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dc.contributor.authorHon, Chung-Chau
dc.contributor.authorRamilowski, Jordan A.
dc.contributor.authorHarshbarger, Jayson
dc.contributor.authorBertin, Nicolas
dc.contributor.authorRackham, Owen J. L.
dc.contributor.authorGough, Julian
dc.contributor.authorDenisenko, Elena
dc.contributor.authorSchmeier, Sebastian
dc.contributor.authorPoulsen, Thomas M.
dc.contributor.authorSeverin, Jessica
dc.contributor.authorLizio, Marina
dc.contributor.authorKawaji, Hideya
dc.contributor.authorKasukawa, Takeya
dc.contributor.authorItoh, Masayoshi
dc.contributor.authorBurroughs, A. Maxwell
dc.contributor.authorNoma, Shohei
dc.contributor.authorDjebali, Sarah
dc.contributor.authorAlam, Tanvir
dc.contributor.authorMedvedeva, Yulia A.
dc.contributor.authorTesta, Alison C.
dc.contributor.authorLipovich, Leonard
dc.contributor.authorYip, Chi-Wai
dc.contributor.authorAbugessaisa, Imad
dc.contributor.authorMendez, Mickaël
dc.contributor.authorHasegawa, Akira
dc.contributor.authorTang, Dave
dc.contributor.authorLassmann, Timo
dc.contributor.authorHeutink, Peter
dc.contributor.authorBabina, Magda
dc.contributor.authorWells, Christine A.
dc.contributor.authorKojima, Soichi
dc.contributor.authorNakamura, Yukio
dc.contributor.authorSuzuki, Harukazu
dc.contributor.authorDaub, Carsten O.
dc.contributor.authorHoon, Michiel J. L. de
dc.contributor.authorArner, Erik
dc.contributor.authorHayashizaki, Yoshihide
dc.contributor.authorCarninci, Piero
dc.contributor.authorForrest, Alistair R. R.
dc.date.accessioned2017-05-31T11:23:05Z
dc.date.available2017-05-31T11:23:05Z
dc.date.issued2017-03-01
dc.identifier.citationHon C-C, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJL, et al. (2017) An atlas of human long non-coding RNAs with accurate 5′ ends. Nature 543: 199–204. Available: http://dx.doi.org/10.1038/nature21374.
dc.identifier.issn0028-0836
dc.identifier.issn1476-4687
dc.identifier.doi10.1038/nature21374
dc.identifier.urihttp://hdl.handle.net/10754/623789
dc.description.abstractLong 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.
dc.description.sponsorshipFANTOM5 was made possible by research grants for the RIKEN Omics Science Center and the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT to Y.H. It was also supported by research grants for the RIKEN Preventive Medicine and Diagnosis Innovation Program (RIKEN PMI) to Y.H. and the RIKEN Centre for Life Science Technologies, Division of Genomic Technologies (RIKEN CLST (DGT)) from the MEXT, Japan. A.R.R.F. is supported by a Senior Cancer Research Fellowship from the Cancer Research Trust, the MACA Ride to Conquer Cancer and the Australian Research Council’s Discovery Projects funding scheme (DP160101960). S.D. is supported by award number U54HG007004 from the National Human Genome Research Institute of the National Institutes of Health, funding from the Ministry of Economy and Competitiveness (MINECO) under grant number BIO2011-26205, and SEV-2012-0208 from the Spanish Ministry of Economy and Competitiveness. Y.A.M. is supported by the Russian Science Foundation, grant 15-14-30002. We thank RIKEN GeNAS for generation of the CAGE and RNA-seq libraries, the Netherlands Brain Bank for brain materials, the RIKEN BioResource Centre for providing cell lines and all members of the FANTOM5 consortium for discussions, in particular H. Ashoor, M. Frith, R. Guigo, A. Tanzer, E. Wood, H. Jia, K. Bailie, J. Harrow, E. Valen, R. Andersson, K. Vitting-Seerup, A. Sandelin, M. Taylor, J. Shin, R. Mori, C. Mungall and T. Meehan.
dc.publisherSpringer Nature
dc.relation.urlhttp://www.nature.com/nature/journal/v543/n7644/full/nature21374.html
dc.titleAn atlas of human long non-coding RNAs with accurate 5′ ends
dc.typeArticle
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.identifier.journalNature
dc.contributor.institutionRIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, , Japan
dc.contributor.institutionRIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, , Japan
dc.contributor.institutionCancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, #12-01, Singapore, 117599, , Singapore
dc.contributor.institutionHuman Longevity Singapore Pte. Ltd., Singapore, , Singapore
dc.contributor.institutionUniversity of Bristol, Department of Computer Science, 24 Tyndall Avenue, Bristol, BS8 1TQ, , United Kingdom
dc.contributor.institutionProgram in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, , Singapore
dc.contributor.institutionInstitute of Natural and Mathematical Sciences, Massey University Auckland, Albany, 0632, , New Zealand
dc.contributor.institutionBiotechnology 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
dc.contributor.institutionRIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Saitama, 351-0198, , Japan
dc.contributor.institutionNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, , United States
dc.contributor.institutionCentre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, , Spain
dc.contributor.institutionUniversitat Pompeu Fabra (UPF), Barcelona Biomedical Research Park (PRBB), Dr Aiguader 88, Barcelona, 08003, , Spain
dc.contributor.institutionGenPhySE, Université de Toulouse, INRA, Castanet Tolosan, , France
dc.contributor.institutionInstitute of Bioengineering, Research Center of Biotechnology RAS, Moscow, 119071, , Russian Federation
dc.contributor.institutionVavilov Institute of General Genetic, RAS, Moscow, 119991, , Russian Federation
dc.contributor.institutionHarry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, University of Western Australia, Nedlands, Western Australia, 6009, , Australia
dc.contributor.institutionCenter for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, , United States
dc.contributor.institutionDepartment of Neurology, School of Medicine, Wayne State University, Detroit, MI, 48201, , United States
dc.contributor.institutionDepartment of Computer Science, University of Toronto, Toronto, ON, , Canada
dc.contributor.institutionTelethon Kids Institute, University of Western Australia, 100 Roberts Road, Subiaco, Subiaco, Western Australia, 6008, , Australia
dc.contributor.institutionGerman Center for Neurodegenerative Diseases (DZNE), Tübingen, D-72076, , Germany
dc.contributor.institutionDepartment of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Berlin, 10117, , Germany
dc.contributor.institutionAustralian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, 4072, , Australia
dc.contributor.institutionFaculty of Medicine, Department of Anatomy and Neuroscience, University of Melbourne, 3010, , Australia
dc.contributor.institutionRIKEN CLST (Division of Bio-Function Dynamics Imaging), Wako, Saitama, 351-0198, , Japan
dc.contributor.institutionCell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, , Japan
dc.contributor.institutionFaculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, , Japan
dc.contributor.institutionDepartment of Biosciences and Nutrition, Karolinska Institutet, Huddinge, 141 83, , Sweden
kaust.personAlam, Tanvir
refterms.dateFOA2020-06-29T12:28:54Z
dc.date.published-online2017-03-01
dc.date.published-print2017-03


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