Titel
Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq)
Autor*in
Julien Lagarde
Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST)
Autor*in
Barbara Uszczynska-Ratajczak
Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST)
Autor*in
Javier Santoyo-Lopez
Genomics and Bioinformatics Platform of Andalusia (GBPA)
... show all
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.
Stichwort
Long non-coding RNAsRNA splicingSequence annotationTranscriptomics
Objekt-Typ
Sprache
Englisch [eng]
Persistent identifier
https://phaidra.univie.ac.at/o:538049
Erschienen in
Titel
Nature Communications
Band
7
Verlag
Springer Nature
Erscheinungsdatum
2016
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