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| Status |
Public on Dec 23, 2011 |
| Title |
Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells |
| Project |
ENCODE
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| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Hundreds of Chromatin Regulators (CRs) control chromatin structure and function by catalyzing and binding histone modifications, yet the rules governing these key processes remain obscure. Here, we present a systematic approach to infer CR function. We developed ChIP-string, a meso-scale assay that combines chromatin immunoprecipitation with a signature readout of 487 representative loci. We applied ChIP-string to screen 145 antibodies, thereby identifying effective reagents, which we used to map the genome-wide binding of 29 CRs in two cell types. We found that specific combinations of CRs co-localize in characteristic patterns at distinct chromatin environments, genes of coherent functions and distal regulatory elements. When comparing between cell types, CRs redistribute to different loci, but maintain their modular and combinatorial associations. Our work provides a multiplex method that substantially enhances the ability to monitor CR binding, presents a large resource of CR maps, and reveals common principles for combinatorial CR function.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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| Overall design |
Study of genom-wide binding of 29 CRs in two cell types.
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| Contributor(s) |
Ram O, Goren A, Bernstein BE |
| Citation(s) |
22196736 |
| BioProject |
PRJNA63443 |
| Submission date |
Sep 30, 2011 |
| Last update date |
Nov 19, 2022 |
| Contact name |
Kevin Dong |
| Organization name |
Dana-Farber Cancer Institute
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| Street address |
360 Longwood Ave
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| City |
Boston |
| State/province |
MASSACHUSETTS |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
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| Samples (59)
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| Relations |
| SRA |
SRP010385 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE32509_RAW.tar |
38.2 Gb |
(http)(custom) |
TAR (of BED, BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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