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Series GSE34518 Query DataSets for GSE34518
Status Public on Feb 01, 2012
Title Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ES cells (ChIP-Seq)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Polycomb repressor complexes (PRCs) are important chromatin modifiers fundamentally implicated in pluripotency and cancer. Polycomb silencing in embryonic stem cells (ESCs) can be accompanied by active chromatin and primed RNA polymerase II (RNAPII), but the relationship between PRCs and RNAPII remains unclear at the genome-wide level. We mapped PRC repression markers and four RNAPII states in ESCs using ChIP-seq, and found that PRC-targets exhibit a range of RNAPII variants. Firstly, developmental PRC-targets are bound by unproductive RNAPII (S5p+S7p- S2p-) genome-wide. Sequential ChIP, Ring1B-depletion and genome-wide correlations show that PRCs and RNAPII-S5p physically bind to the same chromatin and functionally synergize. Secondly, we identify a cohort of genes marked by PRC and elongating RNAPII (S5p+S7p+S2p+); they produce mRNA and protein, and their expression increases upon PRC1 knockdown. We show that this novel group of PRC-targets switch between active and PRC-repressed states within the ESC population, and that many have roles in metabolism.

**Correction (Mar 14, 2012):
Due to curation error, runs for SRX112177 and SRX112179 switched, specifically,
Run SRR391034.1 was removed from experiment SRX112177 (GSM850468) and added to experiment SRX112179 (GSM850470) as SRR391034.3
Run SRR391040.1 was removed from experiment SRX112179 (GSM850470) and added to experiment SRX112177 (GSM850468) as SRR391040.3
Overall design Examination of 4 different RNAPII modifications (S5p, S7p, 8WG16, S2p), and the histone modifications H2Aub1 and H3K36me3 in mouse ES cells
Contributor(s) de Santiago I, Brookes E, Pombo A
Citation(s) 22305566
Submission date Dec 17, 2011
Last update date May 15, 2019
Contact name Ines de Santiago
Phone +44 (0) 2083838526
Organization name MRC Clinical Sciences Centre
Department Epigenetics
Lab Genome Function
Street address Hammersmith Hospital Campus
City London
ZIP/Postal code W12 0NN
Country United Kingdom
Platforms (1)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (9)
GSM850469 RNAPII 8WG16 ChIPSeq
This SubSeries is part of SuperSeries:
GSE34520 Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ES cells
SRA SRP009883
BioProject PRJNA156325

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE34518_RAW.tar 4.5 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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