title: Mechanisms of intron gain and loss in Drosophila.
abstract: BACKGROUND
  It is widely accepted that orthologous genes have lost or gained introns throughout evolution. However, the specific mechanisms that generate these changes have proved elusive. Introns are known to affect nearly every level of gene expression. Therefore, understanding their mechanism of evolution after their initial fixation in eukaryotes is pertinent to understanding the means by which organisms develop greater regulation and complexity.
  
  
  RESULTS
  To investigate possible mechanisms of intron gain and loss, we identified 189 intron gain and 297 intron loss events among 11 Drosophila species. We then investigated these events for signatures of previously proposed mechanisms of intron gain and loss. This work constitutes the first comprehensive study into the specific mechanisms that may generate intron gains and losses in Drosophila. We report evidence of intron gain via transposon insertion; the first intron loss that may have occurred via non-homologous end joining; intron gains via the repair of a double strand break; evidence of intron sliding; and evidence that internal or 5' introns may not frequently be deleted via the self-priming of reverse transcription during mRNA-mediated intron loss. Our data also suggest that the transcription process may promote or result in intron gain.
  
  
  CONCLUSIONS
  Our findings support the occurrence of intron gain via transposon insertion, repair of double strand breaks, as well as intron loss via non-homologous end joining. Furthermore, our data suggest that intron gain may be enabled by or due to transcription, and we shed further light on the exact mechanism of mRNA-mediated intron loss.
authors.affiliation: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Yenerall
authors.forename: Bradlee
authors.initials: B
authors.lastname: Krupa
authors.forename: Leming
authors.initials: L
authors.lastname: Zhou
mesh_terms: D000818:Animals; D001483:Base Sequence; D004251:DNA Transposable Elements; D004330:Drosophila / Q000235:genetics*; D019143:Evolution, Molecular; D007438:Introns / Q000235:genetics*; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D012333:RNA, Messenger / Q000235:genetics; D016415:Sequence Alignment; D017384:Sequence Deletion
chemical_list: D004251:DNA Transposable Elements; D012333:RNA, Messenger