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PXD053494

PXD053494 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleirCLIP-RNP reveals patterns of dynamic protein associations on RNA
DescriptionRNA 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.
HostingRepositoryPRIDE
AnnounceDate2025-01-28
AnnouncementXMLSubmission_2025-01-28_12:39:11.004.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterLuca Ducoli
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-06-28 09:38:55ID requested
12025-01-28 12:39:11announced
Publication List
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;
Keyword List
submitter keyword: mass spectrometry, MS, crisslinking immunoprecipitation, RNA binding proteins,CLIP, RBP
Contact List
Paul Khavari
contact affiliationProgram in Epithelial Biology, Stanford University-School of Medicine, Stanford, CA 94305 USA
contact emailkhavari@stanford.edu
lab head
Luca Ducoli
contact affiliationStanford University
contact emaillducoli@stanford.edu
dataset submitter
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Dataset FTP location
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