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Series GSE104098 Query DataSets for GSE104098
Status Public on Dec 03, 2017
Title The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [ChIP-Seq 2]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Here we show that HNRNPU, the major nuclear matrix attachment factor, is necessary to maintain proper nuclear architecture in mouse hepatocytes. Upon HNRNPU depletion, the interactions between chromatin and nuclear lamina have been changed dramatically;chromatin organization is globally changed; boundaries of topologically associating domains (TADs) become weaker; inter-TAD interactions are increased; thousands of genes are significantly altered coincident with 3D chromatin changes. Mechanically, HNRNPU interacts with CTCF and RAD21, which affects the binding of RAD21 to the chromatin significantly, whereas CTCF bindings are almost unchanged, what’ more, the decrease of binding strengths are highly correlated with the weakness of loop bounded by Rad21. Taken together, we identify HNRNPU as a key regulator of chromatin architecture, and our data suggest the importance of nuclear matrix associating factors in 3D genome organization.
Overall design ChIPseq data of BirA-HNRNPU in AML12 cells
Contributor(s) Wen B, Fan H, Lv P
Citation(s) 29273625
Submission date Sep 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 (6)
GSM2789723 BirA-HNRNPU_ChIPSeq_rep1
GSM2789724 BirA-HNRNPU_ChIPSeq_rep2
GSM2789725 BirA-only_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 PRJNA408237
SRA SRP118474

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE104098_HNRNPU_peaks.bed.gz 128.7 Kb (ftp)(http) BED
GSE104098_RAW.tar 1.1 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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