Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis

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  • dc.contributor.author Pegueroles Queralt, Maria Cinta
  • dc.contributor.author Iraola Guzmán, Susana
  • dc.contributor.author Chorostecki, Uciel
  • dc.contributor.author Ksiezopolska, Ewa
  • dc.contributor.author Saus Martínez, Ester
  • dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
  • dc.date.accessioned 2019-09-17T16:02:06Z
  • dc.date.available 2019-09-17T16:02:06Z
  • dc.date.issued 2019
  • dc.description.abstract Long non-coding RNAs (lncRNAs) are a heterogeneous class of genes that do not code for proteins. Since lncRNAs (or a fraction thereof) are expected to be functional, many efforts have been dedicated to catalog lncRNAs in numerous organisms, but our knowledge of lncRNAs in non vertebrate species remains very limited. Here, we annotated lncRNAs using transcriptomic data from the same larval stage of four Caenorhabditis species. The number of annotated lncRNAs in self-fertile nematodes was lower than in out-crossing species. We used a combination of approaches to identify putatively homologous lncRNAs: synteny, sequence conservation, and structural conservation. We classified a total of 1,532 out of 7,635 genes from the four species into families of lncRNAs with conserved synteny and expression at the larval stage, suggesting that a large fraction of the predicted lncRNAs may be species specific. Despite both sequence and local secondary structure seem to be poorly conserved, sequences within families frequently shared BLASTn hits and short sequence motifs, which were more likely to be unpaired in the predicted structures. We provide the first multi-species catalog of lncRNAs in nematodes and identify groups of lncRNAs with conserved synteny and expression, that share exposed motifs.
  • dc.description.sponsorship This work was supported by the Spanish Ministry of Economy,Industry, and Competitiveness (MEIC), INB Grant (PT17/0009/0023 - ISCIII-SGEFI/ERDF) by the EMBL partnership, and grants ‘Centro de Excelencia Severo Ochoa 2013–2017’ SEV-2012-0208, and BFU2015-67107 cofounded by European Regional 710 Development Fund (ERDF); by the CERCA Programme/Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR857, and grant from the European Union’s Horizon 2020 research and innovation programme under the grant agreement ERC-2016-724173 the Marie Sklodowska-Curie grant agreement No 715 H2020-MSCA-ITN-2014-642095 and the Marie Skłodowska-Curie Actions [H2020-MSCA-IF-2017-793699].
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Pegueroles C, Iraola-Guzmán S, Chorostecki U, Ksiezopolska E, Saus E, Gabaldón T. Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis. RNA Biol. 2019 Mar;16(3):320-9. DOI: 10.1080/15476286.2019.1572438
  • dc.identifier.doi http://dx.doi.org/10.1080/15476286.2019.1572438
  • dc.identifier.issn 1547-6286
  • dc.identifier.uri http://hdl.handle.net/10230/42287
  • dc.language.iso eng
  • dc.publisher Taylor & Francis
  • dc.relation.ispartof RNA Biology. 2019 Mar;16(3):320-9
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2015-67107
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/724173
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/642095
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/793699
  • dc.rights © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited, and is not altered, transformed, or built upon in any way
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/4.0/
  • dc.subject.keyword Lncrna
  • dc.subject.keyword Caenorhabditis
  • dc.subject.keyword Synteny
  • dc.subject.keyword Secondary structure
  • dc.subject.keyword Motifs
  • dc.title Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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