PXD062465

PXD062465 is an original dataset announced via ProteomeXchange.

Title	Pooled scanning of protein variants identifies novel RNA-binding mutants
Description	Binding to RNA has been observed for an ever-increasing number of proteins, which often have other functions. The contributions of RNA binding to protein function are best discerned by studying “separation-of-function” mutants that hamper interaction with RNA without affecting other aspects of protein function. To design these mutants, we need precise knowledge of the residues that contribute to the affinity of the protein to its RNA ligands. Here, we present RBR-scan: a technology to simultaneously measure RNA-binding affinity of a large number of protein variants. We fused individual variants with unique peptide barcodes optimized for detection by mass spectrometry (MS), purified protein pools from single bacterial culture, and assayed proteins in parallel for RNA binding. Mutations in the MS2 coat protein known to impair RNA-binding were correctly identified, as well as a previously unreported mutant, which we validated with orthogonal biochemical methods. We used RBR-scan to discover novel RNA-binding mutants in the cancer-associated splicing regulator SRSF2. Together, our results demonstrate that RBR-scan is a powerful and scalable platform for linking RNA-binding affinity to protein sequence, offering a novel strategy to decode the functional consequences of protein–RNA interactions.
HostingRepository	PRIDE
AnnounceDate	2025-06-20
AnnouncementXML	Submission_2025-06-20_12:41:22.947.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Julia Tasca
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-01 07:22:45	ID requested
⏵ 1	2025-06-20 12:41:23	announced

Tasca JA, Doherty JF, Shields EJ, Mudiyanselage SD, Reich LN, Sarma K, Garcia BA, Bonasio R, Pooled scanning of protein variants identifies novel RNA-binding mutants. bioRxiv, ():(2025) [pubmed]

10.1101/2025.04.02.646914;

submitter keyword: LC-MS, protein-RNA interactions, technology development, RNA-binding proteins, peptide barcodes

Roberto Bonasio
contact affiliation	Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania
contact email	roberto@bonasiolab.org
lab head
Julia Tasca
contact affiliation	University of Pennsylvania
contact email	jtasca@pennmedicine.upenn.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/2025/06/PXD062465

PRIDE project URI

• PRIDE
  1. PXD062465
     1. Label: PRIDE project
     2. Name: Pooled scanning of protein variants identifies novel RNA-binding mutants