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| Status |
Public on May 01, 2024 |
| Title |
Single-cell ATAC-seq analysis of mouse embryonic stem cells before and after Cohesin depletion |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The contrast between the disruption of genome topology upon cohesin loss and the lack of downstream gene expression changes instigates intense debates regarding the structure-function relationship between genome and gene regulation. Here, by analyzing transcriptome at the single-cell level, we discover that, instead of dictating population-wide gene expression levels, cohesin supplies a general function to neutralize stochastic co-expression tendency of cis-linked genes in single cells. Notably, through single-cell ATAC-seq analysis of mouse embryonic stem cells, we found that cohesin loss induces chromatin co-opening tens of million bases apart in cis. Our results support that cohesin arranges nuclear topology to control gene co-expression in single cells.
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| Overall design |
JM8.N4 mouse embryonic stem cells (mESCs) from the C57BL/6N strain were edited by using CRISPR/Cas9 to fuse cohesin subunit RAD21 to the auxin-induced degron (AID) system. The derived cells were used in Smart-SCRB (Smart-Single Cell RNA Barcoding, a highly sensitive single-cell transcriptome assay) analysis and single-cell ATAC-seq analysis under control and acute cohesin loss (6hrs after the auxin treatment) conditions.
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| Web link |
https://www.nature.com/articles/s41588-024-01852-1
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| |
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| Contributor(s) |
Dong P, Liu ZJ |
| Citation(s) |
39048795 |
| |
| Submission date |
Apr 29, 2024 |
| Last update date |
Jul 31, 2024 |
| Contact name |
PENG DONG |
| E-mail(s) |
p.dong@siat.ac.cn
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| Organization name |
Shenzhen Institute of Advanced Technology
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| Street address |
1068 Xueyuan Avenue, Shenzhen University Town
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| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518055 |
| Country |
China |
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| Platforms (1) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA1105866 |
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