RT Journal
A1 Derrien, Thomas
A1 Johnson, Rory
A1 Bussotti, Giovanni
A1 Tanzer, Andrea
A1 Djebali, Sarah
A1 Tilgner, Hagen
A1 Guernec, Gregory
A1 Martin, David
A1 Merkel, Angelika
A1 Knowles, David G.
A1 Lagarde, Julien
A1 Veeravalli, Lavanya
A1 Ruan, Xiaoan
A1 Ruan, Yijun
A1 Lassmann, Timo
A1 Carninci, Piero
A1 Brown, James B.
A1 Lipovich, Leonard
A1 Gonzalez, Jose M.
A1 Thomas, Mark
A1 Davis, Carrie A.
A1 Shiekhattar, Ramin
A1 Gingeras, Thomas R.
A1 Hubbard, Tim J.
A1 Notredame, Cedric
A1 Harrow, Jennifer
A1 Guigó, Roderic
T1 The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
JF Genome Research 
JO Genome Research 
YR 2012 
FD September 01 
VO 22 
IS 9 
SP 1775 
OP 1789 
DO 10.1101/gr.132159.111 
UL http://genome.cshlp.org/content/22/9/1775.abstract 
AB 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.