Post-transcriptional regulatory patterns revealed by protein-RNA interactions

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  • dc.contributor.author Zanzoni, Andreas
  • dc.contributor.author Spinelli, Lionel
  • dc.contributor.author Ribeiro, Diogo M.
  • dc.contributor.author Tartaglia, Gian Gaetano
  • dc.contributor.author Brun, Christine
  • dc.date.accessioned 2019-03-26T09:37:52Z
  • dc.date.available 2019-03-26T09:37:52Z
  • dc.date.issued 2019
  • dc.description.abstract The coordination of the synthesis of functionally-related proteins can be achieved at the post-transcriptional level by the action of common regulatory molecules, such as RNA-binding proteins (RBPs). Despite advances in the genome-wide identification of RBPs and their binding transcripts, the protein-RNA interaction space is still largely unexplored, thus hindering a broader understanding of the extent of the post-transcriptional regulation of related coding RNAs. Here, we propose a computational approach that combines protein-mRNA interaction networks and statistical analyses to provide an inferred regulatory landscape for more than 800 human RBPs and identify the cellular processes that can be regulated at the post-transcriptional level. We show that 10% of the tested sets of functionally-related mRNAs can be post-transcriptionally regulated. Moreover, we propose a classification of (i) the RBPs and (ii) the functionally-related mRNAs, based on their distinct behaviors in the functional landscape, hinting towards mechanistic regulatory hypotheses. In addition, we demonstrate the usefulness of the inferred functional landscape to investigate the cellular role of both well-characterized and novel RBPs in the context of human diseases.
  • dc.description.sponsorship The authors would like to thank Davide Cirillo (CRG, Barcelona), Guillaume Charbonnier (TAGC), Denis Puthier (TAGC) and Thien-Phong Vu Manh (CIML, Marseille) for fruitful discussion and advice; and Elisa Micarelli (TAGC) for providing the list of the RNA biotype targets for the RBPs. 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.). G.G.T. acknowledges the support of the European Research Council (RIBOMYLOME_309545) and the Spanish Ministry of Economy and Competitiveness (BFU2014-55054-P).
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Zanzoni A, Spinelli L, Ribeiro DM, Tartaglia GG, Brun C. Post-transcriptional regulatory patterns revealed by protein-RNA interactions. Sci Rep. 2019 Mar;9(1):4302. DOI: 10.1038/s41598-019-40939-2
  • dc.identifier.doi http://dx.doi.org/10.1038/s41598-019-40939-2
  • dc.identifier.issn 2045-2322
  • dc.identifier.uri http://hdl.handle.net/10230/36964
  • dc.language.iso eng
  • dc.publisher Nature Research
  • dc.relation.ispartof Scientific Reports. 2019 Mar;9(1):4302
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2014-55054-P
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/309545
  • 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 Cellular signalling networks
  • dc.subject.keyword Gene regulatory networks
  • dc.title Post-transcriptional regulatory patterns revealed by protein-RNA interactions
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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