Lucie Y. Guo

All Publications

• Scalable biological signal recording in mammalian cells using Cas12a base editors. Nature chemical biology Kempton, H. R., Love, K. S., Guo, L. Y., Qi, L. S. 2022

  Abstract

  Biological signal recording enables the study of molecular inputs experienced throughout cellular history. However, current methods are limited in their ability to scale up beyond a single signal in mammalian contexts. Here, we develop an approach using a hyper-efficient dCas12a base editor for multi-signal parallel recording in human cells. We link signals of interest to expression of guide RNAs to catalyze specific nucleotide conversions as a permanent record, enabled by Cas12's guide-processing abilities. We show this approach is plug-and-play with diverse biologically relevant inputs and extend it for more sophisticated applications, including recording of time-delimited events and history of chimeric antigen receptor T cells' antigen exposure. We also demonstrate efficient recording of up to four signals in parallel on an endogenous safe-harbor locus. This work provides a versatile platform for scalable recording of signals of interest for a variety of biological applications.

  View details for DOI 10.1038/s41589-022-01034-2

  View details for PubMedID 35637351

• Multiplexed genome regulation in vivo with hyper-efficient Cas12a. Nature cell biology Guo, L. Y., Bian, J., Davis, A. E., Liu, P., Kempton, H. R., Zhang, X., Chemparathy, A., Gu, B., Lin, X., Rane, D. A., Xu, X., Jamiolkowski, R. M., Hu, Y., Wang, S., Qi, L. S. 2022

  Abstract

  Multiplexed modulation of endogenous genes is crucial for sophisticated gene therapy and cell engineering. CRISPR-Cas12a systems enable versatile multiple-genomic-loci targeting by processing numerous CRISPR RNAs (crRNAs) from a single transcript; however, their low efficiency has hindered in vivo applications. Through structure-guided protein engineering, we developed a hyper-efficient Lachnospiraceae bacterium Cas12a variant, termed hyperCas12a, with its catalytically dead version hyperdCas12a showing significantly enhanced efficacy for gene activation, particularly at low concentrations of crRNA. We demonstrate that hyperdCas12a has comparable off-target effects compared with the wild-type system and exhibits enhanced activity for gene editing and repression. Delivery of the hyperdCas12a activator and a single crRNA array simultaneously activating the endogenous Oct4, Sox2 and Klf4 genes in the retina of post-natal mice alters the differentiation of retinal progenitor cells. The hyperCas12a system offers a versatile in vivo tool for a broad range of gene-modulation and gene-therapy applications.

  View details for DOI 10.1038/s41556-022-00870-7

  View details for PubMedID 35414015

• A buoyant mass in the brain: Intraventricular migration of silicone oil. American journal of ophthalmology case reports Guo, L. Y., Jamiolkowski, R. M., Hassan, M., Leng, T. 2022; 25: 101399

  View details for DOI 10.1016/j.ajoc.2022.101399

  View details for PubMedID 35243146

• Inheritance of CENP-A Nucleosomes during DNA Replication Requires HJURP DEVELOPMENTAL CELL Zasadzinska, E., Huang, J., Bailey, A. O., Guo, L. Y., Lee, N. S., Srivastava, S., Wong, K. A., French, B. T., Black, B. E., Foltz, D. R. 2018; 47 (3): 348-+

  View details for DOI 10.1016/j.devcel.2018.09.003

  View details for Web of Science ID 000449415400010

• Centromeres are maintained by fastening CENP-A to DNA and directing an arginine anchor-dependent nucleosome transition. Nature communications Guo, L. Y., Allu, P. K., Zandarashvili, L., McKinley, K. L., Sekulic, N., Dawicki-McKenna, J. M., Fachinetti, D., Logsdon, G. A., Jamiolkowski, R. M., Cleveland, D. W., Cheeseman, I. M., Black, B. E. 2017; 8: 15775

  Abstract

  Maintaining centromere identity relies upon the persistence of the epigenetic mark provided by the histone H3 variant, centromere protein A (CENP-A), but the molecular mechanisms that underlie its remarkable stability remain unclear. Here, we define the contributions of each of the three candidate CENP-A nucleosome-binding domains (two on CENP-C and one on CENP-N) to CENP-A stability using gene replacement and rapid protein degradation. Surprisingly, the most conserved domain, the CENP-C motif, is dispensable. Instead, the stability is conferred by the unfolded central domain of CENP-C and the folded N-terminal domain of CENP-N that becomes rigidified 1,000-fold upon crossbridging CENP-A and its adjacent nucleosomal DNA. Disrupting the 'arginine anchor' on CENP-C for the nucleosomal acidic patch disrupts the CENP-A nucleosome structural transition and removes CENP-A nucleosomes from centromeres. CENP-A nucleosome retention at centromeres requires a core centromeric nucleosome complex where CENP-C clamps down a stable nucleosome conformation and CENP-N fastens CENP-A to the DNA.

  View details for DOI 10.1038/ncomms15775

  View details for PubMedID 28598437

  View details for PubMedCentralID PMC5472775

• A Dual Inhibitory Mechanism Sufficient to Maintain Cell-Cycle-Restricted CENP-A Assembly. Molecular cell Stankovic, A., Guo, L. Y., Mata, J. F., Bodor, D. L., Cao, X. J., Bailey, A. O., Shabanowitz, J., Hunt, D. F., Garcia, B. A., Black, B. E., Jansen, L. E. 2017; 65 (2): 231-246

  Abstract

  Chromatin featuring the H3 variant CENP-A at the centromere is critical for its mitotic function and epigenetic maintenance. Assembly of centromeric chromatin is restricted to G1 phase through inhibitory action of Cdk1/2 kinases in other phases of the cell cycle. Here, we identify the two key targets sufficient to maintain cell-cycle control of CENP-A assembly. We uncovered a single phosphorylation site in the licensing factor M18BP1 and a cyclin A binding site in the CENP-A chaperone, HJURP, that mediated specific inhibitory phosphorylation. Simultaneous expression of mutant proteins lacking these residues results in complete uncoupling from the cell cycle. Consequently, CENP-A assembly is fully recapitulated under high Cdk activities, indistinguishable from G1 assembly. We find that Cdk-mediated inhibition is exerted by sequestering active factors away from the centromere. Finally, we show that displacement of M18BP1 from the centromere is critical for the assembly mechanism of CENP-A.

  View details for DOI 10.1016/j.molcel.2016.11.021

  View details for PubMedID 28017591

  View details for PubMedCentralID PMC5250512

• The CENP-A nucleosome bound by CENP-C and CENP-N is the fundamental unit for maintaining centromere identity. Guo, L. Y., Zandarashvili, L., McKinley, K. L., Sekulic, N., Fachinetti, D., Cleveland, D. W., Cheeseman, I. M., Black, B. E. AMER SOC CELL BIOLOGY. 2016

  View details for Web of Science ID 000394259500160

• The CENP-L-N Complex Forms a Critical Node in an Integrated Meshwork of Interactions at the Centromere-Kinetochore Interface. Molecular cell McKinley, K. L., Sekulic, N., Guo, L. Y., Tsinman, T., Black, B. E., Cheeseman, I. M. 2015; 60 (6): 886-98

  Abstract

  During mitosis, the macromolecular kinetochore complex assembles on the centromere to orchestrate chromosome segregation. The properties and architecture of the 16-subunit Constitutive Centromere-Associated Network (CCAN) that allow it to build a robust platform for kinetochore assembly are poorly understood. Here, we use inducible CRISPR knockouts and biochemical reconstitutions to define the interactions between the human CCAN proteins. We find that the CCAN does not assemble as a linear hierarchy, and instead, each sub-complex requires multiple non-redundant interactions for its localization to centromeres and the structural integrity of the overall assembly. We demonstrate that the CENP-L-N complex plays a crucial role at the core of this assembly through interactions with CENP-C and CENP-H-I-K-M. Finally, we show that the CCAN is remodeled over the cell cycle such that sub-complexes depend on their interactions differentially. Thus, an interdependent meshwork within the CCAN underlies the centromere specificity and stability of the kinetochore.

  View details for DOI 10.1016/j.molcel.2015.10.027

  View details for PubMedID 26698661

  View details for PubMedCentralID PMC4690846

• Chromosomes. CENP-C reshapes and stabilizes CENP-A nucleosomes at the centromere. Science (New York, N.Y.) Falk, S. J., Guo, L. Y., Sekulic, N., Smoak, E. M., Mani, T., Logsdon, G. A., Gupta, K., Jansen, L. E., Van Duyne, G. D., Vinogradov, S. A., Lampson, M. A., Black, B. E. 2015; 348 (6235): 699-703

  Abstract

  Inheritance of each chromosome depends upon its centromere. A histone H3 variant, centromere protein A (CENP-A), is essential for epigenetically marking centromere location. We find that CENP-A is quantitatively retained at the centromere upon which it is initially assembled. CENP-C binds to CENP-A nucleosomes and is a prime candidate to stabilize centromeric chromatin. Using purified components, we find that CENP-C reshapes the octameric histone core of CENP-A nucleosomes, rigidifies both surface and internal nucleosome structure, and modulates terminal DNA to match the loose wrap that is found on native CENP-A nucleosomes at functional human centromeres. Thus, CENP-C affects nucleosome shape and dynamics in a manner analogous to allosteric regulation of enzymes. CENP-C depletion leads to rapid removal of CENP-A from centromeres, indicating their collaboration in maintaining centromere identity.

  View details for DOI 10.1126/science.1259308

  View details for PubMedID 25954010

  View details for PubMedCentralID PMC4610723

• Both tails and the centromere targeting domain of CENP-A are required for centromere establishment. The Journal of cell biology Logsdon, G. A., Barrey, E. J., Bassett, E. A., DeNizio, J. E., Guo, L. Y., Panchenko, T., Dawicki-McKenna, J. M., Heun, P., Black, B. E. 2015; 208 (5): 521-31

  Abstract

  The centromere-defined by the presence of nucleosomes containing the histone H3 variant, CENP-A-is the chromosomal locus required for the accurate segregation of chromosomes during cell division. Although the sequence determinants of human CENP-A required to maintain a centromere were reported, those that are required for early steps in establishing a new centromere are unknown. In this paper, we used gain-of-function histone H3 chimeras containing various regions unique to CENP-A to investigate early events in centromere establishment. We targeted histone H3 chimeras to chromosomally integrated Lac operator sequences by fusing each of the chimeras to the Lac repressor. Using this approach, we found surprising contributions from a small portion of the N-terminal tail and the CENP-A targeting domain in the initial recruitment of two essential constitutive centromere proteins, CENP-C and CENP-T. Our results indicate that the regions of CENP-A required for early events in centromere establishment differ from those that are required for maintaining centromere identity.

  View details for DOI 10.1083/jcb.201412011

  View details for PubMedID 25713413

  View details for PubMedCentralID PMC4347640

• Iron increases APP translation and amyloid-beta production in the retina. Experimental eye research Guo, L. Y., Alekseev, O., Li, Y., Song, Y., Dunaief, J. L. 2014; 129: 31-7

  Abstract

  Age-related macular degeneration (AMD) is the most common cause of blindness among older adults in developed countries, and retinal iron accumulation may exacerbate the disease. Iron can upregulate the production of amyloid precursor protein (APP). Since amyloid-β (Aβ), a byproduct of APP proteolysis, is found in drusen, the histopathological hallmark of AMD, we tested the role of iron in regulating APP and Aβ levels in the retinal pigment epithelial cell line ARPE-19. We found that treatment with ferric ammonium citrate (FAC) increases APP at the translational level. FAC treatment also results in increased generation of APP C-terminal fragments C83 and C99, the products of APP proteolysis by α- and β-secretase, respectively, as well as levels of Aβ42, a highly aggregative amyloid species. Additionally, retinal tissue sections from a patient with aceruloplasminemia, a disease causing iron overload in the retinal pigment epithelium (RPE), showed increased Aβ deposition in the RPE and drusen. Overall, our results suggest that RPE iron overload could contribute to Aβ accumulation in the retina.

  View details for DOI 10.1016/j.exer.2014.10.012

  View details for PubMedID 25456519

  View details for PubMedCentralID PMC4259833

• CENP-C Locks the CENP-A Nucleosome into a Conventionally Shaped Octameric Histone Core that is Incompletely Wrapped with DNA Falk, S. J., Sekulic, N., Guo, L. Y., Mani, T., Gupta, K., Van Duyne, G., Vinogradov, S., Black, B. E. AMER SOC CELL BIOLOGY. 2013

  View details for Web of Science ID 000209348705458

• Aph-1 associates directly with full-length and C-terminal fragments of gamma-secretase substrates. The Journal of biological chemistry Chen, A. C., Guo, L. Y., Ostaszewski, B. L., Selkoe, D. J., LaVoie, M. J. 2010; 285 (15): 11378-91

  Abstract

  Gamma-secretase is a ubiquitous, multiprotein enzyme composed of presenilin, nicastrin, Aph-1, and Pen-2. It mediates the intramembrane proteolysis of many type 1 proteins, plays an essential role in numerous signaling pathways, and helps drive the pathogenesis of Alzheimer disease by excising the hydrophobic, aggregation-prone amyloid beta-peptide from the beta-amyloid precursor protein. A central unresolved question is how its many substrates bind and enter the gamma-secretase complex. Here, we provide evidence that both the beta-amyloid precursor protein holoprotein and its C-terminal fragments, the immediate substrates of gamma-secretase, can associate with Aph-1 at overexpressed as well as endogenous protein levels. This association was observed using bi-directional co-immunoprecipitation in multiple systems and detergent conditions, and an beta-amyloid precursor protein-Aph-1 complex was specifically isolated following in situ cross-linking in living cells. In addition, another endogenous canonical gamma-substrate, Jagged, showed association of both its full-length and C-terminal fragment forms with Aph-1. We were also able to demonstrate that this interaction with substrates was conserved across the multiple isoforms of Aph-1 (beta, alphaS, and alphaL), as they were all able to bind beta-amyloid precursor protein with similar affinity. Finally, two highly conserved intramembrane histidines (His-171 and His-197) within Aph-1, which were recently shown to be important for gamma-secretase activity, are required for efficient binding of substrates. Taken together, our data suggest a dominant role for Aph-1 in interacting with gamma-secretase substrates prior to their processing by the proteolytic complex.

  View details for DOI 10.1074/jbc.M109.088815

  View details for PubMedID 20145246

  View details for PubMedCentralID PMC2857016

• Analysis of methylation-sensitive transcriptome identifies GADD45a as a frequently methylated gene in breast cancer. Oncogene Wang, W., Huper, G., Guo, Y., Murphy, S. K., Olson, J. A., Marks, J. R. 2005; 24 (16): 2705-14

  Abstract

  Treatment of the breast cancer cell line, MDAMB468 with the DNA methylation inhibitor, 5-azacytidine (5-AzaC) results in growth arrest, whereas the growth of the normal breast epithelial line DU99 (telomerase immortalized) is relatively unaffected. Comparing gene expression profiles of these two lines after 5-AzaC treatment, we identified 36 genes that had relatively low basal levels in MDAMB468 cells compared to the DU99 line and were induced in the cancer cell line but not in the normal breast epithelial line. Of these genes, 33 have associated CpG islands greater than 300 bp in length but only three have been previously described as targets for aberrant methylation in human cancer. Northern blotting for five of these genes (alpha-Catenin, DTR, FYN, GADD45a, and Zyxin) verified the array results. Further analysis of one of these genes, GADD45a, showed that 5-AzaC induced expression in five additional breast cancer cell lines with little or no induction in three additional lines derived from normal breast epithelial cells. The CpG island associated with GADD45a was analysed by bisulfite sequencing, sampling over 100 CpG dinucleotides. We found that four CpG's, located approximately 700 bp upstream of the transcriptional start site are methylated in the majority of breast cancer cell lines and primary tumors but not in DNA from normal breast epithelia or matched lymphocytes from cancer patients. Therefore, this simple method of dynamic transcriptional profiling yielded a series of novel methylation-sensitive genes in breast cancer including the BRCA1 and p53 responsive gene, GADD45a.

  View details for DOI 10.1038/sj.onc.1208464

  View details for PubMedID 15735726