PXD022697

PXD022697 is an original dataset announced via ProteomeXchange.

Title	Characterization of R-loop-interacting proteins in embryonic stem cells reveals roles in ribosomal RNA processing and gene expression
Description	Chromatin-associated RNAs have diverse roles in the nucleus. However, their mechanisms of action are poorly understood, in part due to the inability to identify proteins that specifically associate with chromatin-bound RNAs. Here, we address this problem for a subset of chromatin-associated RNAs that form R-loops—RNA-DNA hybrid structures that include a displaced strand of single-stranded DNA. R-loops generally form co-transcriptionally and have important roles in regulation of gene expression, immunoglobulin class switching, and other processes. However, unresolved R-loops can lead to DNA damage and chromosome instability. To identify factors that may bind and potentially regulate R-loop accumulation or mediate R-loop-dependent functions, we used a comparative immunoprecipitation/mass spectrometry approach, with and without RNA-protein crosslinking, to identify a stringent set of R-loop-binding proteins in mouse embryonic stem cells. We identified 365 R-loop-interacting proteins, which were highly enriched for proteins with predicted RNA-binding functions. We characterized several R-loop-interacting proteins of the DEAD-box family of RNA helicases and found that these proteins localize to the nucleolus and, to a lesser degree, the nucleus. Consistent with their localization patterns, we found that these helicases are required for ribosomal RNA processing and regulation of gene expression. Surprisingly, depletion of these helicases resulted in misregulation of highly overlapping sets of protein-coding genes, including many genes that function in differentiation and development. We conclude that R-loop-interacting DEAD-box helicases have non-redundant roles that are critical for maintaining the normal embryonic stem cell transcriptome.
HostingRepository	PRIDE
AnnounceDate	2021-09-21
AnnouncementXML	Submission_2021-09-21_02:40:23.230.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Feixia Chu
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-24 07:51:24	ID requested
1	2021-09-17 07:23:58	announced
⏵ 2	2021-09-21 02:40:24	announced	2021-09-21: Updated project metadata.

10.1016/J.MCPRO.2021.100142;

Wu T, Nance J, Chu F, Fazzio TG, Characterization of R-Loop-Interacting Proteins in Embryonic Stem Cells Reveals Roles in rRNA Processing and Gene Expression. Mol Cell Proteomics, 20():100142(2021) [pubmed]

submitter keyword: R-loop-interacting proteins, immunoprecipitation/mass spectrometry approach, RNA-protein crosslinking

Thomas G. Fazzio, Feixia Chu
contact affiliation	University of Massachusetts Medical School, Department of Molecular, Cell and Cancer Biology, Worcester, MA University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, Durham, NH
contact email	feixia.chu@unh.edu
lab head
Feixia Chu
contact affiliation	University of New Hampshire
contact email	feixia.chu@unh.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD022697

PRIDE project URI

• PRIDE
  1. PXD022697
     1. Label: PRIDE project
     2. Name: Characterization of R-loop-interacting proteins in embryonic stem cells reveals roles in ribosomal RNA processing and gene expression