PXD055956

PXD055956 is an original dataset announced via ProteomeXchange.

Title	lncRNA-protein interactions in hematopoietic progenitor cells by hybridization capture and mass spectrometry
Description	Long non-coding RNAs (lncRNAs) exert regulatory functions in a wide spectrum of biological contexts, and certain regulatory functions involve the formation of RNA-protein complexes. Discovering the structure/function of these complexes may unveil important functional insights. The DDX41 gene encoding the DEAD-box RNA helicase 41 protein (DDX41) is subject to extensive germline genetic variation, and certain variants create a predisposition to develop myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). While the importance of DDX41 for the control of hematopoiesis is established, many questions remain regarding the mechanisms of how DDX41 functions in hematopoietic stem and progenitor cells. Previously, we identified a DDX41-regulated lncRNA, growth arrest-specific 5 (Gas5) (Kim et al.). As Gas5 function in hematopoiesis is unknown, we analyzed protein interactors of Gas5 lncRNA using HyPR-MS (Hybridization Purification of RNA-Protein complexes followed by Mass Spectrometry). 28 proteins were identified as Gas5 lncRNA interactors, five of which were experimentally validated as Gas5 lncRNA interactors by RNA Immunoprecipitation qPCR (RIP-qPCR) analysis. The identification of protein interactors with a DDX41-regulated lncRNA establishes a foundation to guide future mechanistic and biological studies.c
HostingRepository	PRIDE
AnnounceDate	2025-01-13
AnnouncementXML	Submission_2025-01-13_08:32:12.654.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yuling Dai
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	phosphorylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-17 20:01:52	ID requested
⏵ 1	2025-01-13 08:32:13	announced

Dataset with its publication pending

submitter keyword: LC/MS,mouse , HyPR-MS, RNA-protein interaction

Lloyd M. Smith
contact affiliation	University of Wisconsin Madison
contact email	smith@chem.wisc.edu
lab head
Yuling Dai
contact affiliation	University of Wisconsin-Madison
contact email	yulingdai96@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD055956
     1. Label: PRIDE project
     2. Name: lncRNA-protein interactions in hematopoietic progenitor cells by hybridization capture and mass spectrometry