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 are known to 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 main 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.

 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 (Figure 1).

Figure 1

Determining how these events are coordinated is essential to understanding gene expression mechanisms. Our research exploits the powerful genetic systems of budding yeast to examine the function of a complex proposed 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. Mutations in subunits of this complex cause altered DNA damage checkpoint functions, impaired cell cycle progression, and sensitivity to stress. The human orthologues of these proteins are putative oncogenes and have been implicated in regulating hepatitis C virus replication in human cells; thus, understanding the function of this complex is directly relevant to human disease. 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 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 2). 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.

 How RNA Polymerase II contends with barriers throughout the genome 

Transcription of a gene requires the movement of RNA polymerase II (RNAPII) across many thousands of bases in the genome. Throughout the elongation process, RNAPII encounters many barriers to transcription, including DNA damage and nucleosomes. Elongation factors assist RNAPII in transcribing through chromatin and transcription blocks, and completion of transcription across genes requires the coordinated actions of elongation factors and enzymes that remodel chromatin ahead of RNAPII. We are analyzing the pathways that allow RNAPII to navigate the chromatinized genome and how the transcription process aids in the modification of nucleosomes (Figure 3). Using highly purified factors and reconstitution biochemistry, we can monitor the movement of RNAPII and assembly and disassembly of elongation complexes to gain mechanistic insights into how cellular factors promote transcription elongation. 

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

• 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.
   
• Dutta, A., V. Babbarwal, J. Fu, D Brunke-Reese, D.M. Libert, J. Willis and J.C. Reese (2015) Ccr4-Not and TFIIS function cooperatively to rescue arrested RNA polymerase II. Mol. Cell Biol, 35:1915-1925.
   
• Babbarwal, V., J. Fu and J.C. Reese (2014). The Rpb4/7 module of RNA polymerase II is required for Carbon Catabolite Repressor Protein 4-Negative on TATA (Ccr4-Not) complex to promote elongation . J. Biol. Chem., 289:33125-30.