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| Status |
Public on Jun 30, 2019 |
| Title |
Nuclear speckles as a key regulator for the 3D genome organization [HiC] |
| Organism |
Mus musculus |
| Experiment type |
Other
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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 |
HiC data in Control and SRRM2 KD AML12 cells.
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| Contributor(s) |
Hu SB, Lv P, Wen B |
| Citation(s) |
31315647 |
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| Submission date |
May 20, 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 (4)
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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 |
PRJNA543774 |
| SRA |
SRP198906 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE131463_RAW.tar |
4.3 Gb |
(http)(custom) |
TAR (of HIC) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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