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Nat Commun. 2016 Aug 17;7:12339. doi: 10.1038/ncomms12339.

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

Author information

1
Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain.
2
Universitat Pompeu Fabra (UPF), Barcelona, Spain.
3
Genomics and Bioinformatics Platform of Andalusia (GBPA), 41092 Seville, Spain.
4
Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1HH, UK.
5
Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
6
Roche Diagnostics, 08174 Sant Cugat Del Vallès, Barcelona, Spain.
7
Computational Genomics Department, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain.
8
Functional Genomics Node (INB), Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain.

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.

PMID:
27531712
PMCID:
PMC4992054
DOI:
10.1038/ncomms12339
[Indexed for MEDLINE]
Free PMC Article

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