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Series GSE13084 Query DataSets for GSE13084
Status Public on Nov 01, 2008
Title Mapping polycomb complexes in human and mouse embryonic stem cells
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2000 genes. To gain insight into the structure and function of bivalent domains, we mapped key histone modifications and subunits of Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) genomewide in human and mouse ES cells by chromatin immunoprecipitation followed by ultra high-throughput sequencing. We find that bivalent domains can be segregated into two classes: the first occupied by both PRC2 and PRC1 (PRC1-positive) and the second specifically bound by PRC2 (PRC2-only). PRC1-positive bivalent domains appear functionally distinct as they more efficiently retain lysine 27 tri-methylation upon differentiation, show stringent conservation of chromatin state, and associate with an overwhelming number of developmental regulator gene promoters. We also used computational genomics to search for sequence determinants of Polycomb binding. This analysis revealed that the genomewide locations of PRC2 and PRC1 can be largely predicted from the locations, sizes and underlying motif contents of CpG islands. We propose that large CpG islands depleted of activating motifs confer epigenetic memory by recruiting the full repertoire of Polycomb complexes.

Keywords: cell type comparison
Overall design Suz12, Ezh2, Ring1b ChIP-Seq in singlicate from mouse embryonic stem (mES) cells. H3K4me3, H3K27me3, H3K36me3, Ezh2 and Ring1b ChIP-Seq in singlicate from human embyonic stem cells (hES; H9).
Contributor(s) Mikkelsen TS, Ku M, Koche RP, Rheinbay E, Cowan CA, Lander ES, Bernstein BE
Citation(s) 18974828
Submission date Oct 07, 2008
Last update date May 15, 2019
Contact name Tarjei S Mikkelsen
Organization name Broad Institute
Street address 7 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platforms (2)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
GPL9185 Illumina Genome Analyzer (Mus musculus)
Samples (8)
GSM327662 hES_H3K4me3_ChIPSeq
GSM327663 hES_H3K27me3_ChIPSeq
GSM327664 hES_H3K36me3_ChIPSeq
SRA SRP000711
BioProject PRJNA110911

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE13084_RAW.tar 3.3 Gb (http)(custom) TAR (of TXT)
GSE13084_README.aligned.txt 439 b (ftp)(http) TXT
GSE13084_README.densities.txt 705 b (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available on Series record
Raw data are available in SRA

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