An atlas of human long non-coding RNAs with accurate 5′ ends

Chung-Chau Hon, Jordan A. Ramilowski, Jayson Harshbarger, Nicolas Bertin, Owen J. L. Rackham, Julian Gough, Elena Denisenko, Sebastian Schmeier, Thomas M. Poulsen, Jessica Severin, Marina Lizio, Hideya Kawaji, Takeya Kasukawa, Masayoshi Itoh, A. Maxwell Burroughs, Shohei Noma, Sarah Djebali, Tanvir Alam, Yulia A. Medvedeva, Alison C. Testa, Leonard Lipovich, Chi-Wai Yip, Imad Abugessaisa, Mickaël Mendez, Akira Hasegawa, Dave Tang, Timo Lassmann, Peter Heutink, Magda Babina, Christine A. Wells, Soichi Kojima, Yukio Nakamura, Harukazu Suzuki, Carsten O. Daub, Michiel J. L. de Hoon, Erik Arner, Yoshihide Hayashizaki, Piero Carninci () and Alistair R. R. Forrest ()
Additional contact information
Chung-Chau Hon: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Jordan A. Ramilowski: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Jayson Harshbarger: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Nicolas Bertin: RIKEN Omics Science Center (OSC)
Owen J. L. Rackham: University of Bristol, Life Sciences building
Julian Gough: University of Bristol, Life Sciences building
Elena Denisenko: Institute of Natural and Mathematical Sciences, Massey University Auckland
Sebastian Schmeier: Institute of Natural and Mathematical Sciences, Massey University Auckland
Thomas M. Poulsen: Biotechnology Research Institute for Drug Discovery (BRD), National Institute of Advanced Industrial Science and Technology (AIST)
Jessica Severin: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Marina Lizio: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Hideya Kawaji: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Takeya Kasukawa: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Masayoshi Itoh: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
A. Maxwell Burroughs: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Shohei Noma: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Sarah Djebali: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology
Tanvir Alam: Computational Bioscience Research Center; Computer, King Abdullah University of Science and Technology (KAUST)
Yulia A. Medvedeva: Institute of Bioengineering, Research Center of Biotechnology RAS
Alison C. Testa: Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia
Leonard Lipovich: Center for Molecular Medicine and Genetics, Wayne State University
Chi-Wai Yip: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Imad Abugessaisa: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Mickaël Mendez: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Akira Hasegawa: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Dave Tang: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Timo Lassmann: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Peter Heutink: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Magda Babina: Charité Universitätsmedizin Berlin
Christine A. Wells: Australian Institute for Bioengineering and Nanotechnology, The University of Queensland
Soichi Kojima: RIKEN CLST (Division of Bio-Function Dynamics Imaging)
Yukio Nakamura: RIKEN BioResource Center
Harukazu Suzuki: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Carsten O. Daub: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Michiel J. L. de Hoon: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Erik Arner: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Yoshihide Hayashizaki: RIKEN Omics Science Center (OSC)
Piero Carninci: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)
Alistair R. R. Forrest: RIKEN Center for Life Science Technologies (Division of Genomic Technologies)

Nature, 2017, vol. 543, issue 7644, 199-204

Abstract: 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.

Date: 2017
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DOI: 10.1038/nature21374

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