PXD030352

PXD030352 is an original dataset announced via ProteomeXchange.

Title	Proteome-wide quantitative RNA interactome capture (qRIC) identifies phosphorylation sites with regulatory potential in RBM20
Description	Cellular mRNA-binding proteins (mRBPs) are major regulators of gene expression at the post-transcriptional level. While many posttranslational modification sites in mRBPs have been identified, little is known about how these modifications regulate mRBP function. Here, we developed quantitative RNA-interactome capture (qRIC) to quantify the fraction of cellular mRBPs pulled down with polyadenylated mRNAs. Combining qRIC with phosphoproteomics allowed us to systematically compare pull-down efficiencies of phosphorylated and non-phosphorylated forms of mRBPs. Almost 200 phosphorylation events increased or decreased pull-down efficiency compared to the unmodified mRBPs and thus have regulatory potential. Our data captures known regulatory phosphorylation sites in ELAVL1, SF3B1 and UPF1 and identifies new potentially regulatory sites. Follow-up experiments on the cardiac splicing regulator RBM20 revealed that multiple phosphorylation sites in the C-terminal disordered region affect nucleo-cytoplasmic localization, association with cytoplasmic ribonucleoprotein granules and alternative splicing. Together, we show that qRIC in conjunction with phosphoproteomics is a scalable method to identify functional posttranslational modification sites in mRBPs.
HostingRepository	PRIDE
AnnounceDate	2022-09-05
AnnouncementXML	Submission_2022-09-05_04:25:19.961.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Carlos Vieira
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	carbamoylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-12-13 03:02:54	ID requested
⏵ 1	2022-09-05 04:25:20	announced

Vieira-Vieira CH, Dauksaite V, Sporbert A, Gotthardt M, Selbach M, Proteome-wide quantitative RNA-interactome capture identifies phosphorylation sites with regulatory potential in RBM20. Mol Cell, 82(11):2069-2083.e8(2022) [pubmed]

submitter keyword: RNA-binding proteins, RNA-interactome capture, cell signaling, phosphorylation, proteomics, RBM20, alternative splicing, cardiomyopathy

Matthias Selbach
contact affiliation	Max Delbrück Center for Molecular Medicine, Robert-Roessle-Str. 10, D-13092 Berlin, Germany Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
contact email	matthias.selbach@mdc-berlin.de
lab head
Carlos Vieira
contact affiliation	Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft
contact email	carlos.vieira@mdc-berlin.de
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/2022/09/PXD030352

PRIDE project URI

• PRIDE
  1. PXD030352
     1. Label: PRIDE project
     2. Name: Proteome-wide quantitative RNA interactome capture (qRIC) identifies phosphorylation sites with regulatory potential in RBM20