The overall objective of our research is to determine how chromosome structure affects gene expression and how the transcription machinery contends with this structure. Our general strategy has been to focus on an evolutionarily conserved protein complex, SWI/SNF, which is required for expression of a subset of yeast genes and for the activity of several transcriptional activators. Genetic studies in yeast indicate that SWI/SNF facilitates transcription by antagonizing chromatin-mediated transcriptional repression, and our in vitro studies indicate that the ~1 Mda SWI/SNF complex can use the energy derived from ATP hydrolysis to mobilize nucleosomes and disrupt nucleosome structure. Our recent work indicates that SWI/SNF may be unique among remodeling enzymes as its action can disrupt compact heterochromatin, promoting homologous recombination. This proposal continues to exploit the powerful genetic and biochemical opportunities available in yeast to investigate the role of SWI/SNF in vivo and the biochemical mechanism by which SWI/SNF disrupts euchromatic and heterochromatic structures in vitro. Our first objective will dissect the biochemical mechanism by which SWI/SNF remodels heterochromatin structures, including experiments that test whether SWI/SNF contains a unique subunit that interacts with heterochromatin components. In our second objective we will investigate whether SWI/SNF plays a general role in heterochromatin dynamics in vivo. We propose to test if SWI/SNF disrupts the spurious assembly of heterochromatic structures at euchromatic loci, and whether SWI/SNF facilitates Ty5 transposition into heterochromatin. Our third objective will investigate the role of DNA sequence and histone acetylation in regulating the type of remodeling produced due to SWI/SNF action.
This aim i nvolves chromatin biochemistry and single molecule approaches. In our fourth aim, we propose to investigate the structure of SWI/SNF and SWI/SNF- nucleosome complexes by EM methodologies. These studies also involve imaging of complexes that harbor subunit-GFP fusions to map locations of SWI/SNF subunits within the obtained structures.

Public Health Relevance

This proposal describes research that is focused on how chromosome structure affects gene expression and how the normal cellular machinery contends with this structure. Specifically, we propose continued studies on a novel protein machine, SWI/SNF, that facilitates transcription by remodeling chromosome structure. This machine is essential for mammalian development, and its inactivation leads to a variety of cancers.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Method to Extend Research in Time (MERIT) Award (R37)
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Special Emphasis Panel (NSS)
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Carter, Anthony D
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University of Massachusetts Medical School Worcester
Other Basic Sciences
Schools of Medicine
United States
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Watanabe, Shinya; Peterson, Craig L (2016) Response to Comment on ""A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme"". Science 353:358
Krietenstein, Nils; Wal, Megha; Watanabe, Shinya et al. (2016) Genomic Nucleosome Organization Reconstituted with Pure Proteins. Cell 167:709-721.e12
Yu, Lijian; Rege, Mayuri; Peterson, Craig L et al. (2016) RNA polymerase II depletion promotes transcription of alternative mRNA species. BMC Mol Biol 17:20
Watanabe, Shinya; Tan, Dongyan; Lakshminarasimhan, Mahadevan et al. (2015) Structural analyses of the chromatin remodelling enzymes INO80-C and SWR-C. Nat Commun 6:7108
Rege, Mayuri; Subramanian, Vidya; Zhu, Chenchen et al. (2015) Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis. Cell Rep 13:1610-22
Jeronimo, CĂ©lia; Watanabe, Shinya; Kaplan, Craig D et al. (2015) The Histone Chaperones FACT and Spt6 Restrict H2A.Z from Intragenic Locations. Mol Cell 58:1113-23
Xue, Yong; Van, Christopher; Pradhan, Suman K et al. (2015) The Ino80 complex prevents invasion of euchromatin into silent chromatin. Genes Dev 29:350-5
Swygert, Sarah G; Peterson, Craig L (2014) Chromatin dynamics: interplay between remodeling enzymes and histone modifications. Biochim Biophys Acta 1839:728-36
Manning, Benjamin J; Peterson, Craig L (2014) Direct interactions promote eviction of the Sir3 heterochromatin protein by the SWI/SNF chromatin remodeling enzyme. Proc Natl Acad Sci U S A 111:17827-32
Watanabe, Shinya; Peterson, Craig L (2013) Chromatin dynamics: flipping the switch on a chromatin remodeling machine. Cell Cycle 12:2337-8

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