Journal
NATURE COMMUNICATIONS
Volume 10, Issue -, Pages -Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/s41467-019-13235-w
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Funding
- ERC [FLAME-337440, XPRESS-671027]
- ATIP-Avenir
- La Fondation Bettencourt Schueller
- ANR (NoncodiX)
- ARC postdoctoral fellowship [20131200567]
- short-term EMBO fellowship [ESTF324-2015]
- Company of Biologists travel fellowship [JCSTF-150421]
- EMBO long-term fellowship [ALTF 549-2014]
- Fondation pour la Recherche Medicale grant [SPF 20140129387]
- PSL-Biogen PhD fellowship
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Regulatory RNAs exert their cellular functions through RNA-binding proteins (RBPs). Identifying RNA-protein interactions is therefore key for a molecular understanding of regulatory RNAs. To date, RNA-bound proteins have been identified primarily through RNA purification followed by mass spectrometry. Here, we develop incPRINT (in cell protein-RNA interaction), a high-throughput method to identify in-cell RNA-protein interactions revealed by quantifiable luminescence. Applying incPRINT to long noncoding RNAs (lncRNAs), we identify RBPs specifically interacting with the lncRNA Firre and three functionally distinct regions of the lncRNA Xist. incPRINT confirms previously known lncRNA-protein interactions and identifies additional interactions that had evaded detection with other approaches. Importantly, the majority of the incPRINT-defined interactions are specific to individual functional regions of the large Xist transcript. Thus, we present an RNA-centric method that enables reliable identification of RNA-region-specific RBPs and is applicable to any RNA of interest.
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