Identifying lncRNA–Protein Interactions in Hematopoietic Progenitor Cells by Hybridization Capture and Mass Spectrometry Article Swipe
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· 2025
· Open Access
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· DOI: https://doi.org/10.1021/acs.jproteome.5c00334
· OA: W4412822554
Long noncoding 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 and function of these complexes may unveil important functional insights. The <i>DDX41</i> 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 and acute myeloid leukemia. While the importance of <i>DDX41</i> for the control of hematopoiesis is established, many questions remain regarding the mechanisms of how <i>DDX41</i> functions in hematopoietic stem and progenitor cells. Previously, we identified a DDX41-regulated lncRNA, growth-arrest-specific 5 (<i>Gas5</i>). As the <i>Gas5</i> function in hematopoiesis is unknown, we analyzed the protein interactors of <i>Gas5</i> lncRNA using HyPR-MS (hybridization purification of RNA-protein complexes, followed by mass spectrometry). A total of 303 proteins were identified as <i>Gas5</i> lncRNA interactors, five of which were experimentally validated as <i>Gas5</i> lncRNA interactors by RNA immunoprecipitation qPCR (RIP-qPCR) analysis. The identification of protein interactors with a DDX41-regulated lncRNA establishes a foundation on which to guide future mechanistic and biological studies.
