Scientific Publications

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses.

Publication TypeJournal Article
AuthorsCabili, MN, Trapnell C., Goff L., Koziol M., Tazon-Vega B., Regev A., and Rinn JL
AbstractLarge intergenic noncoding RNAs (lincRNAs) are emerging as key regulators of diverse cellular processes. Determining the function of individual lincRNAs remains a challenge. Recent advances in RNA sequencing (RNA-seq) and computational methods allow for an unprecedented analysis of such transcripts. Here, we present an integrative approach to define a reference catalog of >8000 human lincRNAs. Our catalog unifies previously existing annotation sources with transcripts we assembled from RNA-seq data collected from ∼4 billion RNA-seq reads across 24 tissues and cell types. We characterize each lincRNA by a panorama of >30 properties, including sequence, structural, transcriptional, and orthology features. We found that lincRNA expression is strikingly tissue-specific compared with coding genes, and that lincRNAs are typically coexpressed with their neighboring genes, albeit to an extent similar to that of pairs of neighboring protein-coding genes. We distinguish an additional subset of transcripts that have high evolutionary conservation but may include short ORFs and may serve as either lincRNAs or small peptides. Our integrated, comprehensive, yet conservative reference catalog of human lincRNAs reveals the global properties of lincRNAs and will facilitate experimental studies and further functional classification of these genes.
Year of Publication2011
JournalGenes & development
Volume25
Issue18
Pages1915-27
Date Published (YYYY/MM/DD)2011/09/15
ISSN Number0890-9369
DOI10.1101/gad.17446611
PubMedhttp://www.ncbi.nlm.nih.gov/pubmed/21890647?dopt=Abstract