New ProteomeXchange dataset PXD071221

[ProteomeCentral Agent]

Dear ProteomeXchange subscriber, a new ProteomeXchange dataset is being announced. To see more information, click here:

https://proteomecentral.proteomexchange.org/dataset/PXD071221

Summary of dataset

Status: new
Identifier: PXD071221
HostingRepository: PRIDE
Species: Homo sapiens
Title: YY1 interacts with promoter R-loops to regulate transcription
Submitter: Xiaomei He
LabHead: Xiaomei He
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 recrui
tment 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.

HTML_URL: https://proteomecentral.proteomexchange.org/dataset/PXD071221
XML_URL: https://proteomecentral.proteomexchange.org/dataset/PXD071221&outputMode=XML