PXD026484 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Acute depletion of CTCF rewires genome-wide chromatin accessibility |
Description | The transcription factor CTCF appears indispensable in defining topologically associated domain boundaries and maintaining chromatin loop structures within these domains, supported by numerous functional studies. However, acute depletion of CTCF globally reduces chromatin interactions but does not significantly alter transcription. Here we systematically integrated multi-omics data including ATAC-seq, RNA-seq, WGBS, Hi-C, Cut&Run, CRISPR-Cas9 survival dropout screening, time-solved deep proteomic and phosphoproteomic analyses in cells carrying auxin-induced degron at endogenous CTCF locus. Acute CTCF protein degradation markedly rewired genome-wide chromatin accessibility. Increased accessible chromatin regions were largely located adjacent to CTCF-binding sites at promoter regions and insulator sites and were associated with enhanced transcription of nearby genes. In addition, we used CTCF-associated multi-omics data to establish a combinatorial data analysis pipeline to discover CTCF co-regulatory partners in regulating downstream gene expression. We successfully identified 40 candidates, including multiple established partners (i.e., MYC) supported by all layers of evidence. Interestingly, many CTCF co-regulators (e.g., YY1, ZBTB7A) that have evident alterations of respective downstream gene expression do not show changes at their expression levels across the multi-omics measurements upon acute CTCF loss, highlighting the strength of our system to discover hidden co-regulatory partners associated with CTCF-mediated transcription. This study highlights CTCF loss rewires genome-wide chromatin accessibility, which plays a critical role in transcriptional regulation |
HostingRepository | PRIDE |
AnnounceDate | 2021-07-04 |
AnnouncementXML | Submission_2021-07-03_18:14:37.936.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Hong Wang |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | phosphorylated residue |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-06-04 02:52:40 | ID requested | |
⏵ 1 | 2021-07-03 18:14:38 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: CTCF, multiomics, proteome, phosphoproteome, |
Contact List
Hong Wang |
contact affiliation | St Jude Children's Research Hospital |
contact email | hong.wang@stjude.org |
lab head | |
Hong Wang |
contact affiliation | St.Jude children's Research hospi |
contact email | hong.wang@stjude.org |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
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[ - ]
- PRIDE
- PXD026484
- Label: PRIDE project
- Name: Acute depletion of CTCF rewires genome-wide chromatin accessibility