Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs

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• dc.contributor.author Ribeiro, Diogo M.
• dc.contributor.author Zanzoni, Andreas
• dc.contributor.author Cipriano, Andrea
• dc.contributor.author Delli Ponti, Riccardo, 1987-
• dc.contributor.author Spinelli, Lionel
• dc.contributor.author Ballarino, Monica
• dc.contributor.author Bozzoni, Irene
• dc.contributor.author Tartaglia, Gian Gaetano
• dc.contributor.author Brun, Christine
• dc.date.accessioned 2019-11-27T08:34:29Z
• dc.date.available 2019-11-27T08:34:29Z
• dc.date.issued 2018
• dc.description.abstract The human transcriptome contains thousands of long non-coding RNAs (lncRNAs). Characterizing their function is a current challenge. An emerging concept is that lncRNAs serve as protein scaffolds, forming ribonucleoproteins and bringing proteins in proximity. However, only few scaffolding lncRNAs have been characterized and the prevalence of this function is unknown. Here, we propose the first computational approach aimed at predicting scaffolding lncRNAs at large scale. We predicted the largest human lncRNA-protein interaction network to date using the catRAPID omics algorithm. In combination with tissue expression and statistical approaches, we identified 847 lncRNAs (∼5% of the long non-coding transcriptome) predicted to scaffold half of the known protein complexes and network modules. Lastly, we show that the association of certain lncRNAs to disease may involve their scaffolding ability. Overall, our results suggest for the first time that RNA-mediated scaffolding of protein complexes and modules may be a common mechanism in human cells.
• dc.description.sponsorship Work in IB’s lab was partially supported by grants from ERC-2013 [AdG 340172–MUNCODD]; Telethon [GGP16213]; Human Frontiers Science Program Award [RGP0009/2014]; Parent Project Italia, AFM-Telethon [17835]; Epigen-Epigenomics Flagship Project and AriSLA full grant 2014 ‘ARCI’. Work in GGT’s lab was supported by the European Research Council [RIBOMYLOME_309545]; Spanish Ministry of Economy and Competitiveness [BFU2014-55054-P]. The RAINET project leading to this publication has received funding from Excellence Initiative of Aix-Marseille University—A*MIDEX, a French ‘Investissements d’Avenir’ programme (to C.B.). Funding for open access charge: Excellence Initiative of Aix-Marseille University—A*MIDEX [RAINET].
• dc.format.mimetype application/pdf
• dc.identifier.citation Ribeiro DM, Zanzoni A, Cipriano A, Delli Ponti R, Spinelli L, Ballarino M et al. Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs. Nucleic Acids Res. 2018;46(2):917-28. DOI: 10.1093/nar/gkx1169
• dc.identifier.doi http://dx.doi.org/10.1093/nar/gkx1169
• dc.identifier.issn 0305-1048
• dc.identifier.uri http://hdl.handle.net/10230/43003
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.relation.ispartof Nucleic Acids Research. 2018;46(2):917-28
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/340172
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/309545
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2014-55054-P
• dc.rights © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
• dc.subject.keyword RNA
• dc.subject.keyword RNA-protein complexes
• dc.title Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion