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Series GSE94993 Query DataSets for GSE94993
Status Public on May 03, 2017
Title The cohesin release factor WAPL restricts chromatin loop extension. [RNA-Seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The spatial organization of chromosomes influences many nuclear processes including gene expression. The cohesin complex shapes the 3D genome by looping together CTCF sites along chromosomes. We show here that chromatin loop size can be increased, and that the duration with which cohesin embraces DNA determines the degree to which loops are enlarged. Cohesin’s DNA release factor WAPL restricts the degree of this loop extension and also prevents looping between incorrectly oriented CTCF sites. We reveal that the SCC2/SCC4 complex promotes the extension of chromatin loops and the formation of topologically associated domains (TADs). Our data support the model that cohesin structures chromosomes through the processive enlargement of loops and that TADs reflect polyclonal collections of loops in the making. Finally, we find that whereas cohesin promotes chromosomal looping, it rather limits nuclear compartmentalization. We conclude that the balanced activity of SCC2/SCC4 and WAPL enables cohesin to correctly structure chromosomes.
 
Overall design RNAseq was performed in control, ΔWAPL 3.3, ΔWAPL 1.14, ΔSCC4 and ΔWAPL/ΔSCC4 cells in triplicate.
 
Contributor(s) van der Weide RH, de Wit E
Citation(s) 28475897
Submission date Feb 16, 2017
Last update date May 15, 2019
Contact name Robin H. van der Weide
Organization name Hubrecht Institute
Lab Kind Lab
Street address Uppsalalaan 8
City Utrecht
State/province Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (18)
GSM2493886 Hap1 rep A1 RNAseq
GSM2493887 Hap1 rep A2 RNAseq
GSM2493888 Hap1 rep A3 RNAseq
This SubSeries is part of SuperSeries:
GSE95015 The cohesin release factor WAPL restricts chromatin loop extension.
Relations
BioProject PRJNA375741
SRA SRP100153

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
GSE94993_RAW.tar 1.5 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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