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

Moran Cabili, Cole Trapnell, Loyal Goff, Magdalena Koziol, Barbara Tazon-Vega, Aviv Regev, John L. Rinn

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)1915-1927
Number of pages13
JournalGenes and Development
Issue number18
StatePublished - Sep 15 2011
Externally publishedYes


  • Lincrnas
  • Long noncoding rnas
  • Rna sequencing

ASJC Scopus subject areas

  • Genetics
  • Developmental Biology


Dive into the research topics of 'Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses'. Together they form a unique fingerprint.

Cite this