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

Hon, Chung-Chau, Ramilowski, Jordan A., Harshbarger, Jayson, Bertin, Nicolas, Rackham, Owen J. L., Gough, Julian, Denisenko, Elena, Schmeier, Sebastian, Poulsen, Thomas M., Severin, Jessica, Lizio, Marina, Kawaji, Hideya, Kasukawa, Takeya, Itoh, Masayoshi, Burroughs, A. Maxwell, Noma, Shohei, Djebali, Sarah, Alam, Tanvir, Medvedeva, Yulia A., Testa, Alison C., Lipovich, Leonard, Yip, Chi-Wai, Abugessaisa, Imad, Mendez, Mickael, Hasegawa, Akira, Tang, Dave, Lassmann, Timo, Heutink, Peter, Babina, Magda, Wells, Christine A., Kojima, Soichi, Nakamura, Yukio, Suzuki, Harukazu, Daub, Carsten O., de Hoon, Michiel J. L., Arner, Erik, Hayashizaki, Yoshihide, Carninci, Piero and Forrest, Alistair R. R. (2017) An atlas of human long non-coding RNAs with accurate 5′ ends. Nature, 543 7644: 199-204. doi:10.1038/nature21374

Author Hon, Chung-Chau
Ramilowski, Jordan A.
Harshbarger, Jayson
Bertin, Nicolas
Rackham, Owen J. L.
Gough, Julian
Denisenko, Elena
Schmeier, Sebastian
Poulsen, Thomas M.
Severin, Jessica
Lizio, Marina
Kawaji, Hideya
Kasukawa, Takeya
Itoh, Masayoshi
Burroughs, A. Maxwell
Noma, Shohei
Djebali, Sarah
Alam, Tanvir
Medvedeva, Yulia A.
Testa, Alison C.
Lipovich, Leonard
Yip, Chi-Wai
Abugessaisa, Imad
Mendez, Mickael
Hasegawa, Akira
Tang, Dave
Lassmann, Timo
Heutink, Peter
Babina, Magda
Wells, Christine A.
Kojima, Soichi
Nakamura, Yukio
Suzuki, Harukazu
Daub, Carsten O.
de Hoon, Michiel J. L.
Arner, Erik
Hayashizaki, Yoshihide
Carninci, Piero
Forrest, Alistair R. R.
Title An atlas of human long non-coding RNAs with accurate 5′ ends
Journal name Nature   Check publisher's open access policy
ISSN 1476-4687
Publication date 2017-03-01
Sub-type Article (original research)
DOI 10.1038/nature21374
Open Access Status Not yet assessed
Volume 543
Issue 7644
Start page 199
End page 204
Total pages 6
Place of publication London, United Kingdom
Publisher Nature Publishing Group
Language eng
Subject 1000 General
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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
Australian Institute for Bioengineering and Nanotechnology Publications
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Citation counts: TR Web of Science Citation Count  Cited 59 times in Thomson Reuters Web of Science Article | Citations
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