title: Mining mammalian transcript data for functional long non-coding RNAs.
abstract: BACKGROUND
  The role of long non-coding RNAs (lncRNAs) in controlling gene expression has garnered increased interest in recent years. Sequencing projects, such as Fantom3 for mouse and H-InvDB for human, have generated abundant data on transcribed components of mammalian cells, the majority of which appear not to be protein-coding. However, much of the non-protein-coding transcriptome could merely be a consequence of 'transcription noise'. It is therefore essential to use bioinformatic approaches to identify the likely functional candidates in a high throughput manner.
  
  
  RESULTS
  We derived a scheme for classifying and annotating likely functional lncRNAs in mammals. Using the available experimental full-length cDNA data sets for human and mouse, we identified 78 lncRNAs that are either syntenically conserved between human and mouse, or that originate from the same protein-coding genes. Of these, 11 have significant sequence homology. We found that these lncRNAs exhibit: (i) patterns of codon substitution typical of non-coding transcripts; (ii) preservation of sequences in distant mammals such as dog and cow, (iii) significant sequence conservation relative to their corresponding flanking regions (in 50% cases, flanking regions do not have homology at all; and in the remaining, the degree of conservation is significantly less); (iv) existence mostly as single-exon forms (8/11); and, (v) presence of conserved and stable secondary structure motifs within them. We further identified orthologous protein-coding genes that are contributing to the pool of lncRNAs; of which, genes implicated in carcinogenesis are significantly over-represented.
  
  
  CONCLUSIONS
  Our comparative mammalian genomics approach coupled with evolutionary analysis identified a small population of conserved long non-protein-coding RNAs (lncRNAs) that are potentially functional across Mammalia. Additionally, our analysis indicates that amongst the orthologous protein-coding genes that produce lncRNAs, those implicated in cancer pathogenesis are significantly over-represented, suggesting that these lncRNAs could play an important role in cancer pathomechanisms.
authors.affiliation: Department of Biology, McGill University, Montreal, Quebec, Canada. amit.khachane@mail.mcgill.ca
authors.forename: Amit N
authors.initials: AN
authors.lastname: Khachane
authors.forename: Paul M
authors.initials: PM
authors.lastname: Harrison
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D003625:Data Collection; D023281:Genomics; D006801:Humans; D008322:Mammals; D022661:RNA, Untranslated / Q000145:classification / Q000235:genetics / Q000502:physiology*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D022661:RNA, Untranslated