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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 [RNA-Seq] |
Organism |
Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing
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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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Overall design |
RNAseq data in Ctrl and HNRNPU KD AML12 cells.
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Contributor(s) |
Fan H, Lv P, Wen B |
Citation(s) |
29273625 |
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Submission date |
Feb 21, 2017 |
Last update date |
Nov 03, 2021 |
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: |
GSE95116 |
The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture |
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Relations |
BioProject |
PRJNA376129 |
SRA |
SRP100429 |