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Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq)

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dc.contributor.author Lagarde, Julien
dc.contributor.author Uszczynska-Ratajczak, Barbara
dc.contributor.author Santoyo-Lopez, Javier
dc.contributor.author Gonzalez, Jose Manuel
dc.contributor.author Tapanari, Electra
dc.contributor.author Mudge, Jonathan M.
dc.contributor.author Steward, Charles A.
dc.contributor.author Wilming, Laurens
dc.contributor.author Tanzer, Andrea
dc.contributor.author Howald, Cédric
dc.contributor.author Chrast, Jacqueline
dc.contributor.author Vela-Boza, Alicia
dc.contributor.author Rueda, Antonio
dc.contributor.author Lopez-Domingo, Francisco J.
dc.contributor.author Dopazo, Joaquín
dc.contributor.author Reymond, Alexandre
dc.contributor.author Guigó Serra, Roderic
dc.contributor.author Harrow, Jennifer
dc.date.accessioned 2017-01-20T12:11:42Z
dc.date.available 2017-01-20T12:11:42Z
dc.date.issued 2016
dc.identifier.citation Lagarde J, Uszczynska-Ratajczak B, Santoyo-Lopez J, Gonzalez JM, Tapanari E, Mudge JM [et. al.]. Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq). Nature Communications. 2016; 7: 12339. DOI: 10.1038/ncomms12339
dc.identifier.issn 2041-1723
dc.identifier.uri http://hdl.handle.net/10230/27947
dc.description.abstract Long non-coding RNAs (lncRNAs) constitute a large, yet mostly uncharacterized fraction of the mammalian transcriptome. Such characterization requires a comprehensive, high-quality annotation of their gene structure and boundaries, which is currently lacking. Here we describe RACE-Seq, an experimental workflow designed to address this based on RACE (rapid amplification of cDNA ends) and long-read RNA sequencing. We apply RACE-Seq to 398 human lncRNA genes in seven tissues, leading to the discovery of 2,556 on-target, novel transcripts. About 60% of the targeted loci are extended in either 5′ or 3′, often reaching genomic hallmarks of gene boundaries. Analysis of the novel transcripts suggests that lncRNAs are as long, have as many exons and undergo as much alternative splicing as protein-coding genes, contrary to current assumptions. Overall, we show that RACE-Seq is an effective tool to annotate an organism’s deep transcriptome, and compares favourably to other targeted sequencing techniques.
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Nature Publishing Group
dc.relation.ispartof Nature Communications. 2016; 7: 12339
dc.rights © Nature Publishing Group.This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.title Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq)
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1038/ncomms12339
dc.subject.keyword Long non-coding RNAs
dc.subject.keyword RNA splicing
dc.subject.keyword Sequence annotation
dc.subject.keyword Transcriptomics
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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