The discovery potential of RNA processing profiles

Mostra el registre complet Registre parcial de l'ítem

  • dc.contributor.author Pagès Pinós, Amadísca
  • dc.contributor.author Dotu, Ivanca
  • dc.contributor.author Pallarès Albanell, Joanca
  • dc.contributor.author Martí Puig, Eulàliaca
  • dc.contributor.author Guigó Serra, Rodericca
  • dc.contributor.author Eyras Jiménez, Eduardoca
  • dc.date.accessioned 2018-04-11T07:28:28Z
  • dc.date.available 2018-04-11T07:28:28Z
  • dc.date.issued 2018
  • dc.description.abstract Small non-coding RNAs (sncRNAs) are highly abundant molecules that regulate essential cellular processes and are classified according to sequence and structure. Here we argue that read profiles from size-selected RNA sequencing capture the post-transcriptional processing specific to each RNA family, thereby providing functional information independently of sequence and structure. We developed SeRPeNT, a new computational method that exploits reproducibility across replicates and uses dynamic time-warping and density-based clustering algorithms to identify, characterize and compare sncRNAs by harnessing the power of read profiles. We applied SeRPeNT to: (i) generate an extended human annotation with 671 new sncRNAs from known classes and 131 from new potential classes, (ii) show pervasive differential processing of sncRNAs between cell compartments and (iii) predict new molecules with miRNA-like behaviour from snoRNA, tRNA and long non-coding RNA precursors, potentially dependent on the miRNA biogenesis pathway. Furthermore, we validated experimentally four predicted novel non-coding RNAs: a miRNA, a snoRNA-derived miRNA, a processed tRNA and a new uncharacterized sncRNA. SeRPeNT facilitates fast and accurate discovery and characterization of sncRNAs at an unprecedented scale. SeRPeNT code is available under the MIT license at https://github.com/comprna/SeRPeNT.
  • dc.description.sponsorship MINECO (to E.E., A.P.); FEDER [BIO2014-52566-R to E.E., A.P.]; Consolider RNAREG [CSD2009-00080 to E.E., A.P.]; AGAUR [SGR2014-1121 to E.E., A.P.]; European ITN Network RNP-Net [ID:289007 to E.E., A.P.]; Sandra Ibarra Foundation for Cancer [FSI2013 to E.E., A.P.]; MINECO [BIO2011-26205 to R.G., A.P., SAF2014-60551-R to E.M., J.P.A.]; National Human Genome Research Institute of the National Institutes of Health [U54HG007004 to R.G., A.P.]; MINECO Centro de Excelencia Severo Ochoa 2013-2017 [SEV-2012-0208 to R.G., A.P.]; Research Programme on Biomedical Informatics (GRIB), which is member of ELIXIR-Excelerate of the European Union Horizon 2020 Programme 2014-2020 [676559 to E.E., A.P., I.D.]; ELIXIR-Excelerate, European Union Horizon 2020 Spanish National Bioinformatics Institute (INB) [PT13/0001/0023 to E.E., A.P., I.D.]. Funding for open access charge: European ITN Network RNP-Net [ID:289007] and MINECO-FEDER [BIO2014-52566-R].
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Pagès A, Dotu I, Pallarès-Albanell J, Martí E, Guigó R, Eyras E. The discovery potential of RNA processing profiles. Nucleic Acids Res. 2018 Feb 16;46(3):e15. DOI: 10.1093/nar/gkx1115
  • dc.identifier.doi http://dx.doi.org/10.1093/nar/gkx1115
  • dc.identifier.issn 0305-1048
  • dc.identifier.uri http://hdl.handle.net/10230/34335
  • dc.language.iso eng
  • dc.publisher Oxford University Pressca
  • dc.relation.ispartof Nucleic Acids Research. 2018 Feb 16;46(3):e15
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/289007
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/676559
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BIO2014-52566-R
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2011-26205
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/SAF2014-60551-R
  • 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 Small non-coding RNAs
  • dc.title The discovery potential of RNA processing profilesca
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion