Philip C. Hanawalt

All Publications

• A model for transcription-dependent R-loop formation at double-stranded DNA breaks: Implications for their detection and biological effects. Journal of theoretical biology Belotserkovskii, B. P., Hanawalt, P. C. 2024; 595: 111962

  Abstract

  R-loops are structures containing an RNA-DNA duplex and an unpaired DNA strand. During R-loop formation an RNA strand invades the DNA duplex, displacing the homologous DNA strand and binding the complementary DNA strand. Here we analyze a model for transcription-dependent R-loop formation at double-stranded DNA breaks (DSBs). In this model, R-loop formation is preceded by detachment of the non-template DNA strand from the RNA polymerase (RNAP). Then, strand exchange is initiated between the nascent RNA and the non-template DNA strand. During that strand exchange the length of the R-loop could either increase, or decrease in a biased random-walk fashion, in which the bias would depend upon the DNA sequence. Eventually, the restoration of the DNA duplex would completely displace the RNA. However, as long as the RNAP remains bound to the template DNA strand it prevents that displacement. Thus, according to the model, RNAPs stalled at DSBs can increase the lifespan of R-loops, increasing their detectability in experiments, and perhaps enhancing their biological effects.

  View details for DOI 10.1016/j.jtbi.2024.111962

  View details for PubMedID 39384064

• Evelyn M. Witkin (1921-2023). Science (New York, N.Y.) Sweasy, J. B., Hanawalt, P. C. 2023; 381 (6662): 1052

  Abstract

  Pioneer of cell mutagenesis and DNA repair research.

  View details for DOI 10.1126/science.adk1028

  View details for PubMedID 37676948

• Unbalanced Growth, the DNA Replication Cycle and Discovery of Repair Replication. Life (Basel, Switzerland) Hanawalt, P. C. 2023; 13 (4)

  Abstract

  This article recounts my graduate research at Yale University (1954-1958) on unbalanced growth in Eschericia coli during thymine deprivation or following ultraviolet (UV) irradiation, with early evidence for the repair of UV-induced DNA damage. Follow-up studies in Copenhagen (1958-1960) in the laboratory of Ole Maaløe led to my discovery that the DNA replication cycle can be synchronized by inhibiting protein and RNA syntheses and that an RNA synthesis step is essential for initiation of the cycle, but not for its completion. This work set the stage for my subsequent research at Stanford University, where the repair replication of damaged DNA was documented, to provide compelling evidence for an excision-repair pathway. That universal pathway validates the requirement for the redundant information in the complementary strands of duplex DNA to ensure genomic stability.

  View details for DOI 10.3390/life13041052

  View details for PubMedID 37109581

  View details for PubMedCentralID PMC10142232

• Topology and kinetics of R-loop formation. Biophysical journal Belotserkovskii, B. P., Hanawalt, P. C. 2022

  Abstract

  R-loops are structures containing an RNA-DNA duplex and an unpaired DNA strand. They can be formed upon "invasion" of an RNA strand into a DNA duplex, during which the RNA displaces the homologous DNA strand and binds the complementary strand. R-loops have many significant beneficial or deleterious biological effects, so it is important to understand the mechanisms for their generation and processing. We propose a model for co-transcriptional R-loop formation, in which their generation requires passage of the nascent RNA "tail" through the gap between the separated DNA strands. This passage becomes increasingly difficult with lengthening of the RNA tail. The length of the tail increases upon increasing distance between the transcription start site and the site of R-loop initiation. This causes reduced yields of R-loops with greater distance from the transcription start site. However, alternative pathways for R-loop formation are possible, involving either transient disruption of the transcription complex or the hypothetical formation of a triple-stranded structure, as a "collapsed R-loop." These alternative pathways could account for the fact that in many systems R-loops are observed very far from the transcription start site. Our model is consistent with experimental data and makes general predictions about the kinetics of R-loop formation.

  View details for DOI 10.1016/j.bpj.2022.08.026

  View details for PubMedID 36004778

• Perspectives on the processing of R-loops by nucleotide excision repair Hanawalt, P. WILEY. 2022: 62

  View details for Web of Science ID 000841940500145

• Mechanism for R-loop formation remote from the transcription start site: Topological issues and possible facilitation by dissociation of RNA polymerase. DNA repair Belotserkovskii, B. P., Hanawalt, P. C. 1800; 110: 103275

  View details for DOI 10.1016/j.dnarep.2022.103275

  View details for PubMedID 35074657

• Tribute to Sam Wilson: Shining a light on base excision DNA repair. DNA repair Hanawalt, P. C. 2020; 93: 102933

  View details for DOI 10.1016/j.dnarep.2020.102933

  View details for PubMedID 33087270

• Transcription Inhibition by PNA-Induced R-Loops. Methods in molecular biology (Clifton, N.J.) Belotserkovskii, B. P., Ng, S. Y., Hanawalt, P. C. 2020; 2105: 141–55

  Abstract

  R-loops are structures consisting of an RNA-DNA duplex and an unpaired DNA strand. They can form during transcription upon nascent RNA "threadback" invasion into the DNA duplex to displace the non-template DNA strand. R-loops occur naturally in all kingdoms of life, and they have multiple biological effects. Therefore, it is of interest to study the artificial induction of R-loops and to monitor their effects in model in vitro systems to learn mechanisms. Here we describe transcription blockage in vitro by R-loop formation induced by peptide nucleic acid (PNA) binding to the non-template DNA strand.

  View details for DOI 10.1007/978-1-0716-0243-0_8

  View details for PubMedID 32088868

• Mechanistic understanding of cellular responses to genomic stress. Environmental and molecular mutagenesis Hanawalt, P., Sweasy, J. 2019

  Abstract

  Within the past half century we have learned of multiple pathways for repairing damaged DNA, based upon the intrinsic redundancy of information in its complementary double strands. Mechanistic details of these pathways have provided insights into environmental and endogenous threats to genomic stability. Studies on bacterial responses to ultraviolet light led to the discovery of excision-repair, as well as the inducible SOS response to DNA damage. Similar responses in eukaryotes promote upregulation of error-prone translesion DNA polymerases. Recent advances in this burgeoning field include duplex DNA sequencing to provide strikingly accurate profiling of mutational signatures, analyses of gene expression patterns in single cells, CRISPR/Cas9 to generate changes at precise genomic positions, novel roles for RNA in gene expression and DNA repair, phase-separated aqueous environments for specialized cellular transactions, and DNA lesions as epigenetic signals for gene expression. The EMGS, through the broad range of expertise in its membership, stands at the crossroad of basic understanding of mechanisms for genomic maintenance and the field of genetic toxicology, with the need for regulation of exposures to toxic substances. Our future challenges include devising strategies and technologies to identify individuals who are susceptible to specific genomic stresses, along with basic research on the underlying mechanisms of cellular stress responses that promote disease-causing mutations. As the science moves forward it should also be a responsibility for the EMGS to expand its outreach programs for the enlightenment and benefit of all humans and the biosphere. This article is protected by copyright. All rights reserved.

  View details for DOI 10.1002/em.22349

  View details for PubMedID 31793074

• R-loop generation during transcription: Formation, processing and cellular outcomes. DNA repair Belotserkovskii, B. P., Tornaletti, S., D'Souza, A. D., Hanawalt, P. C. 2018

  Abstract

  R-loops are structures consisting of an RNA-DNA duplex and an unpaired DNA strand. They can form during transcription upon nascent RNA "threadback" invasion into the DNA duplex to displace the non-template strand. Although R-loops occur naturally in all kingdoms of life and serve regulatory roles, they are often deleterious and can cause genomic instability. Of particular importance are the disastrous consequences when replication forks or transcription complexes collide with R-loops. The appropriate processing of R-loops is essential to avoid a number of human neurodegenerative and other clinical disorders. We provide a perspective on mechanistic aspects of R-loop formation and their resolution learned from studies in model systems. This should contribute to improved understanding of R-loop biological functions and enable their practical applications. We propose the novel employment of artificially-generated stable R-loops to selectively inactivate tumor cells.

  View details for PubMedID 30190235

• A novel mode for transcription inhibition mediated by PNA-induced R-loops with a model in vitro system BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS D'Souza, A. D., Belotserkovskii, B. P., Hanawalt, P. C. 2018; 1861 (2): 158–66

  Abstract

  The selective inhibition of transcription of a chosen gene by an artificial agent has numerous applications. Usually, these agents are designed to bind a specific nucleotide sequence in the promoter or within the transcribed region of the chosen gene. However, since optimal binding sites might not exist within the gene, it is of interest to explore the possibility of transcription inhibition when the agent is designed to bind at other locations. One of these possibilities arises when an additional transcription initiation site (e.g. secondary promoter) is present upstream from the primary promoter of the target gene. In this case, transcription inhibition might be achieved by inducing the formation of an RNA-DNA hybrid (R-loop) upon transcription from the secondary promoter. The R-loop could extend into the region of the primary promoter, to interfere with promoter recognition by RNA polymerase and thereby inhibit transcription. As a sequence-specific R-loop-inducing agent, a peptide nucleic acid (PNA) could be designed to facilitate R-loop formation by sequestering the non-template DNA strand. To investigate this mode for transcription inhibition, we have employed a model system in which a PNA binding site is localized between the T3 and T7 phage RNA polymerase promoters, which respectively assume the roles of primary and secondary promoters. In accord with our model, we have demonstrated that with PNA-bound DNA substrates, transcription from the T7 promoter reduces transcription from the T3 promoter by 30-fold, while in the absence of PNA binding there is no significant effect of T7 transcription upon T3 transcription.

  View details for PubMedID 29357316

  View details for PubMedCentralID PMC5820110

• Strong transcription blockage mediated by R-loop formation within a G-rich homopurine-homopyrimidine sequence localized in the vicinity of the promoter. Nucleic acids research Belotserkovskii, B. P., Soo Shin, J. H., Hanawalt, P. C. 2017

  Abstract

  Guanine-rich (G-rich) homopurine-homopyrimidine nucleotide sequences can block transcription with an efficiency that depends upon their orientation, composition and length, as well as the presence of negative supercoiling or breaks in the non-template DNA strand. We report that a G-rich sequence in the non-template strand reduces the yield of T7 RNA polymerase transcription by more than an order of magnitude when positioned close (9 bp) to the promoter, in comparison to that for a distal (∼250 bp) location of the same sequence. This transcription blockage is much less pronounced for a C-rich sequence, and is not significant for an A-rich sequence. Remarkably, the blockage is not pronounced if transcription is performed in the presence of RNase H, which specifically digests the RNA strands within RNA-DNA hybrids. The blockage also becomes less pronounced upon reduced RNA polymerase concentration. Based upon these observations and those from control experiments, we conclude that the blockage is primarily due to the formation of stable RNA-DNA hybrids (R-loops), which inhibit successive rounds of transcription. Our results could be relevant to transcription dynamics in vivo (e.g. transcription 'bursting') and may also have practical implications for the design of expression vectors.

  View details for DOI 10.1093/nar/gkx403

  View details for PubMedID 28498974

• Modulation of Cytotoxicity by Transcription-Coupled Nucleotide Excision Repair Is Independent of the Requirement for Bioactivation of Acylfulvene. Chemical research in toxicology Otto, C., Spivak, G., Aloisi, C. M., Menigatti, M., Naegeli, H., Hanawalt, P. C., Tanasova, M., Sturla, S. J. 2017

  Abstract

  Bioactivation as well as DNA repair affects the susceptibility of cancer cells to the action of DNA-alkylating chemotherapeutic drugs. However, information is limited with regard to the relative contributions of these processes to the biological outcome of metabolically activated DNA alkylating agents. We evaluated the influence of cellular bioactivation capacity and DNA repair on cytotoxicity of the DNA alkylating agent acylfulvene (AF). We compared the cytotoxicity and RNA synthesis inhibition by AF and its synthetic activated analogue iso-M0 in a panel of fibroblast cell lines with deficiencies in transcription-coupled (TC-NER) or global genome nucleotide excision repair (GG-NER). We related these data to the inherent bioactivation capacity of each cell type on the basis of mRNA levels. We demonstrated that specific inactivation of TC-NER by siRNA had the largest positive impact on AF activity in a cancer cell line. These findings establish that transcription-coupled DNA repair reduces cellular sensitivity to AF, independent of the requirement for bioactivation.

  View details for DOI 10.1021/acs.chemrestox.6b00240

  View details for PubMedID 28076683

• When transcription goes on Holliday: Double Holliday junctions block RNA polymerase II transcription in vitro. Biochimica et biophysica acta Pipathsouk, A., Belotserkovskii, B. P., Hanawalt, P. C. 2017; 1860 (2): 282-288

  Abstract

  Non-canonical DNA structures can obstruct transcription. This transcription blockage could have various biological consequences, including genomic instability and gratuitous transcription-coupled repair. Among potential structures causing transcription blockage are Holliday junctions (HJs), which can be generated as intermediates in homologous recombination or during processing of stalled replication forks. Of particular interest is the double Holliday junction (DHJ), which contains two HJs. Topological considerations impose the constraint that the total number of helical turns in the DNA duplexes between the junctions cannot be altered as long as the flanking DNA duplexes are intact. Thus, the DHJ structure should strongly resist transient unwinding during transcription; consequently, it is predicted to cause significantly stronger blockage than single HJ structures. The patterns of transcription blockage obtained for RNA polymerase II transcription in HeLa cell nuclear extracts were in accordance with this prediction. However, we did not detect transcription blockage with purified T7 phage RNA polymerase; we discuss a possible explanation for this difference. In general, our findings implicate naturally occurring Holliday junctions in transcription arrest.

  View details for DOI 10.1016/j.bbagrm.2016.12.002

  View details for PubMedID 27923713

  View details for PubMedCentralID PMC5315695

• Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair. Cell Haradhvala, N. J., Polak, P. n., Stojanov, P. n., Covington, K. R., Shinbrot, E. n., Hess, J. M., Rheinbay, E. n., Kim, J. n., Maruvka, Y. E., Braunstein, L. Z., Kamburov, A. n., Hanawalt, P. C., Wheeler, D. A., Koren, A. n., Lawrence, M. S., Getz, G. n. 2016; 164 (3): 538–49

  Abstract

  Mutational processes constantly shape the somatic genome, leading to immunity, aging, cancer, and other diseases. When cancer is the outcome, we are afforded a glimpse into these processes by the clonal expansion of the malignant cell. Here, we characterize a less explored layer of the mutational landscape of cancer: mutational asymmetries between the two DNA strands. Analyzing whole-genome sequences of 590 tumors from 14 different cancer types, we reveal widespread asymmetries across mutagenic processes, with transcriptional ("T-class") asymmetry dominating UV-, smoking-, and liver-cancer-associated mutations and replicative ("R-class") asymmetry dominating POLE-, APOBEC-, and MSI-associated mutations. We report a striking phenomenon of transcription-coupled damage (TCD) on the non-transcribed DNA strand and provide evidence that APOBEC mutagenesis occurs on the lagging-strand template during DNA replication. As more genomes are sequenced, studying and classifying their asymmetries will illuminate the underlying biological mechanisms of DNA damage and repair.

  View details for PubMedID 26806129

• Photobiological Origins of the Field of Genomic Maintenance. Photochemistry and photobiology Ganesan, A., Hanawalt, P. 2016; 92 (1): 52-60

  Abstract

  Although sunlight is essential for life on earth, the ultraviolet (UV) wavelengths in its spectrum constitute a major threat to life. Various cellular responses have evolved to deal with the damage inflicted in DNA by UV, and the study of these responses in model systems has spawned the burgeoning field of DNA repair. Although we now know of many types of deleterious alterations in DNA, the approaches for studying them and the early mechanistic insights have come in large part from pioneering research on the processing of UV-induced bipyrimidine photoproducts in bacteria. It is also notable that UV was one of the first DNA damaging agents for which exposure was directly linked to cancer; the sun-sensitive syndrome, xeroderma pigmentosum, was the first example of a cancer-prone hereditary disease involving a defect in DNA repair. We provide a short history of advances in the broad field of genomic maintenance as they have emerged from research in photochemistry and photobiology.

  View details for DOI 10.1111/php.12542

  View details for PubMedID 26481112

  View details for PubMedCentralID PMC4720547

• Historical perspective on the DNA damage response DNA REPAIR Hanawalt, P. C. 2015; 36: 2-7

  View details for DOI 10.1016/j.dnarep.2015.10.001

  View details for Web of Science ID 000367491900003

• Historical perspective on the DNA damage response. DNA repair Hanawalt, P. C. 2015; 36: 2-7

  Abstract

  The DNA damage response (DDR) has been broadly defined as a complex network of cellular pathways that cooperate to sense and repair lesions in DNA. Multiple types of DNA damage, some natural DNA sequences, nucleotide pool deficiencies and collisions with transcription complexes can cause replication arrest to elicit the DDR. However, in practice, the term DDR as applied to eukaryotic/mammalian cells often refers more specifically to pathways involving the activation of the ATM (ataxia-telangiectasia mutated) and ATR (ATM-Rad3-related) kinases in response to double-strand breaks or arrested replication forks, respectively. Nevertheless, there are distinct responses to particular types of DNA damage that do not involve ATM or ATR. In addition, some of the aberrations that cause replication arrest and elicit the DDR cannot be categorized as direct DNA damage. These include nucleotide pool deficiencies, nucleotide sequences that can adopt non-canonical DNA structures, and collisions between replication forks and transcription complexes. The response to these aberrations can be called the genomic stress response (GSR), a term that is meant to encompass the sensing of all types of DNA aberrations together with the mechanisms involved in coping with them. In addition to fully functional cells, the consequences of processing genomic aberrations may include mutagenesis, genomic rearrangements and lethality.

  View details for DOI 10.1016/j.dnarep.2015.10.001

  View details for PubMedID 26507443

  View details for PubMedCentralID PMC4688148

• PNA binding to the non-template DNA strand interferes with transcription, suggesting a blockage mechanism mediated by R-loop formation MOLECULAR CARCINOGENESIS Belotserkovskii, B. P., Hanawalt, P. C. 2015; 54 (11): 1508-1512

  View details for DOI 10.1002/mc.22209

  View details for PubMedID 25175074

• Transcription blockage by stable H-DNA analogs in vitro. Nucleic acids research Pandey, S., Ogloblina, A. M., Belotserkovskii, B. P., Dolinnaya, N. G., Yakubovskaya, M. G., Mirkin, S. M., Hanawalt, P. C. 2015; 43 (14): 6994-7004

  Abstract

  DNA sequences that can form unusual secondary structures are implicated in regulating gene expression and causing genomic instability. H-palindromes are an important class of such DNA sequences that can form an intramolecular triplex structure, H-DNA. Within an H-palindrome, the H-DNA and canonical B-DNA are in a dynamic equilibrium that shifts toward H-DNA with increased negative supercoiling. The interplay between H- and B-DNA and the fact that the process of transcription affects supercoiling makes it difficult to elucidate the effects of H-DNA upon transcription. We constructed a stable structural analog of H-DNA that cannot flip into B-DNA, and studied the effects of this structure on transcription by T7 RNA polymerase in vitro. We found multiple transcription blockage sites adjacent to and within sequences engaged in this triplex structure. Triplex-mediated transcription blockage varied significantly with changes in ambient conditions: it was exacerbated in the presence of Mn(2+) or by increased concentrations of K(+) and Li(+). Analysis of the detailed pattern of the blockage suggests that RNA polymerase is sterically hindered by H-DNA and has difficulties in unwinding triplex DNA. The implications of these findings for the biological roles of triple-stranded DNA structures are discussed.

  View details for DOI 10.1093/nar/gkv622

  View details for PubMedID 26101261

  View details for PubMedCentralID PMC4538819

• Transcription blockage by stable H-DNA analogs in vitro NUCLEIC ACIDS RESEARCH Pandey, S., Ogloblina, A. M., Belotserkovskii, B. P., Dolinnaya, N. G., Yakubovskaya, M. G., Mirkin, S. M., Hanawalt, P. C. 2015; 43 (14): 6994-7004

  View details for DOI 10.1093/nar/gkv622

  View details for Web of Science ID 000360588200034

• A balanced perspective on unbalanced growth and thymineless death FRONTIERS IN MICROBIOLOGY Hanawalt, P. C. 2015; 6

  Abstract

  The early history of the esoteric phenomenon of thymineless death (TLD) is recounted, from the pioneering discovery by Seymour Cohen and Hazel Barner, through my graduate studies at Yale and postdoctoral research in Copenhagen. My principal contribution was the discovery that restricted synthesis of protein and RNA permits cultures of Escherichia coli to complete their DNA replication cycles without initiating new ones, and that cells held in this physiological state are immune to the lethality of thymine deprivation; unbalanced growth is not the fundamental cause of TLD. The successful synchronization of the DNA replication cycle contributed to formulation of the replicon concept. Studies at Stanford revealed a specific requirement for transcription and led to the discovery of a TLD-resistant mutant in a new gene, termed recQ, with important homologs in humans and most other organisms. The lessons learned from research on TLD underscore the value of basic research in bacterial systems that can have profound implications for human health.

  View details for DOI 10.3389/fmicb.2015.00504

  View details for Web of Science ID 000356344600001

  View details for PubMedID 26097468

  View details for PubMedCentralID PMC4456962

• Photosensitive human syndromes MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS Spivak, G., Hanawalt, P. C. 2015; 776: 24-30

  View details for DOI 10.1016/j.mrfmmm.2014.11.003

  View details for Web of Science ID 000356735900005

• Photosensitive human syndromes. Mutation research Spivak, G., Hanawalt, P. C. 2015; 776: 24-30

  Abstract

  Photosensitivity in humans can result from defects in repair of light-induced DNA lesions, from photoactivation of chemicals (including certain medications) with sunlight to produce toxic mediators, and by immune reactions to sunlight exposures. Deficiencies in DNA repair and the processing of damaged DNA during replication and transcription may result in mutations and genomic instability. We will review current understanding of photosensitivity to short wavelength ultraviolet light (UV) due to genetic defects in particular DNA repair pathways; deficiencies in some are characterized by an extremely high incidence of cancer in sun-exposed tissues, while in others no cancers have been reported.

  View details for DOI 10.1016/j.mrfmmm.2014.11.003

  View details for PubMedID 26255937

  View details for PubMedCentralID PMC4531261

• Altered Minor-Groove Hydrogen Bonds in DNA Block Transcription Elongation by T7 RNA Polymerase CHEMBIOCHEM Tanasova, M., Goeldi, S., Meyer, F., Hanawalt, P. C., Spivak, G., Sturla, S. J. 2015; 16 (8): 1212-1218

  Abstract

  DNA transcription depends upon the highly efficient and selective function of RNA polymerases (RNAPs). Modifications in the template DNA can impact the progression of RNA synthesis, and a number of DNA adducts, as well as abasic sites, arrest or stall transcription. Nonetheless, data are needed to understand why certain modifications to the structure of DNA bases stall RNA polymerases while others are efficiently bypassed. In this study, we evaluate the impact that alterations in dNTP/rNTP base-pair geometry have on transcription. T7 RNA polymerase was used to study transcription over modified purines and pyrimidines with altered H-bonding capacities. The results suggest that introducing wobble base-pairs into the DNA:RNA heteroduplex interferes with transcriptional elongation and stalls RNA polymerase. However, transcriptional stalling is not observed if mismatched base-pairs do not H-bond. Together, these studies show that RNAP is able to discriminate mismatches resulting in wobble base-pairs, and suggest that, in cases of modifications with minor steric impact, DNA:RNA heteroduplex geometry could serve as a controlling factor for initiating transcription-coupled DNA repair.

  View details for DOI 10.1002/cbic.201500077

  View details for Web of Science ID 000354564300013

  View details for PubMedID 25881991

• Thymineless Death Lives On: New Insights into a Classic Phenomenon ANNUAL REVIEW OF MICROBIOLOGY, VOL 69 Khodursky, A., Guzman, E. C., Hanawalt, P. C. 2015; 69: 247-?

  View details for DOI 10.1146/annurev-micro-092412-155749

  View details for PubMedID 26253395

• In memory of John Bruce Hays (1937-2014). DNA repair de Wind, N., Buermeyer, A. B., Hanawalt, P. C. 2014; 16: vi-vii

  View details for DOI 10.1016/S1568-7864(14)00071-8

  View details for PubMedID 24674631

• The awakening of DNA repair at Yale. The Yale journal of biology and medicine Hanawalt, P. C. 2013; 86 (4): 517-23

  Abstract

  As a graduate student with Professor Richard Setlow at Yale in the late 1950s, I studied the effects of ultraviolet and visible light on the syntheses of DNA, RNA, and protein in bacteria. I reflect upon my research in the Yale Biophysics Department, my subsequent postdoctoral experiences, and the eventual analyses in the laboratories of Setlow, Paul Howard-Flanders, and myself that constituted the discovery of the ubiquitous pathway of DNA excision repair in the early 1960s. I then offer a brief perspective on a few more recent developments in the burgeoning DNA repair field and their relationships to human disease.

  View details for PubMedID 24348216

  View details for PubMedCentralID PMC3848106

• DNA Sequences That Interfere with Transcription: Implications for Genome Function and Stability CHEMICAL REVIEWS Belotserkovskii, B. P., Mirkin, S. M., Hanawalt, P. C. 2013; 113 (11): 8620-8637

  View details for DOI 10.1021/cr400078y

  View details for Web of Science ID 000327103200014

  View details for PubMedID 23972098

• Comet-FISH with strand-specific probes reveals transcription-coupled repair of 8-oxoGuanine in human cells NUCLEIC ACIDS RESEARCH Guo, J., Hanawalt, P. C., Spivak, G. 2013; 41 (16): 7700-7712

  Abstract

  Oxidized bases in DNA have been implicated in cancer, aging and neurodegenerative disease. We have developed an approach combining single-cell gel electrophoresis (comet) with fluorescence in situ hybridization (FISH) that enables the comparative quantification of low, physiologically relevant levels of DNA lesions in the respective strands of defined nucleotide sequences and in the genome overall. We have synthesized single-stranded probes targeting the termini of DNA segments of interest using a polymerase chain reaction-based method. These probes facilitate detection of damage at the single-molecule level, as the lesions are converted to DNA strand breaks by lesion-specific endonucleases or glycosylases. To validate our method, we have documented transcription-coupled repair of cyclobutane pyrimidine dimers in the ataxia telangiectasia-mutated (ATM) gene in human fibroblasts irradiated with 254 nm ultraviolet at 0.1 J/m(2), a dose ∼100-fold lower than those typically used. The high specificity and sensitivity of our approach revealed that 7,8-dihydro-8-oxoguanine (8-oxoG) at an incidence of approximately three lesions per megabase is preferentially repaired in the transcribed strand of the ATM gene. We have also demonstrated that the hOGG1, XPA, CSB and UVSSA proteins, as well as actively elongating RNA polymerase II, are required for this process, suggesting cross-talk between DNA repair pathways.

  View details for DOI 10.1093/nar/gkt524

  View details for Web of Science ID 000325173300018

  View details for PubMedID 23775797

• Building on the past, shaping the future: The environmental mutagenesis and genomics society ENVIRONMENTAL AND MOLECULAR MUTAGENESIS Wilson, T. E., DeMarini, D. M., Dertinger, S. D., Engelward, B. P., Hanawalt, P. C., MacGregor, J. T., Smith-Roe, S. L., Witt, K. L., Yauk, C. L., Ljungman, M., Schwartz, J. L., Klein, C. B. 2013; 54 (3): 153-157

  Abstract

  In late 2012, the members of the Environmental Mutagen Society voted to change its name to the Environmental Mutagenesis and Genomics Society. Here, we describe the thought process that led to adoption of the new name, which both respects the rich history of a Society founded in 1969 and reflects the many advances in our understanding of the nature and breadth of gene-environment interactions during the intervening 43 years.

  View details for DOI 10.1002/em.21765

  View details for Web of Science ID 000316227700001

  View details for PubMedID 23444128

• Transcription blockage by homopurine DNA sequences: role of sequence composition and single-strand breaks NUCLEIC ACIDS RESEARCH Belotserkovskii, B. P., Neil, A. J., Saleh, S. S., Shin, J. H., Mirkin, S. M., Hanawalt, P. C. 2013; 41 (3): 1817-1828

  Abstract

  The ability of DNA to adopt non-canonical structures can affect transcription and has broad implications for genome functioning. We have recently reported that guanine-rich (G-rich) homopurine-homopyrimidine sequences cause significant blockage of transcription in vitro in a strictly orientation-dependent manner: when the G-rich strand serves as the non-template strand [Belotserkovskii et al. (2010) Mechanisms and implications of transcription blockage by guanine-rich DNA sequences., Proc. Natl Acad. Sci. USA, 107, 12816-12821]. We have now systematically studied the effect of the sequence composition and single-stranded breaks on this blockage. Although substitution of guanine by any other base reduced the blockage, cytosine and thymine reduced the blockage more significantly than adenine substitutions, affirming the importance of both G-richness and the homopurine-homopyrimidine character of the sequence for this effect. A single-strand break in the non-template strand adjacent to the G-rich stretch dramatically increased the blockage. Breaks in the non-template strand result in much weaker blockage signals extending downstream from the break even in the absence of the G-rich stretch. Our combined data support the notion that transcription blockage at homopurine-homopyrimidine sequences is caused by R-loop formation.

  View details for DOI 10.1093/nar/gks1333

  View details for Web of Science ID 000316351800043

  View details for PubMedID 23275544

  View details for PubMedCentralID PMC3561996

• Transcription blockage by single-strand breaks in various sequences and the general model for transcription blockage by R-loop formation Belotserkovskii, B. P., Neil, A. J., Saleh, S. S., Shin, J. H., Mirkin, S. M., Hanawalt, P. C. TAYLOR & FRANCIS INC. 2013: 83–84

  View details for DOI 10.1080/07391102.2013.786372

  View details for Web of Science ID 000320149400131

• Transcription Blockage by Bulky End Termini at Single-Strand Breaks in the DNA Template: Differential Effects of 5 ' and 3 ' Adducts BIOCHEMISTRY Neil, A. J., Belotserkovskii, B. P., Hanawalt, P. C. 2012; 51 (44): 8964-8970

  Abstract

  RNA polymerases from phage-infected bacteria and mammalian cells have been shown to bypass single-strand breaks (SSBs) with a single-nucleotide gap in the template DNA strand during transcription elongation; however, the SSB bypass efficiency varies significantly depending upon the backbone end chemistries at the break. Using a reconstituted T7 phage transcription system (T7 RNAP) and RNA polymerase II (RNAPII) in HeLa cell nuclear extracts, we observe a slight reduction in the level of transcription arrest at SSBs with no gap as compared to those with a single-nucleotide gap. We have shown that biotin and carbon-chain moieties linked to the 3' side, and in select cases the 5' side, of an SSB in the template strand strongly increase the level of transcription arrest when compared to unmodified SSBs. We also find that a small carbon-chain moiety linked to the upstream side of an SSB aids transcriptional bypass of SSBs for both T7 RNAP and RNAP II. Analysis of transcription across SSBs flanked by bulky 3' adducts reveals the ability of 3' end chemistries to arrest T7 RNAP in a size-dependent manner. T7 RNAP is also completely arrested when 3' adducts or 3'-phosphate groups are placed opposite 5'-phosphate groups at an SSB. We have also observed that a biotinylated thymine in the template strand (without a break) does not pose a strong block to transcription. Taken together, these results emphasize the importance of the size of 3', but usually not 5', end chemistries in arresting transcription at SSBs, substantiating the notion that bulky 3' lesions (e.g., topoisomerase cleavable complexes, 3'-phosphoglycolates, and 3'-unsaturated aldehydes) pose very strong blocks to transcribing RNA polymerases. These findings have implications for the processing of DNA damage through SSB intermediates and the mechanism of SSB bypass by T7 RNAP and mammalian RNAPII.

  View details for DOI 10.1021/bi301240y

  View details for Web of Science ID 000310664200024

  View details for PubMedID 23066636

  View details for PubMedCentralID PMC4153415

• Comet-FISH to Sensitively Assess Global and Transcription-Coupled Repair of DNA Lesions 43rd Annual Meeting of the Environmental-Mutagen-Society (EMS) Guo, J., Spivak, G., Hanawalt, P. WILEY-BLACKWELL. 2012: S35–S35

  View details for Web of Science ID 000307896300093

• A novel XPD mutation in a compound heterozygote; the mutation in the second allele is present in three homozygous patients with mild sun sensitivity ENVIRONMENTAL AND MOLECULAR MUTAGENESIS Falik-Zaccai, T. C., Erel-Segal, R., Horev, L., Bitterman-Deutsch, O., Koka, S., Chaim, S., Keren, Z., Kalfon, L., Gross, B., Segal, Z., Orgal, S., Shoval, Y., Slor, H., Spivak, G., Hanawalt, P. C. 2012; 53 (7): 505-514

  Abstract

  The XPD protein plays a pivotal role in basal transcription and in nucleotide excision repair (NER) as one of the ten known components of the transcription factor TFIIH. Mutations in XPD can result in the DNA repair-deficient diseases xeroderma pigmentosum (XP), trichothiodystrophy (TTD), cerebro-oculo-facial-skeletal syndrome, and in combined phenotypes such as XP/Cockayne syndrome and XP/TTD. We describe here an 18-year-old individual with mild sun sensitivity, no neurological abnormalities and no tumors, who carries a p.R683Q mutation in one allele, and the novel p.R616Q mutation in the other allele of the XPD gene. We also describe four patients from one family, homozygous for the identical p.R683Q mutation in XPD, who exhibit mild skin pigmentation and loss of tendon reflexes. Three homozygous patients presented with late-onset skin tumors, and two with features of premature aging and moderate cognitive decline. Cells from the compound heterozygous individual and from one of the patients homozygous for p.R683Q exhibited similar responses to UV irradiation: reduced viability and defective overall removal of UV-induced cyclobutane pyrimidine dimers, implying deficient global genomic NER. Cells from the compound heterozygous subject also failed to recover RNA synthesis after UV, indicating defective transcription-coupled NER. Mutations affecting codon 616 in XPD generally result in functionally null proteins; we hypothesize that the phenotype of the heterozygous patient results solely from expression of the p.R683Q allele. This study illustrates the importance of detailed follow up with sun sensitive individuals, to ensure appropriate prophylaxis and to understand the mechanistic basis of the implicated hereditary disease.

  View details for DOI 10.1002/em.21716

  View details for Web of Science ID 000307362500003

  View details for PubMedID 22826098

• Transcription-Coupled DNA Repair in Prokaryotes MECHANISMS OF DNA REPAIR Ganesan, A., Spivak, G., Hanawalt, P. C. 2012; 110: 25-40

  Abstract

  Transcription-coupled repair (TCR) is a subpathway of nucleotide excision repair (NER) that acts specifically on lesions in the transcribed strand of expressed genes. First reported in mammalian cells, TCR was then documented in Escherichia coli. In this organism, an RNA polymerase arrested at a lesion is displaced by the transcription repair coupling factor, Mfd. This protein recruits the NER lesion-recognition factor UvrA, and then dissociates from the DNA. UvrA binds UvrB, and the assembled UvrAB* complex initiates repair. In mutants lacking active Mfd, TCR is absent. A gene transcribed by the bacteriophage T7 RNA polymerase in E. coli also requires Mfd for TCR. The CSB protein (missing or defective in cells of patients with Cockayne syndrome, complementation group B) is essential for TCR in humans. CSB and its homologs in higher eukaryotes are likely functional equivalents of Mfd.

  View details for DOI 10.1016/B978-0-12-387665-2.00002-X

  View details for Web of Science ID 000308198900002

  View details for PubMedID 22749141

• Comet-Fish to Sensitively Assess Global and Transcription-Coupled Repair of DNA Lesions. 42nd Annual Meeting of the Environmental-Mutagen-Society Spivak, G., Guo, J., Hanawalt, P. C. WILEY-BLACKWELL. 2011: S37–S37

  View details for Web of Science ID 000297929800100

• DNA slip-outs cause RNA polymerase II arrest in vitro: potential implications for genetic instability NUCLEIC ACIDS RESEARCH Salinas-Rios, V., Belotserkovskii, B. P., Hanawalt, P. C. 2011; 39 (17): 7444-7454

  Abstract

  The abnormal number of repeats found in triplet repeat diseases arises from 'repeat instability', in which the repetitive section of DNA is subject to a change in copy number. Recent studies implicate transcription in a mechanism for repeat instability proposed to involve RNA polymerase II (RNAPII) arrest caused by a CTG slip-out, triggering transcription-coupled repair (TCR), futile cycles of which may lead to repeat expansion or contraction. In the present study, we use defined DNA constructs to directly test whether the structures formed by CAG and CTG repeat slip-outs can cause transcription arrest in vitro. We found that a slip-out of (CAG)(20) or (CTG)(20) repeats on either strand causes RNAPII arrest in HeLa cell nuclear extracts. Perfect hairpins and loops on either strand also cause RNAPII arrest. These findings are consistent with a transcription-induced repeat instability model in which transcription arrest in mammalian cells may initiate a 'gratuitous' TCR event leading to a change in repeat copy number. An understanding of the underlying mechanism of repeat instability could lead to intervention to slow down expansion and delay the onset of many neurodegenerative diseases in which triplet repeat expansion is implicated.

  View details for DOI 10.1093/nar/gkr429

  View details for Web of Science ID 000295184800015

  View details for PubMedID 21666257

  View details for PubMedCentralID PMC3177194

• Anchoring Nascent RNA to the DNA Template Could Interfere with Transcription BIOPHYSICAL JOURNAL Belotserkovskii, B. P., Hanawalt, P. C. 2011; 100 (3): 675-684

  Abstract

  During normal transcription, the nascent RNA product is released from the DNA template. However, in some cases, the RNA remains bound or can become reattached to the template DNA duplex (for example, through R-loop formation). We have analyzed the effect on transcription elongation of nascent RNA anchoring to the template DNA duplex. Because the RNA polymerase follows a helical path along DNA duplex during transcription, the anchoring would result in wrapping the nascent RNA around the DNA in the region between the anchoring point and the translocating polymerase. This wrapping would cause an unfavorable loss of conformation entropy of the nascent RNA. It consequently would create an apparent force to unwrap the RNA by disrupting either the transcription complex or the anchoring structure. We have estimated that this force would be comparable to those required to melt nucleic acid duplexes or to arrest transcription elongation in single-molecule experiments. We predict that this force would create negative supercoiling in the DNA duplex region between the anchoring point and the transcribing RNA polymerase: this can promote the formation of unusual DNA structures and facilitate RNA invasion into the DNA duplex. Potential biological consequences of these effects are discussed.

  View details for DOI 10.1016/j.bpj.2010.12.3709

  View details for Web of Science ID 000286957200018

  View details for PubMedID 21281582

  View details for PubMedCentralID PMC3030168

• Transcription-coupled nucleotide excision repair of a gene transcribed by bacteriophage T7 RNA polymerase in Escherichia coli DNA REPAIR Ganesan, A. K., Hanawalt, P. C. 2010; 9 (9): 958-963

  Abstract

  Transcription-coupled nucleotide excision repair (TC-NER) removes certain kinds of lesions from the transcribed strand of expressed genes. The signal for TC-NER is thought to be RNA polymerase stalled at a lesion in the DNA template. In Escherichia coli, the stalled polymerase is dissociated from the lesion by the transcription repair coupling factor (Mfd protein), which also recruits excision repair proteins to the site resulting in efficient removal of the lesion. TC-NER has been documented in cells from a variety of organisms ranging from bacteria to humans. In each case, the RNA polymerase involved has been a multimeric protein complex. To ascertain whether a gene transcribed by the monomeric RNA polymerase of bacteriophage T7 could be repaired by TC-NER, we constructed strains of E. coli in which the chromosomal lacZ gene is controlled by a T7 promoter. In the absence of T7 RNA polymerase, little or no beta-galactosidase is produced, indicating that the E. coli RNA polymerase does not transcribe lacZ efficiently, if at all, in these strains. By introducing a plasmid (pAR1219) carrying the T7 gene 1 under control of the E. coli lac UV5 promoter into these strains, we obtained derivatives in which the level of T7 RNA polymerase could be regulated. In cultures containing upregulated levels of the polymerase, beta-galactosidase was actively produced indicating that the T7 RNA polymerase transcribes the lacZ gene efficiently. Under these conditions, we observed that UV-induced cyclobutane pyrimidine dimers were removed more rapidly from the transcribed strand of lacZ than from the nontranscribed strand, supporting the conclusion that TC-NER occurred in this gene. This response was absent in an mfd-1 mutant, indicating that the underlying mechanism may be similar to that for the bacterial RNA polymerase.

  View details for DOI 10.1016/j.dnarep.2010.06.007

  View details for Web of Science ID 000282078100003

  View details for PubMedID 20638914

  View details for PubMedCentralID PMC2929277

• Growing up with DNA repair and joining the EMS. Environmental and molecular mutagenesis Hanawalt, P. 2010; 51 (8-9): 890-6

  Abstract

  I recount some personal history, as I rode the crest of the wave of discovery and excitement in the DNA repair field from the early 1960s and eventually came to appreciate that the Environmental Mutagen Society is the appropriate professional "home" for researchers in this field: it places them in the context of the broader genetic, societal, and regulatory issues raised from their studies. In return, the wisdom provided from basic research on cellular processing of damaged DNA is essential to mechanism-based decisions in the domain of genetic toxicology.

  View details for DOI 10.1002/em.20608

  View details for PubMedID 20740638

• Mechanisms and implications of transcription blockage by guanine-rich DNA sequences PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Belotserkovskii, B. P., Liu, R., Tornaletti, S., Krasilnikova, M. M., Mirkin, S. M., Hanawalt, P. C. 2010; 107 (29): 12816-12821

  Abstract

  Various DNA sequences that interfere with transcription due to their unusual structural properties have been implicated in the regulation of gene expression and with genomic instability. An important example is sequences containing G-rich homopurine-homopyrimidine stretches, for which unusual transcriptional behavior is implicated in regulation of immunogenesis and in other processes such as genomic translocations and telomere function. To elucidate the mechanism of the effect of these sequences on transcription we have studied T7 RNA polymerase transcription of G-rich sequences in vitro. We have shown that these sequences produce significant transcription blockage in an orientation-, length- and supercoiling-dependent manner. Based upon the effects of various sequence modifications, solution conditions, and ribonucleotide substitutions, we conclude that transcription blockage is due to formation of unusually stable RNA/DNA hybrids, which could be further exacerbated by triplex formation. These structures are likely responsible for transcription-dependent replication blockage by G-rich sequences in vivo.

  View details for DOI 10.1073/pnas.1007580107

  View details for Web of Science ID 000280144500022

  View details for PubMedID 20616059

  View details for PubMedCentralID PMC2919923

• Thymineless death is associated with loss of essential genetic information from the replication origin MOLECULAR MICROBIOLOGY Sangurdekar, D. P., Hamann, B. L., Smirnov, D., Srienc, F., Hanawalt, P. C., Khodursky, A. B. 2010; 75 (6): 1455-1467

  Abstract

  Thymine starvation results in a terminal cellular condition known as thymineless death (TLD), which is the basis of action for several common antibiotics and anticancer drugs. We characterized the onset and progression of TLD in Escherichia coli and found that DNA damage is the only salient property that distinguishes cells irreversibly senesced under thymine starvation from cells reversibly arrested by the nucleotide limitation. The damage is manifested as the relative loss of genetic material spreading outward from the replication origin: the extent of TLD correlates with the progression of damage. The reduced lethality in mutants deficient in the RecFOR/JQ repair pathway also correlates with the extent of damage, which explains most of the observed variance in cell killing. We propose that such spatially localized and persistent DNA damage is the consequence of transcription-dependent initiation of replication in the thymine-starved cells and may be the underlying cause of TLD.

  View details for DOI 10.1111/j.1365-2958.2010.07072.x

  View details for Web of Science ID 000275396200010

  View details for PubMedID 20132444

• A UV-sensitive syndrome patient with a specific CSA mutation reveals separable roles for CSA in response to UV and oxidative DNA damage PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Nardo, T., Oneda, R., Spivak, G., Vaz, B., Mortier, L., Thomas, P., Orioli, D., Laugel, V., Stary, A., Hanawalt, P. C., Sarasin, A., Stefanini, M. 2009; 106 (15): 6209-6214

  Abstract

  UV-sensitive syndrome (UV(S)S) is a recently-identified autosomal recessive disorder characterized by mild cutaneous symptoms and defective transcription-coupled repair (TC-NER), the subpathway of nucleotide excision repair (NER) that rapidly removes damage that can block progression of the transcription machinery in actively-transcribed regions of DNA. Cockayne syndrome (CS) is another genetic disorder with sun sensitivity and defective TC-NER, caused by mutations in the CSA or CSB genes. The clinical hallmarks of CS include neurological/developmental abnormalities and premature aging. UV(S)S is genetically heterogeneous, in that it appears in individuals with mutations in CSB or in a still-unidentified gene. We report the identification of a UV(S)S patient (UV(S)S1VI) with a novel mutation in the CSA gene (p.trp361cys) that confers hypersensitivity to UV light, but not to inducers of oxidative damage that are notably cytotoxic in cells from CS patients. The defect in UV(S)S1VI cells is corrected by expression of the WT CSA gene. Expression of the p.trp361cys-mutated CSA cDNA increases the resistance of cells from a CS-A patient to oxidative stress, but does not correct their UV hypersensitivity. These findings imply that some mutations in the CSA gene may interfere with the TC-NER-dependent removal of UV-induced damage without affecting its role in the oxidative stress response. The differential sensitivity toward oxidative stress might explain the difference between the range and severity of symptoms in CS and the mild manifestations in UV(s)S patients that are limited to skin photosensitivity without precocious aging or neurodegeneration.

  View details for DOI 10.1073/pnas.0902113106

  View details for Web of Science ID 000265174600034

  View details for PubMedID 19329487

• Peptide Nucleic Acid (PNA) Binding and Its Effect on In Vitro Transcription in Friedreich's Ataxia Triplet Repeats MOLECULAR CARCINOGENESIS Belotserkovskii, B. P., Liu, R., Hanawalt, P. C. 2009; 48 (4): 299-308

  Abstract

  Peptide nucleic acids (PNAs) are DNA mimics in which peptide-like linkages are substituted for the phosphodiester backbone. Homopyrimidine PNAs can invade double-stranded DNA containing the homologous sequence by displacing the homopyrimidine strand from the DNA duplex and forming a PNA/DNA/PNA triplex with the complementary homopurine strand. Among biologically interesting targets for triplex-forming PNA are (GAA/CTT)(n) repeats. Expansion of these repeats results in partial inhibition of transcription in the frataxin gene, causing Friedreich's ataxia. We have studied PNA binding and its effect on T7 RNA polymerase transcription in vitro for short repeats (n = 3) and for long repeats (n = 39), placed in both possible orientations relative to the T7 promoter such that either the GAA-strand, or the CTT-strand serves as the template for transcription. In all cases PNA bound specifically and efficiently to its target sequence. For the short insert, PNA binding to the template strand caused partial transcription blockage with well-defined sites of RNA product truncation in the region of the PNA-binding sequence, whereas binding to the nontemplate strand did not block transcription. However, PNA binding to long repeats, whether in the template or the nontemplate strand, resulted in a dramatic reduction of the amount of full-length transcription product, although in the case of the nontemplate strand there were no predominant truncation sites. Biological implications of these results are discussed.

  View details for DOI 10.1002/mc.20486

  View details for Web of Science ID 000264918500004

  View details for PubMedID 19306309

  View details for PubMedCentralID PMC2664860

• New applications of the Comet assay: Comet-FISH and transcription-coupled DNA repair MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH Spivak, G., Cox, R. A., Hanawalt, P. C. 2009; 681 (1): 44-50

  Abstract

  Transcription-coupled repair (TCR) is a pathway dedicated to the removal of damage from the template strands of actively transcribed genes. Although the detailed mechanism of TCR is not yet understood, it is believed to be triggered when a translocating RNA polymerase is arrested at a lesion or unusual structure in the DNA. Conventional assays for TCR require high doses of DNA damage for the statistical analysis of repair in the individual strands of DNA sequences ranging in size from a few hundred bases to 30kb. The single cell gel electrophoresis (Comet) assay allows detection of single- or double-strand breaks at a 10-100-fold higher level of resolution. Fluorescence in situ hybridization (FISH) combined with the Comet assay (Comet-FISH) affords a heightened level of sensitivity for the assessment of repair in defined DNA sequences of cells treated with physiologically relevant doses of genotoxins. This approach also reveals localized susceptibility to chromosomal breakage in cells from individuals with hypersensitivity to radiation or chemotherapy. Several groups have reported preferential repair in transcriptionally active genes or chromosomal domains using Comet-FISH. The prevailing interpretation of the behavior of DNA in the Comet assay assumes that the DNA is arranged in loops and matrix-attachment sites; that supercoiled, undamaged loops are contained within the nuclear matrix and appear in Comet "heads", and that Comet "tails" consist of relaxed DNA loops containing one or more breaks. According to this model, localization of FISH probes in Comet heads signifies that loops containing the targeted sequences are free of damage. This implies that preferential repair as detected by Comet-FISH might encompass large chromosomal domains containing both transcribed and non-transcribed sequences. We review the existing evidence and discuss the implications in relation to current models for the molecular mechanism of TCR.

  View details for DOI 10.1016/j.mrrev.2007.12.003

  View details for PubMedID 18291710

  View details for PubMedCentralID PMC2667151

• Transcription-coupled DNA repair: two decades of progress and surprises NATURE REVIEWS MOLECULAR CELL BIOLOGY Hanawalt, P. C., Spivak, G. 2008; 9 (12): 958-970

  Abstract

  Expressed genes are scanned by translocating RNA polymerases, which sensitively detect DNA damage and initiate transcription-coupled repair (TCR), a subpathway of nucleotide excision repair that removes lesions from the template DNA strands of actively transcribed genes. Human hereditary diseases that present a deficiency only in TCR are characterized by sunlight sensitivity without enhanced skin cancer. Although multiple gene products are implicated in TCR, we still lack an understanding of the precise signals that can trigger this pathway. Futile cycles of TCR at naturally occurring non-canonical DNA structures might contribute to genomic instability and genetic disease.

  View details for DOI 10.1038/nrm2549

  View details for Web of Science ID 000261126800015

  View details for PubMedID 19023283

• Emerging links between premature ageing and defective DNA repair MECHANISMS OF AGEING AND DEVELOPMENT Hanawalt, P. C. 2008; 129 (7-8): 503-505

  View details for DOI 10.1016/j.mad.2008.03.007

  View details for Web of Science ID 000257816100017

  View details for PubMedID 18440595

  View details for PubMedCentralID PMC2519891

• Inhibitory effect of a short Z-DNA forming sequence on transcription elongation by T7 RNA polymerase NUCLEIC ACIDS RESEARCH Ditlevson, J. V., Tornaletti, S., Belotserkovskii, B. P., Teijeiro, V., Wang, G., Vasquez, K. M., Hanawalt, P. C. 2008; 36 (10): 3163-3170

  Abstract

  DNA sequences capable of forming unusual secondary structures can be a source of genomic instability. In some cases that instability might be affected by transcription, as recently shown for the Z-DNA forming sequence (CG)(14), which causes genomic instability both in mammalian cells and in bacteria, and this effect increases with its transcription. We have investigated the effect of this (CG)(14) sequence on transcription with T7 RNA polymerase in vitro. We detected partial transcription blockage within the sequence; the blockage increased with negative supercoiling of the template DNA. This effect was not observed in a control self-complementary sequence of identical length and base composition as the (CG)(14) sequence, when the purine-pyrimidine alternation required for Z-DNA formation was disrupted. These findings suggest that the inhibitory effect on T7 transcription results from Z-DNA formation in the (CG)(14) sequence rather than from an effect of the sequence composition or from hairpin formation in either the DNA or the RNA product.

  View details for DOI 10.1093/nar/gkn136

  View details for Web of Science ID 000257183200001

  View details for PubMedID 18400779

  View details for PubMedCentralID PMC2425487

• G4-forming sequences in the non-transcribed DNA strand pose blocks to T7 RNA polymerase and mammalian RNA polymerase II JOURNAL OF BIOLOGICAL CHEMISTRY Tornaletti, S., Park-Snyder, S., Hanawalt, P. C. 2008; 283 (19): 12756-12762

  Abstract

  DNA sequences rich in runs of guanine have the potential to form G4 DNA, a four-stranded non-canonical DNA structure stabilized by formation and stacking of G quartets, planar arrays of four hydrogen-bonded guanines. It was reported recently that G4 DNA can be generated in Escherichia coli during transcription of plasmids containing G-rich sequences in the non-transcribed strand. In addition, a stable RNA/DNA hybrid is formed with the transcribed strand. These novel structures, termed G loops, are suppressed in recQ(+) strains, suggesting that their persistence may generate genomic instability and that the RecQ helicase may be involved in their dissolution. However, little is known about how such non-canonical DNA structures are processed when encountered by an elongating polymerase. To assess whether G4-forming sequences interfere with transcription, we studied their effect on transcription elongation by T7 RNA polymerase and mammalian RNA polymerase II. We used a reconstituted transcription system in vitro with purified polymerase and initiation factors and with substrates containing G-rich sequences in either the transcribed or non-transcribed strand downstream of the T7 promoter or the adenovirus major late promoter. We report that G-rich sequences located in the transcribed strand do not affect transcription by either polymerase, but when the sequences are located in the non-transcribed strand, they partially arrest both polymerases. The efficiency of arrest increases with negative supercoiling and also with multiple rounds of transcription compared with single events.

  View details for DOI 10.1074/jbc.M705003200

  View details for Web of Science ID 000255499800011

  View details for PubMedID 18292094

  View details for PubMedCentralID PMC2442332

• Paradigms for the three Rs: DNA replication, recombination, and repair MOLECULAR CELL Hanawalt, P. C. 2007; 28 (5): 702-707

  Abstract

  The recent decade has engendered a convergence of the otherwise distinct fields of DNA replication, recombination, and repair, as we are learning how these essential transactions can operate in coordination to achieve genomic stability and to ensure cellular viability. In the next decade, we can anticipate a functional understanding of the roles of posttranslational protein modifications in the regulation and prioritizing of pathways for genomic maintenance. The fundamental knowledge gained should lead to more effective clinical intervention in human disease.

  View details for DOI 10.1016/j.molcel.2007.11.014

  View details for Web of Science ID 000251926000002

  View details for PubMedID 18082594

• A triplex-forming sequence from the human c-MYC promoter interferes with DNA transcription JOURNAL OF BIOLOGICAL CHEMISTRY Belotserkovskii, B. P., De Silva, E., Tornaletti, S., Wang, G., Vasquez, K. M., Hanawalt, P. C. 2007; 282 (44): 32433-32441

  Abstract

  Naturally occurring DNA sequences that are able to form unusual DNA structures have been shown to be mutagenic, and in some cases the mutagenesis induced by these sequences is enhanced by their transcription. It is possible that transcription-coupled DNA repair induced at sites of transcription arrest might be involved in this mutagenesis. Thus, it is of interest to determine whether there are correlations between the mutagenic effects of such noncanonical DNA structures and their ability to arrest transcription. We have studied T7 RNA polymerase transcription through the sequence from the nuclease-sensitive element of the human c-MYC promoter, which is mutagenic in mammalian cells (Wang, G., and Vasquez, K. M. (2004) Proc. Natl. Acad. Sci. U. S. A. 101, 13448-13453). This element has two mirror-symmetric homopurine-homopyrimidine blocks that potentially can form either DNA triplex (H-DNA) or quadruplex structures. We detected truncated transcription products indicating partial transcription arrest within and closely downstream of the element. The arrest required negative supercoiling and was much more pronounced when the pyrimidine-rich strand of the element served as the template. The exact positions of arrest sites downstream from the element depended upon the downstream flanking sequences. We made various nucleotide substitutions in the wild-type sequence from the c-MYC nuclease-sensitive element that specifically destabilize either the triplex or the quadruplex structure. When these substitutions were ranked for their effects on transcription, the results implicated the triplex structure in the transcription arrest. We suggest that transcription-induced triplex formation enhances pre-existing weak transcription pause sites within the flanking sequences by creating steric obstacles for the transcription machinery.

  View details for DOI 10.1074/jbc.M704618200

  View details for Web of Science ID 000250480300066

  View details for PubMedID 17785457

• Transcription coupled nucleotide excision repair in Escherichia coli can be affected by changing the arginine at position 529 of the p subunit of RNA polymerase DNA REPAIR Ganesan, A. K., Smith, A. J., Savery, N. J., Zamos, P., Hanawalt, P. C. 2007; 6 (10): 1434-1440

  Abstract

  The proposed mechanism for transcription coupled nucleotide excision repair (TCR) invokes RNA polymerase (RNAP) blocked at a DNA lesion as a signal to initiate repair. In Escherichia coli, TCR requires the interaction of RNAP with a transcription-repair coupling factor encoded by the mfd gene. The interaction between RNAP and Mfd depends upon amino acids 117, 118, and 119 of the beta subunit of RNAP; changing any one of these to alanine diminishes the interaction [1]. Using direct assays for TCR, and the lac operon of E. coli containing UV induced cyclobutane pyrimidine dimers (CPDs) as substrate, we have found that a change from arginine to cysteine at amino acid 529 of the beta subunit of the RNAP inactivates TCR, but does not prevent the interaction of RNAP with Mfd. Our results suggest that this interaction may be necessary but not sufficient to facilitate TCR.

  View details for DOI 10.1016/j.dnarep.2007.04.002

  View details for Web of Science ID 000250080300005

  View details for PubMedID 17532270

  View details for PubMedCentralID PMC2578841

• Nucleotide excision repair phenotype of human acute myeloid leukemia cell lines at various stages of differentiation MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS Hsu, P., Hanawalt, P. C., Nouspikel, T. 2007; 614 (1-2): 3-15

  Abstract

  In previous studies it was shown that nucleotide excision repair (NER) is strongly attenuated at the global genome level in terminally differentiated neuron-like cells. NER was measured in several human acute myeloid leukemia cell lines, before and after differentiation into macrophage-like cells. Repair of cisplatin intrastrand GTG crosslinks in differentiated cells was strongly attenuated. There were also some variations between repair levels in naïve cells, but these were not correlated with the degree of differentiation. By contrast, the proficient repair of UV-induced (6-4)pyrimidine-pyrimidone photoproducts [(6-4)PPs] was not affected by differentiation. Although cyclobutane pyrimidine dimers (CPDs) were poorly repaired at the global genome level in all cell lines, differentiated or not, they were very efficiently removed from the transcribed strand of an active gene, indicating that transcription-coupled repair (TCR) is proficient in each cell line. CPDs were also removed from the non-transcribed strand of an active gene better than at the overall global genome level. This relatively efficient repair of the non-transcribed strand of active genes, when compared with global genomic repair (GGR), has been described previously in neuron-like cells and termed differentiation-associated repair (DAR). Here we show that it also can occur in actively growing cells that display poor GGR.

  View details for DOI 10.1016/j.mrfmmm.2006.06.008

  View details for Web of Science ID 000243544900002

  View details for PubMedID 16890248

• Transcription domain-associated repair in human cells MOLECULAR AND CELLULAR BIOLOGY Nouspikel, T. P., Hyka-Nouspikel, N., Hanawalt, P. C. 2006; 26 (23): 8722-8730

  Abstract

  Nucleotide excision repair (NER), which is arguably the most versatile DNA repair system, is strongly attenuated in human cells of the monocytic lineage when they differentiate into macrophages. Within active genes, however, both DNA strands continue to be proficiently repaired. The proficient repair of the nontranscribed strand cannot be explained by the dedicated subpathway of transcription-coupled repair (TCR), which is targeted to the transcribed strand in expressed genes. We now report that the previously termed differentiation-associated repair (DAR) depends upon transcription, but not simply upon RNA polymerase II (RNAPII) encountering a lesion: proficient repair of both DNA strands can occur in a part of a gene that the polymerase never reaches, and even if the translocation of RNAPII is blocked with transcription inhibitors. This suggests that DAR may be a subset of global NER, restricted to the subnuclear compartments or chromatin domains within which transcription occurs. Downregulation of selected NER genes with small interfering RNA has confirmed that DAR relies upon the same genes as global genome repair, rather than upon TCR-specific genes. Our findings support the general view that the genomic domains within which transcription is active are more accessible than the bulk of the genome to the recognition and repair of lesions through the global pathway and that TCR is superimposed upon that pathway of NER.

  View details for DOI 10.1128/MCB.01263-06

  View details for Web of Science ID 000242203700005

  View details for PubMedID 17015469

• Impaired nucleotide excision repair upon macrophage differentiation is corrected by E1 ubiquitin-activating enzyme PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Nouspikel, T., Hanawalt, P. C. 2006; 103 (44): 16188-16193

  Abstract

  Global nucleotide excision repair is greatly attenuated in terminally differentiated mammalian cells. We observed this phenomenon in human neurons and in macrophages, noting that the transcription-coupled repair pathway remains functional and that there is no significant reduction in levels of excision repair enzymes. We have discovered that ubiquitin-activating enzyme E1 complements the repair deficiency in macrophage extracts, and although there is no reduction in the concentration of E1 upon differentiation, our results indicate a reduction in phosphorylation of E1. In preliminary studies, we have identified the basal transcription factor TFIIH as the potential target for ubiquitination. We suggest that this unusual type of regulation at the level of the E1 enzyme is likely to affect numerous cellular processes and may represent a strategy to coordinate multiple phenotypic changes upon differentiation by using E1 as a "master switch."

  View details for DOI 10.1073/pnas.0607769103

  View details for Web of Science ID 000241879500025

  View details for PubMedID 17060614

  View details for PubMedCentralID PMC1621053

• Transcription arrest at an abasic site in the transcribed strand of template DNA CHEMICAL RESEARCH IN TOXICOLOGY Tornaletti, S., Maeda, L. S., Hanawalt, P. C. 2006; 19 (9): 1215-1220

  Abstract

  A dedicated excision repair pathway, termed transcription-coupled repair (TCR), targets the removal of DNA lesions from transcribed strands of expressed genes. Transcription arrest at the site of the lesion has been proposed as the first step for initiation of TCR. In support of this model, a strong correlation between arrest of transcription by a lesion in vitro and TCR of that lesion in vivo has been found in most cases analyzed. TCR has been reported for oxidative DNA damage; however, very little is known about how frequently occurring and spontaneous DNA damage, such as depurination and base deamination, affects progression of the transcription complex. We have previously determined that the oxidative lesion, thymine glycol, is a significant block to transcription by T7 RNA polymerase (T7 RNAP) but has no detectable effect on transcription by RNA polymerase II (RNAP II) in a reconstituted system with all of the required factors. Another oxidative lesion, 8-oxoguanine, only slightly blocked T7 RNAP and caused RNAP II to briefly pause at the lesion before bypassing it. Because an abasic site is an intermediate in the repair of oxidative damage, it was of interest to learn whether it arrested transcription. Using in vitro transcription assays and substrates containing a specifically positioned lesion, we found that an abasic site in the transcribed strand is a 60% block to transcription by T7 RNAP but nearly a complete block to transcription by mammalian RNAP II. An abasic site in the nontranscribed strand did not block either polymerase. Our results clearly indicate that an abasic site is a much stronger block to transcription than either a thymine glycol or an 8-oxoguanine. Because the predominant model for TCR postulates that only lesions that block RNAP will be subject to TCR, our findings suggest that the abasic site may be sufficient to initiate TCR in vivo.

  View details for DOI 10.1021/tx060103g

  View details for PubMedID 16978026

• Research collaborations: Trial, trust, and truth CELL Hanawalt, P. C. 2006; 126 (5): 823-825

  Abstract

  Successful advances in biomedical research increasingly require multigroup collaborations and publication of results in multiauthored papers. It is essential to consider at the outset how to maximize the value of such collaborations while avoiding potential pitfalls.

  View details for DOI 10.1016/j.cell.2006.08.018

  View details for Web of Science ID 000240675000005

  View details for PubMedID 16959557

• Role of DNA replication and repair in thymineless death in Escherichia coli JOURNAL OF BACTERIOLOGY Morganroth, P. A., Hanawalt, P. C. 2006; 188 (14): 5286-5288

  Abstract

  Inhibition of DNA replication with hydroxyurea during thymine starvation of Escherichia coli shows that active DNA synthesis is not required for thymineless death (TLD). Hydroxyurea experiments and thymine starvation of lexA3 and uvrA DNA repair mutants rule out unbalanced growth, the SOS response, and nucleotide excision repair as explanations for TLD.

  View details for DOI 10.1128/JB.00543-06

  View details for Web of Science ID 000239079300029

  View details for PubMedID 16816201

  View details for PubMedCentralID PMC1539979

• Processing of non-canonical DNA structures by RNA polymerase. 37th Annual Meeting of the Environmental-Mutagen-Society VanOverbelke, J. L., DeSilva, E., Wang, G., Vasquez, K. M., Tornaletti, S., Hanawalt, P. C. WILEY-LISS. 2006: 427–27

  View details for Web of Science ID 000239647900110

• Topoisomerase deficiencies subtly enhance global genomic repair of ultraviolet-induced DNA damage in Saccharomyces cerevisiae DNA REPAIR Cline, S. D., Hanawalt, P. C. 2006; 5 (5): 611-617

  Abstract

  Genetic integrity depends upon the precision of all pathways that manipulate DNA. DNA repair mechanisms prevent mutations and aberrant recombination events by removing DNA damage. DNA topoisomerases maintain favorable nucleic acid topology for replication, transcription, and chromosome segregation. However, topoisomerases can also become trapped on DNA at sites of damage, and thereby, might alter the efficiency of DNA repair. The activities of the three nuclear DNA topoisomerases (Top1, Top2, and Top3) in the yeast Saccharomyces cerevisiae were examined for their influence upon the nucleotide excision repair (NER) of DNA damage induced by ultraviolet (UV) irradiation. A 10-20% increase in the global genomic repair (GGR) of cyclobutane pyrimidine dimers (CPDs) was observed with impaired Top1 or Top2 function. The GGR of 6-4 photoproducts (6-4PPs) and the strand-specific removal of CPDs from the yeast RPB2 gene were unaffected by the loss of topoisomerase activity. Even though the deletion of TOP3 conferred UV sensitivity, neither the GGR nor the strand-specific repair of UV-induced DNA damage was compromised in top3Delta yeast. Top1 and Top2 in DNA complexes near CPDs may inhibit GGR recognition of these lesions and produce protein-linked DNA breaks, resulting in CPD repair by an alternate pathway. While the physiological role of topoisomerase association with DNA damage has yet to be determined, these enzymes do not play a direct role in the NER pathways for removing UV-induced lesions in yeast.

  View details for DOI 10.1016/j.dnarep.2006.01.007

  View details for Web of Science ID 000237683700009

  View details for PubMedID 16516562

• Transcriptional inhibition by an oxidized abasic site in DNA CHEMICAL RESEARCH IN TOXICOLOGY Wang, Y. L., Sheppard, T. L., Tornaletti, S., Maeda, L. S., Hanawalt, P. C. 2006; 19 (2): 234-241

  Abstract

  2-Deoxyribonolactone (dL) is an oxidized abasic site in DNA that can be induced by gamma-radiolysis, ultraviolet irradiation, and numerous antitumor drugs. Although this lesion is incised by AP endonucleases, suggesting a base-excision repair mechanism for dL removal, subsequent excision and repair synthesis by DNA polymerase beta is inhibited due to accumulation of a protein-DNA cross-link. This raises the possibility that additional repair pathways might be required to eliminate dL from the genome. Transcription-coupled repair (TCR) is a pathway of excision repair specific to DNA lesions present in transcribed strands of expressed genes. A current model proposes that transcription arrest at the site of DNA damage is required to initiate TCR. In support of this model, a strong correlation between transcription arrest by a lesion in vitro and TCR of the lesion in vivo has been found in most cases analyzed. To assess whether dL might be subject to TCR, we have studied the behavior of bacteriophage T3 and T7 RNA polymerases (T3RNAP, T7RNAP) and of mammalian RNA polymerase II (RNAPII) when they encounter a dL lesion or its "caged" precursor located either in the transcribed or in the nontranscribed strand of template DNA. DNA plasmids containing a specifically located dL downstream of the T3, T7 promoter or the Adenovirus major late promoter were constructed and used for in vitro transcription with purified proteins. We found that both dL and its caged precursor located in the transcribed strand represented a complete block to transcription by T3- and T7RNAP. Similarly, they caused more than 90% arrest when transcription was carried out with mammalian RNAPII. Furthermore, RNAPII complexes arrested at dL were subject to the transcript cleavage reaction mediated by elongation factor TFIIS, indicating that these complexes were stable. A dL in the nontranscribed strand did not block either polymerase.

  View details for DOI 10.1021/tx050292n

  View details for Web of Science ID 000235584800006

  View details for PubMedID 16485899

• Host cell reactivation of plasmids containing oxidative DNA lesions is defective in Cockayne syndrome but normal in UV-sensitive syndrome fibroblasts DNA REPAIR Spivak, G., Hanawalt, P. C. 2006; 5 (1): 13-22

  Abstract

  UV-sensitive syndrome (UV(S)S) is a human DNA repair-deficient disease with mild clinical manifestations. No neurological or developmental abnormalities or predisposition to cancer have been reported. In contrast, Cockayne syndrome (CS) patients exhibit severe developmental and neurological defects, in addition to photosensitivity. The cellular and biochemical responses of UV(S)S and CS cells to UV are indistinguishable, and result from defective transcription-coupled repair (TCR) of photoproducts in expressed genes. We propose that UV(S)S patients develop normally because they are proficient in repair of oxidative base damage. Consistent with our model, we show that Cockayne syndrome cells from complementation groups A and B (CS-A, CS-B) are more sensitive to treatment with hydrogen peroxide than wild type or UV(S)S cells. Using a host cell reactivation assay with plasmids containing UV-induced photoproducts, we find that expression of the plasmid-encoded lacZ gene is reduced in the TCR-deficient CS-B and UV(S)S cells. When the plasmids contain the oxidative base lesion thymine glycol, CS-B cells are defective in recovery of expression, whereas UV(S)S cells show levels of expression similar to those in wild type cells. 8-oxoguanine in the plasmids result in similarly defective host cell reactivation in CS-A and CS-B cells; abasic sites or single strand breaks in the plasmids cause similar decreases in expression in all the cell lines examined. Repair of thymine glycols in the lacZ gene was measured in plasmids extracted from transfected cells; removal of the lesions is efficient and without strand bias in all the cell lines tested.

  View details for DOI 10.1016/j.dnarep.2005.06.017

  View details for Web of Science ID 000234780000002

  View details for PubMedID 16129663

• In vivo assays for transcription-coupled repair DNA REPAIR, PT A Spivak, G., Pfeifer, G. P., Hanawalt, P. 2006; 408: 223-?

  Abstract

  This chapter describes the technologies used in our respective laboratories to study the incidence and repair of lesions induced in specific DNA sequences by ultraviolet light, chemical carcinogens, and products of cellular metabolism. The Southern blot method is suitable for analysis of damage and repair in the individual DNA strands of specific restriction fragments up to 25,000 nucleotides in length, whereas the ligation-mediated polymerase chain reaction approach permits analysis of shorter sequences at the nucleotide level. Both methods have unique advantages and limitations for particular applications.

  View details for DOI 10.1016/S0076-6879(06)08014-1

  View details for Web of Science ID 000238224100014

  View details for PubMedID 16793372

• Comparative TFIIS-mediated transcript cleavage by mammalian RNA polymerase II arrested at a lesion in different transcription systems DNA REPAIR Kalogeraki, V. S., Tornaletti, S., Cooper, P. K., Hanawalt, P. C. 2005; 4 (10): 1075-1087

  Abstract

  Upon prolonged arrest at a cyclobutane pyrimidine dimer (CPD), RNAPII can reverse-translocate, misaligning the 3'-end of the RNA from its active site. Transcription factor SII (TFIIS) is required for cleavage of the disengaged 3'-end and restoration of its correct positioning. We have previously shown in vitro that when RNAPII is arrested at a CPD, TFIIS-induced cleavage results in shortened transcripts. Here, we hypothesized that the pattern of transcript cleavage does not depend solely upon TFIIS itself, but also on some other general transcription factors (GTFs) and/or their effects on RNAPII. To test this hypothesis we compared three in vitro transcription systems which differ with respect to the mode of initiation and the requirement for GTFs. The first consisted of RNAPII and GTFs from rat liver, and required a eukaryotic promoter for initiation. The other two supported transcription in the absence of any GTFs or promoter sequences. In each case, a CPD on the transcribed strand was a complete block for RNAPII translocation. However, the effect of TFIIS on transcript cleavage varied. In the promoter-initiated system, distinct transcripts up to about 20 nucleotides shorter than the uncleaved original one were produced. In the other two systems, the transcripts were degraded nearly completely. Introduction of GTFs partially interfered with cleavage, but failed to reproduce the pattern of transcript lengths observed with the promoter-initiated system. Our results suggest that the extent of TFIIS-mediated transcript cleavage is a well-orchestrated process, depending upon other factors (or their effects on RNAPII), in addition to TFIIS itself.

  View details for DOI 10.1016/j.dnarep.2005.05.007

  View details for Web of Science ID 000232429100004

  View details for PubMedID 16046193

• Nucleotide excision repair activity varies among murine spermatogenic cell types BIOLOGY OF REPRODUCTION Xu, G. G., Spivak, G., Mitchell, D. L., Mori, T., McCarrey, J. R., McMahan, C. A., Walter, R. B., Hanawalt, P. C., Walter, C. A. 2005; 73 (1): 123-130

  Abstract

  Germ cells perform a unique and critical biological function: they propagate the DNA that will be used to direct development of the next generation. Genetic integrity of germ cell DNA is essential for producing healthy and reproductively fit offspring, and yet germ cell DNA is damaged by endogenous and exogenous agents. Nucleotide excision repair (NER) is an important mechanism for coping with a variety of DNA lesions. Little is known about NER activity in spermatogenic cells. We expected that germ cells would be more efficient at DNA repair than somatic cells, and that this efficiency may be reduced with age when the prevalence of spontaneous mutations increases. In the present study, NER was measured in defined spermatogenic cell types, including premeiotic cells (A and B type spermatogonia), meiotic cells (pachytene spermatocytes), and postmeiotic haploid cells (round spermatids) and compared with NER in keratinocytes. Global genome repair and transcription-coupled repair subpathways of NER were examined. All spermatogenic cell types from young mice displayed good repair of (6-4) pyrimidone photoproducts, although the repair rate was slower than in primary keratinocytes. In aged mice, repair of 6-4 pyrimidone photoproducts was depressed in postmeiotic cells. While repair of cyclobutane pyrimidine dimers was not detected in spermatogenic cells or in keratinocytes, the transcribed strands of active genes were repaired with greater efficiency than nontranscribed strands or inactive genes in keratinocytes and in meiotic and postmeiotic cells; spermatogonia displayed low to moderate ability to repair cyclobutane pyrimidine dimers on both DNA strands regardless of transcriptional status. Overall, the data suggest cell type-specific NER activity during murine spermatogenesis, and our results have possible implications for germ cell aging.

  View details for DOI 10.1095/biolreprod.104.039123

  View details for Web of Science ID 000229978700015

  View details for PubMedID 15758148

• Density matters: The semiconservative replication of DNA PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Hanawalt, P. C. 2004; 101 (52): 17889-17894

  Abstract

  The semiconservative mode of DNA replication was originally documented through the classic density labeling experiments of Matthew Meselson and Franklin W. Stahl, as communicated to PNAS by Max Delbruck in May 1958. The ultimate value of their novel approach has extended far beyond the initial implications from that elegant study, through more than four decades of research on DNA replication, recombination, and repair. I provide here a short historical commentary and then an account of some developments in the field of DNA replication, which closely followed the Meselson-Stahl experiment. These developments include the application of density labeling to discover the repair replication of damaged DNA, a "nonconservative" mode of synthesis in which faulty sections of DNA are replaced.

  View details for DOI 10.1073/pnas.0407539101

  View details for Web of Science ID 000226102700003

  View details for PubMedID 15608066

  View details for PubMedCentralID PMC539797

• Malondialdehyde adducts in DNA arrest transcription by T7 RNA polymerase and mammalian RNA polymerase II PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Cline, S. D., Riggins, J. N., Tornaletti, S., Marnett, L. J., Hanawalt, P. C. 2004; 101 (19): 7275-7280

  Abstract

  Malondialdehyde, a genotoxic byproduct of lipid peroxidation, reacts with guanine in DNA to form pyrimido[1,2-alpha]purin-10(3H)one (M(1)dG), the first endogenous DNA lesion found to be a target of nucleotide excision repair enzymes. A subpathway of nucleotide excision repair, transcription-coupled repair, is thought to occur when RNA polymerase (RNAP) is arrested at damage in transcribed DNA strands and might function for efficient removal of M(1)dG in active genes. Results presented here show that M(1)dG and its stable, exocyclic analog 1,N(2)-propanodeoxyguanine (PdG), arrest translocation of T7 RNAP and mammalian RNAPII when located in the transcribed strand of a DNA template. M(1)dG paired with thymine is exocyclic and poses a stronger block to transcription than the acyclic N(2)-(3-oxo-1-propenyl)-dG, formed upon cytosine-catalyzed opening of M(1)dG in duplex DNA. PdG is a complete block to RNAPII regardless of base pairing. The elongation factor TFIIS (SII) induces reversal and RNA transcript cleavage by RNAPII arrested at PdG. Thus, arrested RNAPII complexes may be stable at M(1)dG in cells and may resume transcription once the offending adduct is removed. The conclusion from this work is that malondialdehyde adducts in the transcribed strand of expressed genes are strong blocks to RNAPs and are targets for cellular transcription-coupled repair. If so, then M(1)dG, already known to be highly mutagenic in human cells, also may contribute to apoptosis in the developing tissues of individuals with Cockayne's syndrome, a hereditary disorder characterized by transcription-coupled repair deficiency.

  View details for DOI 10.1073/pnas.0402252101

  View details for Web of Science ID 000221559100015

  View details for PubMedID 15123825

  View details for PubMedCentralID PMC409909

• Effect of 8-oxoguanine on transcription elongation by T7 RNA polymerase and mammalian RNA polymerase II DNA REPAIR Silvia, T. A., Maeda, L. S., Kolodner, R. D., Hanawalt, P. C. 2004; 3 (5): 483-494

  Abstract

  8-Oxoguanine (8-oxoG) is a major oxidative lesion produced in DNA by normal cellular metabolism or after exposure to exogenous sources such as ionizing radiation. Persistence of this lesion in DNA causes G to T transversions, with deleterious consequences for the cell. As a result, several repair processes have evolved to remove this lesion from the genome. It has been reported that 8-oxoG is subject to transcription-coupled repair (TCR), a process dedicated to removal of lesions from transcribed strands of expressed genes. A current model assumes that RNA polymerase arrest at the site of the lesion is required for initiation of TCR. As a first step to understand how TCR of 8-oxoG occurs, we have studied the effect of 8-oxoG on transcription elongation by T7 RNA polymerase (T7 RNAP) and rat liver RNA polymerase II (RNAPII). We have utilized an in vitro transcription system with purified RNA polymerase and initiation factors, and substrates containing a single 8-oxoG in the transcribed or in the non-transcribed strand downstream of the T7 promoter or the Adenovirus major late promoter. We found that 8-oxoG only slightly inhibited T7 RNAP transcription, with a readthrough frequency of up to 95%. Similarly, this lesion only transiently blocked transcription by RNAPII. However, changes in nucleotide concentration affected the extent of RNAPII blockage at the 8-oxoG. When this lesion was positioned in the non-transcribed strand, complete lesion bypass was observed with either polymerase. Binding of the Saccharomyces cerevisiae MSH2-MSH6 complex to 8-oxoG containing substrates did not increase the frequency of RNAPII arrest at the site of the lesion, suggesting that this complex was displaced by the elongating polymerase. These results are discussed in the context of possible models for TCR.

  View details for DOI 10.1016/j.dnarep.2004.01.003

  View details for Web of Science ID 000221156400005

  View details for PubMedID 15084310

• Functional characterization of global genomic DNA repair and its implications for cancer 4th International Conference on Environmental Mutagens in Human Populations (ICEMHP) Hanawalt, P. C., Ford, J. A., Lloyd, D. R. ELSEVIER SCIENCE BV. 2003: 107–14

  Abstract

  The most versatile cellular pathway for dealing with a large variety of structurally-unrelated DNA alterations is nucleotide excision repair (NER). Most genomic damage, if not repaired, may contribute to mutagenesis and carcinogenesis, as well as to cellular lethality. There are two subpathways of NER, termed global genomic repair (GGR) and transcription-coupled repair (TCR); While GGR deals with all repairable lesions throughout the genome, TCR is selective for the transcribed DNA strand in expressed genes. Proteins involved in the initial recognition of lesions for GGR as well as for TCR (i.e. RNA polymerase) may sometimes initiate gratuitous repair events in undamaged DNA. However, the damage recognition enzymes for GGR are normally maintained at very low levels unless the cells are genomically stressed. Following UV irradiation in human fibroblasts the efficiency of GGR is upregulated through activation of the p53 tumor suppressor gene. The transactivation role of p53 includes control of expression of the genes, XPC and XPE, which are implicated in GGR but not TCR. These inducible responses are essential for the efficient repair of the most prominent lesion produced by UV, the cyclobutane pyrimidine dimer (CPD). They are also clinically relevant, as we have shown them to operate upon chemical carcinogen DNA damage at levels to which humans are environmentally exposed (e.g. through smoking). Thus, for benzo(a)pyrene (at 10-50 adducts per 10(8) nucleotides) repair was essentially complete within 1 day in p53(+/+) human fibroblasts while no repair was detected within 3 days in p53(-/-) cells. The levels of all four DNA adducts formed by benzo(g)chrysene, also exhibited p53-dependent control in human fibroblasts. However, unlike humans most rodent tissues are deficient in the p53-dependent GGR pathway. Since rodents are used as surrogates for humans in environmental cancer risk assessment it is very important that we determine how they differ from humans with respect to DNA repair and oncogenic responses to environmental genotoxins.

  View details for DOI 10.1016/j.mrrev.2003.06.002

  View details for PubMedID 14644313

• Four decades of DNA repair: from early insights to current perspectives BIOCHIMIE Hanawalt, P. C. 2003; 85 (11): 1043-1052

  Abstract

  A brief history of the evolution of the DNA repair field over the past four decades is presented, as documented through the Proceedings from a selected series of five scientific meetings, beginning with the 1965 Radiation Microbiology Conference, held at the University of Chicago with only 40 participants, and extending through the 1988 UCLA Symposium on "Mechanisms and Consequences of DNA Damage Processing", convened in Taos, New Mexico, with over 400 participants. The published proceedings and recorded discussions from these early conferences contain notable insights, of which many have turned out to be remarkably clairvoyant while others must be reevaluated in light of recent discoveries and developments in the field.

  View details for DOI 10.1016/j.biochi.2003.11.007

  View details for Web of Science ID 000188616000002

  View details for PubMedID 14726012

• Behavior of T7 RNA polymerase and mammalian RNA polymerase II at site-specific cisplatin adducts in the template DNA JOURNAL OF BIOLOGICAL CHEMISTRY Tornaletti, S., Patrick, S. M., Turchi, J. J., Hanawalt, P. C. 2003; 278 (37): 35791-35797

  Abstract

  Transcription-coupled DNA repair is dedicated to the removal of DNA lesions from transcribed strands of expressed genes. RNA polymerase arrest at a lesion has been proposed as a sensitive signal for recruitment of repair enzymes to the lesion site. To understand how initiation of transcription-coupled repair may occur, we have characterized the properties of the transcription complex when it encounters a lesion in its path. Here we have compared the effect of cisplatin-induced intrastrand cross-links on transcription elongation by T7 RNA polymerase and mammalian RNA polymerase II. We found that a single cisplatin 1,2-d(GG) intrastrand cross-link or a single cisplatin 1,3-d(GTG) intrastrand cross-link is a strong block to both polymerases. Furthermore, the efficiency of the block at a cisplatin 1,2-d(GG) intrastrand cross-link was similar in several different nucleotide sequence contexts. Interestingly, some blockage was also observed when the single cisplatin 1,3-d(GTG) intrastrand cross-link was located in the non-transcribed strand. Transcription complexes arrested at the cisplatin adducts were substrates for the transcript cleavage reaction mediated by the elongation factor TFIIS, indicating that the RNA polymerase II complexes arrested at these lesions are not released from template DNA. Addition of TFIIS yielded a population of transcripts up to 30 nucleotides shorter than those arrested at the lesion. In the presence of nucleoside triphosphates, these shortened transcripts could be re-elongated up to the site of the lesion, indicating that the arrested complexes are stable and competent to resume elongation. These results show that cisplatin-induced lesions in the transcribed DNA strand constitute a strong physical barrier to RNA polymerase progression, and they support current models of transcription arrest and initiation of transcription-coupled repair.

  View details for DOI 10.1074/jbc.M305394200

  View details for PubMedID 12829693

• Transcription arrest at a lesion in the transcribed DNA strand in vitro is not affected by a nearby lesion in the opposite strand JOURNAL OF BIOLOGICAL CHEMISTRY Kalogeraki, V. S., Tornaletti, S., Hanawalt, P. C. 2003; 278 (21): 19558-19564

  Abstract

  Cis-syn cyclobutane pyrimidine dimers (CPDs) are the most frequently formed lesions in UV-irradiated DNA. CPDs are repaired by the nucleotide excision repair pathway. Additionally, they are subject to transcription-coupled DNA repair. In the general model for transcription-coupled DNA repair, an RNA polymerase arrested at a lesion on the transcribed DNA strand facilitates repair by recruiting the repair machinery to the site of the lesion. Consistent with this model, transcription experiments in vitro have shown that CPDs in the transcribed DNA strand interfere with the translocation of prokaryotic and eukaryotic RNA polymerases. Here, we study the behavior of RNA polymerase when transcribing a template that contains two closely spaced lesions, one on each DNA strand. Similar DNA templates containing no CPD, or a single CPD on either the transcribed or the nontranscribed strand were used as controls. Using an in vitro transcription system with purified T7 RNA polymerase (T7 RNAP) or rat liver RNAP II, we characterized transcript length and efficiency of transcription in vitro. We also tested the sensitivity of the arrested RNAP II-DNA-RNA ternary complex, at a CPD in the transcribed strand, to transcription factor TFIIS. The presence of a nearby CPD in the nontranscribed strand did not affect the behavior of either RNA polymerase nor did it affect the reverse translocation ability of the RNAP II-arrested complex. Our results additionally indicate that the sequence context of a CPD affects the efficiency of T7 RNAP arrest more significantly than that of RNAP II.

  View details for DOI 10.1074/jbc.M301060200

  View details for Web of Science ID 000182932200107

  View details for PubMedID 12646562

• Who's on first in the cellular response to DNA damage? NATURE REVIEWS MOLECULAR CELL BIOLOGY Cline, S. D., Hanawalt, P. C. 2003; 4 (5): 361-372

  Abstract

  Cellular DNA-repair pathways involve proteins that have roles in other DNA-metabolic processes, as well as those that are dedicated to damage removal. Several proteins, which have diverse functions and are not known to have roles in DNA repair, also associate with damaged DNA. These newly discovered interactions could either facilitate or hinder the recognition of DNA damage, and so they could have important effects on DNA repair and genetic integrity. The outcome for the cell, and ultimately for the organism, might depend on which proteins arrive first at sites of DNA damage.

  View details for DOI 10.1038/nrm1101

  View details for Web of Science ID 000182687000017

  View details for PubMedID 12728270

• When parsimony backfires: neglecting DNA repair may doom neurons in Alzheimer's disease BIOESSAYS Nouspikel, T., Hanawalt, P. C. 2003; 25 (2): 168-173

  Abstract

  Taking advantage of the fact that they need not replicate their DNA, terminally differentiated neurons only repair their expressed genes and largely dispense with the burden of removing damage from most of their genome. However, they may pay a heavy price for this laxity if unforeseen circumstances, such as a pathological condition like Alzheimer's disease, cause them to re-enter the cell cycle. The lifetime accumulation of unrepaired lesions in the silent genes of neurons is likely to be significant and may result in aborting the mitotic process and triggering cell death if the cells attempt to express these dormant genes and resume DNA replication.

  View details for DOI 10.1002/bies.10227

  View details for Web of Science ID 000180695000011

  View details for PubMedID 12539243

• RecA-dependent recovery of arrested DNA replication forks ANNUAL REVIEW OF GENETICS Courcelle, J., Hanawalt, P. C. 2003; 37: 611-646

  Abstract

  DNA damage encountered during the cellular process of chromosomal replication can disrupt the replication machinery and result in mutagenesis or lethality. The RecA protein of Escherichia coli is essential for survival in this situation: It maintains the integrity of the arrested replication fork and signals the upregulation of over 40 gene products, of which most are required to restore the genomic template and to facilitate the resumption of processive replication. Although RecA was originally discovered as a gene product that was required to change the genetic information during sexual cell cycles, over three decades of research have revealed that it is also the key enzyme required to maintain the genetic information when DNA damage is encountered during replication in asexual cell cycles. In this review, we examine the significant experimental approaches that have led to our current understanding of the RecA-mediated processes that restore replication following encounters with DNA damage.

  View details for DOI 10.1146/annurev.genet.37.110801.142616

  View details for Web of Science ID 000187792500023

  View details for PubMedID 14616075

• Subpathways of nucleotide excision repair and their regulation ONCOGENE Hanawalt, P. C. 2002; 21 (58): 8949-8956

  Abstract

  Nucleotide excision repair provides an important cellular defense against a large variety of structurally unrelated DNA alterations. Most of these alterations, if unrepaired, may contribute to mutagenesis, oncogenesis, and developmental abnormalities, as well as cellular lethality. There are two subpathways of nucleotide excision repair; global genomic repair (GGR) and transcription coupled repair (TCR), that is selective for the transcribed DNA strand in expressed genes. Some of the proteins involved in the recognition of DNA damage (including RNA polymerase) are also responsive to natural variations in the secondary structural features of DNA. Gratuitous repair events in undamaged DNA might then contribute to genomic instability. However, damage recognition enzymes for GGR are normally maintained at very low levels unless the cells are genomically stressed. GGR is controlled through the SOS stress response in E. coli and through the activated p53 tumor suppressor in human cells. These inducible responses in human cells are important, as they have been shown to operate upon chemical carcinogen DNA damage at levels to which humans are environmentally exposed. Interestingly, most rodent tissues are deficient in the p53-dependent GGR pathway. Since rodents are used as surrogates for environmental cancer risk assessment, it is essential that we understand how they differ from humans with respect to DNA repair and oncogenic responses to environmental genotoxins. In the case of terminally differentiated mammalian cells, a new paradigm has appeared in which GGR is attenuated but both strands of expressed genes are repaired efficiently.

  View details for DOI 10.1038/sj.onc.1206096

  View details for Web of Science ID 000179889500006

  View details for PubMedID 12483511

• p53 controls global nucleotide excision repair of low levels of structurally diverse benzo(g)chrysene-DNA adducts in human fibroblasts CANCER RESEARCH Lloyd, D. R., Hanawalt, P. C. 2002; 62 (18): 5288-5294

  Abstract

  Benzo(g)chrysene is a widespread environmental contaminant and potent carcinogen. We have measured the formation and nucleotide excision repair of covalent DNA adducts formed by the DNA-reactive metabolite of this compound in human fibroblasts, in which expression of the p53 tumor suppressor gene could be controlled by a tetracycline-inducible promoter. Cells were exposed for 1 h to 0.01, 0.1, or 1.2 microM (+/-)-anti-benzo(g)chrysene diol-epoxide, and DNA adducts were assessed at various post-treatment times by subjecting isolated DNA to (32)P-postlabeling analysis. Four major DNA adducts were detected, corresponding to the reaction of either the (+)- or (-)-anti-benzo(g)chrysene diol-epoxide stereoisomer with adenine or guanine. Treatment with 1.2 microM resulted in a level of 1100 total adducts/10(8) nucleotides for both p53-proficient and -deficient cells; removal of adducts was not observed in either case. In cells treated with 0.1 microM, the maximum level of total adducts at 24 h was 150/10(8) nucleotides in p53-proficient cells and 210 adducts/10(8) nucleotides in p53-deficient cells. A concentration of 0.01 microM resulted in a maximum of 20 adducts/10(8) nucleotides in p53-proficient cells at 4 h, but 40 adducts/10(8) nucleotides persisted in p53-deficient cells at 24 h. Whereas there were clear differences in the time course of adduct levels in p53-proficient compared with p53-deficient cells treated with 0.1 microM or 0.01 microM, these levels did not decrease extensively over 3 days. This is likely because of the stabilization of the diol-epoxide in cells, and consequent exposure and formation of adducts for many hours after the initial treatment. Furthermore, despite minor quantitative differences, all 4 of the adducts behaved similarly with respect to the effect of p53 expression on their removal. p53 appears to minimize the appearance of benzo(g)chrysene adducts in human cells by up-regulating global nucleotide excision repair and reducing the maximum adduct levels achieved. The fact that this p53-dependent effect is noted at levels of DNA adducts that are commonly found in human tissues (i.e., <100 adducts/10(8) nucleotides) because of environmental factors such as smoking is particularly significant with respect to human carcinogenesis related to environmental exposure.

  View details for Web of Science ID 000178066400028

  View details for PubMedID 12234998

• Ultraviolet-sensitive syndrome cells are defective in transcription-coupled repair of cyclobutane pyrimidine dimers DNA REPAIR Spivak, G., Itoh, T., Matsunaga, T., Nikaido, O., Hanawalt, P., Yamaizumi, M. 2002; 1 (8): 629-643

  Abstract

  Patients with ultraviolet-sensitive syndrome (UV(S)S) are sensitive to sunlight, but present neither developmental nor neurological deficiencies. Complementation studies with hereditary DNA repair syndromes show that UV(S)S is distinct from all known xeroderma pigmentosum (XP) and Cockayne syndrome (CS) groups. UV(S)S cells exhibit some characteristics typical of CS, including normal global genomic (GGR) repair of UV-photoproducts, poor clonal survival and defective recovery of RNA synthesis after UV exposure. Those observations have led us to suggest that UV(S)S cells, like those from CS, are defective in transcription-coupled repair (TCR) of cyclobutane pyrimidine dimers (CPD). We have now examined the repair of CPD in the transcribed and non-transcribed strands of the active dihydrofolate reductase (DHFR) and p53 genes, and of the silent alpha-fetoprotein (AFP) and mid-size neurofilament (NF-M) genes in normal human cells and in cells belonging to UV(S)S and CS complementation group B. Our results provide compelling evidence that the UV(S)S gene is essential for TCR of CPD and probably other bulky DNA lesions. As a possible distinction between UV(S)S and CS patients, we postulate that the UV(S)S gene may not be required for TCR of oxidative lesions. We have also found that repair of CPD in either DNA strand of the genomic fragments examined, occurs at a slower rate in TCR-deficient cells than in the non-transcribed strands in normal cells; we suggest that in the absence of TCR, global repair complexes have hindered access to lesions in genomic regions that extend beyond individual transcription units.

  View details for Web of Science ID 000178248700004

  View details for PubMedID 12509286

• DNA repair in terminally differentiated cells DNA REPAIR Nouspikel, T., Hanawalt, P. C. 2002; 1 (1): 59-75

  Abstract

  Terminally differentiated cells do not replicate their genomic DNA, and could therefore dispense with the task of removing DNA damage from the non-essential bulk of their genome, as long as they are able to maintain the integrity of the genes that must be expressed. There is increasing experimental evidence that this is indeed the case, at least for some repair pathways such as nucleotide excision repair (NER). In this review, we examine a number of terminally differentiated cell systems in which it has been demonstrated that DNA repair is attenuated at the global genome level, but maintained in expressed genes. How these cells manage to repair transcribed genes is not yet fully elucidated, but there are indications that the transcription-coupled repair (TCR) pathway could maintain integrity of the transcribed strand (TS) in the active genes. We have observed in neurons that the non-transcribed strand (NTS) of active genes is also well repaired, a phenomenon that we have named differentiation-associated repair (DAR). It is conceivable that DAR is necessary to maintain the integrity of the template strand that is needed by TCR to complete the repair of lesions in the TS of essential expressed genes with high fidelity.

  View details for Web of Science ID 000182550600004

  View details for PubMedID 12509297

• Effect of thymine glycol on transcription elongation by T7 RNA polymerase and mammalian RNA polymerase II JOURNAL OF BIOLOGICAL CHEMISTRY Tornaletti, S., Maeda, L. S., Lloyd, D. R., Reines, D., Hanawalt, P. C. 2001; 276 (48): 45367-45371

  Abstract

  Thymine glycols are formed in DNA by exposure to ionizing radiation or oxidative stress. Although these lesions are repaired by the base excision repair pathway, they have been shown also to be subject to transcription-coupled repair. A current model for transcription-coupled repair proposes that RNA polymerase II arrested at a DNA lesion provides a signal for recruitment of the repair enzymes to the lesion site. Here we report the effect of thymine glycol on transcription elongation by T7 RNA polymerase and RNA polymerase II from rat liver. DNA substrates containing a single thymine glycol located either in the transcribed or nontranscribed strand were used to carry out in vitro transcription. We found that thymine glycol in the transcribed strand blocked transcription elongation by T7 RNA polymerase approximately 50% of the time but did not block RNA polymerase II. Thymine glycol in the nontranscribed strand did not affect transcription by either polymerase. These results suggest that arrest of RNA polymerase elongation by thymine glycol is not necessary for transcription-coupled repair of this lesion. Additional factors that recognize and bind thymine glycol in DNA may be required to ensure RNA polymerase arrest and the initiation of transcription-coupled repair in vivo.

  View details for Web of Science ID 000172406700132

  View details for PubMedID 11571287

  View details for PubMedCentralID PMC3373304

• Spatially localized generation of nucleotide sequence-specific DNA damage PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Oh, D. H., King, B. A., Boxer, S. G., Hanawalt, P. C. 2001; 98 (20): 11271-11276

  Abstract

  Psoralens linked to triplex-forming oligonucleotides (psoTFOs) have been used in conjunction with laser-induced two-photon excitation (TPE) to damage a specific DNA target sequence. To demonstrate that TPE can initiate photochemistry resulting in psoralen-DNA photoadducts, target DNA sequences were incubated with psoTFOs to form triple-helical complexes and then irradiated in liquid solution with pulsed 765-nm laser light, which is half the quantum energy required for conventional one-photon excitation, as used in psoralen + UV A radiation (320-400 nm) therapy. Target DNA acquired strand-specific psoralen monoadducts in a light dose-dependent fashion. To localize DNA damage in a model tissue-like medium, a DNA-psoTFO mixture was prepared in a polyacrylamide gel and then irradiated with a converging laser beam targeting the rear of the gel. The highest number of photoadducts formed at the rear while relatively sparing DNA at the front of the gel, demonstrating spatial localization of sequence-specific DNA damage by TPE. To assess whether TPE treatment could be extended to cells without significant toxicity, cultured monolayers of normal human dermal fibroblasts were incubated with tritium-labeled psoralen without TFO to maximize detectable damage and irradiated by TPE. DNA from irradiated cells treated with psoralen exhibited a 4- to 7-fold increase in tritium activity relative to untreated controls. Functional survival assays indicated that the psoralen-TPE treatment was not toxic to cells. These results demonstrate that DNA damage can be simultaneously manipulated at the nucleotide level and in three dimensions. This approach for targeting photochemical DNA damage may have photochemotherapeutic applications in skin and other optically accessible tissues.

  View details for Web of Science ID 000171237100054

  View details for PubMedID 11572980

  View details for PubMedCentralID PMC58719

• Participation of recombination proteins in rescue of arrested replication forks in UV-irradiated Escherichia coli need not involve recombination Colloquium on Links Between Recombination and Replication - Vital Roles of Recombination Courcelle, J., Hanawalt, P. C. NATL ACAD SCIENCES. 2001: 8196–8202

  Abstract

  Alternative reproductive cycles make use of different strategies to generate different reproductive products. In Escherichia coli, recA and several other rec genes are required for the generation of recombinant genomes during Hfr conjugation. During normal asexual reproduction, many of these same genes are needed to generate clonal products from UV-irradiated cells. However, unlike conjugation, this latter process also requires the function of the nucleotide excision repair genes. Following UV irradiation, the recovery of DNA replication requires uvrA and uvrC, as well as recA, recF, and recR. The rec genes appear to be required to protect and maintain replication forks that are arrested at DNA lesions, based on the extensive degradation of the nascent DNA that occurs in their absence. The products of the recJ and recQ genes process the blocked replication forks before the resumption of replication and may affect the fidelity of the recovery process. We discuss a model in which several rec gene products process replication forks arrested by DNA damage to facilitate the repair of the blocking DNA lesions by nucleotide excision repair, thereby allowing processive replication to resume with no need for strand exchanges or recombination. The poor survival of cellular populations that depend on recombinational pathways (compared with that in their excision repair proficient counterparts) suggests that at least some of the rec genes may be designed to function together with nucleotide excision repair in a common and predominant pathway by which cells faithfully recover replication and survive following UV-induced DNA damage.

  View details for Web of Science ID 000169967000011

  View details for PubMedID 11459953

• The SOS-dependent upregulation of uvrD is not required for efficient nucleotide excision repair of ultraviolet light induced DNA photoproducts in Escherichia coli MUTATION RESEARCH-DNA REPAIR Crowley, D. J., Hanawalt, P. C. 2001; 485 (4): 319-329

  Abstract

  We have shown previously that induction of the SOS response is required for efficient nucleotide excision repair (NER) of the major ultraviolet light (UV) induced DNA lesion, the cyclobutane pyrimidine dimer (CPD), but not for repair of 6-4 photoproducts (6-4PP) or for transcription-coupled repair of CPDs [1]. We have proposed that the upregulation of cellular NER capacity occurs in the early stages of the SOS response and enhances the rate of repair of the abundant yet poorly recognized genomic CPDs. The expression of three NER genes, uvrA, uvrB, and uvrD, is upregulated as part of the SOS response. UvrD differs from the others in that it is not involved in lesion recognition but rather in promoting the post-incision steps of NER, including turnover of the UvrBC incision complex. Since uvrC is not induced during the SOS response, its turnover would seem to be of great importance in promoting efficient NER. Here we show that the constitutive level of UvrD is adequate for carrying out efficient NER of both CPDs and 6-4PPs. Thus, the upregulation of uvrA and uvrB genes during the SOS response is sufficient for inducible NER of CPDs. We also show that cells with a limited NER capacity, in this case due to deletion of the uvrD gene, repair 6-4PPs but cannot perform transcription-coupled repair of CPDs, indicating that the 6-4PP is a better substrate for NER than is a CPD targeted for transcription-coupled repair.

  View details for Web of Science ID 000168632600004

  View details for PubMedID 11585364

• Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli GENETICS Courcelle, J., Khodursky, A., Peter, B., Brown, P. O., Hanawalt, P. C. 2001; 158 (1): 41-64

  Abstract

  The SOS response in UV-irradiated Escherichia coli includes the upregulation of several dozen genes that are negatively regulated by the LexA repressor. Using DNA microarrays containing amplified DNA fragments from 95.5% of all open reading frames identified on the E. coli chromosome, we have examined the changes in gene expression following UV exposure in both wild-type cells and lexA1 mutants, which are unable to induce genes under LexA control. We report here the time courses of expression of the genes surrounding the 26 documented lexA-regulated regions on the E. coli chromosome. We observed 17 additional sites that responded in a lexA-dependent manner and a large number of genes that were upregulated in a lexA-independent manner although upregulation in this manner was generally not more than twofold. In addition, several transcripts were either downregulated or degraded following UV irradiation. These newly identified UV-responsive genes are discussed with respect to their possible roles in cellular recovery following exposure to UV irradiation.

  View details for PubMedID 11333217

• Therefore, what are recombination proteins there for? BIOESSAYS Courcelle, J., Ganesan, A. K., Hanawalt, P. C. 2001; 23 (5): 463-470

  Abstract

  The order of discovery can have a profound effect upon the way in which we think about the function of a gene. In E. coli, recA is nearly essential for cell survival in the presence of DNA damage. However, recA was originally identified, as a gene required to obtain recombinant DNA molecules in conjugating bacteria. As a result, it has been frequently assumed that recA promotes the survival of bacteria containing DNA damage by recombination in which DNA strand exchanges occur. We now know that several of the processes that interact with or are controlled by recA, such as excision repair and translesion synthesis, operate to ensure that DNA replication occurs processively without strand exchanges. Yet the view persists in the literature that recA functions primarily to promote recombination during DNA repair. With the benefit of hindsight and more than three decades of additional research, we reexamine some of the classical experiments that established the concept of DNA repair by recombination, and we consider the possibilities that recombination is not an efficient mechanism for rescuing damaged cells, and that recA may be important for maintaining processive replication in a manner that does not generally promote recombination.

  View details for Web of Science ID 000168435600012

  View details for PubMedID 11340628

• Controlling the efficiency of excision repair MUTATION RESEARCH-DNA REPAIR Hanawalt, P. C. 2001; 485 (1): 3-13

  Abstract

  The early studies are recounted, that led to the discovery of the ubiquitous process of DNA excision repair, followed by a review of the pathways of transcription-coupled repair (TCR) and global genomic nucleotide excision repair (GGR). Repair replication of damaged DNA in UV-irradiated bacteria was discovered through the use of 5-bromouracil to density-label newly synthesized DNA. This assay was then used in human cells to validate the phenomenon of unscheduled DNA synthesis as a measure of excision repair and to elucidate the first example of a DNA repair disorder, xeroderma pigmentosum. Features of the TCR pathway (that is defective in Cockayne syndrome (CS)) include the possibility of "gratuitous TCR" at transcription pause sites in undamaged DNA. The GGR pathway is shown to be controlled through the SOS stress response in E. coli and through the activated product of the p53 tumor suppressor gene in human cells. These regulatory systems particularly affect the efficiency of repair of the predominant UV-induced photoproduct, the cyclobutane pyrimidine dimer, as well as that of chemical carcinogen adducts, such as benzo(a)pyrene diol-epoxide. Rodent cells (typically lacking the p53-controlled GGR pathway) and tumor virus infected human cells (in which p53 function is abrogated) are unable to carry out efficient GGR of some lesions. Therefore, caution should be exercised in the interpretation of results from such systems for risk assessment in genetic toxicology. Many problems in excision repair remain to be solved, including the mechanism of scanning the DNA for lesions and the subcellular localization of the repair factories. Also there are persisting questions regarding the multiple options of repair, recombination, and translesion synthesis when replication forks encounter lesions in the template DNA. That is where the field of DNA excision repair began four decades ago with studies on the recovery of DNA synthesis in UV-irradiated bacteria.

  View details for Web of Science ID 000167023500002

  View details for PubMedID 11341989

• Revisiting the rodent repairadox ENVIRONMENTAL AND MOLECULAR MUTAGENESIS Hanawalt, P. C. 2001; 38 (2-3): 89-96

  Abstract

  Cultured rodent and human cells typically display similar clonal survival characteristics following exposure to ultraviolet light (UV). However, compared to human cells, cultured cells from mice, rats, and hamsters are generally deficient in excision repair of the most prominent DNA lesion produced by UV, the cyclobutane pyrimidine dimer. In light of recent studies on the control of nucleotide excision repair, we are beginning to understand the basis for this so-called "repairadox." The resolution of this issue is important because rodents are so widely employed as surrogates for humans in genetic toxicology. This article will review the evolution in our understanding of rodent DNA repair and will also "revisit" my early association with my graduate mentor and esteemed colleague, Dick Setlow, in his honor upon the attainment of his 80th birthday.

  View details for Web of Science ID 000172017400002

  View details for PubMedID 11746740

• Reduced global genomic repair of ultraviolet light-induced cyclobutane pyrimidine dimers in simian virus 40-transformed human cells MOLECULAR CARCINOGENESIS Bowman, K. K., Sicard, D. M., Ford, J. M., Hanawalt, P. C. 2000; 29 (1): 17-24

  Abstract

  The p53 tumor-suppressor gene has been implicated in the inducible activation of excision repair of ultraviolet (UV)-induced cyclobutane pyrimidine dimers (CPDs) in human cells. Because the large T antigen (LTAg) of the simian virus 40 (SV40) binds p53 protein and can interfere with its function, it was of interest to study DNA repair in normal human fibroblasts that had been transformed by SV40 compared with that in their nontransformed parental counterparts and to determine whether such transformation attenuated global genomic repair (GGR) of CPDs. Three methods were used to measure GGR in UV-irradiated cells: (i) an immunoassay using monoclonal antibodies specific for CPDs or 6-4 photoproducts (6-4PPs), (ii) zone sedimentation in alkaline sucrose gradients to measure the average DNA strand size after specific nicking at CPD sites in duplex DNA with T4 endonuclease V (TEV), and (iii) Southern hybridization of TEV-treated DNA with strand-specific mRNA probes to assess removal of CPDs from either strand of a defined genetic sequence in an expressed gene. Whereas repair of 6-4PPs was very similar in paired SV40-transformed and primary fibroblasts, GGR of CPDs was significantly reduced in the SV40-transformed cells. In contrast, SV40 transformation did not appreciably affect the efficiency of transcription-coupled repair. These data support the hypothesis that SV40 transformation can result in reduced levels of GGR, most likely because of the inhibition of normal p53 function by LTAg.

  View details for Web of Science ID 000089690900003

  View details for PubMedID 11020243

• Binding and photoreactivity of psoralen linked to triple helix-forming oligonucleotides PHOTOCHEMISTRY AND PHOTOBIOLOGY Oh, D. H., Hanawalt, P. C. 2000; 72 (3): 298-307

  Abstract

  Triple helix-forming oligonucleotides conjugated to a psoralen (psoTFO) have been designed to bind to three distinct purine-rich sequences within the human interstitial collagenase (MMP1) gene. Gel mobility shift assays indicate that these psoTFO bind to and photoreact with model target DNA sequences following ultraviolet A (UVA) irradiation. The dissociation constants for binding of the psoTFO to their targets range from 0.3 to 4 microM. Psoralen monoadducts with the purine-rich target strand and interstrand crosslinks are efficiently formed on targets containing either 5'-ApT-3' or 5'-TpA-3' sequences adjacent to the TFO binding sequence. The dependence of adduct formation on UVA dose has provided quantitative estimates of the overall rate constants for psoralen monoadduct and crosslink formation in the presence of a TFO. When psoralen is tethered to a TFO, the rate of monoadduct formation exceeds that of crosslinking for all sequences studied. This contrasts with the relatively low rate of monoadduct formation that has been reported for free psoralens, suggesting that the bound TFO facilitates the initial photochemistry that generates monoadducts, but does not significantly affect interstrand crosslink formation. psoTFO and UVA treatment inhibit DNA cleavage by a restriction endonuclease when the psoralen covalently reacts directly at the endonuclease site. The particular TFO studied do not completely inhibit endonuclease activity when they are noncovalently bound or when the covalent psoralen adduct does not coincide with the endonuclease site. Our findings confirm that TFO are capable of directing psoralen photoadducts to specific DNA targets and suggest that TFO can significantly modulate psoralen photoreactivity and DNA-protein interactions.

  View details for Web of Science ID 000089212700004

  View details for PubMedID 10989598

• Histone H3 and heat shock protein GRP78 are selectively cross-linked to DNA by photoactivated gilvocarcin V in human fibroblasts CANCER RESEARCH Matsumoto, A., Hanawalt, P. C. 2000; 60 (14): 3921-3926

  Abstract

  Gilvocarcin V (GV) is an antitumor antibiotic with a coumarin-based aromatic structure that promotes protein-DNA cross-linking when photoactivated by near-UV light. We have now identified several proteins that are selectively cross-linked to DNA in human fibroblasts by photoactivated GV, using NH2-terminal amino acid sequencing and Western blot analysis of the purified cross-linked proteins. The selectively cross-linked proteins are histone H3 and GRP78, a heat shock protein belonging to the heat shock protein-70 family. The hydrophobic leader sequence is missing from the cross-linked GRP78, suggesting that only the processed form of the protein is cross-linked to DNA. It is primarily the phosphorylated form of histone H3 that is cross-linked to DNA. Gel retardation analysis from four different GV-treated human fibroblast cell lines revealed two distinct shifted bands, and subsequent immunoblotting confirmed in situ that the slower and the faster bands, respectively, contained GRP78 and histone H3 cross-linked to DNA. The selective cross-linking of these particular proteins is dependent on UV irradiation in the presence of GV, which may help to clarify the unique molecular mechanism of this potent antitumor agent.

  View details for Web of Science ID 000088365300038

  View details for PubMedID 10919670

• p53-mediated DNA repair responses to UV radiation: Studies of mouse cells lacking p53, p21, and/or gadd45 genes MOLECULAR AND CELLULAR BIOLOGY Smith, M. L., Ford, J. M., Hollander, M. C., Bortnick, R. A., Amundson, S. A., Seo, Y. R., Deng, C. X., Hanawalt, P. C., Fornace, A. J. 2000; 20 (10): 3705-3714

  Abstract

  Human cells lacking functional p53 exhibit a partial deficiency in nucleotide excision repair (NER), the pathway for repair of UV-induced DNA damage. The global genomic repair (GGR) subpathway of NER, but not transcription-coupled repair (TCR), is mainly affected by p53 loss or inactivation. We have utilized mouse embryo fibroblasts (MEFs) lacking p53 genes or downstream effector genes of the p53 pathway, gadd45 (Gadd45a) or p21 (Cdkn1a), as well as MEFs lacking both gadd45 and p21 genes to address the potential contribution of these downstream effectors to p53-associated DNA repair. Loss of p53 or gadd45 had a pronounced effect on GGR, while p21 loss had only a marginal effect, determined by measurements of repair synthesis (unscheduled DNA synthesis), by immunoassays to detect removal of UV photoproducts from genomic DNA, and by assays determining strand-specific removal of CPDs from the mouse dhfr gene. Taken together, the evidence suggests a role for Gadd45, but relatively little role for p21, in DNA repair responses to UV radiation. Recent evidence suggests that Gadd45 binds to UV-damaged chromatin and may affect lesion accessibility. MEFs lacking p53 or gadd45 genes exhibited decreased colony-forming ability after UV radiation and cisplatin compared to wild-type MEFs, indicating their sensitivity to DNA damage. We provide evidence that Gadd45 affects chromatin remodelling of templates concurrent with DNA repair, thus indicating that Gadd45 may participate in the coupling between chromatin assembly and DNA repair.

  View details for Web of Science ID 000086698100038

  View details for PubMedID 10779360

  View details for PubMedCentralID PMC85670

• Xeroderma pigmentosum p48 gene enhances global genomic repair and suppresses UV-induced mutagenesis MOLECULAR CELL Tang, J. Y., Hwang, B. J., Ford, J. M., Hanawalt, P. C., Chu, G. 2000; 5 (4): 737-744

  Abstract

  UV-damaged DNA-binding activity (UV-DDB) is deficient in some xeroderma pigmentosum group E individuals due to mutation of the p48 gene, but its role in DNA repair has been obscure. We found that UV-DDB is also deficient in cell lines and primary tissues from rodents. Transfection of p48 conferred UV-DDB to hamster cells, and enhanced removal of cyclobutane pyrimidine dimers (CPDs) from genomic DNA and from the nontranscribed strand of an expressed gene. Expression of p48 suppressed UV-induced mutations arising from the nontranscribed strand, but had no effect on cellular UV sensitivity. These results define the role of p48 in DNA repair, demonstrate the importance of CPDs in mutagenesis, and suggest how rodent models can be improved to better reflect cancer susceptibility in humans.

  View details for PubMedID 10882109

• Terminally differentiated human neurons repair transcribed genes but display attenuated global DNA repair and modulation of repair gene expression MOLECULAR AND CELLULAR BIOLOGY Nouspikel, T., Hanawalt, P. C. 2000; 20 (5): 1562-1570

  Abstract

  Repair of UV-induced DNA lesions in terminally differentiated human hNT neurons was compared to that in their repair-proficient precursor NT2 cells. Global genome repair of (6-4)pyrimidine-pyrimidone photoproducts was significantly slower in hNT neurons than in the precursor cells, and repair of cyclobutane pyrimidine dimers (CPDs) was not detected in the hNT neurons. This deficiency in global genome repair did not appear to be due to denser chromatin structure in hNT neurons. By contrast, CPDs were removed efficiently from both strands of transcribed genes in hNT neurons, with the nontranscribed strand being repaired unexpectedly well. Correlated with these changes in repair during neuronal differentiation were modifications in the expression of several repair genes, in particular an up-regulation of the two structure-specific nucleases XPG and XPF/ERCC1. These results have implications for neuronal dysfunction and aging.

  View details for Web of Science ID 000085342200011

  View details for PubMedID 10669734

• p53-dependent global genomic repair of benzo[a]pyrene-7,8-diol-9,10-epoxide adducts in human cells CANCER RESEARCH Lloyd, D. R., Hanawalt, P. C. 2000; 60 (3): 517-521

  Abstract

  The global genomic repair of DNA adducts formed by the human carcinogen (+/-)-anti-benzo[a]pyrene-7,8-diol-9,10-epoxide (BPDE) has been studied by 32P-postlabeling in human fibroblasts in which p53 expression can be regulated. At low BPDE adduct levels (10-50 adducts/10(8) nucleotides), repair was rapid and essentially complete within 24 h in p53+ cells, whereas no repair was detected within 72 h in similarly treated p53- cells. At 10-fold higher BPDE adduct levels, repair under both conditions was rapid up to 8 h, after which a low level of adducts persisted only in p53- cells. These results demonstrate a dependence on p53 for the efficient repair of BPDE adducts at levels that are relevant to human environmental exposure and, thus, have significant implications for human carcinogenesis.

  View details for Web of Science ID 000085235600004

  View details for PubMedID 10676627

• Regulation of nucleotide excision repair in bacteria and mammalian cells Cold Spring Harbor Symposium on Quantitative Biology Hanawalt, P. C., Crowley, D. J., Ford, J. M., Ganesan, A. K., Lloyd, D. R., Nouspikel, T., Smith, C. A., Spivak, G., Tornaletti, S. COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT. 2000: 183–191

  View details for Web of Science ID 000169676800019

  View details for PubMedID 12760032

• Triple helix-forming oligonucleotides target psoralen adducts to specific chromosomal sequences in human cells NUCLEIC ACIDS RESEARCH Oh, D. H., Hanawalt, P. C. 1999; 27 (24): 4734-4742

  Abstract

  The ability to target photochemical adducts to specific genomic DNA sequences in cells is useful for studying DNA repair and mutagenesis in intact cells, and also as a potential mode of gene-specific therapy. Triple helix-forming DNA oligonucleotides linked to psoralen (psoTFOs) were designed to deliver UVA-induced psoralen photoadducts to two distinct sequences within the human interstitial collagenase gene. A primer extension assay demonstrated that the appropriate psoTFO selectively damages a collagenase cDNA target. Site-specific genomic psoTFO DNA adducts were detected by a single-strand ligation PCR assay. The adduct, formed at a single site by a psoTFO in purified genomic DNA, contrasted with the multiple sites that were damaged within the observed segment of the collagenase gene upon treatment with free psoralen and subsequent photoactivation. When treated with psoTFOs, both repair-deficient fibroblasts from xero- derma pigmentosum complementation group A and HT1080 fibrosarcoma cells exhibited site-specific DNA adducts following UVA irradiation. Addition of phorbol ester, a transcriptional activator of the collagenase gene, to xeroderma pigmentosum cells did not detectably alter the initial levels of damage produced by psoTFOs, suggesting that further stimulation of transcription neither improves accessibility of psoTFOs to their targets nor enhances removal of non-covalently bound psoTFOs.

  View details for Web of Science ID 000084547200009

  View details for PubMedID 10572173

• A phylogenomic study of DNA repair genes, proteins, and processes MUTATION RESEARCH-DNA REPAIR Eisen, J. A., Hanawalt, P. C. 1999; 435 (3): 171-213

  Abstract

  The ability to recognize and repair abnormal DNA structures is common to all forms of life. Studies in a variety of species have identified an incredible diversity of DNA repair pathways. Documenting and characterizing the similarities and differences in repair between species has important value for understanding the origin and evolution of repair pathways as well as for improving our understanding of phenotypes affected by repair (e.g., mutation rates, lifespan, tumorigenesis, survival in extreme environments). Unfortunately, while repair processes have been studied in quite a few species, the ecological and evolutionary diversity of such studies has been limited. Complete genome sequences can provide potential sources of new information about repair in different species. In this paper, we present a global comparative analysis of DNA repair proteins and processes based upon the analysis of available complete genome sequences. We use a new form of analysis that combines genome sequence information and phylogenetic studies into a composite analysis we refer to as phylogenomics. We use this phylogenomic analysis to study the evolution of repair proteins and processes and to predict the repair phenotypes of those species for which we now know the complete genome sequence.

  View details for Web of Science ID 000084300500001

  View details for PubMedID 10606811

• RecQ and RecJ process blocked replication forks prior to the resumption of replication in UV-irradiated Escherichia coli MOLECULAR AND GENERAL GENETICS Courcelle, J., Hanawalt, P. C. 1999; 262 (3): 543-551

  Abstract

  The accurate recovery of replication following DNA damage and repair is critical for the maintenance of genomic integrity. In Escherichia coli, the recovery of replication following UV-induced DNA damage is dependent upon several proteins in the recF pathway, including RecF, RecO, and RecR. Two other recF pathway proteins, the RecQ helicase and the RecJ exonuclease, have been shown to affect the sites and frequencies at which illegitimate rearrangements occur following UV-induced DNA damage, suggesting that they also may function during the recovery of replication. We show here that RecQ and RecJ process the nascent DNA at blocked replication forks prior to the resumption of DNA synthesis. The processing involves selective degradation of the nascent lagging DNA strand and it requires both RecQ and RecJ. We suggest that this processing may serve to lengthen the substrate that can be recognized and stabilized by the RecA protein at the replication fork, thereby helping to ensure the accurate recovery of replication after the obstructing lesion has been repaired.

  View details for Web of Science ID 000083839000018

  View details for PubMedID 10589843

• Structural characterization of RNA polymerase II complexes arrested by a cyclobutane pyrimidine dimer in the transcribed strand of template DNA JOURNAL OF BIOLOGICAL CHEMISTRY Tornaletti, S., Reines, D., Hanawalt, P. C. 1999; 274 (34): 24124-24130

  Abstract

  We have characterized the properties of immunopurified transcription complexes arrested at a specifically located cyclobutane pyrimidine dimer (CPD) using enzymatic probes and an in vitro transcription system with purified RNA polymerase II (RNAP II) and initiation factors. To help understand how RNAP II distinguishes between a natural impediment and a lesion in the DNA to initiate a repair event, we have compared the conformation of RNAP II complexes arrested at a CPD with complexes arrested at a naturally occurring elongation impediment. The footprint of RNAP II arrested at a CPD, using exonuclease III and T4 DNA polymerase's 3'-->5' exonuclease, covers approximately 35 base pairs and is asymmetrically located around the dimer. A similar footprint is observed when RNAP II is arrested at the human histone H3.3 arrest site. Addition of elongation factor SII to RNAP II arrested at a CPD produced shortened transcripts of discrete lengths up to 25 nucleotides shorter than those seen without SII. After addition of photolyase and exposure to visible light, some of the transcripts could be reelongated beyond the dimer, suggesting that SII-mediated transcript cleavage accompanied significant RNAP II backup, thereby providing access of the repair enzyme to the arresting CPD.

  View details for Web of Science ID 000082110900063

  View details for PubMedID 10446184

• Expression and nucleotide excision repair of a UV-irradiated reporter gene in unirradiated human cells MUTATION RESEARCH-DNA REPAIR Ganesan, A. K., Hunt, J., Hanawalt, P. C. 1999; 433 (2): 117-126

  Abstract

  It has been suggested that reactivation of damaged reporter genes introduced into cultured mammalian cells reflects transcription-coupled nucleotide excision repair. To evaluate this possibility directly, we introduced a UV-irradiated shuttle vector, pCMV beta, into unirradiated human cells and compared expression of the reporter gene (lacZ) with repair of cyclobutane pyrimidine dimers (CPDs). Expression of the irradiated reporter gene was more UV resistant in XPC cells, which are deficient in global genome repair, than in CSB cells, which are deficient in transcription-coupled repair. These results are consistent with the idea that repair of the reporter gene is primarily dependent upon transcription-coupled repair. However, when the plasmid DNA was analyzed for removal of CPDs, no clear evidence was obtained for transcription-coupled repair either in XPC cells or in cells with normal repair capacity.

  View details for Web of Science ID 000079208100005

  View details for PubMedID 10102038

• Recovery of DNA replication in UV-irradiated Escherichia coli requires both excision repair and RecF protein function JOURNAL OF BACTERIOLOGY Courcelle, J., Crowley, D. J., Hanawalt, P. C. 1999; 181 (3): 916-922

  Abstract

  After UV doses that disrupt DNA replication, the recovery of replication at replication forks in Escherichia coli requires a functional copy of the recF gene. In recF mutants, replication fails to recover and extensive degradation of the nascent DNA occurs, suggesting that recF function is needed to stabilize the disrupted replication forks and facilitate the process of recovery. We show here that the ability of recF to promote the recovery of replication requires that the disrupting lesions be removed. In the absence of excision repair, recF+ cells protect the nascent DNA at replication forks, but replication does not resume. The classical view is that recombination proteins operate in pathways that are independent from DNA repair, and therefore the functions of Rec proteins have been studied in repair-deficient cells. However, mutations in either uvr or recF result in failure to recover replication at UV doses from which wild-type cells recover efficiently, suggesting that recF and excision repair contribute to a common pathway in the recovery of replication.

  View details for Web of Science ID 000078390600028

  View details for PubMedID 9922256

• Expression of the p48 xeroderma pigmentosum gene is p53-dependent and is involved in global genomic repair PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Hwang, B. J., Ford, J. M., Hanawalt, P. C., Chu, G. 1999; 96 (2): 424-428

  Abstract

  In human cells, efficient global genomic repair of DNA damage induced by ultraviolet radiation requires the p53 tumor suppressor, but the mechanism has been unclear. The p48 gene is required for expression of an ultraviolet radiation-damaged DNA binding activity and is disrupted by mutations in the subset of xeroderma pigmentosum group E cells that lack this activity. Here, we show that p48 mRNA levels strongly depend on basal p53 expression and increase further after DNA damage in a p53-dependent manner. Furthermore, like p53(-/-) cells, xeroderma pigmentosum group E cells are deficient in global genomic repair. These results identify p48 as the link between p53 and the nucleotide excision repair apparatus.

  View details for PubMedID 9892649

• Effect of DNA lesions on transcription elongation BIOCHIMIE Tornaletti, S., Hanawalt, P. C. 1999; 81 (1-2): 139-146

  Abstract

  Some types of damage to cellular DNA have been shown to interfere with the essential transactions of replication and transcription. Not only may the translocation of the polymerase be arrested at the site of the lesion but the bound protein may encumber recognition of the lesion by repair enzymes. In the case of transcription a subpathway of excision repair, termed transcription-coupled repair (TCR) has been shown to operate on lesions in the transcribed strands of expressed genes in bacteria, yeast, mammalian cells and a number of other organisms. Certain genes in mammalian cells (e.g., CSA and CSB) have been uniquely implicated in TCR while others (e.g., XPC-HR23 and XPE) have been shown to operate in the global genomic pathway of nucleotide excision repair, but not in TCR. In order to understand the mechanism of TCR it is important to learn how an RNA polymerase elongation complex interacts with a damaged DNA template. That relationship is explored for different lesions and different RNA polymerase systems in this article.

  View details for Web of Science ID 000079411400015

  View details for PubMedID 10214918

• DNA repair of benzo[a]pyrene diol epoxide-DNA adducts in the DHFR gene of a human embryonic kidney cell line. POLYCYCLIC AROMATIC COMPOUNDS Schild, L. J., Smith, C. A., Hanawalt, P. C., Baird, W. M. 1999; 16 (1-4): 131-139

  View details for Web of Science ID 000086076100015

• Transcription-coupled DNA repair - Which lesions? Which diseases? Conference of the NATO Advanced Study Institute on DNA Damage and Repair - Oxygen Radical Effects, Cellular Protection, and Biological Consequences Hanawalt, P. C., Spivak, G. PLENUM PRESS DIV PLENUM PUBLISHING CORP. 1999: 169–179

  View details for Web of Science ID 000080335400014

• Induction of the SOS response increases the efficiency of global nucleotide excision repair of cyclobutane pyrimidine dimers, but not 6-4 photoproducts, in UV-irradiated Escherichia coli JOURNAL OF BACTERIOLOGY Crowley, D. J., Hanawalt, P. C. 1998; 180 (13): 3345-3352

  Abstract

  Nucleotide excision repair (NER) is responsible for the removal of a variety of lesions from damaged DNA and proceeds through two subpathways, global repair and transcription-coupled repair. In Escherichia coli, both subpathways require UvrA and UvrB, which are induced following DNA damage as part of the SOS response. We found that elimination of the SOS response either genetically or by treatment with the transcription inhibitor rifampin reduced the efficiency of global repair of the major UV-induced lesion, the cyclobutane pyrimidine dimer (CPD), but had no effect on the global repair of 6-4 photoproducts. Mutants in which the SOS response was constitutively derepressed repaired CPDs more rapidly than did wild-type cells, and this rate was not affected by rifampin. Transcription-coupled repair of CPDs occurred in the absence of SOS induction but was undetectable when the response was expressed constitutively. These results suggest that damage-inducible synthesis of UvrA and UvrB is necessary for efficient repair of CPDs and that the levels of these proteins determine the rate of NER of UV photoproducts. We compare our findings with recent data from eukaryotic systems and suggest that damage-inducible stress responses are generally critical for efficient global repair of certain types of genomic damage.

  View details for Web of Science ID 000074416700011

  View details for PubMedID 9642186

• Genomic instability: environmental invasion and the enemies within MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS Hanawalt, P. C. 1998; 400 (1-2): 117-125

  Abstract

  Deleterious alterations in cellular DNA result from endogenous sources of damage, as well as from external radiations and genotoxic chemicals in the environment. Although it is often difficult to ascertain the relative contributions to biological endpoints from endogenous vs. environmental sources of genomic instability, such determinations are highly relevant to risk estimates based upon perceived toxic levels of environmental agents. Of particular concern are the DNA lesions caused by reactive oxygen species that are generated both as a byproduct of oxidative metabolism and as a consequence of exposure to ionizing radiation and some other toxicants. We need to better understand the sequence of biochemical events that occurs between the initial formation of a DNA lesion and the biological outcome. These events may include transcription, replication, and cell cycle regulation, as well as DNA repair. Heterogeneity in the intragenomic distribution of lesions and their repair must also be taken into account. Expressed genes are unusually susceptible to alteration by some agents, and preferential repair of some lesions is targeted to transcribed DNA strands. An arrested RNA polymerase at a lesion may block access of repair enzymes, and it may also serve as a signal for upregulation of repair enzymes, cell cycle arrest and/or apoptosis. Our current understanding of the role of transcription in lesion processing and biological outcomes will be summarized, with particular emphasis upon the information gained from characterization of human genetic diseases expressing defects in the processing of damaged DNA. In some cases, the clinical features of these diseases might be understood in terms of deficiencies in the repair of lesions that arrest transcription.

  View details for Web of Science ID 000075548700012

  View details for PubMedID 9685605

• Human fibroblasts expressing the human papillomavirus E6 gene are deficient in global genomic nucleotide excision repair and sensitive to ultraviolet irradiation CANCER RESEARCH Ford, J. M., Baron, E. L., Hanawalt, P. C. 1998; 58 (4): 599-603

  Abstract

  We investigated the role of wild-type p53 activity in modulating nucleotide excision repair after UV irradiation in normal and p53-deficient primary human fibroblasts created by expression of the human papillomavirus 16 E6 gene. Compared with parental cells, the E6-expressing fibroblasts were deficient in global genomic repair of both UV-induced cyclobutane pyrimidine dimers and 6-4 photoproducts but exhibited normal transcription-coupled repair. The E6-expressing cells were also more sensitive than their parental counterparts to UV irradiation and displayed similar levels of UV-induced apoptosis. These results suggest that disruption of wild-type p53 function by E6 expression results in selective loss of p53-dependent global genomic nucleotide excision repair, but not UV-induced apoptosis, leading to enhanced UV sensitivity.

  View details for PubMedID 9485006

• Nucleotide sequence context effect of a cyclobutane pyrimidine dimer upon RNA polymerase II transcription JOURNAL OF BIOLOGICAL CHEMISTRY Tornaletti, S., Donahue, B. A., Reines, D., Hanawalt, P. C. 1997; 272 (50): 31719-31724

  Abstract

  We have studied the role of sequence context upon RNA polymerase II arrest by a cyclobutane pyrimidine dimer using an in vitro transcription system consisting of templates containing a specifically located cyclobutane pyrimidine dimer (CPD) and purified RNA polymerase II (RNAP II) and initiation factors. We selected a model sequence containing a well characterized site for RNAP II arrest in vitro, the human histone H3.3 gene arrest site. The 13-base pair core of the arrest sequence contains two runs of T in the nontranscribed strand that impose a bend in the DNA. We hypothesized that arrest of RNAP II might be affected by the presence of a CPD, based upon the observation that a CPD located at the center of a dA6.dT6 tract eliminates bending (Wang, C.-I., and Taylor, J.-S. (1991) Proc. Natl. Acad. Sci. U. S. A. 88, 9072-9076). We examined the normal H3.3 sequence and a mutant sequence containing a T --> G transversion, which reduces bending and efficiency of arrest. We show that a CPD in the transcribed strand at either of two locations in the arrest site is a potent block to transcription. However, a CPD in the nontranscribed strand only transiently pauses RNAP II. The CPD in concert with a mutation in the arrest site can reduce the extent of bending of the DNA and improve readthrough efficiency. These results demonstrate the potential importance of sequence context for the effect of CPDs within transcribed sequences.

  View details for Web of Science ID A1997YL41900074

  View details for PubMedID 9395515

• Competent transcription initiation by RNA polymerase II in cell-free extracts from Xeroderma pigmentosum groups B and D in an optimized RNA transcription assay BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION Satoh, M. S., Hanawalt, P. C. 1997; 1354 (3): 241-251

  Abstract

  The human autosomal recessive disease, xeroderma pigmentosum (XP), can result from mutations in any one of seven genes, designated XPA through XPG. Of these, the XPB and XPD genes encode proteins that are subunits of a general transcription factor, TFIIH, involved in both nucleotide excision repair (NER) and initiation of mRNA transcription by RNA polymerase II. In humans, mutation of the XPB or XPD gene impairs NER, resulting in hyper-sensitivity to sunlight and greatly increased skin tumor formation. However, no transcription deficiency has been demonstrated in either XP-B or XP-D. We have employed an optimized cell-free RNA transcription assay to analyze transcription activity of XP-B and XP-D. Although the growth rate was normal, the XP-B and XP-D cells contained reduced amounts of TFIIH. Extracts prepared from XP-B and XP-D lymphoblastoid cells exhibited similar transcription activity from the adenovirus major late promoter when compared to that in extracts from normal cells. Thus, we conclude that the XP-B and XP-D lymphoblastoid cells do not have impaired RNA transcription activity. We consider the possible consequences of the reduced cellular content of TFIIH for the clinical symptoms in XP-B or XP-D patients, and discuss a 'conditional phenotype' that may involve an impairment of cellular function only under certain growth conditions.

  View details for Web of Science ID 000070986500007

  View details for PubMedID 9427533

• Excision-repair patch lengths are similar for transcription-coupled repair and global genome repair in UV-irradiated human cells MUTATION RESEARCH-DNA REPAIR Bowman, K. K., Smith, C. A., Hanawalt, P. C. 1997; 385 (2): 95-105

  Abstract

  We have used the buoyant density shift method to measure excision-repair patch lengths in UV-irradiated repair-proficient human cells and in primary fibroblasts belonging to xeroderma pigmentosum complementation group C (XP-C), in which excision repair of UV-induced photoproducts is dependent upon transcription. The patch size was found to be about 30 nucleotides for both cell types. This agrees with the size of the DNA fragments excised in vitro by the dual incisions of the structure-specific nucleases XPG and ERCC1-XPF. We conclude that the XPC protein is not required to target the excision nucleases to sites of DNA cleavage in transcribed strands of expressed genes or to protect the newly incised DNA from further processing by exonucleases.

  View details for Web of Science ID 000071393900002

  View details for PubMedID 9447231

• Expression of wild-type p53 is required for efficient global genomic nucleotide excision repair in UV-irradiated human fibroblasts JOURNAL OF BIOLOGICAL CHEMISTRY Ford, J. M., Hanawalt, P. C. 1997; 272 (44): 28073-28080

  Abstract

  We have shown previously that Li-Fraumeni syndrome fibroblasts homozygous for p53 mutations are deficient in the removal of UV-induced cyclobutane pyrimidine dimers from genomic DNA, but still proficient in the transcription-coupled repair pathway (Ford, J. M., and Hanawalt, P. C. (1995) Proc. Natl. Acad. Sci. U. S. A. 92, 8876-8880). We have now utilized monoclonal antibodies specific for cyclobutane pyrimidine dimers or 6-4 photoproducts, respectively, to measure their repair in UV-irradiated human fibroblasts. Cells homozygous for p53 mutations were deficient in the repair of both photoproducts, whereas cells heterozygous for mutant p53 exhibited normal repair of 6-4 photoproducts, but decreased initial rates of removal of cyclobutane pyrimidine dimers, compared with normal cells. The specificity of the effect of wild-type p53 on nucleotide excision repair was demonstrated in a p53 homozygous mutant cell line containing a tetracycline-regulated wild-type p53 gene. Wild-type p53 expression and activity were suppressed in the presence of tetracycline, whereas withdrawal of tetracycline resulted in the induction of p53 expression, cell cycle checkpoint activation, and DNA damage-induced apoptosis. The regulated expression of wild-type p53 resulted in the recovery of normal levels of repair of both cyclobutane pyrimidine dimers and 6-4 photoproducts in genomic DNA, but did not alter the transcription-coupled repair of cyclobutane pyrimidine dimers. Therefore, the wild-type p53 gene product is an important determinant of nucleotide excision repair activity in human cells.

  View details for Web of Science ID A1997YD47300087

  View details for PubMedID 9346961

• Preferential mutagenesis of lacZ integrated at unique sites in the Escherichia coli chromosome MOLECULAR AND GENERAL GENETICS Liu, S. K., Tseng, J. N., Shiuan, D., Hanawalt, P. C. 1997; 255 (5): 449-459

  Abstract

  To study the variation in spontaneous mutation frequencies in different chromosomal domains, a mini-Mu-kan-lacZ- transposable element was constructed to insert the lacZ-(Trp570 --> Opal) allele into many different loci in the Escherichia coli chromosome. Papillation on MacConkey lactose plates was used to screen for mini-Mu insertion mutants with elevated levels of spontaneous mutagenesis of lacZop --> LacZ+; candidates were then screened for normal mutation frequencies in other genes. Two different insertion mutants with this enhanced mutagenesis phenotype were isolated from 14000 colonies, and named plm-1 (preferential lacZ mutagenesis) and plm-2. The frequency of LacZ- --> LacZ+ mutations in these plm mutants was over 400-fold higher than that in isogenic strains containing mini-Mu-kan-lacZop insertions at other loci. Six Lac+ reversion (or suppression) mutations obtained from each of the two plm mutants were mapped by P1 transduction and all were found to be linked to the Kan(r) gene in the mini-Mu-kan-lacZop, suggesting that a localized mutagenic event is responsible for the preferential mutagenesis. Furthermore, both the LacZ+ --> LacZ- and Kan(r) --> Kan(s) mutant frequencies of these Lac+ revertants were in the range of 10(-3) to 10(-2), indicating that this putative localized mutagenesis is neither allele nor gene specific. To identify the plm loci, the chromosomal regions flanking the mini-Mu insertion sites were cloned and sequenced. A computer-assisted database search of homologous sequences revealed that the plm-1 locus is identical to the mutS gene; the mini-Mu insertion most probably results in the production of a truncated MutS protein. We suggest that the enhanced lacZ mutation frequency in plm-1 may be associated with an active process involving the putative truncated MutS protein. The DNA sequence of the plm-2 locus matched a putative malate oxidoreductase gene located at 55.5 min of the E. coli chromosome.

  View details for Web of Science ID A1997XT51000001

  View details for PubMedID 9294029

• recF and recR are required for the resumption of replication at DNA replication forks in Escherichia coli PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Courcelle, J., CARSWELLCRUMPTON, C., Hanawalt, P. C. 1997; 94 (8): 3714-3719

  Abstract

  Escherichia coli containing a mutation in recF are hypersensitive to UV. However, they exhibit normal levels of conjugational or transductional recombination unless the major pathway (recBC) is defective. This implies that the UV sensitivity of recF mutants is not due to a defect in recombination such as occurs during conjugation or transduction. Here, we show that when replication is disrupted, at least two genes in the recF pathway, recF and recR, are required for the resumption of replication at DNA replication forks, and that in their absence, localized degradation occurs at the replication forks. Our observations support a model in which recF and recR are required to reassemble a replication holoenzyme at the site of a DNA replication fork. These results, when taken together with previous literature, suggest that the UV hypersensitivity of recF cells is due to an inability to resume replication at disrupted replication forks rather than to a defect in recombination. Current biochemical and genetic data on the conditions under which recF-mediated recombination occurs suggest that the recombinational intermediate also may mimic the structure of a disrupted replication fork.

  View details for Web of Science ID A1997WW81000044

  View details for PubMedID 9108043

• Role of DNA excision repair gene defects in the etiology of cancer GENETIC INSTABILITY AND TUMORIGENESIS Ford, J. M., Hanawalt, P. C. 1997; 221: 47-70

  View details for Web of Science ID A1997BJ47J00005

  View details for PubMedID 8979440

• TFIIH-mediated nucleotide excision repair and initiation of mRNA transcription in an optimized cell-free DNA repair and RNA transcription assay NUCLEIC ACIDS RESEARCH Satoh, M. S., Hanawalt, P. C. 1996; 24 (18): 3576-3582

  Abstract

  In mammalian cells, mRNA transcription is initiated with the aid of transcription initiation factors. Of these, TFIIH has also been shown to play an essential role in nucleotide excision repair (NER), which is a versatile biochemical pathway that corrects a broad range of DNA damage. Since the dual role of TFIIH is conserved among eukaryotes, including yeast and mammalian cells, the sharing of TFIIH between NER and RNA transcription initiation might provide some survival advantage. However, the functional relationship between NER and RNA transcription initiation through TFIIH is not yet understood. We have developed an optimized cell-free assay which allows us to analyze NER and RNA transcription under identical conditions. In this assay, NER did not compete with RNA transcription, probably because the extracts contained sufficient amounts of TFIIH to support both processes. Thus, NER can be considered functionally independent of RNA transcription initiation despite the fact that both processes use the same factor.

  View details for Web of Science ID A1996VK03200014

  View details for PubMedID 8836185

• Recruitment of damaged DNA to the nuclear matrix in hamster cells following ultraviolet irradiation NUCLEIC ACIDS RESEARCH Koehler, D. R., Hanawalt, P. C. 1996; 24 (15): 2877-2884

  Abstract

  We examined the relationship between the nuclear matrix and DNA in the dihydrofolate reductase domain following irradiation of Chinese hamster cells with UV light. The fraction of matrix-bound DNA increased in transcribed and non-transcribed regions during a 3 h period after irradiation. However, no increase was observed with excision repair-deficient cells mutant for the ERCC1 gene. The major UV-induced lesion, the cyclobutane pyrimidine dimer, increased in frequency in the matrix-bound DNA 1 h after irradiation, in both transcribed and non-transcribed regions, but decreased subsequently. This phenomenon was also lacking in excision repair-deficient cells. These data demonstrate that recruitment of lesion-containing DNA to the nuclear matrix occurs following UV irradiation and suggest that this recruitment is dependent upon nucleotide excision repair. This is consistent with the concept of a 'repair factory' residing on the nuclear matrix at which excision repair occurs.

  View details for Web of Science ID A1996VB83200003

  View details for PubMedID 8760868

• Mismatch repair mutants in yeast are not defective in transcription-coupled DNA repair of UV-induced DNA damage GENETICS Sweder, K. S., Verhage, R. A., Crowley, D. J., Crouse, G. F., Brouwer, J., Hanawalt, P. C. 1996; 143 (3): 1127-1135

  Abstract

  Transcription-coupled repair, the targeted repair of the transcribed strands of active genes, is defective in bacteria, yeast, and human cells carrying mutations in mfd, RAD26 and ERCC6, respectively. Other factors probably are also uniquely involved in transcription-repair coupling. Recently, a defect was described in transcription-coupled repair for Escherichia coli mismatch repair mutants and human tumor cell lines with mutations in mismatch repair genes. We examined removal of UV-induced DNA damage in yeast strains mutated in mismatch repair genes in an effort to confirm a defect in transcription-coupled repair in this system. In addition, we determined the contribution of the mismatch repair gene MSH2 to transcription-coupled repair in the absence of global genomic repair using rad7 delta mutants. We also determined whether the Rad26-independent transcription-coupled repair observed in rad26 delta and rad7 delta rad26 delta mutants depends on MSH2 by examining repair deficiencies of rad26 delta msh2 delta and rad7 delta rad26 delta msh2 delta mutants. We found no defects in transcription-coupled repair caused by mutations in the mismatch repair genes MSH2, MLH1, PMS1, and MSH3. Yeast appears to differ from bacteria and human cells in the capacity for transcription-coupled repair in a mismatch repair mutant background.

  View details for Web of Science ID A1996UU74200008

  View details for PubMedID 8807287

• Effects of aminofluorene and acetylaminofluorene DNA adducts on transcriptional elongation by RNA polymerase II JOURNAL OF BIOLOGICAL CHEMISTRY Donahue, B. A., Fuchs, R. P., Reines, D., Hanawalt, P. C. 1996; 271 (18): 10588-10594

  Abstract

  A prominent model for the mechanism of transcription-coupled DNA repair proposes that an arrested RNA polymerase directs the nucleotide excision repair complex to the transcription-blocking lesion. The specific role for RNA polymerase II in this mechanism can be examined by comparing the extent of polymerase arrest with the extent of transcription-coupled repair for a specific DNA lesion. Previously we reported that a cyclobutane pyrimidine dimer that is repaired preferentially in transcribed genes is a strong block to transcript elongation by RNA pol II (Donahue, B.A., Yin, S., Taylor, J.-S., Reines, D., and Hanawalt, P. C. (1994) Proc. Natl. Acad. Sci. U. S. A. 91, 8502-8506). Here we report the extent of RNA polymerase II arrest by the C-8 guanine DNA adduct formed by N-2-aminofluorene, a lesion that does not appear to be preferentially repaired. Templates for an in vitro transcription assay were constructed with either an N-2-aminofluorene adduct or the helix-distorting N-2-acetylaminofluorene adduct situated at a specific site downstream from the major late promoter of adenovirus. Consistent with the model for transcription-coupled repair, an aminofluorene adduct located on the transcribed strand was a weak pause site for RNA polymerase II. An acetylaminofluorene adduct located on the transcribed strand was an absolute block to transcriptional elongation. Either adduct located on the nontranscribed strand enhanced polymerase arrest at a nearby sequence-specific pause site.

  View details for Web of Science ID A1996UJ34200028

  View details for PubMedID 8631860

• Role of transcription-coupled DNA repair in susceptibility to environmental carcinogenesis 2nd International Conference on Environmental Mutagens in Human Populations Hanawalt, P. C. US DEPT HEALTH HUMAN SCIENCES PUBLIC HEALTH SCIENCE. 1996: 547–551

  Abstract

  Susceptibility to environmental carcinogenesis is the consequence of a complex interplay between intrinsic hereditary factors and actual exposures to potential carcinogenic agents. We must learn the nature of these interactions as well as the genetic defects that confer enhanced risk. In some genetic diseases an increased cancer risk correlates with a defect in the repair or replications of damaged DNA. Examples include xeroderma pigmentosum (XP), ataxia telangiectasia, Fanconi's anemia, and Bloom's syndrome. In Cockayne's syndrome the Specific defect in transcription-coupled repair (TCR) does not predispose the patients to the sunlight-induced skin cancer characteristic of XP. The demonstration of TCR in the XP129 partial revertant of XP-A cells indicates that ultraviolet (UV) resistance correlates with repair of cyclobutane pyrimidine dimers in active genes. Repair measured as an average over the genome can be misleading, and it is necessary to consider genomic locations of DNA damage and repair for a meaningful assessment of the biological importance of particular DNA lesions. Mutations in the p53 tumor suppressor gene are found in many human tumors. TCR accounts for the resulting mutational spectra in the p53 gene in certain tumors. Li-Fraumeni syndrome fibroblasts expressing only mutant p53 are more UV-resistant and exhibit less UV-induced apoptosis than normal human cells or heterozygotes for mutations in only one allele of p53. The p53-defective cells are deficient in global excision repair capacity but have retained TCR. The loss of p53 function may lead to greater genomic instability by reducing the efficiency of global DNA repair while cellular resistance may be assured through the operation of TCR and the elimination of apoptosis.

  View details for Web of Science ID A1996UQ08400027

  View details for PubMedID 8781381

• DNA repair deficiencies associated with mutations in genes encoding subunits of transcription initiation factor TFIIH in yeast NUCLEIC ACIDS RESEARCH Sweder, K. S., Chun, R., Mori, T., Hanawalt, P. C. 1996; 24 (8): 1540-1546

  Abstract

  Several proteins, including Rad3 and Rad25(Ssl2), are essential for nucleotide excision repair (NER) and function in the RNA polymerase II transcription initiation complex TFIIH. Mutations in genes encoding two other subunits of TFIIH, TFB1 and SSL1, result in UV sensitivity and have been shown to take part in NER in an in vitro system. However, a deficiency in global NER does not exclude the possibility that such repair-deficient mutants can perform transcription-coupled repair (TCR), as shown for xeroderma pigmentosum group C. To date, temperature-sensitive C-terminal truncations of Tfbl are the only TFIIH mutations that result in intermediate UV sensitivity, which might indicate a deficiency in either the global NER or TCR pathways. We have directly analyzed both TCR and global NER in these mutants. We found that ssl1, rad3 and tfb1 mutants, like rad25(ssl2-xp) mutants, are deficient in both the global NER and TCR pathways. Our results support the view that the mutations in any one of the genes encoding subunits of TFIIH result in deficiencies in both global and TCR pathways of NER. We suggest that when subunits of TFIIH are in limiting amounts, TCR may preclude global NER.

  View details for Web of Science ID A1996UH37000021

  View details for PubMedID 8628689

• Kinetics of pyrimidine(6-4)pyrimidone photoproduct repair in Escherichia coli JOURNAL OF BACTERIOLOGY Koehler, D. R., Courcelle, J., Hanawalt, P. C. 1996; 178 (5): 1347-1350

  Abstract

  We compared the removal of pyrimidine(6-4)pyrimidone photoproducts [(6-4) photoproducts] and cyclobutane pyrimidine dimers (CPDs) from the genome of repair-proficient Escherichia coli, using monoclonal antibodies specific for each type of lesion. We found that (6-4) photoproducts were removed at a higher rate than CPDs in the first 30 min following a moderate UV dose (40 J/m2). The difference in rates was less than that typically reported for cultured mammalian cells, in which the removal of (6-4) photoproducts is far more rapid than that of CPDs.

  View details for Web of Science ID A1996TX75200016

  View details for PubMedID 8631712

• Fine structure mapping of DNA repair within a 100 kb genomic region in Chinese hamster ovary cells 4th International Conference on Mechanisms of Antimutagenesis and Anticarcinogenesis Spivak, G., Hanawalt, P. C. ELSEVIER SCIENCE BV. 1996: 207–16

  Abstract

  We have investigated at a high level of resolution the repair of cyclobutane pyrimidine dimers (CPD) in a large amplified genomic region in Chinese hamster ovary B11 cells. We found strand selective repair in DNA fragments within two active genes, DHFR and an unknown gene adjacent to DHFR. These genes generate divergent transcripts from the same promoter region; their transcribed strands were virtually free of CPD within 24 h after irradiation with 10 j/m2 of ultraviolet light (254nm), while their non-transcribed strands were poorly repaired. We also examined the repair of CPD in three DNA fragments within a 50 kb region downstream of DHFR, in which two origins of replication flanking a matrix attachment site have been characterized from independently derived cell lines with amplified DHFR domains; repair of CPD in this non-transcribed region was similarly poor in both DNA strands. Transcription-coupled repair of CPD in the DHFR gene exhibited the same proficiency throughout the transcription unit: analysis of the efficiency of removal of CPD over time revealed no differences between repair in the 5' and the 3' ends of the DHFR gene. Implications for mechanisms of transcription-coupled repair are discussed.

  View details for Web of Science ID A1996TY15000024

  View details for PubMedID 8657183

• The anti-cancer drug camptothecin inhibits elongation but stimulates initiation of RNA polymerase II transcription CARCINOGENESIS Ljungman, M., Hanawalt, P. C. 1996; 17 (1): 31-35

  Abstract

  Camptothecin is a widely used anti-tumor drug that specifically inhibits DNA topoisomerase I. It is believed that topoisomerase I participates in the process of transcription by relaxing torsional stress induced in the duplex DNA by the elongating RNA polymerase. We have assessed the effects of camptothecin on RNA polymerase II transcription from the dihydrofolate reductase (DHFR) gene in Chinese hamster ovary (CHO) cells. Using in vivo [3H]uridine pulse labeling and in vitro nuclear run-on techniques to estimate relative rates of transcription, it was found that camptothecin stimulated RNA synthesis from promoter-proximal sequences of the DHFR gene, while transcription from promoter-distal sequences was reduced. Furthermore, camptothecin caused a significant accumulation of RNA polymerases in the 5'-end of the DHFR gene. The effect of camptothecin on transcription was reversible, resulting in a wave of RNA synthesis recovery in a 5' to 3' direction through the DHFR gene following a chase with camptothecin-free medium. We conclude that camptothecin stimulates initiation but inhibits elongation of the RNA polymerase II transcribed DHFR gene.

  View details for Web of Science ID A1996UC14800006

  View details for PubMedID 8565133

• LI-FRAUMENI SYNDROME FIBROBLASTS HOMOZYGOUS FOR P53 MUTATIONS ARE DEFICIENT IN GLOBAL DNA-REPAIR BUT EXHIBIT NORMAL TRANSCRIPTION-COUPLED REPAIR AND ENHANCED UV RESISTANCE PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Ford, J. M., Hanawalt, P. C. 1995; 92 (19): 8876-8880

  Abstract

  We investigated whether mutations in the p53 tumor suppressor gene alter UV sensitivity and/or repair of UV-induced DNA damage in primary human skin fibroblasts from patients with Li-Fraumeni syndrome, heterozygous for mutations in one allele of the p53 gene (p53 wt/mut) and sublines expressing only mutant p53 (p53 mut). The p53 mut cells were more resistant than the p53 wt/mut cells to UV cytotoxicity and exhibited less UV-induced apoptosis. DNA repair analysis revealed reduced removal of cyclobutane pyrimidine dimers from overall genomic DNA in vivo in p53 mut cells compared with p53 wt/mut or normal cells. However, p53 mut cells retained the ability to preferentially repair damage in the transcribed strands of expressed genes (transcription-coupled repair). These results suggest that loss of p53 function may lead to greater genomic instability by reducing the efficiency of DNA repair but that cellular resistance to DNA-damaging agents may be enhanced through elimination of apoptosis.

  View details for Web of Science ID A1995RU75900070

  View details for PubMedID 7568035

  View details for PubMedCentralID PMC41070

• EVOLUTION OF THE SNF2 FAMILY OF PROTEINS - SUBFAMILIES WITH DISTINCT SEQUENCES AND FUNCTIONS NUCLEIC ACIDS RESEARCH Eisen, J. A., Sweder, K. S., Hanawalt, P. C. 1995; 23 (14): 2715-2723

  Abstract

  The SNF2 family of proteins includes representatives from a variety of species with roles in cellular processes such as transcriptional regulation (e.g. MOT1, SNF2 and BRM), maintenance of chromosome stability during mitosis (e.g. lodestar) and various aspects of processing of DNA damage, including nucleotide excision repair (e.g. RAD16 and ERCC6), recombinational pathways (e.g. RAD54) and post-replication daughter strand gap repair (e.g. RAD5). This family also includes many proteins with no known function. To better characterize this family of proteins we have used molecular phylogenetic techniques to infer evolutionary relationships among the family members. We have divided the SNF2 family into multiple subfamilies, each of which represents what we propose to be a functionally and evolutionarily distinct group. We have then used the subfamily structure to predict the functions of some of the uncharacterized proteins in the SNF2 family. We discuss possible implications of this evolutionary analysis on the general properties and evolution of the SNF2 family.

  View details for Web of Science ID A1995RN26800022

  View details for PubMedID 7651832

• PRESENCE OF NEGATIVE TORSIONAL TENSION IN THE PROMOTER REGION OF THE TRANSCRIPTIONALLY POISED DIHYDROFOLATE-REDUCTASE GENE IN-VIVO NUCLEIC ACIDS RESEARCH Ljungman, M., Hanawalt, P. C. 1995; 23 (10): 1782-1789

  Abstract

  DNA topology has been suggested to play an important role in the process of transcription. Negative torsional tension has been shown to stimulate both pre-initiation complex formation and promoter clearance on plasmid DNA in vitro. We recently showed that genomic DNA in human cells contains localized torsional tension. In the present study we have further characterized and mapped torsional tension in the dihydrofolate reductase (DHFR) gene in Chinese hamster ovary (CHO) cells and investigated the effects of differential rates of transcription on the magnitude and location of this tension. Using psoralen photo-cross-linking in conjunction with X-irradiation, we found that relaxable psoralen hypersensitivity was specifically localized to the promoter region of the serum-regulated DHFR gene in serum-stimulated, but not in serum-starved, cells. Moreover, this hypersensitivity did not appear to be caused by transcription elongation, since it persisted in cells in which transcription of the DHFR gene had been reduced by the transcription inhibitor 5,6-dichloro-1-beta-D-ribofurano-sylbenzimidazole (DRB). We suggest that the generation of negative torsional tension in DNA may play an important role in gene regulation by poising genes for transcription.

  View details for Web of Science ID A1995RC71200020

  View details for PubMedID 7784183

• DNA-REPAIR COMES OF AGE MUTATION RESEARCH-DNA REPAIR Hanawalt, P. C. 1995; 336 (2): 101-113

  View details for Web of Science ID A1995QL23700001

  View details for PubMedID 7885381

• PREFERENTIAL REPAIR OF THE TRANSCRIBED DNA STRAND IN THE DIHYDROFOLATE-REDUCTASE GENE THROUGHOUT THE CELL-CYCLE IN UV-IRRADIATED HUMAN-CELLS MUTATION RESEARCH-DNA REPAIR Lommel, L., CARSWELLCRUMPTON, C., Hanawalt, P. C. 1995; 336 (2): 181-192

  Abstract

  We examined repair of UV-induced cyclobutane pyrimidine dimers (CPD) in each strand of the expressed dihydrofolate reductase gene in human cells in different phases of the cell cycle: G1, early S, middle S, late S, and G2/M. After 4 h of incubation, repair of the transcribed strand was substantially more efficient than repair of the non-transcribed strand in all phases. Furthermore, we observed no remarkable cell cycle-dependent differences in either the initial lesion frequency or the efficiency of repair of the transcribed strand. We conclude that transcription coupled repair operates generally and with high efficiency throughout the cell cycle.

  View details for Web of Science ID A1995QL23700009

  View details for PubMedID 7885388

• DNA-REPAIR IN THE MYC AND FMS PROTOONCOGENES IN ULTRAVIOLET LIGHT-IRRADIATED HUMAN HL-60 PROMYELOCYTIC CELLS DURING DIFFERENTIATION CANCER RESEARCH Islas, A. L., Hanawalt, P. C. 1995; 55 (2): 336-341

  Abstract

  In order to better understand the role of transcription in cellular processing of damage in specific DNA sequences, we have used an in vitro differentiation system to modulate the activity of the MYC gene. When human HL60 promyelocytic cells differentiate in vitro, the transcriptional activity of the MYC gene is down-regulated. We have shown that in the expressed MYC gene, 56% of UV-induced cyclobutane pyrimidine dimers (CPDs) are removed within 18 h and the transcribed strand is selectively repaired. However, late in differentiation, when the MYC gene is maximally down-regulated, only 15% of the CPDs are removed within the same period. During early differentiation, the MYC gene is regulated by a block to transcription elongation at the 5' end of the first intron. Our results reveal no significant difference in the rate of CPD removal between the restriction fragments upstream and downstream of this elongation block. Furthermore, both strands of each fragment exhibit similar repair characteristics. In contrast, the constitutively expressed FMS gene exhibits proficient removal of CPD in both the differentiated and undifferentiated cells. Furthermore, the repair appears to be more proficient at the 5' end (exon 1) than in the 3' end of the gene about 35 kilobases downstream from exon 1. Since efficient repair of the active FMS gene is maintained in the differentiated cells the loss of repair competence seen in MYC is more likely associated with its reduced transcriptional activity than with a decrease in the overall repair capacity of the terminally differentiated cells.

  View details for Web of Science ID A1995QB80800024

  View details for PubMedID 7529133

• TRANSCRIPTION-COUPLED REPAIR OF PSORALEN CROSS-LINKS BUT NOT MONOADDUCTS IN CHINESE-HAMSTER OVARY CELLS BIOCHEMISTRY Islas, A. L., Baker, F. J., Hanawalt, P. C. 1994; 33 (35): 10794-10799

  Abstract

  We have examined the rate and extent of removal of 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen (HMT) cross-linkable monoadducts and interstrand cross-links from restriction fragments within the amplicon containing the dihydrofolate reductase (DHFR) gene in the Chinese hamster ovary (CHO) cell line B11. The rate and extent of removal of HMT cross-links was significantly greater in an actively transcribed fragment than in a nontranscribed extragenic fragment of similar size. For the 5' half of the DHFR gene, approximately 80% of the HMT cross-links were removed in 8 h, in agreement with results reported by Vos and Wauthier [Vos, J. M., & Wauthier, E. L. (1991) Mol. Cell Biol. 11, 2245-2252, 1991]. However, few cross-links were removed in that period from the nontranscribed fragments, whose 5' end is approximately 7 kb downstream from the DHFR transcription unit and which includes a putative replication initiation site. Even after 24 h, only about 50% of the cross-links had been removed from this fragment. In contrast, both the rate and the extent of removal of cross-linkable HMT monoadducts were similar in the two fragments with 50% of the cross-linkable monoadducts removed in 24 h. Moreover, monoadducts formed in the bulk of the genome were removed in 24 h. Moreover, monoadducts formed in the bulk of the genome were removed at a slightly slower rate and to a lesser extent (30% in 24 hours) than those from either of these specific sequences.(ABSTRACT TRUNCATED AT 250 WORDS)

  View details for Web of Science ID A1994PF19000029

  View details for PubMedID 8075081

• PHOTOACTIVATED GILVOCARCIN-V INDUCES DNA-PROTEIN CROSS-LINKING IN GENES FOR HUMAN RIBOSOMAL-RNA AND DIHYDROFOLATE-REDUCTASE PHOTOCHEMISTRY AND PHOTOBIOLOGY Matsumoto, A., Fujiwara, Y., Elespuru, R. K., Hanawalt, P. C. 1994; 60 (3): 225-230

  Abstract

  The nature of DNA interactions with photoactivated gilvocarcin V has been analyzed at the gene level in both rRNA and dihydrofolate reductase genes of human fibroblasts, utilizing a modified Southern hybridization technique. Neither interstrand DNA crosslinking nor RNA linkage to DNA was detected. However, we consistently observed in both genes retarded DNA bands appearing in a dose-dependent fashion following exposure to photoactivated gilvocarcin V. These retarded bands were enhanced when genomic DNA was prepared without proteinase K treatment, suggesting involvement of protein in this DNA interaction. Because these bands disappear following proteinase K treatment, it is probable that photoactivated gilvocarcin V induces DNA-protein crosslinking.

  View details for Web of Science ID A1994PG81600007

  View details for PubMedID 7972373

• TRANSCRIPT CLEAVAGE BY RNA-POLYMERASE-II ARRESTED BY A CYCLOBUTANE PYRIMIDINE DIMER IN THE DNA-TEMPLATE PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Donahue, B. A., Yin, S., Taylor, J. S., Reines, D., Hanawalt, P. C. 1994; 91 (18): 8502-8506

  Abstract

  A current model for transcription-coupled DNA repair is that RNA polymerase, arrested at a DNA lesion, directs the repair machinery to the transcribed strand of an active gene. To help elucidate this role of RNA polymerase, we constructed DNA templates containing the major late promoter of adenovirus and a cyclobutane pyrimidine dimer (CPD) at a specific site. CPDs, the predominant DNA lesions formed by ultraviolet radiation, are good substrates for transcription-coupled repair. A CPD located on the transcribed strand of the template was a strong block to polymerase movement, whereas a CPD located on the nontranscribed strand had no effect on transcription. Furthermore, the arrested polymerase shielded the CPD from recognition by photolyase, a bacterial DNA repair protein. Transcription elongation factor SII (also called TFIIS) facilitates read-through of a variety of transcriptional pause sites by a process in which RNA polymerase II cleaves the nascent transcript before elongation resumes. We show that SII induces nascent transcript cleavage by RNA polymerase II stalled at a CPD. However, this cleavage does not remove the arrested polymerase from the site of the DNA lesion, nor does it facilitate translesional bypass by the polymerase. The arrested ternary complex is stable and competent to resume elongation, demonstrating that neither the polymerase nor the RNA product dissociates from the DNA template.

  View details for Web of Science ID A1994PE38800040

  View details for PubMedID 8078911

  View details for PubMedCentralID PMC44634

• PREFERENTIAL REPAIR OF ULTRAVIOLET LIGHT-INDUCED DNA-DAMAGE IN THE TRANSCRIBED STRAND OF THE HUMAN P53 GENE MOLECULAR CARCINOGENESIS Ford, J. M., Lommel, L., Hanawalt, P. C. 1994; 10 (2): 105-109

  Abstract

  Mutations in the p53 tumor suppressor gene have been found in most human tumors. Analyses of the spectrum of p53 mutations in certain tumor types have shown a bias for mutations originating from lesions presumed to be in the untranscribed strand of the gene. This implies strand specificity for the formation or repair of DNA damage. We measured the induction and repair of ultraviolet light-induced cyclobutane pyrimidine dimers (CPD) in each strand of the human p53 gene in a normal human lung fibroblast cell line using quantitative Southern hybridization. We found that the removal of CPD from the transcribed strand was more rapid than that from the untranscribed strand of this gene, although the frequency of CPD induction was similar in both strands. Preferential repair of the transcribed strand of the p53 gene may account for the mutational spectra of this gene in human tumors.

  View details for Web of Science ID A1994NV25200007

  View details for PubMedID 8031463

• REPAIR AND TRANSCRIPTION - COLLISION OR COLLUSION CURRENT BIOLOGY Hanawalt, P. C., Donahue, B. A., Sweder, K. S. 1994; 4 (6): 518-521

  Abstract

  While some proteins have distinct responsibilities in both transcription and DNA repair, additional proteins are needed to couple these essential DNA transactions in expressed genes.

  View details for Web of Science ID A1994NU41000005

  View details for PubMedID 7864939

• REMOVAL OF CYCLOBUTANE PYRIMIDINE DIMERS FROM A UV-IRRADIATED SHUTTLE VECTOR INTRODUCED INTO HUMAN-CELLS SOMATIC CELL AND MOLECULAR GENETICS Ganesan, A. K., Hanawalt, P. C. 1994; 20 (3): 233-242

  Abstract

  A shuttle vector (pZH-1) carrying the E. coli lacZ gene under control of the SV40 early promoter was irradiated with UV and introduced into repair-proficient or repair-deficient human cell lines. The expression of irradiated lacZ compared to unirradiated lacZ was greater in repair-proficient cells (HT-1080) than in repair-deficient cells (XP12RO-SV40) belonging to xeroderma pigmentosum complementation group A. To ascertain whether the expression of lacZ in the repair-proficient cells was correlated with the removal of cyclobutane pyrimidine dimers (CPDs), we purified DNA from the recipient cells and used the CPD-specific enzyme T4 endonuclease V to measure the frequency of CPDs remaining in the plasmid as a whole and in two restriction fragments derived from it. We found that removal of CPDs occurred in both fragments in the repair-proficient cells but not in the repair-deficient cells. Our results provide the first direct evidence for the removal of CPDs from UV irradiated plasmids introduced into human cells and support the notion that expression of the UV-damaged lacZ gene in repair-proficient human cells reflects the removal of transcription blocking lesions from the gene.

  View details for Web of Science ID A1994PJ61800008

  View details for PubMedID 7940023

• REPAIR IN RIBOSOMAL-RNA GENES IS DEFICIENT IN XERODERMA-PIGMENTOSUM GROUP-C AND IN COCKAYNES-SYNDROME CELLS MUTATION RESEARCH Christians, F. C., Hanawalt, P. C. 1994; 323 (4): 179-187

  Abstract

  Previous studies have demonstrated transcription-coupled DNA repair in mammalian genes transcribed by RNA polymerase II but not in ribosomal RNA genes (rDNA), which are transcribed by RNA polymerase I. The removal of UV-induced cyclobutane pyrimidine dimers (CPD) from rDNA in repair-proficient human cells has been shown to be slow but detectable and apparently not coupled to transcription. We studied the induction and removal of CPD from rDNA in cultured cells from two repair-deficient human disorders. Primary xeroderma pigmentosum complementation group C (XP-C) cells, whether proliferating or nondividing, removed no CPD from either rDNA strand in 24 h post-UV, a result which supports earlier conclusions that XP-C cells lack the general, transcription-independent pathway of nucleotide excision repair. We also observed lower than normal repair of rDNA in Cockayne's syndrome (CS) cells from complementation groups A and B. In agreement with previous findings, the repair of both strands of the RNA polymerase II-transcribed dihydrofolate reductase gene was also deficient relative to that of normal cells. This strongly suggests that the defect in CS cells is not limited to a deficiency in a transcription-repair coupling factor. Rather, the defect may interfere with the ability of repair proteins to gain access to all expressed genes.

  View details for Web of Science ID A1994NE71200005

  View details for PubMedID 7512688

• THE COOH TERMINUS OF SUPPRESSOR OF STEM-LOOP (SSL2/RAD25) IN YEAST IS ESSENTIAL FOR OVERALL GENOMIC EXCISION-REPAIR AND TRANSCRIPTION-COUPLED REPAIR JOURNAL OF BIOLOGICAL CHEMISTRY Sweder, K. S., Hanawalt, P. C. 1994; 269 (3): 1852-1857

  Abstract

  We examined several yeast strains with different mutations in the essential SSL2 (Suppressor of Stem Loop, also called RAD25) gene for their ability to remove cyclobutane pyrimidine dimers from expressed genes, and from the genome overall. The SSL2 protein has a high degree of amino acid sequence identity to the protein encoded by the human ERCC3 gene (Gulyas, K. D., and Donahue, T. F. (1992) Cell 69, 1031-0142). The mutant allele SSL2-XP encodes a protein resembling the mutated ERCC3 protein from UV-sensitive human cells belonging to xeroderma pigmentosum complementation group B and Cockayne's syndrome (CS) complementation group C (Weeda, G., van Ham, R. C. A., Vermeulen, W., Bootsma, D., van der Eb, A. J., and Hoeijmakers, J. H. J. (1990) Cell 62, 777-791; Gulyas and Donahue, 1992). The SSL2-XP allele confers UV sensitivity on yeast strain KG119. We found that the biochemical basis for the UV sensitivity of KG119 is a complete deficiency in the removal of cyclobutane pyrimidine dimers from the overall genome as well as a deficiency in transcription-coupled repair. This is the first analysis of the DNA repair defect responsible for the UV sensitivity of cells carrying the SSL2-XP allele, and it documents the similarity of the defect to that associated with XP-B/CS-C, and the difference between this defect and that in cells belonging to CS complementation groups A and B.

  View details for Web of Science ID A1994MR98800048

  View details for PubMedID 8294433

• EVOLUTION OF CONCEPTS IN DNA-REPAIR ENVIRONMENTAL AND MOLECULAR MUTAGENESIS Hanawalt, P. C. 1994; 23: 78-85

  Abstract

  A short personalized history of the development of the field of DNA excision repair is presented, beginning with the early insights of radiation biologists and extending to the present-day convergence of the fields of DNA repair and transcription. It is becoming increasingly clear that excision repair is not merely an extraordinary scheme to help UV-exposed cells survive but rather one that operates upon a wide range of structural defects in DNA, some of which are due to environmental chemicals and others are a consequence of normal metabolic activities. It is an important challenge to researchers and risk assessors to determine the relative contributions to biological endpoints from endogenous events and the intrinsic instability of DNA as compared to exogenous environmental exposures. This should be one of the goals of the Environmental Mutagen Society as it embarks upon its second quarter-century.

  View details for Web of Science ID A1994NJ84400016

  View details for PubMedID 8162914

• ANALYSIS OF THE FINE-STRUCTURE OF THE REPAIR OF ANTI-BENZO[A]PYRENE-7,8-DIOL-9,10-EPOXIDE-DNA ADDUCTS IN MAMMALIAN-CELLS BY LASER-INDUCED STRAND CLEAVAGE 14th International Symposium on Polycyclic Aromatic Compounds/1st Biennial Meeting of the International-Society-for-Polycyclic-Aromatic-Compounds Baird, W. M., Smith, C. A., Spivak, G., Mauthe, R. J., Hanawalt, P. C. GORDON BREACH SCI PUBL LTD. 1994: 169–76

  View details for Web of Science ID A1994PG34200022

• TRANSCRIPTION-COUPLED DNA-REPAIR SCIENCE Sweder, K. S., Hanawalt, P. C. 1993; 262 (5132): 439-439

  View details for Web of Science ID A1993MB85900064

  View details for PubMedID 8211165

• LACK OF TRANSCRIPTION-COUPLED REPAIR IN MAMMALIAN RIBOSOMAL-RNA GENES BIOCHEMISTRY Christians, F. C., Hanawalt, P. C. 1993; 32 (39): 10512-10518

  Abstract

  We studied the induction and removal of UV-induced cyclobutane pyrimidine dimers (CPDs) in the ribosomal RNA genes (rDNA) in cultured hamster and human cells. In these genes, which are transcribed by RNA polymerase I, we found no evidence for transcription-coupled repair. The induction of CPDs was heterogeneous in rDNA due to nucleotide sequence: it was lower on the transcribed strand than on the nontranscribed strand and slightly lower in the coding region than in the nontranscribed spacer. Nevertheless, no dramatic difference in CPD induction was observed between rDNA and the dihydrofolate reductase (DHFR) gene. In Chinese hamster ovary cells, we observed no removal of CPDs from either rDNA strand within 24 h after UV irradiation. In these experiments, we did observe efficient repair of the transcribed, but not the nontranscribed, strand of the DHFR gene, in agreement with published results. In human cells, repair of rDNA was observed, but it showed no strand preference and was slower than that reported for the genome overall. No significant differences in repair were observed between restriction fragments from transcribed and nontranscribed regions or between growth-arrested and proliferating human cells, with presumably different levels of transcription of rDNA. We conclude that the modest level of rDNA repair is accomplished by a transcription-independent repair system and that repair is impeded by the nucleolar compartmentalization of rDNA. We discuss the possibility that recombination, rather than repair, maintains the normal sequence of rDNA in mammalian cells.

  View details for Web of Science ID A1993MA66400030

  View details for PubMedID 8399197

• RECA MUTATIONS THAT REDUCE THE CONSTITUTIVE COPROTEASE ACTIVITY OF THE RECA1202(PRT(C)) PROTEIN - POSSIBLE INVOLVEMENT OF INTERFILAMENT ASSOCIATION IN PROTEOLYTIC AND RECOMBINATION ACTIVITIES JOURNAL OF BACTERIOLOGY Liu, S. K., Eisen, J. A., Hanawalt, P. C., Tessman, I. 1993; 175 (20): 6518-6529

  Abstract

  Twenty-eight recA mutants, isolated after spontaneous mutagenesis generated by the combined action of RecA1202(Prtc) and UmuDC proteins, were characterized and sequenced. The mutations are intragenic suppressors of the recA1202 allele and were detected by the reduced coprotease activity of the gene product. Twenty distinct mutation sites were found, among which two mutations, recA1620 (V-275-->D) and recA1631 (I-284-->N), were mapped in the C-terminal portion of the interfilament contact region (IFCR) in the RecA crystal. An interaction of this region with the part of the IFCR in which the recA1202 mutation (Q-184-->K) is mapped could occur only intermolecularly. Thus, altered IFCR and the likely resulting change in interfilament association appear to be important aspects of the formation of a constitutively active RecA coprotease. This observation is consistent with the filament-bundle theory (R. M. Story, I. T. Weber, and T. A. Steitz, Nature (London) 335:318-325, 1992). Furthermore, we found that among the 20 suppressor mutations, 3 missense mutations that lead to recombination-defective (Rec-) phenotypes also mapped in the IFCR, suggesting that the IFCR, with its putative function in interfilament association, is required for the recombinase activity of RecA. We propose that RecA-DNA complexes may form bundles analogous to the RecA bundles (lacking DNA) described by Story et al. and that these RecA-DNA bundles play a role in homologous recombination.

  View details for Web of Science ID A1993MC02300019

  View details for PubMedID 8407828

• CLOSE-FITTING SLEEVES - RECOGNITION OF STRUCTURAL DEFECTS IN DUPLEX DNA MUTATION RESEARCH Hanawalt, P. C. 1993; 289 (1): 7-15

  Abstract

  The first step in the ubiquitous cellular process of nucleotide excision-repair must involve the recognition of a lesion or structural distortion in DNA. This is followed by incision in the strand perceived as damaged; and then coordinated steps of local degradation and re-synthesis occur to replace the defective DNA segment with a new stretch of nucleotides, making use of the intact complementary strand as template. The repair patch is ultimately ligated at its 3' end to the contiguous preexisting DNA strand to restore the integrity of the normal DNA structure. Crucial to this repair scheme is the fact that the genome consists of double-stranded DNA, so that when one strand is damaged the information for its repair can, in principle, be recovered from the other strand. We will review a bit of the early speculation about the nature of the damage recognition step and then discuss the complexity of that event as we currently understand it. An important conceptual contribution to this field resulted from my collaboration with Robert Haynes in which we suggested that "the recognition step in the repair mechanism could be formally equivalent to threading the DNA through a close-fitting 'sleeve' which gauges the closeness-of-fit to the Watson-Crick structure" (Hanawalt and Haynes, 1965).

  View details for Web of Science ID A1993LV53600003

  View details for PubMedID 7689165

• DIGESTION OF DAMAGED DNA BY THE T7 DNA POLYMERASE-EXONUCLEASE BIOCHEMICAL JOURNAL Koehler, D. R., Hanawalt, P. C. 1993; 293: 451-453

  Abstract

  We have investigated the 3'-5'-exonuclease activity of phage T7 DNA polymerase for its usefulness as an approach for the detection of lesions in DNA. Unlike the T4 DNA polymerase-exonuclease, which is commonly used to map the position and frequency of lesions in very small DNA fragments, T7 DNA polymerase-exonuclease is able to hydrolyse almost completely the large fragments from KpnI-restricted mammalian DNA. However, we found that the exonuclease was also able to hydrolyse DNA containing several kinds of lesions: cyclobutane pyrimidine dimers, thymine glycols, and mono-adducts of 4'-hydroxymethyl-4,5',8-trimethylpsoralen and 5'-methyl-isopsoralen. Modifications of the reaction conditions did not significantly alter the extent of hydrolysis. These properties distinguish the T7 DNA polymerase-exonuclease from the T4 DNA polymerase-exonuclease and make the T7 DNA polymerase-exonuclease unsuitable for detecting several types of lesions in DNA.

  View details for Web of Science ID A1993LP71300023

  View details for PubMedID 8343124

• INCREASED UV RESISTANCE OF A XERODERMA-PIGMENTOSUM REVERTANT CELL-LINE IS CORRELATED WITH SELECTIVE REPAIR OF THE TRANSCRIBED STRAND OF AN EXPRESSED GENE MOLECULAR AND CELLULAR BIOLOGY Lommel, L., Hanawalt, P. C. 1993; 13 (2): 970-976

  Abstract

  A UV-resistant revertant (XP129) of a xeroderma pigmentosum group A cell line has been reported to be totally deficient in repair of cyclobutane pyrimidine dimers (CPDs) but proficient in repair of 6-4 photoproducts. This finding has been interpreted to mean that CPDs play no role in cell killing by UV. We have analyzed the fine structure of repair of CPDs in the dihydrofolate reductase gene in the revertant. In this essential, active gene, we observe that repair of the transcribed strand is as efficient as that in normal, repair-proficient human cells, but repair of the nontranscribed strand is not. Within 4 h after UV at 7.5 J/m2, over 50% of the CPDs were removed, and by 8 h, 80% of the CPDs were removed. In contrast, there was essentially no removal from the nontranscribed strand even by 24 h. Our results demonstrate that overall repair measurements can be misleading, and they support the hypothesis that removal of CPDs from the transcribed strands of expressed genes is essential for UV resistance.

  View details for Web of Science ID A1993KH79300027

  View details for PubMedID 8423816

• STRANDED IN AN ACTIVE GENE CURRENT BIOLOGY Hanawalt, P., Mellon, I. 1993; 3 (1): 67-69

  View details for Web of Science ID A1993LL95300017

  View details for PubMedID 15335889

• GENOMIC HETEROGENEITY OF DNA-REPAIR - ROLE IN AGING ANNALS OF THE NEW YORK ACADEMY OF SCIENCES Hanawalt, P. C., Gee, P., Ho, L., Hsu, R. K., Kane, C. J. 1992; 663: 17-25

  Abstract

  The introduction and repair of DNA lesions are generally heterogeneous with respect to different genomic domains. In particular, the repair of helix-distorting damage, such as the cyclobutane pyrimidine dimers (CPD) induced by ultraviolet light occurs selectively in expressed genes. This is due in large part to the preferential repair of transcribed DNA strands, which is then reflected in a bias toward mutagenesis from persisting lesions in nontranscribed strands. Consequently, determination of overall genomic repair efficiencies may not be a good indicator of cellular sensitivity to agents that damage DNA. Although some studies suggest an age-related accumulation of altered nucleotides in DNA, we do not know the intragenomic distribution of those changes and whether they are relevant to the physiological aspects of aging. Subtle changes in the pattern of preferential repair during maturation could have profound effects on cell and tissue function. DNA repair has been analyzed in differentiating cell systems as possible models for aging. We have observed attenuated overall repair of CPD in differentiated rat myoblasts or PC12 neuron-like cells. In both model systems, several expressed genes have been shown to be repaired relatively efficiently but without strand specificity. In another model system of human HT1080 fibroblasts differentiating in the presence of dexamethasone, we demonstrated enhanced repair in the gene for plasminogen activator inhibitor I whose transcription is induced and, correspondingly, a reduced repair rate in the urokinase plasminogen activator gene whose transcription is suppressed. We conclude that any attempted correlation of the phenomena of aging with DNA repair should focus on the relevant genes in the tissue of interest.

  View details for Web of Science ID A1992KJ58100003

  View details for PubMedID 1482051

• PREFERENTIAL REPAIR OF CYCLOBUTANE PYRIMIDINE DIMERS IN THE TRANSCRIBED STRAND OF A GENE IN YEAST CHROMOSOMES AND PLASMIDS IS DEPENDENT ON TRANSCRIPTION PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Sweder, K. S., Hanawalt, P. C. 1992; 89 (22): 10696-10700

  Abstract

  While preferential repair of the transcribed strands within active genes has been demonstrated in organisms as diverse as humans and Escherichia coli, it has not previously been shown to occur in chromosomal genes in the yeast Saccharomyces cerevisiae. We found that repair of cyclobutane pyrimidine dimers in the transcribed strand of the expressed RPB2 gene in the chromosome of a repair-proficient strain is much more rapid than that in the nontranscribed strand. Furthermore, a copy of the RPB2 gene borne on a centromeric ARS1 plasmid showed the same strand bias in repair. To investigate the relation of this strand bias to transcription, we studied repair in a yeast strain with the temperature-sensitive mutation, rpb1-1, in the largest subunit of RNA polymerase II. When exponentially growing rpb1-1 cells are shifted to the nonpermissive temperature, they rapidly cease mRNA synthesis. At the permissive temperature, both rpb1-1 and the wild-type, parental cells exhibited rapid, proficient repair in the transcribed strand of chromosomal and plasmid-borne copies of the RPB2 gene. At the nonpermissive temperature, the rate of repair in the transcribed strand in rpb1-1 cells was reduced to that in the nontranscribed strand. These findings establish the dependence of strand bias in repair on transcription by RNA polymerase II in the chromosomes and in plasmids, and they validate the use of plasmids for analysis of the relation of repair to transcription in yeast.

  View details for Web of Science ID A1992JY87400028

  View details for PubMedID 1438266

• INTRAGENOMIC REPAIR HETEROGENEITY OF DNA DAMAGE ENVIRONMENTAL HEALTH PERSPECTIVES Scicchitano, D. A., Hanawalt, P. C. 1992; 98: 45-51

  Abstract

  The mutagenic and carcinogenic consequences of unrepaired DNA damage depend upon its precise location with respect to the relevant genomic sites. Therefore, it is important to learn the fine structure of DNA damage, in particular, proto-oncogenes, tumor-suppressor genes, and other DNA sequences implicated in tumorigenesis. Both the introduction and the repair of many types of DNA lesions are heterogeneous with respect to chromatin structure and/or gene activity. For example, cyclobutane pyrimidine dimers are removed more efficiently from the transcribed than the nontranscribed strand of the dhfr gene in Chinese hamster ovary cells. In contrast, preferential strand repair of alkali-labile sites is not found at this locus. In mouse 3T3 cells, dimers are more efficiently removed from an expressed proto-oncogene than from a silent one. Persistent damage in nontranscribed domains may account for genomic instability in those regions, particularly during cell proliferation as lesions are encountered by replication forks. The preferential repair of certain lesions in the transcribed strands of active genes results in a bias toward mutagenesis owing to persistent lesions in the nontranscribed strands. Risk assessment in environmental genetic toxicology requires assays that determine effective levels of DNA damage of producing malignancy. The existence of nonrandom repair in the mammalian genome casts doubt on the reliability of overall indicators of carcinogen-DNA binding and lesion repair for such determinations. Tissue-specific and cell-specific differences in the coordinate regulation of gene expression and DNA repair may account for corresponding differences in the carcinogenic response to particular environmental agents.

  View details for Web of Science ID A1992KG63700006

  View details for PubMedID 1486861

• INHIBITION OF TRANSCRIPTION AND STRAND-SPECIFIC DNA-REPAIR BY ALPHA-AMANITIN IN CHINESE-HAMSTER OVARY CELLS MUTATION RESEARCH Christians, F. C., Hanawalt, P. C. 1992; 274 (2): 93-101

  Abstract

  Recent studies have shown preferential repair of UV-induced cyclobutane pyrimidine dimers (CPD) in the transcribed strand of the expressed dihydrofolate reductase (DHFR) gene in human and rodent cells. We have tested the hypothesis that the strand-specific repair of such transcription-blocking lesions is dependent upon concurrent transcription. Chinese hamster ovary (CHO) B11 cells with an amplified DHFR gene were treated with alpha-amanitin before irradiation with UV (254 nm) and during post-irradiation incubation. Nuclear run-off analysis verified inhibition of transcription in the DHFR gene. CsCl density gradient analysis showed that alpha-amanitin at the levels used does not significantly interfere with overall genomic repair replication or semiconservative replication. However, we did observe a dramatic reduction in the removal of CPD from the transcribed strand in the 14 kb KpnI fragment within the DHFR gene in treated cells. We conclude that strand-specific repair of an active gene in CHO cells is dependent upon the activity of the transcribing RNA polymerase. Our results support the model that transcription complexes stalled at CPD signal the repair machinery to achieve efficient repair of the transcribed strand in active genes.

  View details for Web of Science ID A1992JC64900004

  View details for PubMedID 1378211

• TRANSLESION DNA-SYNTHESIS IN THE DIHYDROFOLATE-REDUCTASE DOMAIN OF UV-IRRADIATED CHO CELLS BIOCHEMISTRY Spivak, G., Hanawalt, P. C. 1992; 31 (29): 6794-6800

  Abstract

  The studies that document the coupling of strand-specific DNA repair to transcription of active genes exclude replicated DNA from the analysis. Yet cyclobutane pyrimidine dimers (CPD) induced by ultraviolet light (UV) persist in most of the genome in surviving Chinese hamster ovary (CHO) cells. The mechanisms that allow DNA replication to occur in the presence of damaged templates are poorly understood. We have investigated the distribution of CPD in the dihydrofolate reductase gene (DHFR) domain in replicated DNA. CHO B11 cells were incubated in the presence of BrdUrd after UV irradiation; the replicated DNA was separated from the unreplicated DNA by isopycnic sedimentation in CsCl, and then the parental and daughter strands were resolved in alkaline CsCl. We determined the fraction of a 14-kb KpnI fragment of the DHFR gene that was resistant to digestion by T4 endonuclease V, a CPD-specific enzyme. In both parental and unreplicated DNA, approximately 80% of the CPD were removed from the transcribed strands while approximately 20% were removed from the nontranscribed strands of DHFR within 24 h. In a 15-kb KpnI fragment that contains an origin of replication and is located approximately 15 kb downstream of DHFR, we found very low repair levels, whether it had been replicated or not. We detected no CPD in the daughter strands of either fragment analyzed. These results suggest that the replication forks can move through the damaged DNA in the absence of significant levels of repair or strand exchange and that the repair of CPD is not affected by replication in these cells.

  View details for Web of Science ID A1992JF65400021

  View details for PubMedID 1637815

• LOCALIZED TORSIONAL TENSION IN THE DNA OF HUMAN-CELLS PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Ljungman, M., Hanawalt, P. C. 1992; 89 (13): 6055-6059

  Abstract

  Torsional tension in DNA may be both a prerequisite for the efficient initiation of transcription and a consequence of the transcription process itself with the generation of positive torsional tension in front of the RNA polymerase and negative torsional tension behind it. To examine torsional tension in specific regions of genomic DNA in vivo, we developed an assay using photoactivated psoralen as a probe for unconstrained DNA superhelicity and x-rays as a means to relax DNA. Psoralen intercalates more readily into DNA underwound by negative torsional tension than into relaxed. DNA, and it can form interstrand DNA cross-links upon UVA irradiation. By comparing the amount of psoralen-induced DNA cross-links in cells irradiated with x-rays either before or after the psoralen treatment, we examined the topological state of the DNA in specific regions of the genome in cultured human 6A3 cells. We found that although no net torsional tension was detected in the bulk of the genome, localized tension was prominent in the DNA of two active genes. Negative torsional tension was found in the 5' end of the amplified dihydrofolate reductase gene and in a region near the 5' end of the 45S rRNA transcription unit, whereas a low level of positive torsional tension was found in a region near the 3' end of the dihydrofolate reductase gene. These results document an intragenomic heterogeneity of DNA torsional tension and lend support to the twin supercoiled domain model for transcription in the genome of intact human cells.

  View details for Web of Science ID A1992JC86800073

  View details for PubMedID 1631091

• EFFICIENT PROTECTION AGAINST OXIDATIVE DNA DAMAGE IN CHROMATIN MOLECULAR CARCINOGENESIS Ljungman, M., Hanawalt, P. C. 1992; 5 (4): 264-269

  Abstract

  The role of histones and higher order chromatin structures in protecting against oxidative DNA damage was investigated using an in vitro system consisting of nuclear and nucleoid monolayers as model chromatin substrates. These substrates, derived from human skin fibroblasts, were challenged with hydroxyl radicals produced via a Fenton reaction involving Fe(II)-ethylenediaminetetraacetic acid and ascorbic acid. The resulting DNA strand breaks were measured using the alkaline unwinding technique. The sequential removal of chromosomal proteins from the DNA by pretreating nuclear monolayers with increasing concentrations of salt dramatically increased the frequency of hydroxyl radical-induced DNA strand breaks. Furthermore, the DNA in decondensed chromatin was found to contain 14-fold fewer DNA strand breaks than naked, supercoiled DNA, whereas the DNA of "native" chromatin and "condensed" chromatin contained 100-fold and 300-fold fewer breaks, respectively. We conclude that the binding of histones to the DNA and its organization into higher order chromatin structures dramatically protects the DNA against hydroxyl radical-induced DNA strand breaks and thus should be considered part of the cellular defense against the induction of oxidative DNA damage.

  View details for Web of Science ID A1992JB22100004

  View details for PubMedID 1323299

• GENOMIC HETEROGENEITY OF DNA-REPAIR - ROLE IN AGING CONF ON AGING AND CELLULAR DEFENSE MECHANISMS Hanawalt, P. C., Gee, P., Ho, L., Hsu, R. K., Kane, C. J. NEW YORK ACAD SCIENCES. 1992: 17–25

  Abstract

  The introduction and repair of DNA lesions are generally heterogeneous with respect to different genomic domains. In particular, the repair of helix-distorting damage, such as the cyclobutane pyrimidine dimers (CPD) induced by ultraviolet light occurs selectively in expressed genes. This is due in large part to the preferential repair of transcribed DNA strands, which is then reflected in a bias toward mutagenesis from persisting lesions in nontranscribed strands. Consequently, determination of overall genomic repair efficiencies may not be a good indicator of cellular sensitivity to agents that damage DNA. Although some studies suggest an age-related accumulation of altered nucleotides in DNA, we do not know the intragenomic distribution of those changes and whether they are relevant to the physiological aspects of aging. Subtle changes in the pattern of preferential repair during maturation could have profound effects on cell and tissue function. DNA repair has been analyzed in differentiating cell systems as possible models for aging. We have observed attenuated overall repair of CPD in differentiated rat myoblasts or PC12 neuron-like cells. In both model systems, several expressed genes have been shown to be repaired relatively efficiently but without strand specificity. In another model system of human HT1080 fibroblasts differentiating in the presence of dexamethasone, we demonstrated enhanced repair in the gene for plasminogen activator inhibitor I whose transcription is induced and, correspondingly, a reduced repair rate in the urokinase plasminogen activator gene whose transcription is suppressed. We conclude that any attempted correlation of the phenomena of aging with DNA repair should focus on the relevant genes in the tissue of interest.

  View details for Web of Science ID A1992BX33J00003

• GENE-SPECIFIC DNA-REPAIR IN TERMINALLY DIFFERENTIATING RAT MYOBLASTS MUTATION RESEARCH Ho, L., Hanawalt, P. C. 1991; 255 (2): 123-141

  Abstract

  Preferential DNA repair in expressed genes has been well documented in proliferating mammalian cells following ultraviolet irradiation. It was of interest to learn whether excision repair is similarly selective in terminally differentiating cells. We have measured the removal of ultraviolet-induced cyclobutane pyrimidine dimers (detected as T4 endonuclease V-sensitive sites) from various genes in cultured L8 rat skeletal myoblasts. In these cells, the transcription of muscle-specific genes such as the embryonic myosin heavy chain (MHCemb) gene can be regulated by inducing cells to differentiate. L8 myoblasts are somewhat more sensitive than Chinese hamster ovary cells to ultraviolet radiation, and they exhibit relatively poor overall DNA-repair rates throughout differentiation. Irradiation severely reduces the rates of transcription and steady-state RNA levels for the genes studied. Although differences in kinetics are seen between the repair of active and inactive genes, repair rates are low relative to those previously measured in proliferating rodent cell lines. Repair efficiency in the MHCemb gene increases as it is activated during differentiation and, in fact, approaches 100% within 5 days, while that in the silent GAP43 gene is much lower. While repair efficiencies generally correlate with expression in the genes studied, the overall time course of repair appears to be prolonged in these cells compared to that in proliferating cells. These terminally differentiating cells seem to maintain a DNA damage surveillance and repair capacity for selected genes and/or genomic domains.

  View details for Web of Science ID A1991GF75400002

  View details for PubMedID 1717842

• THE GENETIC-DEFECT IN THE CHINESE-HAMSTER OVARY CELL MUTANT UV61 PERMITS MODERATE SELECTIVE REPAIR OF CYCLOBUTANE PYRIMIDINE DIMERS IN AN EXPRESSED GENE MUTATION RESEARCH Lommel, L., Hanawalt, P. C. 1991; 255 (2): 183-191

  Abstract

  We examined removal of cyclobutane pyrimidine dimers (CPDs) from the dihydrofolate reductase (DHFR) gene in ultraviolet-irradiated Chinese hamster ovary (CHO) UV61 and UV5 cells. The sensitivity of UV61 cells to UV-irradiation is intermediate between that of the parental CHO cells and that of mutants such as UV5 that are highly defective in excision repair. UV61 cells have been characterized as having normal repair of pyrimidine(6-4)pyrimidone photoproducts (6-4 PPs) but no detectable removal of CPDs from the genome overall. We find that the extent of removal of CPDs from the DHFR gene in UV61 cells is intermediate between that of the parental CHO cells and that of the UV5 mutant, and the observed repair appears to be confined to the transcribed strand. We detected no removal of CPDs from the DHFR gene in UV5 cells. Our findings in UV61 cells demonstrate a correlation between survival after UV-irradiation and CPD repair in an expressed gene in a cell line with moderate UV-sensitivity and yet no apparent removal of CPDs from the genome as a whole. We have thus demonstrated that overall repair measurements can be misleading. Our results have implications for the determination of the relative biological importance of the CPD and the 6-4 PP, and they further support the hypothesis that removal of CPDs from transcriptionally active DNA is crucial for UV-resistance.

  View details for Web of Science ID A1991GF75400007

  View details for PubMedID 1922150

• DIRECT EVIDENCE FOR SPATIAL AND TEMPORAL REGULATION OF TRANSFORMING GROWTH-FACTOR BETA-1 EXPRESSION DURING CUTANEOUS WOUND-HEALING JOURNAL OF CELLULAR PHYSIOLOGY Kane, C. J., Hebda, P. A., MANSBRIDGE, J. N., Hanawalt, P. C. 1991; 148 (1): 157-173

  Abstract

  The expression of transforming growth factor (TGF beta 1) protein in human and porcine skin has been analyzed by immunohistochemistry with two polyclonal antibodies (anti-CC and anti-LC) following cutaneous injury. The anti-LC antibody binds intracellular TGF beta 1 constitutively expressed in the nonproliferating, differentiated suprabasal keratinocytes in the epidermis of normal human skin, while the anti-CC antibody does not react with the form of TGF beta 1 present in normal skin as previously shown. TGF beta 1 may play a role in wound healing as suggested by its effect on multiple cell types in vitro and its acceleration of wound repair in animals. We have evaluated the natural expression and localization of TGF beta 1 protein in situ during initiation, progression, and resolution of the wound healing response in two models of cutaneous injury: the human suction blister and the dermatome excision of partial thickness procine skin. Anti-CC reactive TGF beta 1 in the epidermis is rapidly induced within 5 minutes following injury and progresses outward from the site of injury. The induction reflects a structural or conformational change in TGF beta 1 protein and can be blocked by the protease inhibitor leupeptin or by EDTA, suggesting a change in TGF beta 1 activity. One day post-injury anti-CC reactive TGF beta 1 is present in all epidermal keratinocytes adjacent to the wound including the basal cells. This corresponds temporally to the transient block of the basal keratinocyte mitotic burst following epithelial injury. Three to 4 days post-injury anti-CC reactive TGF beta 1 is localized around the suprabasal keratinocytes, in blood vessels, and in the papillary dermis in cellular infiltrates. The exclusion of TGF beta 1 from the rapidly proliferating basal cells and its extracellular association with suprabasal keratinocytes may represent physiological compartmentation of TGF beta 1 activity. Anti-CC staining is strong in the leading edge of the migrating epithelial sheet. The constitutive anti-LC reactivity with suprabasal keratinocytes seen in normal epidermis is neither relocalized nor abolished adjacent to the injury, but anti-LC staining is absent in the keratinocytes migrating within the wound. As the wound healing response resolves and the skin returns to normal, anti-CC reactive TGF beta 1 disappears while constitutive anti-LC reactive TGF beta 1 persists. Thus, changes in the structure or conformation of TGF beta 1, its localization, and perhaps its activity vary in a spatial and temporal manner following cutaneous injury and correlate with physiological changes during wound healing.

  View details for Web of Science ID A1991GA08100018

  View details for PubMedID 1907288

• DIFFERENTIAL INTRODUCTION AND REPAIR OF PSORALEN PHOTOADDUCTS TO DNA IN SPECIFIC HUMAN GENES CANCER RESEARCH Islas, A. L., Vos, J. M., Hanawalt, P. C. 1991; 51 (11): 2867-2873

  Abstract

  We have developed a novel procedure to measure interstrand DNA cross-linking in specific DNA sequences. After alkaline denaturation, CsCl gradient equilibrium sedimentation at pH 10.8 is used to resolve cross-linked double-stranded DNA from un-cross-linked single-stranded DNA. The DNA in gradient fractions is slot-blotted and hybridized with 32P-labeled DNA probes for the sequences of interest. After densitometric quantitation of the autoradiograms, the fraction of DNA cross-linked is determined by the ratio of cross-linked DNA to total DNA (the sum of cross-linked and un-cross-linked DNA). We have used this approach to measure the initial levels of production and extent of repair of the photoadducts of 4'-hydroxymethyl-4,5',8-trimethylpsoralen, i.e., both interstrand cross-links and cross-linkable monoadducts, in specific DNA sequences in cultured human cells. Under conditions in which DNA fragments carrying the expressed dihydrofolate reductase gene were extensively modified, with approximately 92% of the fragments cross-linked, only 37% of the fragments containing the unexpressed fms protooncogene were cross-linked. The overall level of cross-linking for bulk DNA was 74%. Within 24 h, 90% of the cross-linking had been removed from the dihydrofolate reductase gene, whereas little removal was detected in fms, and the bulk DNA showed 31% removal. From this study, we conclude that both the introduction and removal of 4'-hydroxymethyl-4,5',8-trimethylpsoralen adducts are dependent upon the target DNA sequence and its transcriptional activity. The implications for DNA repair of chromatin structure and active transcription are discussed in relation to our results.

  View details for Web of Science ID A1991FM97800019

  View details for PubMedID 2032227

• HETEROGENEITY OF DNA-REPAIR AT THE GENE LEVEL MUTATION RESEARCH Hanawalt, P. C. 1991; 247 (2): 203-211

  Abstract

  Overall genomic DNA repair efficiencies do not necessarily correlate with cellular sensitivities to radiation and other DNA-damaging agents. My colleagues and I have developed experimental approaches to measure DNA lesions and their repair in defined DNA sequences and we have discovered that for some types of damage, such as the cyclobutane pyrimidine dimers produced in DNA by ultraviolet light (UV), repair is highly selective for transcribed DNA strands in active genes: repair may be directly coupled to the transcription apparatus. Freely diffusing repair complexes may account for the much lower repair efficiencies observed in silent genomic domains. The viability of mammalian cells may be ensured through selective repair of transcription-blocking DNA damage in essential, expressed genes rather than as a consequence of overall genomic repair. Persisting damage in non-transcribed domains may account for some cell-specific mutagenic and carcinogenic phenomena. In UV-irradiated cells from xeroderma pigmentosum (complementation group C) there is a deficiency in the removal of pyrimidine dimers from silent genomic domains, while in Cockayne's syndrome the defect appears to involve the preferential repair of active genes. In contrast to the cancer-prone characteristic of xeroderma pigmentosum the victims of Cockayne's syndrome do not suffer enhanced skin cancer induction by sunlight. Susceptibility to cancer and other biological endpoints is clearly dependent upon the fine structure detail of the DNA repair response.

  View details for Web of Science ID A1991FH26300005

  View details for PubMedID 2011138

• LACK OF SEQUENCE-SPECIFIC REMOVAL OF N-METHYLPURINES FROM CELLULAR DNA MUTATION RESEARCH Scicchitano, D. A., Hanawalt, P. C. 1990; 233 (1-2): 31-37

  Abstract

  The removal of N-methylpurines from the DHFR gene and an unexpressed adjacent locus located downstream occurs at similar rates and to a similar extent in dimethyl sulfate treated Chinese hamster ovary B11 cells. Furthermore, no significant differences in repair rates are observed between the strands of the active gene. These data primarily reflect the removal of the most abundant lesion produced by dimethyl sulfate, 7-methylguanine, and are in contrast to the results obtained for the removal of ultraviolet-induced cyclobutane pyrimidine dimers from the same region of the genome. Pyrimidine dimers are cleared preferentially from the transcribed strand of the DHFR gene and are removed poorly from the non-transcribed complementary strand and unexpressed adjacent regions. The results suggest that DNA lesions such as dimers that block transcription are removed preferentially from active genes, whereas lesions that do not interfere with nucleic acid synthesis (i.e. 7-methylguanine) are removed at similar rates from expressed and silent loci.

  View details for Web of Science ID A1990EJ42300005

  View details for PubMedID 2233810

• TRANSFORMING GROWTH FACTOR-BETA-1 LOCALIZATION IN NORMAL AND PSORIATIC EPIDERMAL-KERATINOCYTES INSITU JOURNAL OF CELLULAR PHYSIOLOGY Kane, C. J., KNAPP, A. M., MANSBRIDGE, J. N., Hanawalt, P. C. 1990; 144 (1): 144-150

  Abstract

  Transforming growth factor-beta 1 (TGF beta 1) is a potent inhibitor of epithelial cell proliferation and its effects on growth and differentiation have been extensively characterized in cultured keratinocytes. We used two TGF beta 1-specific polyclonal antibodies (anti-LC and anti-CC) to determine the presence of TGF beta 1 peptide in keratinocytes in sections of normal human skin in situ and in both plaque and nonplaque skin from individuals with psoriasis. In contrast to the differentiation phenotype expressed by keratinocytes in normal epidermis, keratinocytes in the psoriatic plaque exhibit a hyperproliferative/regenerative differentiation phenotype. Anti-TGF beta 1 staining was observed primarily in the epidermis. Anti-LC TGF beta 1 antibody stained nonproliferating, differentiated suprabasal keratinocytes intracellularly in normal skin but did not stain psoriatic plaques from five of seven patients. In contrast, anti-CC TGF beta 1 antibody stained suprabasal keratinocytes extracellularly in psoriatic plaques, but did not stain normal skin. Both anti-LC and anti-CC stained suprabasal keratinocytes intracellularly in nonplaque psoriatic skin. Thus, the conformation or structure of TGF beta 1 and its localization vary in keratinocytes with distinct differentiation phenotypes suggesting that TGF beta 1 is a potential modulator of keratinocyte differentiation in vivo. Selective association of TGF beta 1 with nonproliferating keratinocytes in the suprabasal layers of the epidermis and its exclusion from the proliferating keratinocytes in the basal layer suggest that it may be a physiological regulator of keratinocyte proliferation. In addition, the intracellular localization of TGF beta 1 peptide in both normal and psoriatic keratinocytes suggests that it is constitutively synthesized by epidermal keratinocytes in vivo.

  View details for Web of Science ID A1990DN56900018

  View details for PubMedID 1694857

• DIFFERENTIAL REPAIR AND REPLICATION OF DAMAGED DNA IN RIBOSOMAL-RNA GENES IN DIFFERENT CHO CELL-LINES JOURNAL OF CELLULAR BIOCHEMISTRY WAUTHIER, E. L., Hanawalt, P. C., Vos, J. M. 1990; 43 (2): 173-183

  Abstract

  We studied the repair of psoralen adducts in the pol I-transcribed ribosomal RNA (rRNA) genes of excision repair competent Chinese hamster ovary (CHO) cell lines, their UV sensitive mutant derivatives, and their UV resistant transformants, which express a human excision repair gene. In the parental cell line CHO-AA8, both monoadducts and interstrand crosslinks are removed efficiently from the rRNA genes, whereas neither adduct is removed in the UV sensitive derivative UV5; removal of both adducts is restored in the UV resistant transformant CHO-5T4 carrying the human excision repair gene ERCC-2. In contrast, removal of psoralen adducts from the rRNA genes is not detected in another parental CHO cell line CHO-9, neither in its UV sensitive derivative 43-3B, nor in its UV resistant transformant 83-G5 carrying the human excision repair gene ERCC-1. In contrast to such intergenomic heterogeneity of repair, persistence of psoralen monoadducts during replication of the rRNA genes occurs equally well in all CHO cell lines tested. From these data, we conclude that: 1) the repair efficiency of DNA damage in the rRNA genes varies between established parental CHO cell lines; 2) the repair pathways of intrastrand adducts and interstrand crosslinks in mammalian cells share, at least, one gene product, i.e., the excision repair gene ERCC-2; 3) replicational bypass of psoralen monoadducts at the CHO rRNA locus occurs similarly on both DNA strands.

  View details for Web of Science ID A1990DG83500007

  View details for PubMedID 2380262

• Selective DNA repair in expressed genes in mammalian cells. Progress in clinical and biological research Hanawalt, P. C. 1990; 340A: 213-222

  View details for PubMedID 2201974

• DNA-REPAIR IN DIFFERENTIATING CELLS IN RELATION TO AGING COLLOQUIUM ON MOLECULAR BIOLOGY OF AGING Hanawalt, P. C., Gee, P., Ho, L. WILEY-LISS, INC. 1990: 45–51

  View details for Web of Science ID A1990BQ98Z00004

• SELECTIVE DNA-REPAIR IN ACTIVE GENES INTERNATIONAL SYMP ON DNA REPAIR, CHROMOSOME ALTERATIONS, AND CHROMATIN STRUCTURE UNDER ENVIRONMENTAL POLLUTIONS Hanawalt, P. C. AKADEMIAI KIADO RT. 1990: 77–91

  Abstract

  My colleagues and I have discovered intragenomic heterogeneity in DNA repair in mammalian cells. Consequences of unrepaired DNA damage depend upon the precise location of the damage with respect to relevant genes. It is therefore important to understand rules governing accessibility of specific DNA sequences in chromatin to damage and repair. The efficiency of removal of pyrimidine dimers has been mapped in the active dihydrofolate reductase (DHFR) gene in Chinese hamster ovary (CHO) cells. Repair within the gene was shown to be much more efficient than that in silent downstream sequences or in the genome overall. Preferential repair of active and essential genes such as DHFR may account for the fact that rodent cells are as UV-resistant as human cells in spite of their much lower overall repair efficiencies. In repair proficient human cells the rate of repair in the DHFR gene is greater than that in the overall genome or in non-transcribed alpha DNA sequences. The efficiency of removal of pyrimidine dimers is much higher in the transcribed than the non-transcribed DNA strands of the DHFR gene in both CHO and human cells. An excision-repair complex may be directly coupled to the transcription machinery to ensure early removal of transcription-blocking lesions in active genes. Sequences in the active c-abl protooncogene are repaired much more efficiently than are sequences containing the inactive c-mos protooncogene in Swiss mouse 3T3 cells. Tissue specific and cell specific differences in the coordinate regulation of protooncogene expression and DNA repair may account for corresponding differences in the carcinogenic response. Efficient replicative bypass of persisting psoralen monoadducts, but not interstrand crosslinks, was demonstrated in the human DHFR gene. It is likely that most bulky lesions in mammalina DNA, other than crosslinks, do not pose insurmountable problems for replication in vivo, but they must be removed from essential transcribed sequences to maintain cellular viability.

  View details for Web of Science ID A1990FA42900009

  View details for PubMedID 2094132

• INDUCTION OF THE ESCHERICHIA-COLI LACTOSE OPERON SELECTIVELY INCREASES REPAIR OF ITS TRANSCRIBED DNA STRAND NATURE Mellon, I., Hanawalt, P. C. 1989; 342 (6245): 95-98

  Abstract

  Nucleotide excision repair helps to ameliorate the lethal and mutagenic consequences of DNA damage by removing helix-distorting lesions from cellular genomes. We have previously analysed the removal of ultraviolet-induced cyclobutane pyrimidine dimers from specific DNA sequences in mammalian cells and demonstrated that transcriptionally active genes are preferentially repaired. Additionally, we found that in rodent and human cells only the transcribed strand of the dihydrofolate reductase gene is selectively repaired. Transcription is blocked by pyrimidine dimers in template DNA and the selective removal of these lesions seems to be important for cell survival after irradiation with ultraviolet light. To determine whether this feature of repair is common to prokaryotes and eukaryotes and better to understand its mechanism, we have investigated repair in the two separate DNA strands of the lactose operon of ultraviolet-irradiated Escherichia coli. We find a dramatic difference in the repair of the two strands only when transcription is induced. Most dimers are removed from the transcribed strand of the induced operon within five minutes of irradiation. In the nontranscribed strand, repair is significantly slower and resembles that found in both strands of the uninduced operon. Thus there seems to be a mechanism that couples nucleotide excision repair and transcription.

  View details for Web of Science ID A1989AX86800066

  View details for PubMedID 2554145

• TRANSLESION SYNTHESIS IS THE MAIN COMPONENT OF SOS REPAIR IN BACTERIOPHAGE-LAMBDA DNA JOURNAL OF BACTERIOLOGY Defais, M., Lesca, C., Monsarrat, B., Hanawalt, P. 1989; 171 (9): 4938-4944

  Abstract

  Agents that interfere with DNA replication in Escherichia coli induce physiological adaptations that increase the probability of survival after DNA damage and the frequency of mutants among the survivors (the SOS response). Such agents also increase the survival rate and mutation frequency of irradiated bacteriophage after infection of treated bacteria, a phenomenon known as Weigle reactivation. In UV-irradiated single-stranded DNA phage, Weigle reactivation is thought to occur via induced, error-prone replication through template lesions (translesion synthesis [P. Caillet-Fauquet, M: Defais, and M. Radman, J. Mol. Biol. 117:95-112, 1977]). Weigle reactivation occurs with higher efficiency in double-stranded DNA phages such as lambda, and we therefore asked if another process, recombination between partially replicated daughter molecules, plays a major role in this case. To distinguish between translesion synthesis and recombinational repair, we studied the early replication of UV-irradiated bacteriophage lambda in SOS-induced and uninduced bacteria. To avoid complications arising from excision of UV lesions, we used bacterial uvrA mutants, in which such excision does not occur. Our evidence suggests that translesion synthesis is the primary component of Weigle reactivation of lambda phage in the absence of excision repair. The greater efficiency in Weigle reactivation of double-stranded DNA phage could thus be attributed to some inducible excision repair unable to occur on single-stranded DNA. In addition, after irradiation, lambda phage replication seems to switch prematurely from the theta mode to the rolling circle mode.

  View details for Web of Science ID A1989AM27300055

  View details for PubMedID 2527845

• QUANTIFICATION OF AMINOFLUORENE ADDUCT FORMATION AND REPAIR IN DEFINED DNA-SEQUENCES IN MAMMALIAN-CELLS USING THE UVRABC NUCLEASE JOURNAL OF BIOLOGICAL CHEMISTRY Tang, M. S., Bohr, V. A., Zhang, X. S., Pierce, J., Hanawalt, P. C. 1989; 264 (24): 14455-14462

  Abstract

  Using the UVRABC nuclease as a reagent coupled with DNA restriction and hybridization analysis we have developed a method to quantify N-acetoxy-2-acetylaminofluorene (NAAAF)-induced DNA damage in the coding and noncoding sequences of the dihydrofolate reductase (DHFR) gene in Chinese hamster ovary (CHO) cells. High performance liquid chromatography analysis shows that the only DNA adduct formed in NAAAF-treated CHO cells is N-(deoxyguanosine-C8-yl)-2-aminofluorene (dG-C8-AF). DNA sequencing analysis demonstrates that the UVRABC nuclease incises at all potential sites in which dG-C8-AF adduct may form in linear DNA fragments. We have found that the formation and removal of dG-C8-AF adducts in the coding and 3' downstream noncoding sequences of the DHFR domain are similar in cells treated with 10 microM NAAAF (3.1 adducts/14 kilobases); DNA adduct removal attains 70% for both sequences within 24 h. This result contrasts with that obtained for the repair of cyclobutane dipyrimidines in the DHFR gene, in which the repair efficiency is much higher in the coding region than in the 3' downstream noncoding region. Our results suggest that in CHO cells the repair pathway for aminofluorene DNA adducts is not the same as that for cyclobutane dipyrimidines. This new technique has the potential to detect a variety of chemical carcinogen induced DNA adducts at the gene level in cultured cells and in DNA isolated from animal tissues.

  View details for Web of Science ID A1989AL23300076

  View details for PubMedID 2760069

• DNA INTERSTRAND CROSS-LINKS PROMOTE CHROMOSOMAL INTEGRATION OF A SELECTED GENE IN HUMAN-CELLS MOLECULAR AND CELLULAR BIOLOGY Vos, J. M., Hanawalt, P. C. 1989; 9 (7): 2897-2905

  Abstract

  We have used integrative pSV2 plasmids to learn how DNA lesions affect nonhomologous recombination with human chromosomes. Enhanced stable transformation of fibrosarcoma cells with a selectable gene was observed after chemical modification of the plasmid DNA; thus, cells transfected with plasmid pSV2-gpt carrying photoadducts of the cross-linking agent 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT) yielded four- to sevenfold-higher levels of Gpt+ transformants than were obtained with untreated plasmid. The enhancement due to HMT interstrand cross-links was at least as great as that due to the monoadducts. DNA hybridization analysis indicated that the enhanced transformation frequency resulted from an increased number of cells carrying integrated plasmid sequences rather than from a higher copy number per transformant. The enhancement was not seen with a plasmid missing the sequences flanking the minimal simian virus 40 gpt transcription unit. Cotransfection with untreated and HMT-treated plasmids suggested that the HMT-containing DNA interacted preferentially with some cellular factor that promoted chromosomal integration of the plasmid DNA. It is concluded that (i) interstrand cross-linking as well as intrastrand DNA adducts promote nonhomologous recombination in human chromatin and (ii) DNA sequences flanking the selectable genes are the targets for such recombinational events.

  View details for Web of Science ID A1989AC45000015

  View details for PubMedID 2779552

• REPAIR ANALYSIS OF MITOMYCIN C-INDUCED DNA CROSSLINKING IN RIBOSOMAL-RNA GENES IN LYMPHOBLASTOID-CELLS FROM FANCONIS ANEMIA PATIENTS MUTATION RESEARCH Matsumoto, A., Vos, J. M., Hanawalt, P. C. 1989; 217 (3): 185-192

  Abstract

  The repair of mitomycin C (MMC)-induced DNA crosslinking was analyzed by denaturation-renaturation gel electrophoresis in ribosomal RNA genes in lymphoblastoid cell lines from 4 patients with Fanconi's anemia (FA). In comparison to normal lymphoblastoid cell lines, 2 lines of FA cells belonging to complementation group A clearly exhibited higher sensitivity to MMC and an almost identical deficiency in the removal of DNA crosslinking. A complementation group B cell line, HSC 62, exhibited a lower sensitivity than group A cells and a lesser deficiency in crosslink repair. Another 'non-A' group cell line, HSC 230, reproducibly exhibited even higher sensitivity to MMC than group A cells. The results on MMC crosslinkage removal at the molecular level correlated well with cell survival. The observed subtle differences of repair among the 4 FA cell lines might represent possible genetic differences in the respective FA complementation groups.

  View details for Web of Science ID A1989U510800002

  View details for PubMedID 2497343

• REPAIR OF N-METHYLPURINES IN SPECIFIC DNA-SEQUENCES IN CHINESE-HAMSTER OVARY CELLS - ABSENCE OF STRAND SPECIFICITY IN THE DIHYDROFOLATE-REDUCTASE GENE PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Scicchitano, D. A., Hanawalt, P. C. 1989; 86 (9): 3050-3054

  Abstract

  We have developed a quantitative method for examining the removal of N-methylpurines from specific genes to investigate their possible differential repair throughout the genome. Chinese hamster ovary cells were exposed to dimethyl sulfate, and the isolated DNA was treated with an appropriate restriction endonuclease. The DNA was heated to convert remaining N-methylpurines to apurinic sites to render them alkaline-labile. Duplicate samples heated in the presence of methoxyamine to protect the apurinic sites from alkaline hydrolysis provided controls to assess total DNA. After alkaline hydrolysis, agarose gel electrophoresis, Southern transfer, and probing for the fragment of interest, the ratios of band intensities of the test DNA sample to its methoxyamine-treated control counterpart were calculated to yield the percentage of fragments containing no alkaline-labile sites. The frequency of N-methylpurines was measured at different times after dimethyl sulfate treatment to study repair. We found no differences between the rates of repair of N-methylpurines in the active dihydrofolate reductase gene and a nontranscribed region located downstream from it in treated cells. Also, similar rates of repair were observed in the transcribed and nontranscribed strands of the gene, in contrast to previous results for the removal of cyclobutane pyrimidine dimers. Thus, there does not appear to be a coupling of N-methylpurine repair to transcription in Chinese hamster ovary cells. However, the repair in the dihydrofolate reductase domain appears to be somewhat more efficient than that in the genome overall. Our method permits the quantifying at the defined gene level of abasic sites or of any DNA adduct that can be converted to them.

  View details for Web of Science ID A1989U446200014

  View details for PubMedID 2785688

• DEMETHYLATION ENHANCES REMOVAL OF PYRIMIDINE DIMERS FROM THE OVERALL GENOME AND FROM SPECIFIC DNA-SEQUENCES IN CHINESE-HAMSTER OVARY CELLS MOLECULAR AND CELLULAR BIOLOGY Ho, L., Bohr, V. A., Hanawalt, P. C. 1989; 9 (4): 1594-1603

  Abstract

  We have examined the effects of changes in cytosine methylation on DNA repair in UV-irradiated Chinese hamster ovary (CHO) cells. A hypomethylated derivative of the CHO K1B11 line, B11aza, was established by passaging B11 cells over several months in increasing concentrations of 5-azacytidine; greater than 60% demethylation was consistently demonstrated in these conditioned cells. Following a UV dose of 10 J/m2, the amount of repair replication performed within 24 h was approximately twofold higher in B11aza cells than in control B11 cells. Removal of T4 endonuclease V-sensitive sites (ESS) from specific restriction fragments within and around the dihydrofolate reductase (DHFR) gene was then examined in B11aza cells and compared with that in B11 cells. Although demethylation had little or no effect on repair in the 5' half of the DHFR gene, within a nontranscribed sequence immediately downstream from the gene, or within an extragenic region further downstream from the DHFR gene, significant increases in repair were observed at the 3' end of the DHFR gene and within an extragenic region upstream of the DHFR gene. However, the increases in DNA repair were not accompanied by any changes in overall cellular resistance to UV when colony-forming ability was assayed. We suggest that the level of DNA methylation may play an indirect role in the regulation of DNA repair, perhaps through an effect on chromatin structure or transcriptional activity.

  View details for Web of Science ID A1989T862900023

  View details for PubMedID 2725518

• EFFECT OF DNA DAMAGE ON STABLE TRANSFORMATION OF MAMMALIAN-CELLS WITH INTEGRATIVE AND EPISOMAL PLASMIDS MUTATION RESEARCH Vos, J. M., Hanawalt, P. C. 1989; 220 (2-3): 205-220

  Abstract

  The efficiency of stable transformation of human cells by integrative (non-replicating) plasmids carrying a selectable gene has been shown to be markedly enhanced by the introduction into the plasmid DNA of bulky damage, such as cyclobutane pyrimidine dimers or psoralen photoadducts. Enhanced transformation (ET) occurs in all human cells tested, including DNA repair-deficient cells from the hereditary syndrome xeroderma pigmentosum, but significantly less, if at all, in rodent cells. ET has been observed with a variety of integrative plasmid constructs, suggesting the generality of the phenomenon; as expected, ET is due to an increase in the number of cells carrying integrated plasmid sequences. In contrast to integrative plasmids, stable transformation by episomal (autonomously replicating) plasmids derived from the Epstein-Barr virus is only depressed by the introduction of photoproducts; furthermore, pronounced inactivation of transformation mediated by episomal plasmids becomes apparent in xeroderma pigmentosum cells. Altogether, these results suggest that DNA damage increases the probability of stable insertion of heterologous non-replicating DNA into human chromosomes. Moreover, the differential sensitivity to DNA damage of human cell transformation mediated by integrative versus episomal plasmids suggests caution in using such assay to measure host cell reactivation capacity; processing of DNA damage in mammalian cells might differ significantly between intra- versus extra-chromosomal DNA. Since ET may be induced by damage outside the selectable gene carried on integrative plasmids, we propose a model that involves local disruption of chromatin structure by helix-distorting DNA lesions flanking actively transcribed sequences; alternatively, reorganization of such altered DNA structure might be favored by the presence of topoisomerase-like activities in the proximity of active genes. Because ET can also be induced by DNA damage to the recipient cells, it is speculated that similar mechanism(s) might be involved in the generation of other types of non-homologous DNA recombination in damaged human chromosomes, including oncogenic cell transformation mediated by integrative DNA viruses.

  View details for Web of Science ID A1989T814800018

  View details for PubMedID 2927424

• CONCEPTS AND MODELS FOR DNA-REPAIR - FROM ESCHERICHIA-COLI TO MAMMALIAN-CELLS ENVIRONMENTAL AND MOLECULAR MUTAGENESIS Hanawalt, P. C. 1989; 14: 90-98

  Abstract

  Much of our early understanding of the mechanisms of excision-repair and its roles in maintaining genome integrity and cellular viability was derived from studies with bacteria. In fact, the discoveries of damage excision and repair replication were made in ultraviolet (UV)-irradiated Escherichia coli. Recent advances in recombinant DNA technology have helped to further our understanding of the manner in which mammalian cells deal with damage in their complex genomes. These include the discovery that expressed genes may be preferentially repaired and, furthermore, that the transcribed DNA strand, for some types of damage, is selectively repaired within an active gene. The latter finding has now been documented in E. coli as well, so it is likely that it is of widespread importance as a mechanism to ensure the expression of active genes in otherwise damaged cells. It is certain that studies with bacterial systems as models will continue to have an important impact on the development of the field of mammalian DNA repair.

  View details for Web of Science ID A1989AE31300016

  View details for PubMedID 2659338

• RELATIONSHIPS BETWEEN DNA-REPAIR AND TRANSCRIPTION IN DEFINED DNA-SEQUENCES IN MAMMALIAN-CELLS NATO ADVANCED RESEARCH WORKSHOP ON DNA REPAIR MECHANISMS AND THEIR BIOLOGICAL IMPLICATIONS IN MAMMALIAN CELLS Hanawalt, P., Mellon, I., SCICCHITANO, D., Spivak, G. PLENUM PRESS DIV PLENUM PUBLISHING CORP. 1989: 325–337

  View details for Web of Science ID A1989BR19Z00028

• PREFERENTIAL REPAIR OF DAMAGE IN ACTIVELY TRANSCRIBED DNA-SEQUENCES INVIVO 16TH INTERNATIONAL CONGRESS OF GENETICS : GENETICS AND THE UNITY OF BIOLOGY Hanawalt, P. C. NATL RESEARCH COUNCIL CANADA. 1989: 605–11

  Abstract

  My colleagues and I have discovered intragenomic heterogeneity in DNA repair in mammalian cells. Consequences of unrepaired DNA damage depend upon the precise location of the damage with respect to relevant genes. It is therefore important to understand rules governing accessibility of specific DNA sequences in chromatin to damage and repair. The efficiency of removal of pyrimidine dimers has been determined in the active dihydrofolate reductase (DHFR) gene in Chinese hamster ovary (CHO) cells. Repair within the gene was shown to be much more efficient than that in nontranscribed downstream sequences or in the genome overall. Preferential repair of active and essential genes such as DHFR may account for the fact that rodent cells are as uv-resistant as human cells in spite of their much lower overall repair efficiencies. In repair-proficient human cells the rate of repair in the DHFR gene is greater than that in the overall genome or in nontranscribed alpha-DNA sequences. The efficiency of removal of pyrimidine dimers is much higher in the transcribed than the nontranscribed DNA strands of the DHFR gene in both CHO and human cells. An excision-repair complex may be directly coupled to the transcription machinery to ensure early removal of transcription-blocking lesions in active genes. Sequences in the active c-abl proto-oncogene are repaired much more efficiently than are sequences containing the inactive c-mos proto-oncogene in Swiss mouse 3T3 cells. Tissue-specific and cell-specific differences in the coordinate regulation of proto-oncogene expression and DNA repair may account for corresponding differences in the carcinogenic response.(ABSTRACT TRUNCATED AT 250 WORDS)

  View details for Web of Science ID A1989CL22100018

  View details for PubMedID 2698835

• DNA DAMAGE STIMULATES HUMAN CELL-TRANSFORMATION BY INTEGRATIVE BUT NOT EPISOMAL EPSTEIN-BARR VIRUS-DERIVED PLASMID MOLECULAR CARCINOGENESIS Vos, J. M., WAUTHIER, E. L., Hanawalt, P. C. 1989; 2 (5): 237-244

  Abstract

  Previous work has demonstrated that ultraviolet (UV) irradiation of SV40-based plasmids can strikingly enhance the frequency of stable transformation of human cells. In this study we compared the effect of UV-induced DNA damage on transformation mediated by integrative versus autonomously replicating plasmids derived from human Epstein-Barr virus (EBV). We report that transfection of human fibroblasts with UV-irradiated integrative EBV-based plasmid results in enhanced transformation. However, transfection of UV-damaged episomal EBV-based constructs into the same human cell line does not enhance transformation; in fact, the extrachromosomal status of the plasmid is maintained irrespective of the UV dose to the plasmid. We conclude that enhanced transformation of human cells by damaged DNA requires its chromosomal integration.

  View details for Web of Science ID A1989CF69500002

  View details for PubMedID 2557855

• TEMPERATURE-DEPENDENT SURVIVAL OF UV-IRRADIATED ESCHERICHIA-COLI-K12 MOLECULAR & GENERAL GENETICS Ganesan, A. K., Hunt, J., Hanawalt, P. C. 1988; 214 (2): 198-203

  Abstract

  We have found that several excision deficient derivatives of Escherichia coli K12 survive better after UV irradiation if incubated at 42 degrees C than if incubated at 30 degrees C. The highest survival was observed when incubation at 42 degrees C followed UV irradiation and was maintained for at least 16 h. Our results indicate that this temperature dependent resistance (TDR) requires a functional recA gene, but not uvrA, uvrB, recF, or recB genes, or the recA441 (tif-1) mutation which allows thermoinduction of the recA-lexA regulon. Our data are consistent with the idea that the increase in survival observed at 42 degrees C reflects enhanced daughter-strand gap repair by DNA strand exchange. Although the conditions used to elicit TDR can induce heat shock proteins and thermotolerance in E. coli, the relationship between the two responses remains to be elucidated.

  View details for Web of Science ID A1988Q513500003

  View details for PubMedID 3070347

• COMPARATIVE REMOVAL OF PYRIMIDINE DIMERS FROM HUMAN EPIDERMAL-KERATINOCYTES INVIVO AND INVITRO JOURNAL OF INVESTIGATIVE DERMATOLOGY REUSCH, M. K., Meager, K., Leadon, S. A., Hanawalt, P. C. 1988; 91 (4): 349-352

  Abstract

  We have compared the kinetics for repair of UV-induced cyclobutane pyrimidine dimers in the DNA of keratinocytes in human skin and in cell culture. A small area of the buttocks of volunteers was exposed to UVB-irradiation and biopsies were taken at various time intervals. Epidermal keratinocytes in culture from the same subjects were exposed to UVC with doses chosen to elicit comparable yields of dimers in cellular DNA. The initial density of pyrimidine dimers and the kinetics of their removal were assessed utilizing the dimer-specific T4 endonuclease V and sedimentation of the unlabeled DNA through alkaline sucrose gradients. The position of DNA in the gradients was determined using a monoclonal antibody against random sequences of single-stranded DNA in a sensitive immunoassay. The initial dimer frequency was 3.9-6.7 per 10(8) daltons DNA. About 40% of the dimers were removed within 1 h, 70% in 6 h, and 90% in 24 h for both in vivo and in vitro samples. The early rapid removal phase may represent preferential repair of actively transcribed genes. Our findings reaffirm the usefulness and applicability of cell culture systems to model in vivo repair phenomena. The use of monoclonal antibodies to detect single-stranded DNA in alkaline sucrose gradients may be of value in a variety of studies involving human tissues in which it is not possible to use radioactive labeling of the DNA for the analysis.

  View details for Web of Science ID A1988Q217500014

  View details for PubMedID 2459263

• HUMAN REPAIR GENE RESTORES NORMAL PATTERN OF PREFERENTIAL DNA-REPAIR IN REPAIR DEFECTIVE CHO CELLS NUCLEIC ACIDS RESEARCH Bohr, V. A., CHU, E. H., VANDUIN, M., Hanawalt, P. C., OKUMOTO, D. S. 1988; 16 (15): 7397-7403

  Abstract

  The pattern of preferential DNA repair of UV-induced pyrimidine dimers was studied in repair-deficient Chinese hamster ovary (CHO) cells transfected with the human excision repair gene, ERCC-1. Repair efficiency was measured in the active dihydrofolate reductase (DHFR) gene and in its flanking, non-transcribed sequences in three cell lines: Wild type CHO cells, a UV-sensitive excision deficient CHO mutant, and the transfected line of the mutant carrying the expressed ERCC-1 gene. The CHO cells transformed with the human ERCC-1 gene repaired the active DHFR gene much more efficiently than the non-transcribed sequences, a pattern similar to that seen in wild type CHO cells. This pattern differs from that previously reported in CHO cells transfected with the denV gene of bacteriophage T4, in which both active and non-transcribed DNA sequences were efficiently repaired (Bohr and Hanawalt, Carcinogenesis 8: 1333-1336, 1987). The ERCC-1 gene product may specifically substitute for the repair enzyme present in normal hamster cells while the denV product, T4 endonuclease V, does not be appear to be constrained in its access to inactive chromatin.

  View details for Web of Science ID A1988P685100013

  View details for PubMedID 3412890

• HIGH-EFFICIENCY TRANSFORMATION OF BACTERIAL-CELLS BY ELECTROPORATION JOURNAL OF BACTERIOLOGY CALVIN, N. M., Hanawalt, P. C. 1988; 170 (6): 2796-2801

  Abstract

  We have developed a method for efficiently generating transient pores in the outer membranes of Escherichia coli K-12 derivatives by using a new type of electroporation apparatus. The pores are large enough and persist long enough to facilitate the equilibration of plasmid molecules between the intracellular and extracellular spaces. The method has been used to transform bacterial cells with an efficiency greater than 10(9) transformants per microgram of plasmid. It has also been used to extract intact plasmid from transformed cells with efficiencies comparable to those of the traditional alkaline lysis or CsCl equilibrium density gradient techniques. The technique is simple and rapid, allowing a transformation or the preparation of microgram quantities of plasmid to be accomplished in minutes.

  View details for Web of Science ID A1988N699900056

  View details for PubMedID 3286620

  View details for PubMedCentralID PMC211205

• ROLE OF TRANSFORMING GROWTH FACTOR-BETA IN THE MATURATION OF HUMAN EPIDERMAL-KERATINOCYTES JOURNAL OF INVESTIGATIVE DERMATOLOGY MANSBRIDGE, J. N., Hanawalt, P. C. 1988; 90 (3): 336-341

  Abstract

  Changes in protein synthesis and phosphorylation in cultured human keratinocytes in response to TGF-beta have been examined by one and two dimensional electrophoresis. Transforming growth factor beta has been shown to cause little change in the rate of methionine incorporation in the concentration range in which growth is reversibly arrested. It does, however, prevent the labeling of certain specific bands detected on gels of triton-soluble proteins after 3 days of treatment. Phosphorylation of triton-soluble proteins is inhibited at concentrations of TGF-beta rather higher than the Kd of its receptor and may represent a nonphysiological effect. Nonetheless, the phosphorylation of certain prominent species is reduced. In keratinocytes cultured in delipidated serum, which show some expression of keratin 1 (67 kd) characteristic of normal maturation, TGF-beta reduces the incorporation of methionine into this keratin 1 and increases labeling of keratins 6 and 16. Transforming growth factor beta thus promotes regenerative maturation, which is normally expressed during wound healing. The ability of TGF-beta to arrest keratinocyte growth in a reversible manner and to stimulate regenerative maturation, supports its physiological role in controlling the balance between cell division, migration and maturation during epidermal wound healing.

  View details for Web of Science ID A1988M543400015

  View details for PubMedID 2450142

• ENHANCED TRANSFORMING ACTIVITY OF PSV2 PLASMIDS IN HUMAN-CELLS DEPENDS UPON THE TYPE OF DAMAGE INTRODUCED INTO THE PLASMID MUTATION RESEARCH Spivak, G., Leadon, S. A., Vos, J. M., Meade, S., Hanawalt, P. C., Ganesan, A. K. 1988; 193 (2): 97-108

  Abstract

  When pSV2-gpt or pSV2-neo plasmids are introduced into human cells by calcium phosphate coprecipitation, the yield of stable transformants (Gpt+ or Neo+) is increased by irradiating the respective plasmid DNA in vitro with UV (254 nm). To identify specific lesions that can increase the transforming activity of plasmids in human cells we examined pSV2 plasmids containing different types of damage. Of the lesions tested, cyclobutane pyrimidine dimers produced the greatest increase, and can nearly fully account for the effect of 254 nm UV on transformation. The enhancement of transformation produced by UV was not altered by the additional treatment of the plasmid DNA with T4 endonuclease V, an enzyme that nicks DNA specifically at pyrimidine dimers. Treatment of plasmid DNA with osmium tetroxide to produce thymine glycols, or with acid and heat to produce apurinic sites did not affect transformation frequency. The enhancement occurred in all the human cell lines tested, whether they contained or not sequences homologous to those in the plasmids, and was independent of the repair capacity of the recipient cells.

  View details for Web of Science ID A1988M516700002

  View details for PubMedID 2831452

• DNA-REPAIR IN GENES PHARMACOLOGY & THERAPEUTICS Bohr, V. A., Hanawalt, P. C. 1988; 38 (3): 305-319

  View details for Web of Science ID A1988Q589900002

  View details for PubMedID 3057514

• HETEROGENEOUS DNA DAMAGE AND REPAIR IN THE MAMMALIAN GENOME CANCER RESEARCH Bohr, V. A., Phillips, D. H., Hanawalt, P. C. 1987; 47 (24): 6426-6436

  View details for Web of Science ID A1987L355500001

  View details for PubMedID 3315187

• PREFERENTIAL DNA-REPAIR IN EXPRESSED GENES ENVIRONMENTAL HEALTH PERSPECTIVES Hanawalt, P. C. 1987; 76: 9-14

  Abstract

  Potentially deleterious alterations to DNA occur nonrandomly within the mammalian genome. These alterations include the adducts produced by many chemical carcinogens, but not the UV-induced cyclobutane pyrimidine dimer, which may be an exception. Recent studies in our laboratory have shown that the excision repair of pyrimidine dimers and certain other lesions is nonrandom in the mammalian genome, exhibiting a distinct preference for actively transcribed DNA sequences. An important consequence of this fact is that mutagenesis and carcinogenesis may be determined in part by the activities of the relevant genes. Repair may also be processive, and a model is proposed in which excision repair is coupled to transcription at the nuclear matrix. Similar but freely diffusing repair complexes may account for the lower overall repair efficiencies in the silent domains of the genome. Risk assessment in relation to chemical carcinogenesis requires assays that determine effective levels of DNA damage for producing malignancy. The existence of nonrandom repair in the genome casts into doubt the reliability of overall indicators of DNA binding and lesion repair for such determinations. Furthermore, some apparent differences between the intragenomic repair heterogeneity in rodent cells and that in human cells mandate a reevaluation of rodent test systems for human risk assessment. Tissue-specific and cell-specific differences in the coordinate regulation of gene expression and DNA repair may account for corresponding differences in the carcinogenic response.

  View details for Web of Science ID A1987M423800002

  View details for PubMedID 3447906

• SELECTIVE REMOVAL OF TRANSCRIPTION-BLOCKING DNA DAMAGE FROM THE TRANSCRIBED STRAND OF THE MAMMALIAN DHFR GENE CELL Mellon, I., Spivak, G., Hanawalt, P. C. 1987; 51 (2): 241-249

  Abstract

  We find a dramatic difference in the efficiency of removal of UV-induced pyrimidine dimers from the transcribed and nontranscribed strands of the dihydrofolate reductase (DHFR) gene in cultured hamster and human cells. In hamster cells, 80% of the dimers are removed from the transcribed strand in 4 hr, but little repair occurs in the nontranscribed strand even after 24 hr. In human cells, repair is significantly faster in the transcribed strand than in the other strand. Furthermore, in the 5' flanking region of the human DHFR gene, selective rapid repair occurs in the opposite DNA strand relative to the transcribed strand of the DHFR gene. This strand is thought to serve as a template for transcription of a divergent transcript. These results have important implications for excision repair pathways and mutagenesis in mammalian cells.

  View details for Web of Science ID A1987K595600009

  View details for PubMedID 3664636

• ENHANCED TRANSFORMING ACTIVITY OF ULTRAVIOLET-IRRADIATED PSV2-GPT IS DUE TO DAMAGE OUTSIDE THE GPT TRANSCRIPTION UNIT PLASMID Leadon, S. A., Ganesan, A. K., Hanawalt, P. C. 1987; 18 (2): 135-141

  Abstract

  We have shown that when pSV2-gpt is introduced into human cells by calcium phosphate coprecipitation, the yield of Gpt+ transformants is increased by irradiating the plasmid with 254 nm uv. To elucidate the mechanism underlying this response, we constructed pSV2-gpt molecules in which the uv damage was confined to a particular region: a 3.0-kb region containing the pBR322 sequences and simian virus 40 (SV40) sequences not required for expression of the gpt gene, or a 2.3-kb fragment containing the Escherichia coli gpt gene together with the SV40 early promoter and sequences needed for splicing and polyadenylation. The transforming activity of the plasmid was greatly enhanced by uv damage confined to the 3.0-kb pBR322 region and increased linearly with uv dose up to 1 kJ/m2, but remained relatively constant at doses between 2 and 8 kJ/m2. Positioning the damaged region upstream, or both upstream and downstream, from the gpt transcription unit increased the uv enhancement slightly compared to positioning the damaged region only downstream. In contrast, transforming activity was significantly decreased by damage in the 2.3-kb gpt transcription unit. These results suggest that uv damage outside a selectable marker gene in a plasmid can increase the probability of stable integration of the plasmid into the genome of recipient cells without inhibiting expression of of the gene.

  View details for Web of Science ID A1987L108600005

  View details for PubMedID 2829251

• ENHANCED REPAIR OF PYRIMIDINE DIMERS IN CODING AND NONCODING GENOMIC SEQUENCES IN CHO CELLS EXPRESSING A PROKARYOTIC DNA-REPAIR GENE CARCINOGENESIS Bohr, V. A., Hanawalt, P. C. 1987; 8 (9): 1333-1336

  Abstract

  We have previously demonstrated that the active dihydrofolate reductase (DHFR) gene is efficiently repaired in Chinese hamster ovary (CHO) cells which remove only a small fraction of u.v.-induced pyrimidine dimers from the overall genome. Preferential DNA repair of essential genes may explain why the u.v. resistance of normal CHO cells is as high as that of fully repair-proficient normal human cells. In this report, we have studied the removal of pyrimidine dimers in a CHO cell line expressing the cloned denV gene from bacteriophage T4 which codes for the pyrimidine dimer specific enzyme T4 endonuclease V (T4 endo V). This cell line was derived from a u.v.-sensitive excision deficient mutant of a CHO wild type line by transformation with the denV gene, and partial restoration of u.v. resistance was achieved. We have examined an important aspect of the u.v. excision repair in these denV+ cells by studying the repair efficiencies in the active DHFR gene and in a non-coding sequence located downstream from it. In the u.v.-sensitive CHO mutant cell line from which the denV+ was derived, we detected no pyrimidine dimer removal from the gene or from the downstream sequence after irradiation of the cells with 20 J/m2 u.v. (254 nm) light. In the wild type CHO cells, approximately 50% of the pyrimidine dimers were removed from a sequence in the DHFR gene within 8 h, whereas none were removed from the downstream sequence in that period. This represents the normal pattern of preferential DNA repair of active genes, which we have described in previous communications. In the denV+ cells, approximately 70% of the pyrimidine dimers were removed from both the DHFR gene and from the downstream sequence; these cells thus repair both coding and non-coding regions of the genome and show no pattern of preferential repair. The endogenous activity that initiates excision repair in normal CHO cells is evidently much more restricted in its accessibility to DNA lesions in chromatin than is the activity in cells containing substantial amounts of the small T4 endo V enzyme.

  View details for Web of Science ID A1987J921300029

  View details for PubMedID 3621470

• PROCESSING OF PSORALEN ADDUCTS IN AN ACTIVE HUMAN-GENE - REPAIR AND REPLICATION OF DNA CONTAINING MONOADDUCTS AND INTERSTRAND CROSS-LINKS CELL Vos, J. M., Hanawalt, P. C. 1987; 50 (5): 789-799

  Abstract

  We have examined DNA repair in the dihydrofolate reductase (DHFR) gene in cultured human cells treated with 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT) using a newly developed assay for interstrand DNA cross-linking in defined genomic sequences. Within 24 hr, 80% of the cross-links, but only 45% of the monoadducts, were removed from a 32 kb transcribed sequence, demonstrating that repair efficiency in an active human gene varies with the nature of the damage. HMT monoadducts were also detected in the replicated DHFR sequence at frequencies indicating little interference with replication. The existence of cross-linkable monoadduct sites in the replicated DNA implies strand continuity opposite those sites and a relatively error-free mechanism of bypass. Translesion replication could circumvent transcription blockage in a damaged gene. These findings have important implications for mechanisms of mutagenesis and DNA lesion tolerance in human cells.

  View details for Web of Science ID A1987J846900015

  View details for PubMedID 3621344

• PHOTOADDUCTS OF 8-METHOXYPSORALEN TO CYTOSINE IN DNA PHOTOCHEMISTRY AND PHOTOBIOLOGY CALVIN, N. M., Hanawalt, P. C. 1987; 45 (3): 323-330

  View details for Web of Science ID A1987G283200002

  View details for PubMedID 3550835

• TOPICAL TREATMENT OF PSORIASIS WITH THE TOPOISOMERASE INHIBITORS NOVOBIOCIN AND NALIDIXIC-ACID - A PILOT-STUDY ARCHIVES OF DERMATOLOGICAL RESEARCH Bohr, V. A., Abel, E. A., Farber, E. M., Hanawalt, P. C. 1987; 279 (3): 147-150

  Abstract

  Our studies in human epidermal keratinocytes as a model system have suggested that the antibiotic topoisomerase II inhibitors, novobiocin and nalidixic acid, may be of value for the treatment of hyperproliferative skin disorders. We have therefore conducted a pilot study of the clinical efficacy of these compounds for the treatment of psoriasis. The compounds were administered topically to psoriatic plaques in seven healthy patients over a period of 6 weeks. Nalidixic acid (2%) or novobiocin (2% or 5%) in methylcellulose were applied twice daily under occlusion, and methylcellulose alone was used as a control. In six of the seven patients, one or both compounds effected somewhat greater improvement than in the control within 3 weeks of treatment.

  View details for Web of Science ID A1987G300500002

  View details for PubMedID 3036023

• CHARACTERIZATION OF A DNA-REPAIR DOMAIN CONTAINING THE DIHYDROFOLATE-REDUCTASE GENE IN CHINESE-HAMSTER OVARY CELLS JOURNAL OF BIOLOGICAL CHEMISTRY Bohr, V. A., OKUMOTO, D. S., Ho, L., Hanawalt, P. C. 1986; 261 (35): 6666-6672

  View details for Web of Science ID A1986F247600059

• Characterization of a DNA repair domain containing the dihydrofolate reductase gene in Chinese hamster ovary cells. journal of biological chemistry Bohr, V. A., OKUMOTO, D. S., Ho, L., Hanawalt, P. C. 1986; 261 (35): 16666-16672

  Abstract

  The formation and removal of UV-induced pyrimidine dimers were measured in restriction fragments near and within the essential dihydrofolate reductase (DHFR) gene in Chinese hamster ovary cells in order to map the genomic fine structure of DNA repair. Dimer frequencies were determined at 0, 8, and 24 h after irradiating the cells with 20 J/m2 UV light (254 nm). Within 8 h, the cells had removed more than 40% of the dimers from sequences near the 5' end of the gene, somewhat fewer from the 3' end, but only 2% from the 3' flanking region and 10% from a region upstream from the gene. The corresponding extent of repair in the genome as a whole is 5-10% in the 8-h period. Isoschizomeric restriction enzyme analysis was used to detect the level of methylation in the fragments in which repair was measured. We found that the only hypomethylated sites in and around the DHFR gene were in the fragment near its 5' end, which displayed maximal DNA repair efficiency. The size of the region of preferential DNA repair at the DHFR locus appears to be in the range of 50-80 kilobases, and this finding is discussed in relation to genomic domains and the structure of mammalian chromatin.

  View details for PubMedID 3023360

• PREFERENTIAL DNA-REPAIR OF AN ACTIVE GENE IN HUMAN-CELLS PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Mellon, I., Bohr, V. A., Smith, C. A., Hanawalt, P. C. 1986; 83 (23): 8878-8882

  Abstract

  Removal of pyrimidine dimers was measured in defined sequences in human cells amplified for the dihydrofolate reductase (DHFR) gene. We quantitated repair in specific restriction fragments by using the dimer-specific bacteriophage T4 endonuclease V and analysis by Southern blotting. Within 4 hr after 5- or 10-J/m2 UV irradiation, more than 60% of the dimers had been removed from a 20-kilobase fragment that lies entirely within the transcription unit of the DHFR gene and from a 25-kilobase fragment located in the 5' flanking region of the gene. Repair in the overall genome was measured by analyzing cellular DNA treated with T4 endonuclease V in alkaline sucrose gradients. Sixty-nine percent of the dimers were removed from the genome overall within 24 hr after irradiation, but only 25% were removed within 4 hr and 38% were removed within 8 hr. These results demonstrate a strong preferential rate of removal of dimers from the 50-kilobase region that includes the transcriptionally active DHFR gene compared to that in total cellular DNA. We confirmed that DHFR-containing DNA is repaired more rapidly than bulk DNA by using an approach that provides a direct comparison between repair in specific sequences and repair in total cellular DNA. We also show that the DHFR-containing sequences are repaired more rapidly than the nontranscribed repetitive alpha DNA sequences. Our finding of preferential early repair in a transcriptionally active region in overall repair-proficient cells suggests that selective dimer removal from active sequences may be a general characteristic of mammalian DNA repair.

  View details for Web of Science ID A1986F147100013

  View details for PubMedID 3466163

• PROCESSIVITY OF T4 ENDONUCLEASE-V IS SENSITIVE TO NACL CONCENTRATION BIOCHEMISTRY Ganesan, A. K., SEAWELL, P. C., Lewis, R. J., Hanawalt, P. C. 1986; 25 (19): 5751-5755

  Abstract

  We previously reported that endonuclease V of bacteriophage T4 reacts processively with pyrimidine dimers in UV-irradiated DNA, tending to react with all of the dimers on one DNA molecule before reacting with any dimers on another DNA molecule [Lloyd, R. S., Hanawalt, P. C., & Dodson, M. L. (1980) Nucleic Acids Res. 8, 5113-5127]. In this paper we show that this processivity depends upon salt concentration: it can be detected in 10 mM NaCl but not, by our methods, in 100 mM NaCl. In addition, we show that endonuclease V binds to unirradiated DNA in 10 mM NaCl but not in 100 mM NaCl. We conclude that T4 endonuclease V binds to pyrimidine dimers in a two-step process in 10 mM NaCl. It first binds electrostatically to undamaged sections of DNA, and it remains bound during the second step in which it "searches" for pyrimidine dimers. Our conclusion is analogous to the expanded target theory developed for Lac repressor [Berg, O. G., Winter, R. B., & von Hippel, P. H. (1981) Biochemistry 20, 6929-6948].

  View details for Web of Science ID A1986E242300059

  View details for PubMedID 3535887

• RAPID REPAIR OF THE DHFR GENE IN HUMAN-CELLS Mellon, I., Bohr, V., Smith, C. A., Hanawalt, P. C. NATURE PUBLISHING GROUP. 1986: 361–61

  View details for Web of Science ID A1986D515300067

• CELL-CYCLE-DEPENDENT REPAIR OF DAMAGE IN ALPHA-DNA AND BULK DNA OF MONKEY CELLS MUTATION RESEARCH Leadon, S. A., Hanawalt, P. C. 1986; 166 (1): 71-77

  Abstract

  Excision repair of bulky chemical adducts in alpha DNA of confluent cultures of African green monkey cells has previously been shown to be deficient relative to that in the overall genome. We have compared the removal of adducts produced by treatment with aflatoxin B1 (AFB1) and N-acetoxy-2-acetylamino-fluorene (NA-AAF) from alpha DNA sequences in synchronized and exponentially growing cultures of monkey cells. Proficient removal of AFB1 adducts in alpha DNA was observed in exponentially growing cultures. However, as the cultures approached confluence, adduct removal from alpha DNA became deficient. Cells synchronized by subculturing confluent cultures exhibited proficient removal of adducts from both alpha and bulk DNA when treated in early G1 or late S/G2 while those cells treated in early S phase did not remove adducts from either alpha or bulk DNA. We conclude that the accessibility of chemical adducts to repair in alpha chromatin is influenced by the growth state and the cell cycle stage.

  View details for Web of Science ID A1986D081200009

  View details for PubMedID 3088442

• SURVIVAL OF UV-IRRADIATED MAMMALIAN-CELLS CORRELATES WITH EFFICIENT DNA-REPAIR IN AN ESSENTIAL GENE PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Bohr, V. A., OKUMOTO, D. S., Hanawalt, P. C. 1986; 83 (11): 3830-3833

  Abstract

  The survival of UV-irradiated mammalian cells is not necessarily correlated with their overall capacity to carry out DNA repair. Human cells typically remove 80% of the pyrimidine dimers produced by a UV dose of 5 J/m2 within 24 hr. In contrast, a Chinese hamster ovary (CHO) cell line survives UV irradiation equally well while removing only 15% of the dimers. Using a newly developed technique to measure dimer frequencies in single-copy specific sequences, we find that the CHO cells remove 70% of the dimers from the essential dihydrofolate reductase (DHFR) gene but only 20% from sequences located 30 kilobases or more upstream from the 5' end of the gene in a 24-hr period. Repair-deficient human cells from xeroderma pigmentosum complementation group C (XPC) are similar to the CHO cells in overall repair levels, but they are extremely sensitive to killing by UV irradiation. In the XPC cells, we find little or no repair in the DHFR gene; in contrast, in normal human fibroblasts and epidermal keratinocytes, greater than 80% of the dimers induced in the gene by 20 J/m2 are removed in 24 hr. Since the CHO and normal human cells exhibit similar UV resistance, much higher than that of XPC cells, our findings suggest a correlation between efficient repair of essential genes and resistance to DNA-damaging agents such as UV light.

  View details for Web of Science ID A1986C590700056

  View details for PubMedID 3459159

• COMPARATIVE EFFECTS OF GROWTH-INHIBITORS ON DNA-REPLICATION, DNA-REPAIR, AND PROTEIN-SYNTHESIS IN HUMAN EPIDERMAL-KERATINOCYTES CANCER RESEARCH Bohr, V., Mansbridge, J., Hanawalt, P. 1986; 46 (6): 2929-2935

  Abstract

  Cultured human epidermal keratinocytes were used as a model system for testing compounds with potential therapeutic effect against hyperproliferative skin disorders. We have investigated whether each test compound caused direct damage to the DNA or inhibited DNA repair and/or seminconservative replication of DNA, as well as its effect on the overall rate of protein synthesis and on expression of specific keratin genes. The following compounds were studied: (a) inhibitors of DNA polymerase alpha [aphidicolin and its derivative aphidicolin glycine], (b) inhibitors of topoisomerases [novobiocin, nalidixic acid, teniposide, etoposide, and 4'-(9-acridylamine) methanesulfon-m-anisidide], (c) modifiers of chromatin structure [sodium butyrate, 3-aminobenzamide, and nicotinamide], (d) inhibitors of calmodulin activation and protein kinase C [chlorpromazine and trifluoperazine]; and (e) drugs used in clinical dermatology [anthralin, fluocinolone acetonide, ketoconazole, and hydroxyurea]. The compounds were tested at concentrations at which they were known from the literature to be effective in their respective actions. Among the groups of compounds studied, the topoisomerase inhibitors were particularly interesting since they caused no detectable damage to DNA but exhibited maximal inhibitory effect on replication combined with minimal inhibition of DNA repair. In addition most of the topoisomerase inhibitors, particularly novobiocin, changed the pattern of gene expression by inhibiting the synthesis of certain keratins and inducing a Mr 67,000 protein in the prekeratin fraction. These properties combined with minimal systemic side effects may encourage the clinical exploration of some topoisomerase inhibitors for antiproliferative therapy of skin disorders.

  View details for Web of Science ID A1986C502100051

  View details for PubMedID 2421888

• DIFFERENTIAL DNA-REPAIR IN TRANSCRIPTIONALLY ACTIVE AND INACTIVE PROTOONCOGENES - C-ABL AND C-MOS CELL Madhani, H. D., Bohr, V. A., Hanawalt, P. C. 1986; 45 (3): 417-423

  Abstract

  DNA repair was examined in the c-abl and c-mos proto-oncogenes in UV-irradiated mouse 3T3 fibroblasts using an optimized assay for measuring pyrimidine dimers in single-copy nucleotide sequences. We found similar initial dimer frequencies in the two genes. Within 24 hr, 85% of the dimers were removed from the 20 kb intragenic BamHl restriction fragment of the expressed c-abl gene, while only 22% of the dimers were removed from the 15 kb EcoRl fragment that spans the transcriptionally inactive c-mos locus. Quiescent and actively growing cells showed similar relative efficiencies of repair in the two regions. This is the first demonstration of differential DNA repair in two different genes. These findings have important implications for the mechanisms of proto-oncogene activation.

  View details for Web of Science ID A1986C319600011

  View details for PubMedID 3698104

• CANCER-PRONE HEREDITARY-DISEASES WITH DNA PROCESSING ABNORMALITIES TRENDS IN GENETICS Hanawalt, P. C., Sarasin, A. 1986; 2 (5): 124-129

  View details for Web of Science ID A1986C587800003

• ALPHA-DNA IN AFRICAN-GREEN MONKEY CELLS IS ORGANIZED INTO EXTREMELY LONG TANDEM ARRAYS JOURNAL OF BIOLOGICAL CHEMISTRY Madhani, H. D., Leadon, S. A., Smith, C. A., Hanawalt, P. C. 1986; 261 (5): 2314-2318

  Abstract

  We have determined the size of arrays formed by tandemly repeated monomers of alpha DNA in African green monkey cells. DNA fragments containing intact alpha DNA arrays were generated by digestion of genomic DNA with restriction endonuclease that do not have sites in the alpha DNA consensus sequence. Their size was determined by Southern analysis and by sedimentation through neutral sucrose gradients followed by probing of each fraction for alpha sequences. The restriction fragments varied in size with the most frequent being 78 kilobase pairs long. We have also shown that they contain very little non-alpha DNA sequences. This suggests a minimum array of 450 tandemly repeated alpha DNA monomers, which is more than an order of magnitude larger than previously supposed.

  View details for Web of Science ID A1986A006900053

  View details for PubMedID 3003109

• SUBSTRATE RANGE OF THE 40000-DALTON DNA-PHOTOREACTIVATING ENZYME FROM ESCHERICHIA-COLI BIOCHEMISTRY Sutherland, B. M., Oliveira, O. M., Ciarrocchi, G., Brash, D. E., Haseltine, W. A., Lewis, R. J., Hanawalt, P. C. 1986; 25 (3): 681-687

  Abstract

  We determined the ability of the 40 000-dalton Escherichia coli photoreactivating enzyme to act on a variety of pyrimidine-pyrimidine photoproduct substrates in nucleic acids. The enzyme is at least as active on cis-syn-cyclobutylpyrimidine dimers in supercoiled DNA as in linear DNA, but inactive on dimers in RNA. Both the phosphodiester bond internal to the deoxyriboses of the pyrimidines of the dimer and the N-glycosyl bond joining the pyrimidine to deoxyribose must be intact for enzyme action. The enzyme has no activity toward (6-4) pyrimidine-cytosine products in DNA.

  View details for Web of Science ID A1986A007000026

  View details for PubMedID 3513832

• EFFECT OF A LEXA41(TS) MUTATION ON DNA-REPAIR IN RECA(DEF) DERIVATIVES OF ESCHERICHIA-COLI K-12 MOLECULAR AND GENERAL GENETICS Ganesan, A. K., Hanawalt, P. C. 1985; 201 (3): 201-387

  View details for Web of Science ID A1985AVU2300005

• Effect of a lexA41(Ts) mutation on DNA repair in recA(Def) derivatives of Escherichia coli K-12. Molecular & general genetics : MGG Ganesan, A. K., Hanawalt, P. C. 1985; 201 (3): 387-392

  Abstract

  Derivatives of Escherichia coli K-12 carrying a deletion of the recA gene survive exposure to UV (254 nm) better if they also contain the lexA41 mutation which codes for a labile LexA protein. This effect of the lexA41 mutation is not observed in comparable strains carrying a uvr A6 mutation. Using two independent methods to detect pyrimidine dimers we found that UV irradiated RecA deficient cells removed dimers from their DNA more rapidly if they contained the lexA41 mutation than if they contained the wild-type lexA gene. Our results are consistent with the idea that a relatively high level of UvrABC incision nuclease resulting from inefficient repression of the corresponding genes by the labile LexA41 protein facilitates excision of pyrimidine dimers from the DNA of UV irradiated cells.

  View details for PubMedID 3911024

• ROLE OF SOLAR CONDITIONING IN DNA-REPAIR RESPONSE AND SURVIVAL OF HUMAN EPIDERMAL-KERATINOCYTES FOLLOWING UV IRRADIATION JOURNAL OF INVESTIGATIVE DERMATOLOGY Liu, S. C., Meagher, K., Hanawalt, P. C. 1985; 85 (2): 93-97

  Abstract

  We have investigated the cumulative effects of sunlight exposure upon the excision-repair of UV radiation damage to DNA in epidermal keratinocytes from human donors of different ages as well as the possible effect on DNA repair of periodic conditioning of the cultured keratinocytes with sublethal UV radiation exposures. We have also compared the growth properties of UV-irradiated keratinocytes derived from habitually sun-exposed and nonexposed areas from the bodies of young and aged donors. DNA repair replication in keratinocytes from habitually sun-exposed facial skin and the less sun-exposed abdominal skin of middle-aged adults was found to be similar, with respect to both the UV dose response and the time course of repair after 20 J/m2, 254 nm. Growth and survival (after exposure up to 50 J/m2, 254 nm) were greater for keratinocytes from protected areas of the upper arm of young donors (under 18 years) than for cells from their own sun-exposed areas. Growth and survival were markedly reduced for all keratinocyte cultures from aged donors, especially those cultures developed from sun-exposed areas. Nevertheless, the DNA repair response to UV radiation was similar in all cases. The evident uncoupling of UV sensitivity from DNA repair capacity remains to be understood. Our studies confirm that the cumulative effect of sunlight exposure indeed contributes to some skin aging processes. However, we have found no indication that an overall reduction in capacity for excision-repair of UV photoproducts in keratinocyte DNA accompanies senescence in human skin.

  View details for Web of Science ID A1985AND4300003

  View details for PubMedID 4020165

• DNA-REPAIR IN AN ACTIVE GENE - REMOVAL OF PYRIMIDINE DIMERS FROM THE DHFR GENE OF CHO CELLS IS MUCH MORE EFFICIENT THAN IN THE GENOME OVERALL CELL Bohr, V. A., Smith, C. A., OKUMOTO, D. S., Hanawalt, P. C. 1985; 40 (2): 359-369

  Abstract

  DNA repair was measured in the dihydrofolate reductase gene in Chinese hamster ovary cells, amplified for the gene, by quantitating pyrimidine dimers with a specific UV-endonuclease. More than two thirds of the dimers had been removed from a 14.1 kb restriction fragment of the gene by 26 hr after irradiation (20 J/m2), while little removal was detected in fragments upstream of the gene and only 15% were removed from the genome overall. This suggests that damage processing can vary according to function or activity of affected sequences, which has general implications for correlations of DNA repair with survival and mutagenesis. Perhaps preferential repair of vital sequences facilitates UV-resistance of these cells despite low overall repair levels.

  View details for Web of Science ID A1985AFE4800016

  View details for PubMedID 3838150

• TOWARD A RATIONAL THERAPY FOR PSORIASIS CUTIS Bohr, V., Hanawalt, P. C. 1985; 35 (1): 37-37

  View details for Web of Science ID A1985AAS0900004

  View details for PubMedID 3967514

• Repair of furocoumarin adducts in mammalian cells. National Cancer Institute monograph Zolan, M. E., Smith, C. A., Hanawalt, P. C. 1984; 66: 137-142

  Abstract

  We studied DNA repair in cultured mammalian cells treated with the furocoumarins 8-methoxypsoralen (8-MOP), aminomethyl trioxsalen, or angelicin and irradiated with near UV light. The amount of DNA cross-linked by 8-MOP in normal human cells decreased by about one-half in 24 hours after treatment; no decrease was observed in xeroderma pigmentosum cells, group A. At present, it is not known to what extent this decrease represents complete repair events at the sites of cross-links. Furocoumarin adducts elicited excision repair in normal human and monkey cells but not in xeroderma pigmentosum group A cells. This excision repair resembled in several aspects that elicited by pyrimidine dimers, formed in DNA by irradiation with 254-nm UV light; however, it appeared that for at least 8-MOP and aminomethyl trioxsalen, removal of adducts was not as efficient as was the removal of pyrimidine dimers. We also compared repair in the 172-base-pair repetitive alpha-DNA component of monkey cells to repair in the bulk of the genome. Although repair elicited by pyrimidine dimers in alpha-DNA was the same as in the bulk DNA, that following treatment of cells with either aminomethyl trioxsalen or angelicin and near UV was markedly deficient in alpha-DNA. This deficiency reflected the removal of fewer adducts from alpha-DNA after the same initial adduct frequencies. These results could mean that each furocoumarin may produce several structurally distinct adducts to DNA in cells and that the capacity of cellular repair systems to remove these various adducts may vary greatly.(ABSTRACT TRUNCATED AT 250 WORDS)

  View details for PubMedID 6531019

• ULTRAVIOLET-IRRADIATION OF MONKEY CELLS ENHANCES THE REPAIR OF DNA ADDUCTS IN ALPHA-DNA CARCINOGENESIS Leadon, S. A., Hanawalt, P. C. 1984; 5 (11): 1505-1510

  Abstract

  Excision repair of bulky adducts in alpha DNA of African green monkey cells has previously been shown to be deficient relative to that in the overall genome. We have found that u.v. irradiation of these cells results in the enhanced removal of both aflatoxin B1 (AFB1) and acetylaminofluorene (AAF) adducts from the alpha DNA sequences without affecting repair in the bulk of the DNA. The degree of enhanced removal of AFB1 is dependent upon the u.v. dose and the time interval between irradiation and AFB1 treatment. The u.v. enhancement is not inhibited by cycloheximide. Exposure of the cells to dimethylsulfate or gamma-rays does not affect AFB1 adduct repair. The formation and removal of N-acetoxy-2-acetylaminofluorene (NA-AAF) adducts from alpha and bulk DNA was studied in detail. A higher initial level of the acetylated C8 adduct of guanine was found in alpha DNA than in bulk DNA. Although both the acetylated and deacetylated C8 adducts were removed from the two DNA species, the level of repair was significantly greater in the bulk DNA. Irradiation of cells with u.v. prior to treatment with NA-AAF enhanced the removal of both adducts from alpha DNA with little or no effect on repair in bulk DNA. We conclude that the presence of u.v. photoproducts or some intermediate in their processing alters the chromatin structure of alpha DNA thereby rendering bulky adducts accessible to repair enzymes. In addition, the differential formation and repair of AAF adducts in alpha DNA compared with that in the bulk of the genome supports the hypothesis of an altered chromatin structure for alpha domains.

  View details for Web of Science ID A1984TR42600018

  View details for PubMedID 6435903

• Factors that affect the initiation of excision-repair in chromatin. Nucleic acids symposium series Bohr, V., Hanawalt, P. 1984: 109-125

  View details for PubMedID 6093060

• ELECTROPHORETIC SEPARATION OF FUROCOUMARIN - DNA PHOTOADDUCTS PHOTOCHEMISTRY AND PHOTOBIOLOGY CALVIN, N. M., Hanawalt, P. C. 1984; 40 (2): 161-170

  View details for Web of Science ID A1984TG19300002

  View details for PubMedID 6483994

• FORMATION AND REPAIR OF FUROCOUMARIN ADDUCTS IN ALPHA-DEOXYRIBONUCLEIC ACID AND BULK DEOXYRIBONUCLEIC-ACID OF MONKEY CELLS BIOCHEMISTRY Zolan, M. E., Smith, C. A., Hanawalt, P. C. 1984; 23 (1): 63-69

  Abstract

  We have extended our previous finding that excision repair of furocoumarin photoadducts is deficient in the highly repetitive alpha DNA sequences in cultured African green monkey cells. The formation and removal from DNA of the individual photoadducts of 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen (HMT) were monitored by analysis of DNA hydrolysates using a high-pressure liquid chromatography procedure that separated the major adducts from each other and also resolved the two diastereomers of the most frequent monoadduct. The overall deficiency in removal of HMT adducts from alpha DNA was similar to that previously observed by us with 4'-(aminomethyl)-4,5',8-trimethylpsoralen and angelicin. The two diastereomers of the furan-T monoadducts were formed in the same relative amounts in alpha DNA and bulk DNA whether photoaddition was in vivo or in vitro, and they were removed from cellular DNA at the same relative rates. Therefore, the deficient removal of furocoumarin adducts from alpha cannot be due to preferential formation of some adduct inherently refractory to repair. However, in vivo, the photochemical conversion of the furan-T monoadducts to diadducts was markedly reduced in alpha DNA, relative to that in bulk DNA. This indicates a possible conformational constraint in the internucleosomal DNA in alpha-chromatin which may account for the deficiency in repair.

  View details for Web of Science ID A1984RX92500010

  View details for PubMedID 6691967

• DNA repair in cultured keratinocytes. journal of investigative dermatology Liu, S. C., Parsons, S., Hanawalt, P. C. 1983; 81 (1): 179s-83s

  Abstract

  Most of our understanding of DNA repair mechanisms in human cells has come from the study of these processes in cultured fibroblasts. The unique properties of keratinocytes and their pattern of terminal differentiation led us to a comparative examination of their DNA repair properties. We have examined the relative repair capabilities of the basal cells and the differentiated epidermal keratinocytes as well as possible correlations of DNA repair capacity with respect to age of the donor. In addition, since portions of human skin are chronically exposed to sunlight, we have assessed the repair response to ultraviolet (UV) irradiation (254 nm) when the cells are conditioned by chronic low-level UV irradiation. The methods of Liu and Karasek were used to grow pure keratinocytes on collagen gels following their isolation from abdominal skin of newborns and adults at autopsy. Density labeling with 5-bromodeoxyuridine was used to resolve repair replication from the semiconservative mode. We found similar repair characteristics in human epidermal keratinocytes to those previously reported for cultured fibroblasts. However, the DNA repair response in basal cells was much greater than that in differentiated cells from the same skin preparation. Our comparative studies of DNA repair in keratinocytes from infant and aged donors have revealed no significant age-related differences for repair of UV-induced damage to DNA. Sublethal UV conditioning of cells from infant skin had no appreciable effect on either the repair or normal replication response to higher, challenge doses of UVL. However, such conditioning resulted in attenuated repair in keratinocytes from adult skin after UV doses above 25 J/m2. In addition, a surprising enhancement in replication was seen in conditioned cells from adult following challenge UV doses.

  View details for PubMedID 6863989

• RESTRICTED REPAIR OF AFLATOXIN-B1 INDUCED DAMAGE IN ALPHA-DNA OF MONKEY CELLS NUCLEIC ACIDS RESEARCH Leadon, S. A., Zolan, M. E., Hanawalt, P. C. 1983; 11 (16): 5675-5689

  Abstract

  We have investigated the processing of adducts formed by covalent binding of aflatoxin B1 (AFB1) to DNA in confluent cultures of African green monkey cells. Repair synthesis elicited by AFB1 adducts was deficient in alpha DNA sequences compared to that in bulk DNA, although the initial levels of modification were the same for these DNAs. The removal of the primary initial adduct, AFB1-N7-Guanine, was deficient in alpha DNA and the kinetics of its loss resembled those previously reported for removal from total DNA in xeroderma pigmentosum cells of complementation group A. Spontaneous loss of the AFB1 moiety or the concomitant loss of the guanine to yield an apurinic site account for these results. The formation of the more chemically stable secondary product, AFB1-triamino-Pyrimidine, occurred more rapidly and to a greater extent in alpha DNA than in bulk DNA, probably because of slower removal of the primary product. The excision repair patch size for AFB1 adducts in alpha DNA was only 10 nucleotides compared to 20 nucleotides for repair of AFB1 adducts in bulk DNA. Irradiation of cells with low doses of UV prior to or immediately after treatment with AFB1 increased the rate and extent of removal of AFB1 adducts from alpha DNA to the levels found in the bulk DNA, indicating that the formation of pyrimidine dimers or their repair may alter the chromatin structure of alpha DNA sufficiently to facilitate its repair.

  View details for Web of Science ID A1983RE05200027

  View details for PubMedID 6412212

• VIRAL PROBES FOR DNA-REPAIR ADVANCES IN RADIATION BIOLOGY DEFAIS, M. J., Hanawalt, P. C., SARASIN, A. R. 1983; 10: 1-37

  View details for Web of Science ID A1983QS81400001

• MONOCLONAL-ANTIBODY TO DNA CONTAINING THYMINE GLYCOL MUTATION RESEARCH Leadon, S. A., Hanawalt, P. C. 1983; 112 (4): 191-200

  Abstract

  Exposure of DNA to ionizing or near ultraviolet radiation modifies thymine to form ring-saturated products. One of the major products formed is 5,6-dihydroxy-5,6-dihydrothymine (thymine glycol). Thymine glycol can also be selectively formed by oxidizing DNA with OsO4. We have isolated hybrids that produce monoclonal antibodies against thymine glycol by fusing mouse myeloma cells (P3X63-Ag8-6.5.3) with spleen cells from BALB/c mice immunized with OsO4-oxidized poly(dT) complexed with methylated bovine serum albumin. This report describes the characterization of the antibody from one hybridoma using a competitive enzyme-linked immunosorbent assay (ELISA). The antibody reacted with both single- and double-stranded DNA treated with OsO4, and with OsO4-treated poly(dA-dT) and poly(dT); it did not crossreact with unmodified or apurinic DNA. It also reacted with DNA treated with H2O2 or with gamma-rays at doses as low as 250 rad. We were able to detect 2 fmoles of thymine glycol in OsO4-treated DNA and could quantitate 1 thymine glycol per 220 000 thymines. Using the antibody and the ELISA, the formation and removal of thymine glycol was examined in cultures of African green monkey cells irradiated with 25 krad of gamma-rays. The antibody reactive sites produced by irradiation (8.5 per 10(6) thymines) were efficiently removed from the cellular DNA.

  View details for Web of Science ID A1983RF58700001

  View details for PubMedID 6888408

• DNA-REPAIR IN CULTURED KERATINOCYTES JOURNAL OF INVESTIGATIVE DERMATOLOGY Liu, S. C., Parsons, S., Hanawalt, P. C. 1983; 81 (1): S179-S183

  View details for Web of Science ID A1983QZ98700033

• DEFICIENT REPAIR OF CHEMICAL ADDUCTS IN ALPHA-DNA OF MONKEY CELLS CELL Zolan, M. E., Cortopassi, G. A., Smith, C. A., Hanawalt, P. C. 1982; 28 (3): 613-619

  Abstract

  We have examined excision repair of DNA damage in the highly repeated alpha DNA sequence of cultured African green monkey cells. Irradiation of cells with 254 nm ultraviolet light resulted in the same frequency of pyrimidine dimers in alpha DNA and the bulk of the DNA. The rate and extent of pyrimidine dimer removal, as judged by measurement of repair synthesis, was also similar for alpha DNA and bulk DNA. In cells treated with furocoumarins and long-wave-length ultraviolet light, however, repair synthesis in alpha DNA was only 30% of that in bulk DNA, although it followed the same time course. We found that this reduced repair was not caused by different initial amounts of furocoumarin damage or by different sizes of repair patches, as we found these to be similar in the two DNA species. Direct quantification demonstrated that fewer furocoumarin adducts were removed from alpha DNA than from bulk DNA. In cells treated with another chemical DNA-damaging agent, N-acetoxy-2-acetylaminofluorene, repair synthesis in alpha DNA was 60% of that in bulk DNA. These results show that the repair of different kinds of DNA damage can be affected to different extents by some property of this tandemly repeated heterochromatic DNA. To our knowledge, this is the first demonstration in primate cells of differential repair of cellular DNA sequences.

  View details for Web of Science ID A1982NG44200023

  View details for PubMedID 7074686

• DNA-REPAIR RESPONSE IN HUMAN EPIDERMAL-KERATINOCYTES FROM DONORS OF DIFFERENT AGE JOURNAL OF INVESTIGATIVE DERMATOLOGY LIU, S. C., Parsons, C. S., Hanawalt, P. C. 1982; 79 (5): 330-335

  Abstract

  We have compared the excision-repair and growth properties of epidermal keratinocytes from humans of different ages. Keratinocytes isolated from newborn and adult abdominal skin at autopsy were cultured on collagen gels. Repair replication was assayed by the 5-bromodeoxyuridine density-labeling method following ultraviolet (UV) irradiation (254 nm) of the cultures. The keratinocytes from newborn donors proliferated more rapidly and attained a higher concentration at confluence than did those from aged donors. Semiconservative DNA replication was inhibited by UV radiation to an equal extent in cell cultures from newborns and adults. After a UV dose of 13 J/m2, the time course of DNA repair was similar for the respective cultures. Furthermore, there were no significant differences in the time course of repair for keratinocytes in the proliferative or the plateau phase of growth. The dose-response curves for repair replication in cells from both young and old donors maximized at about 50 J/m2 but the attenuation in repair at higher doses appeared somewhat greater in cells from older donors. We conclude that no significant age-related differences exist in the rate and extent of the repair-replication response of human epidermal keratinocytes to UV-radiation damage in DNA. However, it remains to be determined whether other cellular recovery responses to damaged DNA are also relatively unrelated to age.

  View details for Web of Science ID A1982PP31600013

  View details for PubMedID 7130746

• ALKALI-SENSITIVE SITES IN DNA FROM HUMAN-CELLS TREATED WITH ULTRAVIOLET-LIGHT, 1'-ACETOXYSAFROLE OR 1'-ACETOXYESTRAGOLE CARCINOGENESIS Phillips, D. H., Hanawalt, P. C. 1982; 3 (8): 935-940

  Abstract

  The formation and repair of alkali-labile sites in the DNA of human cells treated with 254 nm u.v. light, 1'-acetoxyestragole (1'-AcO-E) or 1'-acetoxysafrole (1'-AcO-S) have been studied. DNA was analysed by sedimentation in alkaline sucrose gradients after the cells had been layered on the gradients in lysis solution for 15 h (long lysis) or for only 0.75 h (short lysis). With the long lysis technique, a dose of 20 J/m2 resulted in 0.2-0.4 strand breaks/10(8) daltons while treatment of cells with 0.5 mM 1'-AcO-E or 1'-AcO-S caused 0.1-0.3 strand breaks/10(8) daltons. In excision repair proficient T98G cells, one third to two thirds of these strand breaks disappeared upon 4 h incubation after exposure to each of the three agents. In excision repair deficient xeroderma pigmentosum fibroblasts (XPA), the alkali-labile sites produced by 1'-AcO-E or 1'-AcO-S were still repaired, although those resulting from u.v.-irradiation were not. Similar characteristics were observed after the short lysis period. The sedimentation velocities of nucleoids, prepared from treated XPA cells, in neutral sucrose gradients containing ethidium bromide, did not reveal the presence of overt strand breaks in the DNA, suggesting that the lesions were of a type in which the sugar-phosphate backbone was intact but sensitive to hydrolysis by alkali. The contribution of this type of damage to the total DNA damage produced by the agents was estimated to be less than 1% for u.v., and less than 2.5% for 1'-AcO-E and 1'-AcO-S.

  View details for Web of Science ID A1982PF37900017

  View details for PubMedID 7127674

• LIGATION OF OLIGONUCLEOTIDES BY PYRIMIDINE DIMERS - A MISSING LINK IN THE ORIGIN OF LIFE NATURE Lewis, R. J., Hanawalt, P. C. 1982; 298 (5872): 393-396

  Abstract

  One of the principal photochemical reactions of DNA on exposure to UV is the formation of intrastrand cyclobutane-type pyrimidine dimers. The efficiency of this reaction depends on both the wavelength of the UV2 and the specific nucleotide sequence in the DNA. The formation of the pyrimidine dimer and its repair in living cells have been studied extensively. We have examined the possibility that pyrimidines at the ends of DNA strands may be adequately juxtaposed for dimer formation by the presence of a complementary strand, even when no phosphodiester linkage joins their sugars. In these conditions the formation of a dimer will 'ligate' two DNA strands end-to-end. We report here that thymidine oligonucleotides annealed to polydeoxyadenylate can be ligated end-to-end by UV irradiation, via thymine dimerization of the terminal nucleotides in adjacent oligonucleotides. The linkages are susceptible to direct photoreversal by 254 nm UV, as expected for cyclobutane-type thymine dimers, but they are not cleaved by the bacteriophage T4 endonuclease V, a dimer-specific DNA repair enzyme. We demonstrate that the ligating dimers are also resistant to photolyase from Escherichia coli. Although the phosphodiester backbone is not required for dimer formation, it is required for recognition of dimers by these DNA repair enzymes. We discuss the possibility that high molecular weight polynucleotides in primordial seas might have been generated from oligonucleotides by pyrimidine dimerization under the intense solar UV flux unattenuated by an ozone layer.

  View details for Web of Science ID A1982NY37400051

  View details for PubMedID 6283388

• REPAIR REPLICATION CHARACTERISTICS OF HUMAN-CELLS EXPOSED TO 1'-ACETOXYSAFROLE OR 1'-ACETOXYESTRAGOLE CARCINOGENESIS Phillips, D. H., Hanawalt, P. C. 1982; 3 (8): 929-934

  Abstract

  The response of cultured human cells to treatment with 1'-acetoxysafrole (1'-AcO-S) and 1'-acetoxyestragole (1'-AcO-E), which are electrophilic and mutagenic, has been examined. Fifty percent survival of T98G cells followed exposure to 0.2 mM 1'-AcO-E. Fifty percent inhibition of DNA synthesis rate occurred after exposure to 0.3-0.5 mM of either compound. DNA repair replication in treated cells was measured by the combined 5-bromodeoxyuridine density and radioisotope labelling method. Detectable levels of repair over a 4 h time period appeared following exposure to 0.1 mM or higher concentrations of either compound. However, the maximum level of repair in 1'-AcO-S-treated cells was only 15% of the value seen after a saturating dose of u.v. (254 nm), and that for 1'-AcO-E was only 10% of the u.v. maximum. The time course for repair was similar for u.v. and 1'-AcO-S up to at least 11 h after treatment. Normal human fibroblasts (GM38) exhibited a similar ability to that of T98G cells for repair of 1'-AcO-S-induced damage. Even SV40-transformed fibroblasts from a xeroderma pigmentosum patient (complementation group A) exhibited a low but significant amount of repair after treatment with 0.5 mM 1'-AcO-S. The repair patch size distribution in T98G cells treated wih 1'-AcO-S or 1'-AcO-E was 19-23 nucleotides, -70% of the value obtained by the density-labelling method in u.v.-irradiated human cells.

  View details for Web of Science ID A1982PF37900016

  View details for PubMedID 7127673

• REARRANGEMENT OF MAMMALIAN CHROMATIN STRUCTURE FOLLOWING EXCISION REPAIR NATURE Zolan, M. E., Smith, C. A., CALVIN, N. M., Hanawalt, P. C. 1982; 299 (5882): 462-464

  View details for Web of Science ID A1982PJ15200056

  View details for PubMedID 7121585

• REPAIR RESPONSES TO DNA DAMAGE - ENZYMATIC PATHWAYS IN ESCHERICHIA-COLI AND HUMAN-CELLS JOURNAL OF CELLULAR BIOCHEMISTRY Hanawalt, P. C., Cooper, P. K., Ganesan, A. K., Lloyd, R. S., Smith, C. A., Zolan, M. E. 1982; 18 (3): 271-283

  View details for Web of Science ID A1982NM03100002

  View details for PubMedID 7040432

• REPAIR IN ALPHA-DNA OF AFRICAN-GREEN MONKEY CELLS Zolan, M. E., Smith, C. A., Hanawalt, P. C. ROCKEFELLER UNIV PRESS. 1981: A74–A74

  View details for Web of Science ID A1981NT31300280

• EXPRESSION OF THE DENV GENE OF BACTERIOPHAGE-T4 CLONED IN ESCHERICHIA-COLI PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES Lloyd, R. S., Hanawalt, P. C. 1981; 78 (5): 2796-2800

  Abstract

  The denV gene of bacteriophage T4 has been cloned into Escherichia coli K-12 by inserting appropriate fragments of cytosine-containing T4 DNA into the Sal I site of the plasmid pBR322. The denV gene codes for an enzyme that initiates the excision repair of pyrimidine dimers produced in DNA by UV. In uvrA recA mutants, deficient in an early step in excision repair, the cloned DNA results in enhanced UV resistance that is more pronounced in stationary- than in exponential-phase cultures. The expression of the cloned DNA also results in the enhanced survival of UV-irradiated phage lambda or of a denV mutant of phage T4 and in removal of dimers from the DNA of UV-irradiated cells.

  View details for Web of Science ID A1981LS91000027

  View details for PubMedID 6265912

• DNA-REPAIR RESPONSES IN HUMAN-SKIN CELLS JOURNAL OF INVESTIGATIVE DERMATOLOGY Hanawalt, P. C., Liu, S. C., Parsons, C. S. 1981; 77 (1): 86-90

  Abstract

  Sunlight and some environmental chemical agents produce lesions in the DNA of human skin cells that if unrepaired may interfere with normal functioning of these cells. The most serious outcome of such interactions may be malignancy. It is therefore important to develop an understanding of mechanisms by which the lesions may be repaired or tolerated without deleterious consequences. Our models for the molecular processing of damaged DNA have been derived largely from the study of bacterial systems. Some similarities but significant differences are revealed when human cell responses are tested against these models. It is also of importance to learn DNA repair responses of epidermal keratinocytes for comparison with the more extensive studies that have been carried out with dermal fibroblasts. Our experimental results thus far indicate similarities for the excision-repair of ultraviolet-induced pyrimidine dimers in human keratinocytes and fibroblasts. Both the monoadducts and the interstrand crosslinks produced in DNA by photoactivated 8-methoxypsoralen (PUVA) can be repaired in normal human fibroblasts but not in those from xeroderma pigmentosum patients. The monoadducts, like pyrimidine dimers, are probably the more mutagenic/carcinogenic lesions while the crosslinks are less easily repaired and probably result in more effective blocking of DNA function. It is suggested that a split-dose protocol that maximizes the production of crosslinks while minimizing the yield of monoadducts may be more effective and potentially less carcinogenic than the single ultraviolet exposure regimen in PUVA therapy for psoriasis.

  View details for Web of Science ID A1981LZ25700014

  View details for PubMedID 7252262

• THE INVIVO FORMATION AND REPAIR OF DNA ADDUCTS FROM 1'-HYDROXYSAFROLE JOURNAL OF SUPRAMOLECULAR STRUCTURE AND CELLULAR BIOCHEMISTRY Phillips, D. H., Hanawalt, P. C., Miller, J. A., Miller, E. C. 1981; 16 (1): 83-90

  Abstract

  1'-Hydroxysafrole is a proximate carcinogenic metabolite of the naturally occurring hepatocarcinogen safrole. Comparison by high-performance liquid chromatography of the nucleoside adducts obtained from hepatic DNA of adult female mice treated with [2',3'-3H]1'-hydroxysafrole with those formed by reaction of deoxyribonucleosides with electrophilic derivatives of 1'-hydroxysafrole indicated that the four in vivo adducts studied were derived from an ester of 1'-hydroxysafrole. Three of the four adducts comigrated with products of the reaction of 1'-acetoxysafrole with deoxyguanosine, whereas the fourth adduct comigrated with the major reaction product of the ester with deoxyadenosine. Analysis of the three deoxyguanosine adducts indicated that all three involve substitution on the 2-amino group of guanine. A sample of ther major adduct prepared from deoxyguanylic acid has been characterized from its NMR spectrum as N2-(trans-isosafrol-3'-yl)-deoxyguanosine, and the deoxyadenosine adduct has been similarly characterized as N6-(trans-isosafrol-3'-yl)-deoxyadenosine. Repair replication was measured in cultured human T98G cells exposed to 1'-acetoxysafrole using the combined 5-bromodeoxyuridine density label and radioisotopic label method. At a concentration of 1 mM 1'-acetoxysafrole, the amount of repair synthesis approached maximum values only about 15% of those obtained after saturating doses of ultraviolet light. Repair patch size distribution was found to be similar in cells treated with ultraviolet light or 1'-acetoxysafrole as determined by the density of repair-labeled DNA relative to that of parental DNA.

  View details for Web of Science ID A1981ML89400007

  View details for PubMedID 7299840

• SENSITIVE DETERMINATION OF PYRIMIDINE DIMERS IN DNA OF UV-IRRADIATED MAMMALIAN-CELLS - INTRODUCTION OF T4 ENDONUCLEASE-V INTO FROZEN AND THAWED CELLS MUTATION RESEARCH VanZeeland, A. A., Smith, C. A., Hanawalt, P. C. 1981; 82 (1): 173-189

  Abstract

  Endonuclease V from E. coli infected with phage T4 was used to evaluate the frequency and the removal of pyrimidine dimers from DNA in cultured mammalian cells. Cellular membranes were made permeable to the enzyme by two cycles of rapid freezing and thawing. The number of endonuclease-sensitive sites in DNA was assayed by sedimentation in alkaline sucrose gradients upon which the cells were lysed directly. Comparison of the frequency of endonuclease-sensitive sites with the frequency of pyrimidine dimers determined by chromatographic analysis of hydrolysed DNA indicated that about 50% of the dimers in the permeabilized cells were substrates for T4 endonuclease V. This was confirmed by observation that when DNA treated with the enzyme in situ was purified, it contained the expected additional number of endonuclease-sensitive sites if again treated with the enzyme. The percentage of pyrimidine dimers recognized by T4 endonuclease V was enhanced to nearly 100% by exposing the permeabilized cells to 2 M NaCl before the enzyme was introduced. This method allowed the measurement of frequencies of endonuclease-sensitive sites after doses of UV irradiation at low as 0.5 J/m2. Loss of endonuclease sites from cellular DNA was observed during post-irradiation incubation of V79 Chinese hamster cells and several human cell strains. A comparison of the results obtained in human cells with or without the high-salt exposure before endonuclease treatment suggested that the dimers recognized under low-salt conditions may be removed slightly faster than those recognized only after high-salt exposure.

  View details for Web of Science ID A1981LT18900017

  View details for PubMedID 6267456

• DNA-REPAIR IN HUMAN-CELLS CONTAINING PHOTOADDUCTS OF 8-METHOXYPSORALEN OR ANGELICIN CANCER RESEARCH Kaye, J., Smith, C. A., Hanawalt, P. C. 1980; 40 (3): 696-702

  Abstract

  Photoactivated 8-methoxypsoralen (8-MOP) has been proven to be clinically effective for a number of dermatological conditions including lichen planus, mycosis fungoides, and psoriasis. 8-MOP forms two types of covalent photoproducts with DNA, monoadducts, and bifunctional adducts which cross-link the two DNA strands. Angelicin is a congener of 8-MOP which forms only monoadducts. We have used the combined density and isotopic labeling technique to study repair replication in cultured human fibroblasts treated with either of these compounds and exposed to near-ultraviolet light. In human diploid fibroblasts (WI-38), the time course of repair replication for both compounds is similar. Drug concentration and ultraviolet dose responses are also similar for 8-MOP and angelicin. No repair replication was stimulated by either compound in xeroderma pigmentosum cells from Complementation Group A (XP12BE). These results suggest that repair replication in response to 8-MOP is primarily a response to monoadducts and that the enzymatic pathway for this repair synthesis shares at least one step with the pathway for repair of pyrimidine dimers. Cross-link persistence in treated cells was assayed by use of the single-strand-specific S1 nuclease to digest DNA that did not renature readily following heat denaturation. Partial removal of cross-links was observed in normal, xeroderma pigmentosum variant, and Fanconi's anemia fibroblasts, but not in xeroderma pigmentosum Group A cells.

  View details for Web of Science ID A1980JG46100035

  View details for PubMedID 7471088

• REPLICATION OF ULTRAVIOLET-IRRADIATED SIMIAN VIRUS-40 IN MONKEY KIDNEY-CELLS JOURNAL OF MOLECULAR BIOLOGY SARASIN, A. R., Hanawalt, P. C. 1980; 138 (2): 299-319

  View details for Web of Science ID A1980JN48100007

  View details for PubMedID 6251226

• PROCESSIVE ACTION OF T4 ENDONUCLEASE-V ON ULTRAVIOLET-IRRADIATED DNA NUCLEIC ACIDS RESEARCH Lloyd, R. S., Hanawalt, P. C., Dodson, M. L. 1980; 8 (21): 5113-5127

  Abstract

  The action of the dimer-specific endonuclease V of bacteriophage T4 was studied on UV-irradiated, covalently-closed circular DNa. Form I ColE1 DNA preparations containing average dimer frequencies ranging from 2.5 to 35 pyrimidine dimers per molecule were treated with T4 endonuclease V and analysed by agarose gel electrophoresis. At all dimer frequencies examined, the production of form III DNA was linear with time and the double-strand scissions were made randomly on the ColE1 DNA genome. Since the observed fraction of form III DNA increased with increasing dimer frequency but the initial rate of loss of form I decreased with increasing dimer frequency, it was postulated that multiple single-strand scissions could be produced in a subset of the DNA population while some DNA molecules contained no scissions. When DNA containing an average of 25 dimers per circle was incubated with limiting enzyme concentrations, scissions appeared at most if not all dimmer sites in some molecules before additional strand scissions were produced in other DNA molecules. The results support a processive model for the interaction of T4 endonuclease V with UV-irradiated DNA.

  View details for Web of Science ID A1980KQ40400021

  View details for PubMedID 6255442

• DNA-REPAIR IN BACTERIA AND MAMMALIAN-CELLS ANNUAL REVIEW OF BIOCHEMISTRY Hanawalt, P. C., Cooper, P. K., Ganesan, A. K., Smith, C. A. 1979; 48: 783-836

  View details for Web of Science ID A1979HD84900027

  View details for PubMedID 382997

• PHAGE-T4 ENDONUCLEASE-V STIMULATES DNA-REPAIR REPLICATION IN ISOLATED-NUCLEI FROM ULTRAVIOLET-IRRADIATED HUMAN CELLS, INCLUDING XERODERMA PIGMENTOSUM FIBROBLASTS PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Smith, C. A., Hanawalt, P. C. 1978; 75 (6): 2598-2602

  Abstract

  The repair mode of DNA replication has been demonstrated in isolated nuclei from UV-irradiated human cells. Nuclei are incubated in a mixture containing [(3)H]thymidine triphosphate and bromodeoxyuridine triphosphate in a 1:5 ratio. The (3)H at the density of parental DNA in alkaline CsCl density gradients is then a measure of repair. In nuclei prepared from WI38 cells 30 min after irradiation, repair replication is UV dependent and proceeds at approximately the in vivo rate for 5 min. Repair replication is reduced in irradiated nuclei or in nuclei prepared immediately after irradiation. It is Mg(2+)-dependent and stimulated by added ATP and deoxyribonucleoside triphosphates. No repair replication is observed in nuclei from xeroderma pigmentosum (complementation group A) cells. However, upon addition of coliphage T4 endonuclease V, which specifically nicks DNA containing pyrimidine dimers, repair replication is observed in nuclei from irradiated xeroderma pigmentosum cells and is stimulated in WI38 nuclei. The reaction then persists for an hour and is dependent upon added ATP and deoxyribonucleoside triphosphates. The repair label is in stretches of roughly 35 nucleotides, as it is in intact cells. Added pancreatic DNase does not promote UV-dependent repair synthesis. Our results support the view that xeroderma pigmentosum (group A) cells are defective in the incision step of the DNA excision repair pathway, and demonstrate the utility of this system for probing DNA repair mechanisms.

  View details for Web of Science ID A1978FF05900015

  View details for PubMedID 275829

• CARCINOGENS ENHANCE SURVIVAL OF UV-IRRADIATED SIMIAN-VIRUS 40 IN TREATED MONKEY KIDNEY CELLS - INDUCTION OF A RECOVERY PATHWAY PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA SARASIN, A. R., Hanawalt, P. C. 1978; 75 (1): 346-350

  Abstract

  Treatment of monkey kidney cells with low doses of carcinogen enhances the survival of UV-irradiated simian virus 40 (SV40). This is true for compounds with UV-like effects (metabolites of aflatoxin B1, N-acetoxyacetylaminofluorene) and compounds with x-ray-like effects (methyl methanesulfonate, ethyl methanesulfonate). This phenomenon resembles the UV-reactivation of viruses in eukaryotic cells. The carcinogen-induced enhancement of the survival of UV-irradiated SV40 is correlated with the inhibition of host-cell DNA synthesis, suggesting that the inhibition is an inducing agent. An enhancement of UV-irradiated SV40 survival is also obtained in cells treated with hydroxyurea or cycloheximide for long enough that there is still inhibition of host DNA synthesis during the early stage of SV40 infection. We hypothesize that treatment of host cells with carcinogens induces a new recovery pathway that facilitates the replication of damaged DNA, bypassing the lesions and resulting in the enhanced survival of UV-irradiated SV40. This inducible process might represent the expression of "SOS repair" functions in eukaryotic cells analogous to the previously demonstrated induction of SOS repair in bacteria after UV or carcinogen treatment.

  View details for Web of Science ID A1978EM12800077

  View details for PubMedID 203936

  View details for PubMedCentralID PMC411245

• REPAIR OF DNA IN HUMAN CELLS AFTER TREATMENT WITH ACTIVATED AFLATOXIN-B1 CANCER RESEARCH SARASIN, A. R., Smith, C. A., Hanawalt, P. C. 1977; 37 (6): 1786-1793

  Abstract

  Repair replication was examined in cultured human cells exposed to the hepatocarcinogen aflatoxin B1 using the combined bromodeoxyuridine density label and radioisotopic label method. Semiconservative DNA synthesis was strongly inhibited, and the repair replication mode was stimulated in diploid fibroblasts (W138) and in their SV40 transformants (VA13) only when exposure to aflatoxin B1 was in the presence of an activating system containing rat liver microsomal enzymes. The maximum amount of repair synthesis was about 20% of that obtained after saturating doses of ultraviolet light (UV). The time course of repair synthesis was similar to that seen after UV, and most of the synthesis was in 30- to 50-nucleotide "short patches." A line of SV40-transformed xeroderma pigmentosum cells (Group A) deficient in repair after exposure to UV was similarly deficient in repair replication after aflatoxin treatment. Treatment with aflatoxin resulted in a 25 to 45% inhibition of UV-induced repair replication, suggesting that in addition to producing lesions in DNA, which are substrates for the excision repair system, the toxin also inhibits excision repair. CsC1 gradients of DNA treated in vitro with activated aflatoxin demonstrated binding of the drug to DNA. Alkaline sucrose gradient sedimentation gave no indication that single-strand breaks or alkali labile bonds were introduced into DNA by treatment of cells with activated aflatoxin.

  View details for Web of Science ID A1977DG87600034

  View details for PubMedID 192462

• REPAIR REPLICATION IN HUMAN CELLS - SIMPLIFIED DETERMINATION UTILIZING HYDROXYUREA BIOCHIMICA ET BIOPHYSICA ACTA Smith, C. A., Hanawalt, P. C. 1976; 432 (3): 336-347

  Abstract

  A simplified and shortened procedure has been developed for the determination of repair replication of DNA in cultured mammalian cells. The procedure, using the bromodeoxyuridine density label and a radio-isotopic label has been applied to normal diploid human cells (WI38) and to their SV40 transformants (VA13). After incubation with the repair label the cells are lysed and digested for two hours at 50 degrees C with proteinase K. This digest can then be immediately subjected to alkaline cesium chloride density gradient centrifugation with no need for DNA extraction. Hydroxyurea is used to reduce the level of semi-conservative synthesis that a quantitative determination of repair replication can be accomplished by a single centrifugation. The method is not affected by variation in the effectiveness of the inhibitor although a small amount of semi-conservative synthesis normally occurs in the presence of the drug. The time course of repair replication in WI38 cells is unaffected by the drug. The apparent amount of repair synthesis in ultraviolet irradiated cells is increased 25 to 40% in the presence of hydroxyurea when thymidine is used as tracer. Under certain conditions in which the level of semiconservative synthesis is low (e.g., contact inhibited cells, high ultraviolet doses) the use of hydroxyurea is unnecessary.

  View details for Web of Science ID A1976BS79100010

  View details for PubMedID 178379

• REPAIR REPLICATION IN CULTURED NORMAL AND TRANSFORMED HUMAN FIBROBLASTS BIOCHIMICA ET BIOPHYSICA ACTA Smith, C. A., Hanawalt, P. C. 1976; 447 (2): 121-132

  Abstract

  Repair replication in response to ultraviolet irradiation has been studied in normal human diploid fibroblast cultures, W138, and an SV40 transformant, VA13. Quantitative comparisons have been made using the combined isotopic and density labeling method for assaying repair replication. We find no significant difference in the amount of repair replication performed its dose response, or the time course between growing and confluent W138 cells, early passage and senescent cells, or normal W138 cells and the transformed VA13 cells. When [3H]dThd was employed as the isotopic label in the presence of a 30-200 fold excess of unlabelled BrdUrd, apparent differences in repair replication were seen between W138 cells shortly after subcultivation and cells which had been allowed to reach confluence. These differences were the same over a wide dose range and regardless of the passage number of the cells, but could be influenced by using different serum lots. The differences were not seen, however, when [3H]BrdUrd provided the isotopic label; thus they reflect either impurities in the [3H]dThd or a slight discrimination by some cellular process.

  View details for Web of Science ID A1976CG36600001

  View details for PubMedID 184836