title: Evidence for the dissemination of cryptic non-coding RNAs transcribed from intronic and intergenic segments by retroposition.
abstract: BACKGROUND
  Insertion of DNA segments is one mechanism by which genomes evolve. The bulk of genomic segments are now known to be transcribed into long and short non-coding RNAs (ncRNAs), promoter-associated transcripts and enhancer-templated transcripts. These various cryptic ncRNAs are thought to be dispersed in the human and other genomes by retroposition.
  
  
  RESULTS
  In this study, I report clear evidence for dissemination of cryptic ncRNAs transcribed from intronic and intergenic segments by retroposition. I used highly stringent conditions to find recently retroposed ncRNAs that had a poly(A) tract and were flanked by target site duplication. I identified 73 instances of retroposition in the human, mouse, and rat genomes (12, 36 and 25 instances, respectively). The inserted segments, in some cases, served as a novel exon or promoter for the associated gene, resulting in novel transcript variants. Some disseminated sequences showed sequence conservation across animals, implying a possible regulatory role. My results indicate that retroposition is one of the mechanisms for dispersion of ncRNAs. I propose that these newly inserted segments may play a role in genome evolution by potentially functioning as novel exons, promoters or enhancers.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Korea. yoonsoo.hahn@gmail.com
authors: Yoonsoo
authors: Y
authors: Hahn
mesh_terms: D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence; D021901:DNA, Intergenic / Q000737:chemistry; D019143:Evolution, Molecular; D005091:Exons; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D007438:Introns; D051379:Mice; D011401:Promoter Regions, Genetic; D022661:RNA, Untranslated / Q000096:biosynthesis / Q000235:genetics*; D051381:Rats
chemical_list: D021901:DNA, Intergenic; D022661:RNA, Untranslated