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| Status |
Public on Jan 30, 2023 |
| Title |
Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels [RNA-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Cohesin mediates sister chromatid cohesion and organizes the genome through the formation of chromatin loops. Two versions of the complex carrying either STAG1 or STAG2 show overlapping and specific functions and both are required to fulfill embryonic development. Cohesin-STAG1 displays longer residence time on chromatin that depends on CTCF and ESCO1 and establishes longer, long-lived chromatin loops together with CTCF. Cohesin-STAG2 shows a preferential interaction with WAPL and mediates shorter loops involved in tissue-specific transcription independently of CTCF. Here we show that the two variants respond in opposite ways to knock down of NIPBL, the putative cohesin loader that is also essential for loop extrusion. Cohesin-STAG1 levels increase on chromatin under this condition and the complex accumulates further at CTCF positions while cohesin-STAG2 is diminished genome-wide. Our data support a model in which NIPBL is not required for association of cohesin with chromatin but it is for loop extrusion, which in turn facilitates stabilization of cohesin-STAG2 at CTCF positions after being loaded elsewhere. In contrast, cohesin-STAG1 is preferentially loaded at CTCF sites independently of NIPBL. Nevertheless, loop formation by these chromatin-bound complexes is impaired and gene expression is severely affected, resembling alterations in Cornelia de Lange patients
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| Overall design |
RNA-seq was performed in triplicates in MCF10A cells mock transfected or transfected with siRNAs for NIPBL.
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| Contributor(s) |
Gimenez-Llorente D, Cuadrado A, del Pilar Alonso-Gil D, Rodríguez-Corsino M, Losada A |
| Citation(s) |
36898992 |
| Submission date |
Jun 28, 2022 |
| Last update date |
May 08, 2023 |
| Contact name |
Daniel Gimenez |
| E-mail(s) |
dgimenezl@cnio.es
|
| Organization name |
CNIO
|
| Street address |
Calle de Melchor Fernández Almagro, 3
|
| City |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
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| Platforms (1) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE207116 |
Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels |
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| Relations |
| BioProject |
PRJNA853746 |
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