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Series GSE104888 Query DataSets for GSE104888
Status Public on Oct 13, 2017
Title Cohesin loss eliminates all loop domains [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The human genome folds to create thousands of intervals, called “contact domains,” that exhibit enhanced contact frequency within themselves. “Loop domains” form because of tethering between two loci – almost always bound by CTCF and cohesin – lying on the same chromosome. “Compartment domains” form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loss of loop domains does not lead to widespread ectopic gene activation, but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes, and affecting the regulation of nearby genes. We then restore cohesin and monitor the re-formation of each loop. Although re-formation rates vary greatly, many megabase-sized loops recovered in under an hour, consistent with a model where loop extrusion is rapid.
 
Overall design we use in situ Hi-C, ChIP-Seq and PRO-Seq to probe nuclear architecture, the epigenome and transcription during cohesin loss and recovery
 
Contributor(s) Rao S, Aiden EL
Citation(s) 28985562
Submission date Oct 12, 2017
Last update date May 15, 2019
Contact name Suhas Rao
E-mail(s) suhasrao@post.harvard.edu
Organization name Baylor College of Medicine
Department Molecular and Human Genetics
Lab The Center for Genome Architecture
Street address 1 Baylor Plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (39)
GSM2809609 Rao-2017-CHIP001-RAD21-untreated
GSM2809610 Rao-2017-CHIP002-RAD21-treated
GSM2809611 Rao-2017-CHIP003-SMC1-untreated
This SubSeries is part of SuperSeries:
GSE104334 Cohesin loss eliminates all loop domains
Relations
BioProject PRJNA414094
SRA SRP119849

Download family Format
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Supplementary file Size Download File type/resource
GSE104888_RAW.tar 16.1 Gb (http)(custom) TAR (of BW)
GSE104888_Rao-2017-ChIP-Seq-README.txt.gz 570 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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