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| Status |
Public on Jul 13, 2020 |
| Title |
Cohesin-dependent and independent mechanisms support chromosomal contacts between promoters and enhancers (SLAM-Seq) |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
It is currently assumed that 3D chromosomal organisation plays a central role in transcriptional control. However, recent evidence shows that steady-state transcription of only a minority of genes is affected by depletion of architectural proteins such as cohesin and CTCF. Here, we have used Capture Hi-C to interrogate the dynamics of chromosomal contacts of all human gene promoters upon rapid architectural protein degradation. We show that promoter contacts lost in these conditions tend to be long-range, with at least one interaction partner localising in the vicinity of topologically associated domain (TAD) boundaries. In contrast, many shorter-range chromosomal contacts, particularly those that connect active promoters with each other and with active enhancers remain unaffected by cohesin and CTCF depletion. We demonstrate that the effects of cohesin depletion on nascent transcription can be explained by changes in the connectivity of their enhancers. Jointly, these results provide a mechanistic explanation to the limited, but consistent effects of cohesin and CTCF on steady-state transcription and point towards the existence of alternative enhancer-promoter pairing mechanisms that are independent of these proteins.
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| Overall design |
SLAM-seq was performed on HeLa kyoto cells in which SCC1 was raplidly and selectively depleted using an Auxin inducible degron and on control cells (without Auxin)
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| Contributor(s) |
Muhar M, Wutz G |
| Citation(s) |
32698000 |
| |
| Submission date |
Feb 21, 2020 |
| Last update date |
Aug 03, 2020 |
| Contact name |
Michiel Johannes Thiecke |
| Organization name |
Babraham research institute
|
| Department |
Nuclear dynamics
|
| Lab |
Spivakov
|
| Street address |
Babraham Hall
|
| City |
Cambridge |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB22 3AT |
| Country |
United Kingdom |
| |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE145736 |
Cohesin-dependent and independent mechanisms support chromosomal contacts between promoters and enhancers |
|
| Relations |
| BioProject |
PRJNA608020 |
| SRA |
SRP250332 |
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