title: The distribution and evolution of Arabidopsis thaliana cis natural antisense transcripts.
abstract: BACKGROUND
  Natural antisense transcripts (NATs) are regulatory RNAs that contain sequence complementary to other RNAs, these other RNAs usually being messenger RNAs. In eukaryotic genomes, cis-NATs overlap the gene they complement.
  
  
  RESULTS
  Here, our goal is to analyze the distribution and evolutionary conservation of cis-NATs for a variety of available data sets for Arabidopsis thaliana, to gain insights into cis-NAT functional mechanisms and their significance. Cis-NATs derived from traditional sequencing are largely validated by other data sets, although different cis-NAT data sets have different prevalent cis-NAT topologies with respect to overlapping protein-coding genes. A. thaliana cis-NATs have substantial conservation (28-35% in the three substantive data sets analyzed) of expression in A. lyrata. We examined evolutionary sequence conservation at cis-NAT loci in Arabidopsis thaliana across nine sequenced Brassicaceae species (picked for optimal discernment of purifying selection), focussing on the parts of their sequences not overlapping protein-coding transcripts (dubbed 'NOLPs'). We found significant NOLP sequence conservation for 28-34% NATs across different cis-NAT sets. This NAT NOLP sequence conservation versus A. lyrata is generally significantly correlated with conservation of expression. We discover a significant enrichment of transcription factor binding sites (as evidenced by CHIP-seq data) in NOLPs compared to randomly sampled near-gene NOLP-like DNA , that is linked to significant sequence conservation. Conversely, there is no such evidence for a general significant link between NOLPs and formation of small interfering RNAs (siRNAs), with the substantial majority of unique siRNAs arising from the overlapping portions of the cis-NATs.
  
  
  CONCLUSIONS
  In aggregate, our results suggest that many cis-NAT NOLPs function in the regulation of conserved promoter/regulatory elements that they 'over-hang'.
authors.affiliation: Department of Biology, McGill University, Montreal, QC, Canada. johnathan.bouchard@mail.mcgill.ca.
authors.forename: Johnathan
authors.initials: J
authors.lastname: Bouchard
authors.affiliation: Department of Biology, McGill University, Montreal, QC, Canada. carlos.gonzalez.oliver@gmail.com.
authors.forename: Carlos
authors.initials: C
authors.lastname: Oliver
authors.affiliation: Department of Biology, McGill University, Montreal, QC, Canada. paul.harrison@mcgill.ca.
authors.forename: Paul M
authors.initials: PM
authors.lastname: Harrison
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001665:Binding Sites; D001937:Brassica / Q000145:classification / Q000235:genetics; D017124:Conserved Sequence; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D016372:RNA, Antisense / Q000032:analysis*; D018749:RNA, Plant / Q000032:analysis*; D034741:RNA, Small Interfering / Q000032:analysis* / Q000737:chemistry; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D016372:RNA, Antisense; D018749:RNA, Plant; D034741:RNA, Small Interfering