title: Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses.
abstract: Large 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.
authors: Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA.
authors: Moran N
authors: MN
authors: Cabili
authors: Cole
authors: C
authors: Trapnell
authors: Loyal
authors: L
authors: Goff
authors: Magdalena
authors: M
authors: Koziol
authors: Barbara
authors: B
authors: Tazon-Vega
authors: Aviv
authors: A
authors: Regev
authors: John L
authors: JL
authors: Rinn
mesh_terms: D017398:Alternative Splicing; D004742:Enhancer Elements, Genetic / Q000235:genetics; D005786:Gene Expression Regulation; D005807:Genes, Overlapping; D006801:Humans; D058977:Molecular Sequence Annotation / Q000379:methods*; D022661:RNA, Untranslated / Q000145:classification / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D022661:RNA, Untranslated