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GEO help: Mouse over screen elements for information. |
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| 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
Other
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| 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.
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| Overall design |
Hi-C and mRNA-seq experiments in Cohesin and CTCF depleted HEK293 cells
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| 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 |
| E-mail(s) |
jedixon@salk.edu
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| Organization name |
Salk Institute for Biological Studies
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| Lab |
PBL-D
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| Street address |
10010 N. Torrey Pines Rd.
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (18)
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| 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 |
| GSM1081529 |
Hi-C, RAD21cv HEK293, HRV treated, replicate two |
| GSM1081530 |
Hi-C, HEK293 siRNA Control, replicate one |
| GSM1081531 |
Hi-C, HEK293 siRNA Control, replicate two |
| GSM1081532 |
Hi-C, HEK293 siRNA CTCF, replicate one |
| GSM1081533 |
Hi-C, HEK293 siRNA CTCF, replicate two |
| GSM1081534 |
mRNA-seq, RAD21cv HEK293, TEV treated, replicate one |
| GSM1081535 |
mRNA-seq, RAD21cv HEK293, TEV treated, replicate two |
| GSM1081536 |
mRNA-seq, RAD21cv HEK293, HRV treated, replicate one |
| GSM1081537 |
mRNA-seq, RAD21cv HEK293, HRV treated, replicate two |
| GSM1081538 |
mRNA-seq, HEK293 siRNA Control, replicate one |
| GSM1081539 |
mRNA-seq, HEK293 siRNA Control, replicate two |
| GSM1081540 |
mRNA-seq, HEK293 siRNA CTCF, replicate one |
| GSM1081541 |
mRNA-seq, HEK293 siRNA CTCF, replicate two |
| GSM1081542 |
Smc3 ChIP-seq, RAD21cv HEK293, TEV Treated |
| GSM1081543 |
Input ChIP-seq, RAD21cv HEK293, TEV Treated |
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| Relations |
| BioProject |
PRJNA189267 |
| SRA |
SRP018571 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE44267_RAW.tar |
3.2 Gb |
(http)(custom) |
TAR (of BW, RPKM, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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