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| Status |
Public on Dec 03, 2017 |
| Title |
The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [ChIP-Seq 1] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Higher-order chromatin conformation plays critical role in regulating gene expression and biological development, here we show that HNRNPU, a nuclear matrix attachment factor, is a regulator of 3D genome architecture at multiple levels in mouse hepatocytes. We demonstrate that depletion of HNRNPU results into a global reorganization of nuclear bodies and re-localization of chromatin towards nuclear periphery. Additionally, upon HNRNPU depletion, chromatin interactions between A-type (active) and B-type (inactive) compartments increase significantly but those among same types of compartments decrease significantly, which associate with global gene expression changes. While TADs remain largely invariant, both inter- and intra-TAD interactions increase significantly in A-type compartments but decrease in B-type compartments. Mechanically, HNRNPU complexes with structural proteins CTCF and RAD21; depletion of HNRNPU specifically weakens the bindings of RAD21 to the chromatin, which is highly correlated with the weakness of chromatin loops.
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| |
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| Overall design |
ChIP-seq data of CTCF, RAD21 in Ctrl and HNRNPU KD AML12 cells.
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| |
|
| Contributor(s) |
Fan H, Lv P, Wen B |
| Citation(s) |
29273625 |
| |
| Submission date |
Feb 21, 2017 |
| Last update date |
Nov 03, 2021 |
| Contact name |
Bo Wen |
| E-mail(s) |
bowen75@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Department |
Institutes of Biomedical Sciences
|
| Street address |
130 DongAn Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
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| Platforms (1) |
|
| Samples (10)
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| This SubSeries is part of SuperSeries: |
| GSE95116 |
The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture |
|
| Relations |
| BioProject |
PRJNA376127 |
| SRA |
SRP100432 |
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