The regulation of gene expression is a fundamental process in cells, and alterations in this process have been linked to numerous disease states in humans. It is regulated at multiple levels, and determining how these events are coordinated is central to understanding gene expression. The yeast Ccr4-Not complex was originally described as a regulator of the general transcription factor TFIID. Remarkably, it has now been implicated in multiple aspects of gene regulation including mRNA degradation, translational silencing, histone methylation and protein ubiquitylation. Its myriad of functions is quite fascinating and suggests it regulates gene expression from the birth to death of a gene product. Our study of TFIID and DNA damage inducible genes led us to characterize this complex, as it appears to play a role in regulating DNA damage stress responses. Over the last funding period we established it as a bona-fide elongation factor that directly activates arrested RNA polymerase II (RNAPII). Interestingly, Ccr4-Not appears to function via a mechanism unique from other elongation factors characterized to date;thus, analyzing its function has the potential to reveal novel insights into how factors regulate RNAPII. We have a developed a number of powerful assays to fully exploit the biochemistry, powerful genetics and genomics of yeast to characterize its mechanism of action and the role it plays in gene expression in vivo. The goals of the studies described in this proposal are to investigate the structure of arrested elongation complexes bound by Ccr4-Not to gain a greater understanding of how it promotes elongation;to explore its collaboration with other elongation factors to regulate RNAPII activity;to analyze the physiological functions of the complex in vivo by mapping changes in RNAPII arrest across the genome in Ccr4-Not mutants. The long term goals of this project are to understand how this multi-functional complex regulates multiple steps in gene regulation to maintain normal development and the integrity of the genome in eukaryotic cells.
Numerous human diseases and syndromes are caused by disturbances in gene expression. A multitude of transcription factors coordinate their activities to regulate this important process. The goal of the work described here is to understand how a multi-functional transcription factor complex, Ccr4-Not, controls gene expression. This complex has been implicated in DNA damage resistance, cell proliferation and cardiovascular development;thus, the work described here is directly relevant to human health.!
|Miller, Jason E; Zhang, Liye; Jiang, Haoyang et al. (2018) Genome-Wide Mapping of Decay Factor-mRNA Interactions in Yeast Identifies Nutrient-Responsive Transcripts as Targets of the Deadenylase Ccr4. G3 (Bethesda) 8:315-330|
|Crickard, John B; Lee, Jaehyoun; Lee, Tae-Hee et al. (2017) The elongation factor Spt4/5 regulates RNA polymerase II transcription through the nucleosome. Nucleic Acids Res 45:6362-6374|
|Crickard, J Brooks; Fu, Jianhua; Reese, Joseph C (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 Chem 291:9853-70|
|Dutta, Arnob; Babbarwal, Vinod; Fu, Jianhua et al. (2015) Ccr4-Not and TFIIS Function Cooperatively To Rescue Arrested RNA Polymerase II. Mol Cell Biol 35:1915-25|
|Zheng, Suting; Crickard, J Brooks; Srikanth, Abhinaya et al. (2014) A highly conserved region within H2B is important for FACT to act on nucleosomes. Mol Cell Biol 34:303-14|
|Collart, Martine A; Reese, Joseph C (2014) Gene expression as a circular process: cross-talk between transcription and mRNA degradation in eukaryotes; International University of Andalusia (UNIA) Baeza, Spain. RNA Biol 11:320-3|
|Babbarwal, Vinod; Fu, Jianhua; Reese, Joseph C (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|
|Reese, Joseph C (2013) The control of elongation by the yeast Ccr4-not complex. Biochim Biophys Acta 1829:127-33|
|Bhargava, Purnima; Reese, Joseph C (2013) Transcription by Odd Pols. Biochim Biophys Acta 1829:249-50|
|Miller, Jason E; Reese, Joseph C (2012) Ccr4-Not complex: the control freak of eukaryotic cells. Crit Rev Biochem Mol Biol 47:315-33|
Showing the most recent 10 out of 32 publications