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Series GSE95113 Query DataSets for GSE95113
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.
Overall design ChIP-seq data of CTCF, RAD21 in Ctrl and HNRNPU KD AML12 cells.
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
Organization name Fudan University
Department Institutes of Biomedical Sciences
Street address 130 DongAn Road
City Shanghai
ZIP/Postal code 200032
Country China
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (10)
GSM2496432 shCtrl_CTCF_ChIPSeq_rep1
GSM2496433 shCtrl_CTCF_ChIPSeq_rep2
GSM2496434 shU_CTCF_ChIPSeq_rep1
This SubSeries is part of SuperSeries:
GSE95116 The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture
BioProject PRJNA376127
SRA SRP100432

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Supplementary file Size Download File type/resource
GSE95113_RAW.tar 2.0 Gb (http)(custom) TAR (of BW)
GSE95113_shCtrl_CTCF_merge_peaks.bed.gz 467.9 Kb (ftp)(http) BED
GSE95113_shCtrl_RAD21_merge_peaks.bed.gz 269.4 Kb (ftp)(http) BED
GSE95113_shU_CTCF_merge_peaks.bed.gz 437.7 Kb (ftp)(http) BED
GSE95113_shU_RAD21_merge_peaks.bed.gz 211.6 Kb (ftp)(http) BED
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Processed data are available on Series record

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