Joseph C. Reese

About Me

Joseph Reese obtained his B.A. in Biology from Boston University, where he conducted research on steroid hormone receptors in subavian species. He obtained in Ph.D. in Molecular Physiology from the University of Illinois Champaign-Urbana studying the molecular actions of estrogen agonists and antagonists. He was a Damon Runyon Walter Winchell Cancer Research Fund postdoctoral fellow at U Massachusetts Medical Center-HHMI with Michael Green. As a postdoc he discovered and characterized yeast TBP-associated factors. He joined the faculty in 1997. 

Program or Departmental Affiliations

Centers

Research Summary

Stress-induced gene expression and UV resistance pathways

The accumulation of genetic and cellular damage can result in uncontrolled cell proliferation and diseases such as cancer. Eukaryotic cells respond to these challenges by activating DNA damage sensing, signaling, and repair pathways that are stimulated by damage to DNA and other stresses. Activation of these pathways causes the execution of cell cycle delays, referred to as checkpoints, and the expression of DNA repair genes. Alterations in these functions predispose people to cancer and other diseases. Our laboratory uses a combination of biochemistry, genetics, genomics, and molecular biology to study the mechanisms controlling stress-induced changes in gene expression in eukaryotes. The two focus areas of the lab are the role of transcription and mRNA decay factors in regulating the DNA damage response and the control of transcription elongation by protein complexes and chromatin. We use both the powerful genetic system of budding yeast and mammalian cells to study these processes.

 Regulation of mRNAs from birth to death during stress responses

Gene expression is controlled at multiple levels, requiring highly organized and integrated events, including chromatin remodeling, initiation, elongation, processing, transport, and, ultimately the destruction of mRNA. Determining how these events are coordinated is essential to understanding gene expression mechanisms. Our research focuses on a complex that integrates stress signals to perform multiple steps in gene regulation: the Ccr4-Not complex. The Ccr4-Not complex is highly conserved across the eukaryotic kingdom. Initially purposed to be a nuclear transcription regulatory complex in yeast, it has since been identified as the major mRNA deadenylase in the cytoplasm and implicated in protein destruction and micro RNA (miRNA) mediated gene repression (Figure 1). Mutations in subunits of this complex cause altered DNA damage checkpoint functions, impaired cell cycle progression, and sensitivity to stress. The complex also has been implicated in brain and heart development. Our goals are to (1) uncover how multiple steps in gene expression are coordinated and regulated; (2) define the functions of Ccr4-Not in gene regulation; (3) identifying how specific mRNAs are marked for post-transcriptional control during stress responses.

Targeted protein degradation during transcriptional stress
The Not4 (cNOT4 in human) subunit of the Ccr4-Not complex is an E3 RING domain-containing protein that promotes the covalent attachment of ubiquitin onto proteins. Ubiquitylation of protein can change protein activity or target it for degradation by the proteasome. Ccr4-Not travels with elongating RNA polymerase II (RNAPII) to prevent arrest, and we recently have shown it is involved in the ubiquitylation and degradation of RNAPII arrested over DNA lesions (Figure 1). It is likely Not4 ubiquitylates other proteins associated with the RNAPII elongation complex. We are currently utilizing genetics, molecular biology, cell imaging, and proteomics to identify novel Not4 substrates and determine the consequences of this modification on transcription and DNA repair.

Functions of the human Ccr4-Not complex. 

The subunits of the Ccr4-Not complex, first identified in yeast, is conserved across all eukaryotes. Some gene regulation pathways, such as miRNA control of mRNAs and heterochromatin formation, are not present in budding yeast. Thus, new functions of the human Ccr4-Not (hCccr4-Not) complex are yet to be discovered. Characterization of hCcr4-Not lags behind its yeast counterpart. Advances in CRISPR-Cas9 gene editing capabilities provide an opportunity to characterize the functions of hCcr4-Not thoroughly. We use gene editing technologies to deplete and modify hCcr4-Not subunit genes, followed by multi-omics approaches to analyze the functions of hCcr4-Not in gene expression control, cell cycle regulation, and DNA damage responses.

Funding:

Sponsor:       National Institutes of Health; NIGMS; MIRA, R35 GM136353 

Title:               “Activities of yeast Ccr4-Not transcription factor complex”

Sponsor:       National Institutes of Health; NIGMS; T32 GM125592

Title:               “Eukaryotic Gene Regulation Predoctoral Training Program”

Honors and Awards

• Fellow, American Association for the Advancement of Science (elected 2015)
   
• Howard B. Palmer Faculty Mentoring Award 
   
• Established Investigator of the American Heart Association, National Program
   
• Damon Runyon-Walter Winchell Cancer Research Fund Postdoctoral Fellow 

Selected Publications

• Oluwasegun T Akinniyi, Shardul Kulkarni, Mikayla M Hribal, Cheryl A Keller, Belinda Giardine, Joseph C. Reese (2024) The DNA damage response and RNA Polymerase II regulator Def1 has posttranscriptional functions in the cytoplasm. bioRxiv 2024.09.16.613278; doi: https://doi.org/10.1101/2024.09.16.613278

  Shardul Kulkarni, Alexis Morrissey, Aswathy Sebastian, Cheryl A Keller, Belinda Giardine, Courtney Smith, OluwasegunT Akinniyi, Alexei Arnaoutov, Istvan Albert, Shaun Mahony, Joseph C. Reese (2024) Human CCR4-NOT is a global regulator of gene expression and is a novel silencer of retrotransposon activation. bioRxiv 2024.09.10.612038; doi: https://doi.org/10.1101/2024.09.10.612038

• Pfannenstein J, Tyryshkin M, Gulden ME, Doud EH, Mosley AL, Reese JC. (2024) Characterization of BioID tagging systems in budding yeast and exploring the interactome of the Ccr4-Not complex. G3 (Bethesda). 2024 Sep 13:jkae221. doi: 10.1093/g3journal/jkae221. PMID: 39271111
• Reese, J.C. (2023) New roles for elongation factors in RNA polymerase II ubiquitylation and degradation. BBA- Gene Regulatory Mechanisms.  Jun 16:194956
• Akinniyi,  O.T. and Reese, J.C. (2021). Def1: Much more than an RNA polymerase degradation factor. DNA Repair 107:103202 
• Huynh, M., Yadav, S.,  Reese, J.C. and T-H Lee (2020). Nucleosome dynamics     during transcription elongation.  ACS Chem Biol. 15:3133-3142
• Jiang, H., M. Wolgast, L.M. Beebe and J.C. Reese (2019). Ccr4-Not maintains genomic integrity by controlling the ubiquitylation and degradation of arrested RNAPII. Genes and Development 33:705-717.
• Crickard, J.B. and J.C. Reese (2019). Biochemical Methods to Characterize RNA Polymerase II Elongation Complexes. Methods S1046-2023:30296-2.
• Miller, J.E., L. Zhang, H. Jiang, Y. Li, B.F. Pugh and J.C. Reese (2018). Genome-Wide Mapping of Decay Factor-mRNA Interactions in Yeast Identifies Nutrient Responsive Transcripts as Targets of the Deadenylase Ccr4. G3 8:315-330.
• Crickard, J.B. , Lee, J, Lee, T-H and Reese, J.C.  (2017). The elongation factor Spt4/5 regulates RNA polymerase II transcription through the nucleosome. Nucleic Acids Research, 45:6362-6374.
• Crickard, J.B., J. Fu and J.C. Reese. (2016). Biochemical Analysis of Yeast Suppressor of Ty 4/5 (Spt4/5) Reveals the Importance of Nucleic Acid Interactions in the Prevention of RNA Polymerase II Arrest J. Biol. Chemistry 291, 9853-9870.
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