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Series GSE102884 Query DataSets for GSE102884
Status Public on Dec 07, 2017
Title Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL and PDS5 proteins
Organism Homo sapiens
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Summary Mammalian genomes are organized into compartments, topologically-associating domains (TADs) and loops to facilitate gene regulation and other chromosomal functions. Compartments are formed by nucleosomal interactions, but how TADs and loops are generated is unknown. It has been proposed that cohesin forms these structures by extruding loops until it encounters CTCF, but direct evidence for this hypothesis is missing. Here we show that cohesin suppresses compartments but is essential for TADs and loops, that CTCF defines their boundaries, and that WAPL and its PDS5 binding partners control the length of chromatin loops. In the absence of WAPL and PDS5 proteins, cohesin passes CTCF sites with increased frequency, forms extended chromatin loops, accumulates in axial chromosomal positions (vermicelli) and condenses chromosomes to an extent normally only seen in mitosis. These results show that cohesin has an essential genome-wide function in mediating long-range chromatin interactions and support the hypothesis that cohesin creates these by loop extrusion, until it is delayed by CTCF in a manner dependent on PDS5 proteins, or until it is released from DNA by WAPL.
 
Overall design Analysis of chromatin structure by HiC and ChIP-Seq upon RNAi depletion and auxin-inducible degron (AID) systems.
 
Contributor(s) Stocsits RR, Wutz G
Citation(s) 29217591
Submission date Aug 21, 2017
Last update date May 15, 2019
Contact name Roman R Stocsits
E-mail(s) roman.stocsits@imp.ac.at
Organization name IMP - Research Institute of Molecular Pathology
Lab Jan Michael Peters' Lab
Street address Campus-Vienna-Biocenter 1
City Vienna
ZIP/Postal code 1030
Country Austria
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (30)
GSM2747738 Hi-C: G1 control sync.
GSM2747739 Hi-C: Wapl RNAi
GSM2747740 Hi-C: Pds5SA/B RNAi
Relations
BioProject PRJNA399157
SRA SRP115913

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

Supplementary file Size Download File type/resource
GSE102884_RAW.tar 11.9 Gb (http)(custom) TAR (of HIC, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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