|
| Status |
Public on May 31, 2018 |
| Title |
Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
|
| Summary |
In addition to mediating sister chromatid cohesion, cohesin plays a central role in DNA looping and segmentation of the genome into contact domains (TADs). Two variant cohesin complexes that contain either STAG/SA1 or SA2 are present in all cell types. Here we addressed their specific contribution to genome architecture in non-transformed human cells. We found that cohesin-SA1 drives stacking of cohesin rings at CTCF-bound sites and thereby contributes to the stabilization and preservation of TAD boundaries. In contrast, a more dynamic cohesin-SA2 promotes cell type-specific contacts between enhancers and promoters within TADs independently of CTCF. SA2 loss, a condition frequently observed in cancer cells, results in increased intra-TAD interactions, likely altering the expression of key cell identity genes.
|
| |
|
| Overall design |
ChIP-seq for cohesin subunits SMC1, SA1 and SA2 was performed in 3 different cell lines (MCF10A, HMEC, HCAEC) and peak calling was done against the input sample from the corresponding cell line. RNA-seq was performed in triplicates in MCF10A cells control depleated from SA1, SA2 or CTCF by means of Dharmacon SMART pool siRNAs. HiC-seq was performed in two replicates in MCF10A cells control and depleated from SA1 and SA2 by means of Dharmacon SMART pool siRNAs. 4C-seq was performed in MCF10A cells control and depleated from SA2 or CTCF.
|
| |
|
| Contributor(s) |
Kojic A, Cuadrado A, Gimenez D, De Koninck M, Rodríguez-Corsino M, Gómez-López G, Le Dily F, Marti-Renom MA, Losada A |
| Citation(s) |
29867216 |
| |
| Submission date |
Jul 26, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Ana Losada |
| E-mail(s) |
[email protected]
|
| Phone |
+34 - 917 328 000
|
| Organization name |
Centro Nacional de Investigaciones Oncológicas (CNIO)
|
| Department |
Molecular Oncology Programme
|
| Lab |
Chromosome Dynamics Group
|
| Street address |
C/ Melchor Fernández Almagro, 3.
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platforms (3) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (45)
|
|
| Relations |
| BioProject |
PRJNA395931 |
| SRA |
SRP113633 |
Less...
More...