Anthony Harris

All Publications

• Multi-signal regulation of the GSK-3β homolog Rim11 controls meiosis entry in budding yeast. The EMBO journal Kociemba, J., Jørgensen, A. C., Tadić, N., Harris, A., Sideri, T., Chan, W. Y., Ibrahim, F., Ünal, E., Skehel, M., Shahrezaei, V., Argüello-Miranda, O., van Werven, F. J. 2024; 43 (15): 3256-3286

  Abstract

  Starvation in diploid budding yeast cells triggers a cell-fate program culminating in meiosis and spore formation. Transcriptional activation of early meiotic genes (EMGs) hinges on the master regulator Ime1, its DNA-binding partner Ume6, and GSK-3β kinase Rim11. Phosphorylation of Ume6 by Rim11 is required for EMG activation. We report here that Rim11 functions as the central signal integrator for controlling Ume6 phosphorylation and EMG transcription. In nutrient-rich conditions, PKA suppresses Rim11 levels, while TORC1 retains Rim11 in the cytoplasm. Inhibition of PKA and TORC1 induces Rim11 expression and nuclear localization. Remarkably, nuclear Rim11 is required, but not sufficient, for Rim11-dependent Ume6 phosphorylation. In addition, Ime1 is an anchor protein enabling Ume6 phosphorylation by Rim11. Subsequently, Ume6-Ime1 coactivator complexes form and induce EMG transcription. Our results demonstrate how various signaling inputs (PKA/TORC1/Ime1) converge through Rim11 to regulate EMG expression and meiosis initiation. We posit that the signaling-regulatory network elucidated here generates robustness in cell-fate control.

  View details for DOI 10.1038/s44318-024-00149-7

  View details for PubMedID 38886580

  View details for PubMedCentralID PMC11294583

• The transcriptional regulator Ume6 is a major driver of early gene expression during gametogenesis. Genetics Harris, A., Ünal, E. 2023; 225 (2)

  Abstract

  The process of gametogenesis is orchestrated by a dynamic gene expression program, where a vital subset constitutes the early meiotic genes. In budding yeast, the transcription factor Ume6 represses early meiotic gene expression during mitotic growth. However, during the transition from mitotic to meiotic cell fate, early meiotic genes are activated in response to the transcriptional regulator Ime1 through its interaction with Ume6. While it is known that binding of Ime1 to Ume6 promotes early meiotic gene expression, the mechanism of early meiotic gene activation remains elusive. Two competing models have been proposed whereby Ime1 either forms an activator complex with Ume6 or promotes Ume6 degradation. Here, we resolve this controversy. First, we identify the set of genes that are directly regulated by Ume6, including UME6 itself. While Ume6 protein levels increase in response to Ime1, Ume6 degradation occurs much later in meiosis. Importantly, we found that depletion of Ume6 shortly before meiotic entry is detrimental to early meiotic gene activation and gamete formation, whereas tethering of Ume6 to a heterologous activation domain is sufficient to trigger early meiotic gene expression and produce viable gametes in the absence of Ime1. We conclude that Ime1 and Ume6 form an activator complex. While Ume6 is indispensable for early meiotic gene expression, Ime1 primarily serves as a transactivator for Ume6.

  View details for DOI 10.1093/genetics/iyad123

  View details for PubMedID 37431893

  View details for PubMedCentralID PMC10550318

• Meiotic Cells Counteract Programmed Retrotransposon Activation via RNA-Binding Translational Repressor Assemblies. Developmental cell Laureau, R., Dyatel, A., Dursuk, G., Brown, S., Adeoye, H., Yue, J. X., De Chiara, M., Harris, A., Ünal, E., Liti, G., Adams, I. R., Berchowitz, L. E. 2021; 56 (1): 22-35.e7

  Abstract

  Retrotransposon proliferation poses a threat to germline integrity. While retrotransposons must be activated in developing germ cells in order to survive and propagate, how they are selectively activated in the context of meiosis is unclear. We demonstrate that the transcriptional activation of Ty3/Gypsy retrotransposons and host defense are controlled by master meiotic regulators. We show that budding yeast Ty3/Gypsy co-opts binding sites of the essential meiotic transcription factor Ndt80 upstream of the integration site, thereby tightly linking its transcriptional activation to meiotic progression. We also elucidate how yeast cells thwart Ty3/Gypsy proliferation by blocking translation of the retrotransposon mRNA using amyloid-like assemblies of the RNA-binding protein Rim4. In mammals, several inactive Ty3/Gypsy elements are undergoing domestication. We show that mammals utilize equivalent master meiotic regulators (Stra8, Mybl1, Dazl) to regulate Ty3/Gypsy-derived genes in developing gametes. Our findings inform how genes that are evolving from retrotransposons can build upon existing regulatory networks during domestication.

  View details for DOI 10.1016/j.devcel.2020.11.008

  View details for PubMedID 33278343

  View details for PubMedCentralID PMC7116619

• Comparison of sequencing the D2 region of the large subunit ribosomal RNA gene (MicroSEQ®) versus the internal transcribed spacer (ITS) regions using two public databases for identification of common and uncommon clinically relevant fungal species. Journal of microbiological methods Arbefeville, S., Harris, A., Ferrieri, P. 2017; 140: 40-46

  Abstract

  Fungal infections cause considerable morbidity and mortality in immunocompromised patients. Rapid and accurate identification of fungi is essential to guide accurately targeted antifungal therapy. With the advent of molecular methods, clinical laboratories can use new technologies to supplement traditional phenotypic identification of fungi.The aims of the study were to evaluate the sole commercially available MicroSEQ® D2 LSU rDNA Fungal Identification Kit compared to the in-house developed internal transcribed spacer (ITS) regions assay in identifying moulds, using two well-known online public databases to analyze sequenced data.85 common and uncommon clinically relevant fungi isolated from clinical specimens were sequenced for the D2 region of the large subunit (LSU) of ribosomal RNA (rRNA) gene with the MicroSEQ® Kit and the ITS regions with the in house developed assay. The generated sequenced data were analyzed with the online GenBank and MycoBank public databases.The D2 region of the LSU rRNA gene identified 89.4% or 92.9% of the 85 isolates to the genus level and the full ITS region (f-ITS) 96.5% or 100%, using GenBank or MycoBank, respectively, when compared to the consensus ID. When comparing species-level designations to the consensus ID, D2 region of the LSU rRNA gene aligned with 44.7% (38/85) or 52.9% (45/85) of these isolates in GenBank or MycoBank, respectively. By comparison, f-ITS possessed greater specificity, followed by ITS1, then ITS2 regions using GenBank or MycoBank. Using GenBank or MycoBank, D2 region of the LSU rRNA gene outperformed phenotypic based ID at the genus level. Comparing rates of ID between D2 region of the LSU rRNA gene and the ITS regions in GenBank or MycoBank at the species level against the consensus ID, f-ITS and ITS2 exceeded performance of the D2 region of the LSU rRNA gene, but ITS1 had similar performance to the D2 region of the LSU rRNA gene using MycoBank.Our results indicated that the MicroSEQ® D2 LSU rDNA Fungal Identification Kit was equivalent to the in-house developed ITS regions assay to identify fungi at the genus level. The MycoBank database gave a better curated database and thus allowed a better genus and species identification for both D2 region of the LSU rRNA gene and ITS regions.

  View details for DOI 10.1016/j.mimet.2017.06.015

  View details for PubMedID 28647582

• Immunolocalization on Whole Anther Chromosome Spreads for Male Meiosis. Methods in molecular biology (Clifton, N.J.) Dukowic-Schulze, S., Harris, A., Chen, C. 2016; 1429: 161-75

  Abstract

  Immunolocalization of cells undergoing meiosis has proven to be one of the most important tools to decipher chromatin-associated protein dynamics and causal relationships. Here, we describe a protocol established for maize which is easily adaptable to other plants, for example, with minor modifications to Arabidopsis as stated here. In contrast to many other protocols, the following protocol is based on fixation by a 3:1 mixture of ethanol and acetic acid. Spreading of cells is followed by freeze-shattering, protein antigenicity retrieval by a hot citrate buffer bath, antibody incubations and washes, and DNA staining.

  View details for DOI 10.1007/978-1-4939-3622-9_13

  View details for PubMedID 27511174

• Pasteurella multocida Bacteremia With Associated Knee Arthroplasty Infection in an 80-Year-Old Caucasian Man. Laboratory medicine Arbefeville, S., Harris, A., Dittes, S., Ferrieri, P. 2016; 47 (3): 241-5

  Abstract

  To identify the gram-negative rods grown from blood cultures and a right-knee fluid aspirate from an 80-year-old caucasian man who had undergone a total right knee arthroplastic procedure 6 years ago, and to assess the genetic similarity between the 2 isolates.We used 3 different approaches: biochemical testing, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry, and 16S ribosomal RNA (rRNA) gene sequencing.The 3 methods identified the gram-negative rods as Pasteurella multocida; 16S rRNA gene sequencing further identified the organisms as P. multocida subsp. septica.A concordant identification of P. multocida was observed using biochemical testing, mass spectrometry, and 16S rRNA gene sequencing. Only 16S rRNA sequencing was able to determine the subspecies of P. multocida and to determine the genetic relatedness of the 2 isolates.

  View details for DOI 10.1093/labmed/lmw034

  View details for PubMedID 27378482

  View details for PubMedCentralID PMC4985777

• Comparative transcriptomics of early meiosis in Arabidopsis and maize. Journal of genetics and genomics = Yi chuan xue bao Dukowic-Schulze, S., Harris, A., Li, J., Sundararajan, A., Mudge, J., Retzel, E. F., Pawlowski, W. P., Chen, C. 2014; 41 (3): 139-52

  Abstract

  Though sexually reproductive plants share the same principle and most processes in meiosis, there are distinct features detectable. To address the similarities and differences of early meiosis transcriptomes from the dicot model system Arabidopsis and monocot model system maize, we performed comparative analyses of RNA-seq data of isolated meiocytes, anthers and seedlings from both species separately and via orthologous genes. Overall gene expression showed similarities, such as an increased number of reads mapping to unannotated features, and differences, such as the amount of differentially expressed genes. We detected major similarities and differences in functional annotations of genes up-regulated in meiocytes, which point to conserved features as well as unique features. Transcriptional regulation seems to be quite similar in Arabidopsis and maize, and we could reveal known and novel transcription factors and cis-regulatory elements acting in early meiosis. Taken together, meiosis between Arabidopsis and maize is conserved in many ways, but displays key distinctions that lie in the patterns of gene expression.

  View details for DOI 10.1016/j.jgg.2013.11.007

  View details for PubMedID 24656234