|
| Status |
Public on Jan 10, 2011 |
| Title |
Lamin binding profiles in the ENCODE regions |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
|
| Summary |
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.
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| |
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| Overall design |
ChIP-chip analysis of lamin A/C and lamin B in HeLa S3 cells
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| |
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| Contributor(s) |
Euskirchen GM, Auerbach RK, Davidov E, Gianoulis TA, Rozowsky J, Zhong G, Bhardwaj N, Gerstein MB, Snyder MP |
| Citation(s) |
21408204 |
| |
| Submission date |
Sep 27, 2010 |
| Last update date |
Mar 22, 2012 |
| Contact name |
Ghia Euskirchen |
| E-mail(s) |
ghia.euskirchen@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Lab |
Snyder
|
| Street address |
1501 S. California Ave.
|
| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94304 |
| Country |
USA |
| |
|
| Platforms (1) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE24398 |
Diverse roles and interactions of the SWI/SNF chromatin-remodeling complex revealed using global approaches |
|
| Relations |
| BioProject |
PRJNA133473 |
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