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Series GSE78826 Query DataSets for GSE78826
Status Public on Mar 21, 2016
Title The cohesin associated protein Wapal is required for proper polycomb-mediated gene silencing [Ring1b ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The cohesin complex consists of multiple core subunits that play critical roles in mitosis and transcriptional regulation. The cohesin-associated protein Wapal plays a central role in offloading cohesin to facilitate sister chromatid separation, but its role in regulating mammalian gene expression is not understood. We used embryonic stem cells (ESCs) as a model given the well-defined transcriptional regulatory circuits established through master transcription factors and epigenetic pathways that regulate their ability to maintain a pluripotent state. RNAi-mediated depletion of Wapal causes a loss of pluripotency, phenocopying loss of core cohesin subunits. Using chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) we determine that Wapal occupies genomic sites distal to genes in combination with CTCF and core cohesin subunits such as Rad21. Interestingly, genomic sites occupied by Wapal appear enriched for cohesin, implying Wapal does not offload cohesin at regions it occupies. Wapal depletion induces derepression of Polycomb Group (PcG) target genes without altering total levels of Polycomb-mediated histone modifications, implying that PcG enzymatic activity is preserved. By integrating ChIP-seq and gene expression changes data we identify that Wapal binding is enriched at the promoters of PcG silenced genes and is required for proper Polycomb Repressive Complex 2 (PRC2) recruitment. Lastly, we demonstrate that Wapal is required for the interaction of a distal cis-regulatory element (CRE) with the ­c-Fos promoter. Collectively, this work indicates that Wapal plays a critical role in silencing of PcG target genes through the interaction of distal CREs with promoters.
Overall design ChIP-seq for Ring1b, before or after depletion of Wapal by RNAi
Contributor(s) Rao S
Citation(s) 27087855
Submission date Mar 02, 2016
Last update date May 15, 2019
Contact name Sridhar Rao
Phone 4149373841
Organization name BloodCenter of Wisconsin
Department Blood Research Institute
Street address 8727 Watertown Plank Road
City Milwaukee
State/province WI
ZIP/Postal code 53226
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (20)
GSM2078257 Wapal shRNA#1-1
GSM2078258 Wapal shRNA#1-2
GSM2078259 Wapal shRNA#1-3
This SubSeries is part of SuperSeries:
GSE63325 The cohesin associated factor Wapal is required for proper polycomb-mediated gene silencing
BioProject PRJNA314075
SRA SRP071063

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Supplementary file Size Download File type/resource
GSE78826_EMPTYVECTOR_RING1B_VS_BothINPUT_normalized.wig.gz 252.9 Mb (ftp)(http) WIG
GSE78826_W_RING1B_VS_BOTHINPUT_normalized.wig.gz 297.8 Mb (ftp)(http) WIG
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Raw data are available in SRA
Processed data are available on Series record

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