PXD027138

PXD027138 is an original dataset announced via ProteomeXchange.

Title	Quantitative RNA interactome capture (qRIC) identifies phosphorylation sites with regulatory potential - RBM20 BioID
Description	RNA binding proteins (RBPs) are major regulators of gene expression at the post-transcriptional level. While many posttranslational modification sites in RBPs have been identified, less is known about how these modifications regulate RBP function. Here, we develop quantitative RNA-interactome capture (qRIC) to quantify the fraction of cellular RBPs pulled down with polyadenylated mRNAs. Applying qRIC to HEK293T cells quantified pulldown efficiencies of over 300 mRBPs. Combining qRIC with phosphoproteomics allowed us to systematically compare pulldown efficiencies of phosphorylated and non-phosphorylated forms of mRBPs. Over hundred phosphorylation sites show increased or decreased pull-down efficiency compared to their host RBPs 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 shuttling, association with cytosolic RNA granules and alternative splicing. Together, we show that qRIC is a scalable method to identify the function of posttranslational modifications in RBPs.
HostingRepository	PRIDE
AnnounceDate	2022-09-05
AnnouncementXML	Submission_2022-09-05_04:25:07.531.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	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-07 00:43:51	ID requested
⏵ 1	2022-09-05 04:25:08	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: SILAC, LC-MSMS, BioID, RBM20

Matthias Selbach
contact affiliation	Max Delbruck Center for Molecular Medicine, Robert-Rössle-Str. 10, D-13092 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

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PRIDE project URI

• PRIDE
  1. PXD027138
     1. Label: PRIDE project
     2. Name: Quantitative RNA interactome capture (qRIC) identifies phosphorylation sites with regulatory potential - RBM20 BioID