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

TitleAn atlas of human long non-coding RNAs with accurate 5' ends.
Publication TypeJournal Article
Year of Publication2017
AuthorsHon, C-C, Ramilowski, JA, Harshbarger, J, Bertin, N, Rackham, OJL, Gough, J, Denisenko, E, Schmeier, S, Poulsen, TM, Severin, J, Lizio, M, Kawaji, H, Kasukawa, T, Itoh, M, A Burroughs, M, Noma, S, Djebali, S, Alam, T, Medvedeva, YA, Testa, AC, Lipovich, L, Yip, C-W, Abugessaisa, I, Mendez, M, Hasegawa, A, Tang, D, Lassmann, T, Heutink, P, Babina, M, Wells, CA, Kojima, S, Nakamura, Y, Suzuki, H, Daub, CO, de Hoon, MJL, Arner, E, Hayashizaki, Y, Carninci, P, Forrest, ARR
JournalNature
Volume543
Issue7644
Pagination199-204
Date Published2017 Mar 09
ISSN1476-4687
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.

DOI10.1038/nature21374
Alternate JournalNature
PubMed ID28241135