Post-transcriptional regulatory patterns revealed by protein-RNA interactions

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 protei...

Descripción completa

Detalles Bibliográficos
Autores: Zanzoni, Andreas, Spinelli, Lionel, Ribeiro, Diogo M., Tartaglia, Gian Gaetano, Brun, Christine
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2019
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/36964
Acceso en línea:http://hdl.handle.net/10230/36964
http://dx.doi.org/10.1038/s41598-019-40939-2
Access Level:acceso abierto
Palabra clave:Cellular signalling networks
Gene regulatory networks
id ES_5bb33cd60f68167a0e2f3a3fb95f84a1
oai_identifier_str oai:recercat.cat:10230/36964
network_acronym_str ES
network_name_str España
repository_id_str
spelling Post-transcriptional regulatory patterns revealed by protein-RNA interactionsZanzoni, AndreasSpinelli, LionelRibeiro, Diogo M.Tartaglia, Gian GaetanoBrun, ChristineCellular signalling networksGene regulatory networksThe 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.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).Nature Research201920192019info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/36964http://dx.doi.org/10.1038/s41598-019-40939-2reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésScientific Reports. 2019 Mar;9(1):4302info:eu-repo/grantAgreement/ES/1PE/BFU2014-55054-Pinfo:eu-repo/grantAgreement/EC/FP7/309545© 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/.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/369642026-05-29T05:05:01Z
dc.title.none.fl_str_mv Post-transcriptional regulatory patterns revealed by protein-RNA interactions
title Post-transcriptional regulatory patterns revealed by protein-RNA interactions
spellingShingle Post-transcriptional regulatory patterns revealed by protein-RNA interactions
Zanzoni, Andreas
Cellular signalling networks
Gene regulatory networks
title_short Post-transcriptional regulatory patterns revealed by protein-RNA interactions
title_full Post-transcriptional regulatory patterns revealed by protein-RNA interactions
title_fullStr Post-transcriptional regulatory patterns revealed by protein-RNA interactions
title_full_unstemmed Post-transcriptional regulatory patterns revealed by protein-RNA interactions
title_sort Post-transcriptional regulatory patterns revealed by protein-RNA interactions
dc.creator.none.fl_str_mv Zanzoni, Andreas
Spinelli, Lionel
Ribeiro, Diogo M.
Tartaglia, Gian Gaetano
Brun, Christine
author Zanzoni, Andreas
author_facet Zanzoni, Andreas
Spinelli, Lionel
Ribeiro, Diogo M.
Tartaglia, Gian Gaetano
Brun, Christine
author_role author
author2 Spinelli, Lionel
Ribeiro, Diogo M.
Tartaglia, Gian Gaetano
Brun, Christine
author2_role author
author
author
author
dc.subject.none.fl_str_mv Cellular signalling networks
Gene regulatory networks
topic Cellular signalling networks
Gene regulatory networks
description 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.
publishDate 2019
dc.date.none.fl_str_mv 2019
2019
2019
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/36964
http://dx.doi.org/10.1038/s41598-019-40939-2
url http://hdl.handle.net/10230/36964
http://dx.doi.org/10.1038/s41598-019-40939-2
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Scientific Reports. 2019 Mar;9(1):4302
info:eu-repo/grantAgreement/ES/1PE/BFU2014-55054-P
info:eu-repo/grantAgreement/EC/FP7/309545
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Nature Research
publisher.none.fl_str_mv Nature Research
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869408821550514176
score 15,812429

Similares en LA Referencia