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, requiring highly coordinated and integrated events including chromatin remodeling, initiation, elongation, processing and ultimately the destruction of mRNA. Determining how these events are coordinated is central to understanding gene expression. The overall objective of this proposal is to understand how transcription factor complexes coordinate multiple steps in gene regulation. This proposal will examine the functions of the Ccr4-Not complex, exploiting the powerful genetic system of yeast. The Ccr4-Not complex has many ties to the general transcription factor complex TFIID, particularly the TAFII subunits. Genetic, biochemical and molecular approaches are proposed.
Aim 1 will characterize the functions of the Ccr4- Not transcription complex in the process of transcription. This complex displays multiple physical and genetic links to TFIID, the general transcription machinery and elongation factors. Its role in multiple stages in the transcription cycle will be examined using RNR3 as a model gene.
Aim 2 will identify the targeting mechanism for Ccr4-Not. It regulates a subset of genes, and appears not be universally required for all transcription in the cell. We will explore the DNA sequence and transcription factor requirements for its recruitment and function at RNR3.
Aim 3 will employ genomics based approaches to identify novel Ccr4-Not dependent genes and identify the features of the genome that specifies regulation by this complex. The intersection of these approaches will allow for a greater understanding of the coordination of multiple steps in transcription. The completion of these aims will: (1) uncover how multiple steps in gene expression are coordinated and regulated;(2) define the functions of a highly conserved eukaryotic transcription factor complex implicated in human disease;(3) lay the groundwork for identifying how specific mRNAs are marked for post-transcriptional control. Project Narrative - Relevance: Cells require precise control over the expression of their genes, and 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 transcription factors control the level of gene expression;thus, completion of this work is directly relevant to human health.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Molecular Genetics A Study Section (MGA)
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Tompkins, Laurie
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Pennsylvania State University
Schools of Arts and Sciences
University Park
United States
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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
Dutta, Arnob; Zheng, Suting; Jain, Deepti et al. (2011) Intermolecular interactions within the abundant DEAD-box protein Dhh1 regulate its activity in vivo. J Biol Chem 286:27454-70

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