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 & 19 others Leonard Lipovich, Chi Wai Yip, Imad Abugessaisa, Mickal 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, Alistair R R Forrest

Research output: Contribution to journalArticle

274 Citations (Scopus)

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.      © 2017 Macmillan Publishers Limited, part of Springer Nature

Original languageEnglish
Pages (from-to)199-204
Number of pages6
JournalNature
Volume543
Issue number7644
DOIs
Publication statusPublished - 9 Mar 2017

    Fingerprint

Cite this

Hon, C. C., Ramilowski, J. A., Harshbarger, J., Bertin, N., Rackham, O. J. L., Gough, J., ... Forrest, A. R. R. (2017). An atlas of human long non-coding RNAs with accurate 5′ ends. Nature, 543(7644), 199-204. https://doi.org/10.1038/nature21374