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Series GSE44267 Query DataSets for GSE44267
Status Public on Dec 16, 2013
Title Cohesin and CTCF Differentially Affect the Chromatin Architecture and Gene Expression in Human Cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Recent studies of genome-wide chromatin interactions have revealed that the human genome is partitioned into many self-associating topological domains. The boundary sequences are enriched for binding sites of CTCF and the cohesin complex, implicating these two factors in the establishment or maintenance of topological domains. To determine the role of cohesin and CTCF in higher order chromatin architecture in human cells, we proteolytically cleaved the cohesin complex from interphase chromatin and examined changes in chromosomal organization as well as transcriptome. We observed a general loss of local chromosomal interactions upon disruption of cohesin complex, but the topological domains remain intact. However, we found that depletion of CTCF by RNA interference in these cells not only reduced intra-domain interactions but also increased inter-domain interactions. Further more, distinct groups of genes become mis-regulated upon depletion of cohesin and CTCF. Taken together, these observations suggest that CTCF and cohesin contribute in different ways to chromatin organization and gene regulation.
Overall design Hi-C and mRNA-seq experiments in Cohesin and CTCF depleted HEK293 cells
Contributor(s) Dixon J, Ren B, Wendt K
Citation(s) 24335803
Submission date Feb 12, 2013
Last update date May 15, 2019
Contact name Jesse R Dixon
Organization name Salk Institute for Biological Studies
Street address 10010 N. Torrey Pines Rd.
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (18)
GSM1081526 Hi-C, RAD21cv HEK293, TEV treated, replicate one
GSM1081527 Hi-C, RAD21cv HEK293, TEV treated, replicate two
GSM1081528 Hi-C, RAD21cv HEK293, HRV treated, replicate one
BioProject PRJNA189267
SRA SRP018571

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Supplementary file Size Download File type/resource
GSE44267_RAW.tar 3.2 Gb (http)(custom) TAR (of BW, RPKM, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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