In-cell identification and measurement of RNA-protein interactions

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  • dc.contributor.author Graindorge, Antoine
  • dc.contributor.author Pinheiro, Inês
  • dc.contributor.author Nawrocka, Anna
  • dc.contributor.author Mallory, Allison C.
  • dc.contributor.author Tsvetkov, Peter
  • dc.contributor.author Gil, Noa
  • dc.contributor.author Carolis, Carlo
  • dc.contributor.author Buchholz, Frank
  • dc.contributor.author Ulitsky, Igor
  • dc.contributor.author Heard, Edith
  • dc.contributor.author Taipale, Mikko
  • dc.contributor.author Shkumatava, Alena
  • dc.date.accessioned 2020-04-01T08:42:55Z
  • dc.date.available 2020-04-01T08:42:55Z
  • dc.date.issued 2019
  • dc.description.abstract 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.
  • dc.description.sponsorship This work was supported by grants from ERC (FLAME-337440), ATIP-Avenir, and La Fondation Bettencourt Schueller to A.S.; and by ERC (XPRESS-671027) and ANR (NoncodiX) to E.H. A.G. was supported by the ARC postdoctoral fellowship (20131200567), short-term EMBO (ESTF324-2015) and Company of Biologists travel (JCSTF-150421) fellowships. I.P. was supported by the EMBO long-term fellowship (ALTF 549-2014), and Fondation pour la Recherche Medicale grant SPF 20140129387, A.N. was supported by the PSL-Biogen PhD fellowship. The imaging experiments were performed in the Cell and Tissue Imaging Facility/UMR3215 (PICT-IBiSA) of the Institut Curie, member of the French National Research Infrastructure France-BioImaging (ANR-10-INBS-04).
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Graindorge A, Pinheiro I, Nawrocka A, Mallory AC, Tsvetkov P, Gil N, Carolis C, Buchholz F, Ulitsky I, Heard E, Taipale M, Shkumatava A. In-cell identification and measurement of RNA-protein interactions. Nat Commun. 2019; 10(1):5317. DOI: 10.1038/s41467-019-13235-w
  • dc.identifier.doi http://dx.doi.org/10.1038/s41467-019-13235-w
  • dc.identifier.issn 2041-1723
  • dc.identifier.uri http://hdl.handle.net/10230/44135
  • dc.language.iso eng
  • dc.publisher Nature Research
  • dc.relation.ispartof Nat Commun. 2019; 10(1):5317
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/337440
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/671027
  • dc.rights © The Author(s) 2019. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword Non-coding RNAs
  • dc.subject.keyword RNA
  • dc.title In-cell identification and measurement of RNA-protein interactions
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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