. The goal of this project is to define the interactions between RNA polymerase II, the basal transcription factors, and the chromatin template that lead to accurate transcription initiation and productive elongation. Using a combination of approaches in the yeast Saccharomyces cerevisiae model system, several fundamental aspects of gene expression will be studied. In the first specific aim, initiation and elongation complexes formed under various conditions will be purified on immobilized chromatin templates and then analyzed by quantitative mass spectrometry. It is possible some new factors associated with transcription complexes will be identified, but what is of greater interest is the exchange of factors that occur at various stages of transcription. Using various mutant or depleted extracts, factor interdependencies will be revealed. We will ask whether different activators recruit distinct co-activators, and how different promoters and transcribed sequences influence the associated proteins. The second specific aim will probe the function of the Set1/COMPASS complex, which methylates histone H3 at lysine 4 (H3K4). Methylation is co- transcriptional, and H3K4 trimethylation is strongest at the nucleosome nearest the transcription start site, while dimethylation predominates further downstream through the next few nucleosomes. We will explore how Set1/COMPASS is recruited to transcription complexes and how this gradient of methylation is achieved.
This aim will also address how levels of COMPASS are controlled. The third specific aim of this project will study the downstream effects of the co-transcriptional histone methylations at H3K4 and H3K36. We will continue our work on the Set3 histone deacetylase complex, which recognizes H3K4me2, and the Rpd3S histone deacetylase complex that recognizes H3K36me2/3. Preliminary data suggests that the Set3 complex strongly affects the kinetics of transcription induction and repression, and several molecular models to explain these effects will be tested. The role of H3K4me3 in recruiting various chromatin modifying complexes will also be explored. The experiments in these three specific aims will significantly increase our understanding of the RNA polymerase II transcription reaction and its interactions with the chromatin template. This fundamental knowledge is essential for understanding how mutations in transcription factors and histone modifying enzymes lead to diseases such as cancer and developmental defects.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM046498-23
Application #
8515442
Study Section
Molecular Genetics A Study Section (MGA)
Program Officer
Sledjeski, Darren D
Project Start
1991-07-06
Project End
2016-06-30
Budget Start
2013-07-01
Budget End
2014-06-30
Support Year
23
Fiscal Year
2013
Total Cost
$381,428
Indirect Cost
$156,397
Name
Harvard University
Department
Biochemistry
Type
Schools of Medicine
DUNS #
047006379
City
Boston
State
MA
Country
United States
Zip Code
02115
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Marquardt, Sebastian; Escalante-Chong, Renan; Pho, Nam et al. (2014) A chromatin-based mechanism for limiting divergent noncoding transcription. Cell 157:1712-23
Suh, Hyunsuk; Hazelbaker, Dane Z; Soares, Luis M et al. (2013) The C-terminal domain of Rpb1 functions on other RNA polymerase II subunits. Mol Cell 51:850-8
Soares, Luis M; Buratowski, Stephen (2013) Histone Crosstalk: H2Bub and H3K4 Methylation. Mol Cell 49:1019-20
Terzi, Nihal; Churchman, L Stirling; Vasiljeva, Lidia et al. (2011) H3K4 trimethylation by Set1 promotes efficient termination by the Nrd1-Nab3-Sen1 pathway. Mol Cell Biol 31:3569-83
Lenstra, Tineke L; Benschop, Joris J; Kim, Taesoo et al. (2011) The specificity and topology of chromatin interaction pathways in yeast. Mol Cell 42:536-49
Kim, TaeSoo; Buratowski, Stephen (2009) Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5'transcribed regions. Cell 137:259-72
Sikorski, Timothy W; Buratowski, Stephen (2009) The basal initiation machinery: beyond the general transcription factors. Curr Opin Cell Biol 21:344-51
Ahn, Seong Hoon; Keogh, Michael-Christopher; Buratowski, Stephen (2009) Ctk1 promotes dissociation of basal transcription factors from elongating RNA polymerase II. EMBO J 28:205-12
Johnson, Aaron; Li, Geng; Sikorski, Timothy W et al. (2009) Reconstitution of heterochromatin-dependent transcriptional gene silencing. Mol Cell 35:769-81

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