PXD071221

PXD071221 is an original dataset announced via ProteomeXchange.

Title	YY1 interacts with promoter R-loops to regulate transcription
Description	R-loops are three-stranded nucleic acid structures consisting of a DNA-RNA hybrid and a displaced single-stranded DNA (ssDNA). R-loops are facilitators of gene expression and genome stability that play both regulatory and potentially deleterious roles in cells. To elucidate the protein-based mechanisms of R-loop regulation, we developed an APEX-based proximity proteomics using a catalytically inactive mutant of RNase H1 (APEX-RNH1D210N) to profile the proximal proteome of R-loops in cells. Our proteomics results identified a list of known and potential R-loop-binding proteins with diverse molecular functions, and confirmed YY1 as a novel R-loop-binding protein through a series of in-vitro binding assays. YY1 is a DNA-binding protein recognizing a consensus motif or G-quadruplex (G4) structure. Our binding results indicated YY1's notably stronger affinity for R-loops compared to RNA/DNA hybrid, DNA G4 and DNA without a consensus motif, implying R-loops' role in YY1 recruitment to genomic regions lacking a YY1-binding motif. To investigate YY1-R-loop interaction in cells, we introduced R-loop structures into specific genomic regions vis CRISPR-dCas9 targeting, followed by DRIP-qPCR, YY1-ChIP-qPCR and RT-qPCR experiments. Increased R-loop levels corresponded with heightened YY1 occupancy and differential gene expression, suggesting YY1-R-loop interactions contribute to transcriptional regulation. More importantly, our RNA-seq and YY1-ChIP-seq results revealed that the interactions between YY1 and promoter R-loops were involved in global transcriptional regulation, especially in the positive regulation of transcription. Together, we identified YY1 as a novel R-loop-binding protein and uncovered a mechanism wherein YY1-R-loop interactions regulate gene expression.
HostingRepository	PRIDE
AnnounceDate	2026-03-09
AnnouncementXML	Submission_2026-03-09_15:10:22.185.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Xiaomei He
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2025-11-25 15:03:54	ID requested
⏵ 1	2026-03-09 15:10:22	announced

10.1021/JACS.5C22130;

submitter keyword: LC-MS/MS, proximity proteomics, transcription regulation, YY1, R-loop

Xiaomei He
contact affiliation	Department of Biology, East Carolina University
contact email	hex24@ecu.edu
lab head
Xiaomei He
contact affiliation	East Carolina University
contact email	hex24@ecu.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD071221
     1. Label: PRIDE project
     2. Name: YY1 interacts with promoter R-loops to regulate transcription