Journal article
An atlas of human long non-coding RNAs with accurate 5′ ends
CC Hon, JA Ramilowski, J Harshbarger, N Bertin, OJL Rackham, J Gough, E Denisenko, S Schmeier, TM Poulsen, J Severin, M Lizio, H Kawaji, T Kasukawa, M Itoh, AM Burroughs, S Noma, S Djebali, T Alam, YA Medvedeva, AC Testa Show all
Nature | Published : 2017
DOI: 10.1038/nature21374
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 type..
View full abstractGrants
Awarded by Australian Research Council
Funding Acknowledgements
FANTOM5 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.