Genomics

Dataset Information

297

Genome-wide profile of the SWI/SNF chromatin remodeling complex


ABSTRACT: A systems understanding of nuclear organization and events is critical for determining how cells divide, differentiate and respond to stimuli and for identifying the causes of diseases. Chromatin remodeling complexes such as SWI/SNF have been implicated in a wide variety of cellular processes including gene expression, nuclear organization, centromere function and chromosomal stability, and mutations in SWI/SNF components have been linked to several types of cancer. To better understand the biological processes in which chromatin remodeling proteins participate we globally mapped binding regions for several components of the SWI/SNF complex throughout the human genome using ChIP-Seq. SWI/SNF components were found to lie near regulatory elements integral to transcription (e.g. 5’ ends, RNA Polymerases II and III and enhancers) as well as regions critical for chromosome organization (e.g. CTCF, lamins and DNA replication origins). To further elucidate the association of SWI/SNF subunits with each other as well as with other nuclear proteins we also analyzed SWI/SNF immunoprecipitated complexes by mass spectrometry. Individual SWI/SNF factors are associated with their own family members as well as with cellular constituents such as nuclear matrix proteins, key transcription factors and centromere components implying a ubiquitous role in gene regulation and nuclear function. We find an overrepresentation of both SWI/SNF-associated regions and proteins in cell cycle and chromosome organization. Taken together the results from our ChIP and immunoprecipitation experiments suggest that SWI/SNF facilitates gene regulation and genome function more broadly and through a greater diversity of interactions than previously appreciated. ChIP-Seq analysis of the SWI/SNF subunits Ini1, Brg1, BAF155 and BAF170 in HeLa S3 cells

ORGANISM(S): Homo sapiens  

SUBMITTER: Joel Rozowsky   Michael P Snyder  Raymond K Auerbach  Mark B Gerstein  Tara A Gianoulis  Ghia Euskirchen  Guoneng Zhong  Ghia M Euskirchen  Nitin Bhardwaj  Eugene Davidov 

PROVIDER: E-GEOD-24397 | ArrayExpress | 2011-01-10

SECONDARY ACCESSION(S): SRP003634GSE24397PRJNA133475

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches.

Euskirchen Ghia M GM   Auerbach Raymond K RK   Davidov Eugene E   Gianoulis Tara A TA   Zhong Guoneng G   Rozowsky Joel J   Bhardwaj Nitin N   Gerstein Mark B MB   Snyder Michael M  

PLoS genetics 20110303 3


A systems understanding of nuclear organization and events is critical for determining how cells divide, differentiate, and respond to stimuli and for identifying the causes of diseases. Chromatin remodeling complexes such as SWI/SNF have been implicated in a wide variety of cellular processes including gene expression, nuclear organization, centromere function, and chromosomal stability, and mutations in SWI/SNF components have been linked to several types of cancer. To better understand the bi  ...[more]

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