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PXD026484-1

PXD026484 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleAcute depletion of CTCF rewires genome-wide chromatin accessibility
DescriptionThe 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
HostingRepositoryPRIDE
AnnounceDate2021-07-04
AnnouncementXMLSubmission_2021-07-03_18:14:37.936.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterHong Wang
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListphosphorylated residue
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-06-04 02:52:40ID requested
12021-07-03 18:14:38announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: CTCF, multiomics, proteome, phosphoproteome,
Contact List
Hong Wang
contact affiliationSt Jude Children's Research Hospital
contact emailhong.wang@stjude.org
lab head
Hong Wang
contact affiliationSt.Jude children's Research hospi
contact emailhong.wang@stjude.org
dataset submitter
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Dataset FTP location
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