PXD053494

PXD053494 is an original dataset announced via ProteomeXchange.

Title	irCLIP-RNP reveals patterns of dynamic protein associations on RNA
Description	RNA binding proteins (RBPs) interact with RNA targets to control an array of processes, including RNA splicing, stability, transport, and translation1-3. Dysfunctional RNA-RBP interactions contribute to pathogenesis of a plethora of human diseases1,4,5, underscoring the need for a greater understanding of the nature and dynamics of RNA-protein assemblies. The capacity to study native RNA-dependent protein assemblies in living cells, however, has been limited. To address this, non-isotopic ligation-based ultraviolet crosslinking immunoprecipitation6 was combined with mass spectrometry (irCLIP-RNP) to identify RNA-dependent associated proteins (RDAPs) co-bound to RNA with specific RBPs of interest. irCLIP-RNP defined landscapes of complex and multimeric protein assemblies on RNA, uncovering previously unknown patterns of RBP associations on RNA. This included cell-type-selective patterned relationships between RDAPs and primary RBPs, such as cell context-dependent reciprocal impacts of HNRNPU and NONO on each other’s RDAP landscapes. irCLIP-RNP also defined dynamic RDAP remodeling patterns in response to epidermal growth factor (EGF) and uncovered EGF-induced recruitment of UPF1 adjacent to HNRNPC to effect splicing surveillance of mRNAs that mediate cell proliferation. The development of sequential immunoprecipitation irCLIP (RE-irCLIP) supported the same-RNA-molecule co-localization of irCLIP-RNP-identified associations. Thus, irCLIP-RNP and RE-irCLIP provide a framework to identify and characterize dynamic RNA-protein assemblies in living cells.
HostingRepository	PRIDE
AnnounceDate	2025-01-28
AnnouncementXML	Submission_2025-01-28_12:39:11.004.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Luca Ducoli
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-28 09:38:55	ID requested
⏵ 1	2025-01-28 12:39:11	announced

Ducoli L, Zarnegar BJ, Porter DF, Meyers RM, Miao W, Riley NM, Srinivasan S, Jackrazi LV, Yang YY, Li Z, Wang Y, Bertozzi CR, Flynn RA, Khavari PA, irCLIP-RNP and Re-CLIP reveal patterns of dynamic protein associations on RNA. bioRxiv, ():(2024) [pubmed]

10.1101/2024.09.27.615518;

submitter keyword: mass spectrometry, MS, crisslinking immunoprecipitation, RNA binding proteins,CLIP, RBP

Paul Khavari
contact affiliation	Program in Epithelial Biology, Stanford University-School of Medicine, Stanford, CA 94305 USA
contact email	khavari@stanford.edu
lab head
Luca Ducoli
contact affiliation	Stanford University
contact email	lducoli@stanford.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/2025/01/PXD053494

PRIDE project URI

• PRIDE
  1. PXD053494
     1. Label: PRIDE project
     2. Name: irCLIP-RNP reveals patterns of dynamic protein associations on RNA