The ATP-dependent chromatin remodeler SWI/SNF regulates transcription and DNA recombination by making DNA more accessible. The objective of this study is to find the mechanism used by SWI/SNF to move and disassemble nucleosomes. Nucleosome remodeling will be examined at two levels: changes in histone- DNA interactions and the corresponding changes in the interactions of SWI/SNF with histones and DNA. Ultimately the goal is to correlate these two different sets of interactions with each other in a temporal manner to provide an unprecedented view of the process of nucleosome remodeling. We propose to apply the relatively new technology of an expanded genetic code to site-specifically incorporate a photoreactive amino acid analog for examining protein-protein and protein-DNA interactions both in vivo and in vitro. Domains in the catalytic subunit of SWI/SNF other than the ATPase domain will be systematically studied with the basic premise that these domains make critical contributions to mobilizing nucleosomes in coordination and cooperation with the ATPase domain. Several domains have already been identified that are necessary for SWI/SNF remodeling. Single molecule magnetic tweezer and DNA unwinding optical trap type experiments will be done to determine if these domains are important for DNA translocation and nucleosome remodeling. The effect of histone H3 acetylation on SWI/SNF remodeling will be examined to determine at which stage in remodeling it modulates the activity of SWI/SNF and RSC. SWI/SNF has many important regulatory roles such as in stem cell self renewal, cellular differentiation, chromatin maintenance and stability, and oncogenesis. While the yeast system has provided us with important insights as to how this enzyme functions and the corresponding models, there still remain many questions as to how SWI/SNF regulates chromatin structure. In this proposal we continue to take advantage of the yeast system to examine these questions at a biophysical, biochemical, and molecular genetic level.

Public Health Relevance

. SWI/SNF is involved in regulation of transcription and DNA repair. Often mutations in SWI/SNF are associated with the onset of cancer and several of the proteins in SWI/SNF are from known tumor suppressor genes. We are investigating the mechanism of SWI/SNF that is used to regulate the epigenome and how it regulates chromatin structure and function.

Agency
National Institute of Health (NIH)
Type
Research Project (R01)
Project #
5R01GM048413-21
Application #
8681461
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Carter, Anthony D
Project Start
Project End
Budget Start
Budget End
Support Year
21
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of Texas MD Anderson Cancer Center
Department
Internal Medicine/Medicine
Type
Overall Medical
DUNS #
City
Houston
State
TX
Country
United States
Zip Code
77030
Harada, Bryan T; Hwang, William L; Deindl, Sebastian et al. (2016) Stepwise nucleosome translocation by RSC remodeling complexes. Elife 5:
Prasad, Rashmi; D'Arcy, Sheena; Hada, Arjan et al. (2016) Coordinated Action of Nap1 and RSC in Disassembly of Tandem Nucleosomes. Mol Cell Biol 36:2262-71
Chatterjee, Nilanjana; North, Justin A; Dechassa, Mekonnen Lemma et al. (2015) Histone Acetylation near the Nucleosome Dyad Axis Enhances Nucleosome Disassembly by RSC and SWI/SNF. Mol Cell Biol 35:4083-92
Kim, Sang-Ah; Chatterjee, Nilanjana; Jennings, Matthew J et al. (2015) Extranucleosomal DNA enhances the activity of the LSD1/CoREST histone demethylase complex. Nucleic Acids Res 43:4868-80
Kapoor, Prabodh; Bao, Yunhe; Xiao, Jing et al. (2015) Regulation of Mec1 kinase activity by the SWI/SNF chromatin remodeling complex. Genes Dev 29:591-602
Bartholomew, Blaine (2014) Regulating the chromatin landscape: structural and mechanistic perspectives. Annu Rev Biochem 83:671-96
Sen, Payel; Vivas, Paula; Dechassa, Mekonnen Lemma et al. (2013) The SnAC domain of SWI/SNF is a histone anchor required for remodeling. Mol Cell Biol 33:360-70
Hota, Swetansu K; Bhardwaj, Saurabh K; Deindl, Sebastian et al. (2013) Nucleosome mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains. Nat Struct Mol Biol 20:222-9
Dechassa, Mekonnen Lemma; Hota, Swetansu K; Sen, Payel et al. (2012) Disparity in the DNA translocase domains of SWI/SNF and ISW2. Nucleic Acids Res 40:4412-21
Chatterjee, Nilanjana; Sinha, Divya; Lemma-Dechassa, Mekonnen et al. (2011) Histone H3 tail acetylation modulates ATP-dependent remodeling through multiple mechanisms. Nucleic Acids Res 39:8378-91

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