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

Author

Listed:
  • Julien Lagarde

    (Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST)
    Universitat Pompeu Fabra (UPF))

  • Barbara Uszczynska-Ratajczak

    (Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST)
    Universitat Pompeu Fabra (UPF))

  • Javier Santoyo-Lopez

    (Genomics and Bioinformatics Platform of Andalusia (GBPA)
    Present address: Edinburgh Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK)

  • Jose Manuel Gonzalez

    (Wellcome Trust Sanger Institute, Hinxton)

  • Electra Tapanari

    (Wellcome Trust Sanger Institute, Hinxton
    Present address: European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK)

  • 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)
    Universitat Pompeu Fabra (UPF)
    Present address: Department of Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, 1090 Vienna, Austria)

  • Cédric Howald

    (Center for Integrative Genomics, University of Lausanne
    Present address: Division of Genetic Medicine, Geneva University Hospitals, Geneva, Switzerland)

  • Jacqueline Chrast

    (Center for Integrative Genomics, University of Lausanne)

  • Alicia Vela-Boza

    (Genomics and Bioinformatics Platform of Andalusia (GBPA)
    Roche Diagnostics)

  • 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)
    Centro de Investigación Príncipe Felipe
    Functional Genomics Node (INB), Centro de Investigación Príncipe Felipe)

  • Alexandre Reymond

    (Center for Integrative Genomics, University of Lausanne)

  • Roderic Guigó

    (Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST)
    Universitat Pompeu Fabra (UPF))

  • Jennifer Harrow

    (Wellcome Trust Sanger Institute, Hinxton)

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.

Suggested Citation

  • Julien Lagarde & Barbara Uszczynska-Ratajczak & Javier Santoyo-Lopez & Jose Manuel Gonzalez & Electra Tapanari & Jonathan M. Mudge & Charles A. Steward & Laurens Wilming & Andrea Tanzer & Cédric Howal, 2016. "Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq)," Nature Communications, Nature, vol. 7(1), pages 1-11, November.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms12339
    DOI: 10.1038/ncomms12339
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