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Status |
Public on Jun 30, 2019 |
Title |
Nuclear speckles as a key regulator for the 3D genome organization [RNA-Seq] |
Organism |
Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
The nuclei of eukaryotes contain various higher-order chromatin architectures and nuclear bodies (NBs), which are critical for proper nuclear functions. By using mouse hepatocytes as the model, we knocked-down SRRM2, a core protein component scaffolding NSs, and performed Hi-C experiments to examine genome-wide chromatin interactions. We found that Srrm2 depletion disrupted the NSs and changes expression of about 1,000 genes. The intra-chromosomal interactions were decreased in type A (active) compartments and increased in type B (repressive) compartments. Furthermore, upon Srrm2 knockdown, the insulation of TADs was decreased specifically in active compartments, and the most significant reduction was found in the A1 sub-compartments. We showed that disruption of NSs by Srrm2 knockdown led to a global decrease of chromatin interactions in active compartments, indicating critical functions of NSs in the organization of the 3D genome.
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Overall design |
RNAseq data in Control and SRRM2 KD AML12 cells.
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Contributor(s) |
Hu SB, Lv P, Wen B |
Citation(s) |
31315647 |
Submission date |
May 07, 2019 |
Last update date |
Jul 29, 2019 |
Contact name |
Bo Wen |
E-mail(s) |
bowen75@fudan.edu.cn
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Organization name |
Fudan University
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Department |
Institutes of Biomedical Sciences
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Street address |
130 DongAn Road
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City |
Shanghai |
ZIP/Postal code |
200032 |
Country |
China |
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Platforms (1) |
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Samples (9)
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This SubSeries is part of SuperSeries: |
GSE131466 |
Nuclear speckles as a key regulator for the 3D genome organization |
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Relations |
BioProject |
PRJNA541491 |
SRA |
SRP195765 |