RGD Reference Report - The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. - Rat Genome Database

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The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.

Authors: Derrien, Thomas  Johnson, Rory  Bussotti, Giovanni  Tanzer, Andrea  Djebali, Sarah  Tilgner, Hagen  Guernec, Gregory  Martin, David  Merkel, Angelika  Knowles, David G  Lagarde, Julien  Veeravalli, Lavanya  Ruan, Xiaoan  Ruan, Yijun  Lassmann, Timo  Carninci, Piero  Brown, James B  Lipovich, Leonard  Gonzalez, Jose M  Thomas, Mark  Davis, Carrie A  Shiekhattar, Ramin  Gingeras, Thomas R  Hubbard, Tim J  Notredame, Cedric  Harrow, Jennifer  Guig√≥, Roderic 
Citation: Derrien T, etal., Genome Res. 2012 Sep;22(9):1775-89. doi: 10.1101/gr.132159.111.
RGD ID: 18182915
Pubmed: PMID:22955988   (View Abstract at PubMed)
PMCID: PMC3431493   (View Article at PubMed Central)
DOI: DOI:10.1101/gr.132159.111   (Journal Full-text)

The human genome contains many thousands of long noncoding RNAs (lncRNAs). While several studies have demonstrated compelling biological and disease roles for individual examples, analytical and experimental approaches to investigate these genes have been hampered by the lack of comprehensive lncRNA annotation. Here, we present and analyze the most complete human lncRNA annotation to date, produced by the GENCODE consortium within the framework of the ENCODE project and comprising 9277 manually annotated genes producing 14,880 transcripts. Our analyses indicate that lncRNAs are generated through pathways similar to that of protein-coding genes, with similar histone-modification profiles, splicing signals, and exon/intron lengths. In contrast to protein-coding genes, however, lncRNAs display a striking bias toward two-exon transcripts, they are predominantly localized in the chromatin and nucleus, and a fraction appear to be preferentially processed into small RNAs. They are under stronger selective pressure than neutrally evolving sequences-particularly in their promoter regions, which display levels of selection comparable to protein-coding genes. Importantly, about one-third seem to have arisen within the primate lineage. Comprehensive analysis of their expression in multiple human organs and brain regions shows that lncRNAs are generally lower expressed than protein-coding genes, and display more tissue-specific expression patterns, with a large fraction of tissue-specific lncRNAs expressed in the brain. Expression correlation analysis indicates that lncRNAs show particularly striking positive correlation with the expression of antisense coding genes. This GENCODE annotation represents a valuable resource for future studies of lncRNAs.

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