title: Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).
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.
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Julien
authors.initials: J
authors.lastname: Lagarde
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Barbara
authors.identifier: 0000-0003-0150-3841
authors.initials: B
authors.lastname: Uszczynska-Ratajczak
authors.affiliation: Genomics and Bioinformatics Platform of Andalusia (GBPA), 41092 Seville, Spain.
authors.forename: Javier
authors.identifier: 0000-0003-1988-5059
authors.initials: J
authors.lastname: Santoyo-Lopez
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1HH, UK.
authors.forename: Jose Manuel
authors.initials: JM
authors.lastname: Gonzalez
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1HH, UK.
authors.forename: Electra
authors.initials: E
authors.lastname: Tapanari
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1HH, UK.
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Mudge
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1HH, UK.
authors.forename: Charles A
authors.initials: CA
authors.lastname: Steward
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1HH, UK.
authors.forename: Laurens
authors.initials: L
authors.lastname: Wilming
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Andrea
authors.identifier: 0000-0003-2873-4236
authors.initials: A
authors.lastname: Tanzer
authors.affiliation: Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
authors.forename: Cédric
authors.initials: C
authors.lastname: Howald
authors.affiliation: Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Chrast
authors.affiliation: Genomics and Bioinformatics Platform of Andalusia (GBPA), 41092 Seville, Spain.|Roche Diagnostics, 08174 Sant Cugat Del Vallès, Barcelona, Spain.
authors.forename: Alicia
authors.initials: A
authors.lastname: Vela-Boza
authors.affiliation: Genomics and Bioinformatics Platform of Andalusia (GBPA), 41092 Seville, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Rueda
authors.affiliation: Genomics and Bioinformatics Platform of Andalusia (GBPA), 41092 Seville, Spain.
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Lopez-Domingo
authors.affiliation: Genomics and Bioinformatics Platform of Andalusia (GBPA), 41092 Seville, Spain.|Computational Genomics Department, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain.|Functional Genomics Node (INB), Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain.
authors.forename: Joaquin
authors.initials: J
authors.lastname: Dopazo
authors.affiliation: Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Reymond
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigó
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1HH, UK.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Harrow
mesh_terms: D005091:Exons / Q000235:genetics; D056426:Genetic Loci; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D058977:Molecular Sequence Annotation; D009928:Organ Specificity / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000379:methods*; D000075082:Proof of Concept Study; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D022821:RNA Splice Sites / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics
chemical_list: D020033:Protein Isoforms; D022821:RNA Splice Sites; D062085:RNA, Long Noncoding; D012333:RNA, Messenger