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

Julien Lagarde, Barbara Uszczynska-Ratajczak, Javier Santoyo-Lopez, Jose Manuel Gonzalez, Electra Tapanari, Jonathan M. Mudge, Charles A. Steward, Laurens Wilming, Andrea Tanzer, Cédric Howald, Jacqueline Chrast, Alicia Vela-Boza, Antonio Rueda, Francisco J. Lopez-Domingo, Joaquin Dopazo, Alexandre Reymond, Roderic Guigó () and Jennifer Harrow ()
Additional contact information
Julien Lagarde: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST)
Barbara Uszczynska-Ratajczak: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST)
Javier Santoyo-Lopez: Genomics and Bioinformatics Platform of Andalusia (GBPA)
Jose Manuel Gonzalez: Wellcome Trust Sanger Institute, Hinxton
Electra Tapanari: Wellcome Trust Sanger Institute, Hinxton
Jonathan M. Mudge: Wellcome Trust Sanger Institute, Hinxton
Charles A. Steward: Wellcome Trust Sanger Institute, Hinxton
Laurens Wilming: Wellcome Trust Sanger Institute, Hinxton
Andrea Tanzer: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST)
Cédric Howald: Center for Integrative Genomics, University of Lausanne
Jacqueline Chrast: Center for Integrative Genomics, University of Lausanne
Alicia Vela-Boza: Genomics and Bioinformatics Platform of Andalusia (GBPA)
Antonio Rueda: Genomics and Bioinformatics Platform of Andalusia (GBPA)
Francisco J. Lopez-Domingo: Genomics and Bioinformatics Platform of Andalusia (GBPA)
Joaquin Dopazo: Genomics and Bioinformatics Platform of Andalusia (GBPA)
Alexandre Reymond: Center for Integrative Genomics, University of Lausanne
Roderic Guigó: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST)
Jennifer Harrow: Wellcome Trust Sanger Institute, Hinxton

Nature Communications, 2016, vol. 7, issue 1, 1-11

Abstract: 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.

Date: 2016
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DOI: 10.1038/ncomms12339

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