title: An atlas of human long non-coding RNAs with accurate 5' ends.
abstract: Long non-coding RNAs (lncRNAs) are largely heterogeneous and functionally uncharacterized. Here, using FANTOM5 cap analysis of gene expression (CAGE) data, we integrate multiple transcript collections to generate a comprehensive atlas of 27,919 human lncRNA genes with high-confidence 5' ends and expression profiles across 1,829 samples from the major human primary cell types and tissues. Genomic and epigenomic classification of these lncRNAs reveals that most intergenic lncRNAs originate from enhancers rather than from promoters. Incorporating genetic and expression data, we show that lncRNAs overlapping trait-associated single nucleotide polymorphisms are specifically expressed in cell types relevant to the traits, implicating these lncRNAs in multiple diseases. We further demonstrate that lncRNAs overlapping expression quantitative trait loci (eQTL)-associated single nucleotide polymorphisms of messenger RNAs are co-expressed with the corresponding messenger RNAs, suggesting their potential roles in transcriptional regulation. Combining these findings with conservation data, we identify 19,175 potentially functional lncRNAs in the human genome.
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.
authors.forename: Chung-Chau
authors.initials: CC
authors.lastname: Hon
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
authors.forename: Jordan A
authors.initials: JA
authors.lastname: Ramilowski
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
authors.forename: Jayson
authors.initials: J
authors.lastname: Harshbarger
authors.affiliation: RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.|Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, #12-01, Singapore 117599, Singapore.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Bertin
authors.affiliation: University of Bristol, Department of Computer Science, Life Sciences building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.|Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, 169857 Singapore.
authors.forename: Owen J L
authors.initials: OJ
authors.lastname: Rackham
authors.affiliation: University of Bristol, Department of Computer Science, Life Sciences building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
authors.forename: Julian
authors.initials: J
authors.lastname: Gough
authors.affiliation: Institute of Natural and Mathematical Sciences, Massey University Auckland, Albany 0632, New Zealand.
authors.forename: Elena
authors.initials: E
authors.lastname: Denisenko
authors.affiliation: Institute of Natural and Mathematical Sciences, Massey University Auckland, Albany 0632, New Zealand.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Schmeier
authors.affiliation: Biotechnology Research Institute for Drug Discovery (BRD), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan.
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Poulsen
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
authors.forename: Jessica
authors.initials: J
authors.lastname: Severin
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
authors.forename: Marina
authors.initials: M
authors.lastname: Lizio
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.|RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
authors.forename: Hideya
authors.initials: H
authors.lastname: Kawaji
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.
authors.forename: Takeya
authors.initials: T
authors.lastname: Kasukawa
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.|RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
authors.forename: Masayoshi
authors.initials: M
authors.lastname: Itoh
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.|National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
authors.forename: A Maxwell
authors.initials: AM
authors.lastname: Burroughs
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
authors.forename: Shohei
authors.initials: S
authors.lastname: Noma
authors.affiliation: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.|Universitat Pompeu Fabra (UPF), Barcelona Biomedical Research Park (PRBB), Dr Aiguader 88, Barcelona 08003, Spain.
authors.forename: Sarah
authors.initials: S
authors.lastname: Djebali
authors.affiliation: Computational Bioscience Research Center; Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
authors.forename: Tanvir
authors.initials: T
authors.lastname: Alam
authors.affiliation: Institute of Bioengineering, Research Center of Biotechnology RAS, Moscow 119071, Russia.|Vavilov Institute of General Genetic, RAS, Moscow 119991, Russia.
authors.forename: Yulia A
authors.initials: YA
authors.lastname: Medvedeva
authors.affiliation: Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands 6009, Western Australia, Australia.
authors.forename: Alison C
authors.initials: AC
authors.lastname: Testa
authors.affiliation: Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA.|Department of Neurology, School of Medicine, Wayne State University, Detroit, Michigan 48201, USA.
authors.forename: Leonard
authors.initials: L
authors.lastname: Lipovich
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.
authors.forename: Chi-Wai
authors.initials: CW
authors.lastname: Yip
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.
authors.forename: Imad
authors.initials: I
authors.lastname: Abugessaisa
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
authors.forename: Mickaël
authors.initials: M
authors.lastname: Mendez
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Hasegawa
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.|Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, Subiaco, 6008, Western Australia, Australia.
authors.forename: Dave
authors.initials: D
authors.lastname: Tang
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.|Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, Subiaco, 6008, Western Australia, Australia.
authors.forename: Timo
authors.initials: T
authors.lastname: Lassmann
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|German Center for Neurodegenerative Diseases (DZNE), D-72076 Tübingen, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Heutink
authors.affiliation: Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.
authors.forename: Magda
authors.initials: M
authors.lastname: Babina
authors.affiliation: Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane 4072, Australia.|Faculty of Medicine, Department of Anatomy and Neuroscience, The University of Melbourne, 3010, Australia.
authors.forename: Christine A
authors.initials: CA
authors.lastname: Wells
authors.affiliation: RIKEN CLST (Division of Bio-Function Dynamics Imaging), Wako, Saitama 351-0198, Japan.
authors.forename: Soichi
authors.initials: S
authors.lastname: Kojima
authors.affiliation: Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan.|Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan.
authors.forename: Yukio
authors.initials: Y
authors.lastname: Nakamura
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
authors.forename: Harukazu
authors.initials: H
authors.lastname: Suzuki
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.|Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden.
authors.forename: Carsten O
authors.initials: CO
authors.lastname: Daub
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
authors.forename: Michiel J L
authors.initials: MJ
authors.lastname: de Hoon
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
authors.forename: Erik
authors.initials: E
authors.lastname: Arner
authors.affiliation: RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.|RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.affiliation: RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.|RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.|Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands 6009, Western Australia, Australia.
authors.forename: Alistair R R
authors.initials: AR
authors.lastname: Forrest
mesh_terms: D002478:Cells, Cultured; D017124:Conserved Sequence / Q000235:genetics; D030541:Databases, Genetic; D066264:Datasets as Topic; D004742:Enhancer Elements, Genetic / Q000235:genetics; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D015894:Genome, Human / Q000235:genetics; D055106:Genome-Wide Association Study; D023281:Genomics; D006801:Humans; D020407:Internet; D058977:Molecular Sequence Annotation; D009928:Organ Specificity / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics; D020871:RNA Stability; D062085:RNA, Long Noncoding / Q000737:chemistry* / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger