@Article{Hiller:Findeiss:Lein:Conse_intro_revea:2009,
  author =	 {Hiller, Michael and Findeiss, Sven and Lein, Sandro and 
                  Marz, Manja and Nickel, Claudia and Rose, Dominic and 
                  Schulz, Christine and Backofen, Rolf and Prohaska, Sonja J. 
                  and Reuter, Gunter and Stadler, Peter F.},
  title =	 {Conserved introns reveal novel transcripts in {Drosophila} 
                  melanogaster},
  journal =	 {Genome Res},
  issn =         {1088-9051},
  year =	 {2009},
  volume =	 {19},
  number =	 {7},
  pages =	 {1289-300},
  user =	 {backofen},
  pmid =	 {19458021},
  doi = 	 {10.1101/gr.090050.108},
  abstract =	 {Noncoding RNAs that are-like mRNAs-spliced, capped, and 
                  polyadenylated have important functions in cellular 
                  processes. The inventory of these mRNA-like noncoding RNAs 
                  (mlncRNAs), however, is incomplete even in well-studied 
                  organisms, and so far, no computational methods exist to 
                  predict such RNAs from genomic sequences only. The subclass 
                  of these transcripts that is evolutionarily conserved 
                  usually has conserved intron positions. We demonstrate here 
                  that a genome-wide comparative genomics approach searching 
                  for short conserved introns is capable of identifying 
                  conserved transcripts with a high specificity. Our approach 
                  requires neither an open reading frame nor substantial 
                  sequence or secondary structure conservation in the 
                  surrounding exons. Thus it identifies spliced transcripts in 
                  an unbiased way. After applying our approach to insect 
                  genomes, we predict 369 introns outside annotated coding 
                  transcripts, of which 131 are confirmed by expressed 
                  sequence tags (ESTs) and/or noncoding FlyBase transcripts. 
                  Of the remaining 238 novel introns, about half are 
                  associated with protein-coding genes-either extending coding 
                  or untranslated regions or likely belonging to unannotated 
                  coding genes. The remaining 129 introns belong to novel 
                  mlncRNAs that are largely unstructured. Using RT-PCR, we 
                  verified seven of 12 tested introns in novel mlncRNAs and 11 
                  of 17 introns in novel coding genes. The expression level of 
                  all verified mlncRNA transcripts is low but varies during 
                  development, which suggests regulation. As conserved introns 
                  indicate both purifying selection on the exon-intron 
                  structure and conserved expression of the transcript in 
                  related species, the novel mlncRNAs are good candidates for 
                  functional transcripts.}
}