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

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

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Exons / genetics
  • Genetic Loci
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Molecular Sequence Annotation
  • Organ Specificity / genetics
  • Polymerase Chain Reaction / methods*
  • Proof of Concept Study
  • Protein Isoforms / genetics
  • Protein Isoforms / metabolism
  • RNA Splice Sites / genetics
  • RNA, Long Noncoding / genetics*
  • RNA, Long Noncoding / metabolism
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Sequence Analysis, RNA / methods*
  • Transcriptome / genetics

Substances

  • Protein Isoforms
  • RNA Splice Sites
  • RNA, Long Noncoding
  • RNA, Messenger