TY - JOUR
T1 - Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq)
AU - Lagarde, Julien
AU - Uszczynska-Ratajczak, Barbara
AU - Santoyo-Lopez, Javier
AU - Gonzalez, Jose Manuel
AU - Tapanari, Electra
AU - Mudge, Jonathan M.
AU - Steward, Charles A.
AU - Wilming, Laurens
AU - Tanzer, Andrea
AU - Howald, Cédric
AU - Chrast, Jacqueline
AU - Vela-Boza, Alicia
AU - Rueda, Antonio
AU - Lopez-Domingo, Francisco J.
AU - Dopazo, Joaquin
AU - Reymond, Alexandre
AU - Guigó, Roderic
AU - Harrow, Jennifer
PY - 2016/8/17
Y1 - 2016/8/17
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84983446019&partnerID=8YFLogxK
U2 - 10.1038/ncomms12339
DO - 10.1038/ncomms12339
M3 - Article
AN - SCOPUS:84983446019
SN - 2041-1723
VL - 7
JO - Nature Communications
JF - Nature Communications
M1 - 12339
ER -