title: Prediction of trans-antisense transcripts in Arabidopsis thaliana.
abstract: BACKGROUND
  Natural antisense transcripts (NATs) are coding or non-coding RNAs with sequence complementarity to other transcripts (sense transcripts). These RNAs could potentially regulate the expression of their sense partner(s) at either the transcriptional or post-transcriptional level. Experimental and computational methods have demonstrated the widespread occurrence of NATs in eukaryotes. However, most previous studies only focused on cis-NATs with little attention being paid to NATs that originate in trans.
  
  
  RESULTS
  We have performed a genome-wide screen of trans-NATs in Arabidopsis thaliana and identified 1,320 putative trans-NAT pairs. An RNA annealing program predicted that most trans-NATs could form extended double-stranded RNA duplexes with their sense partners. Among trans-NATs with available expression data, more than 85% were found in the same tissue as their sense partners; of these, 67% were found in the same cell as their sense partners at comparable expression levels. For about 60% of Arabidopsis trans-NATs, orthologs of at least one transcript of the pair also had trans-NAT partners in either Populus trichocarpa or Oryza sativa. The observation that 430 transcripts had both putative cis- and trans-NATs implicates multiple regulations by antisense transcripts. The potential roles of trans-NATs in inducing post-transcriptional gene silencing and in regulating alternative splicing were also examined.
  
  
  CONCLUSIONS
  The Arabidopsis transcriptome contains a fairly large number of trans-NATs, whose possible functions include silencing of the corresponding sense transcripts or altering their splicing patterns. The interlaced relationships observed in some cis- and trans-NAT pairs suggest that antisense transcripts could be involved in complex regulatory networks in eukaryotes.
authors.affiliation: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China. hwang@genetics.ac.cn
authors.forename: Huan
authors.initials: H
authors.lastname: Wang
authors.forename: Nam-Hai
authors.initials: NH
authors.lastname: Chua
authors.forename: Xiu-Jie
authors.initials: XJ
authors.lastname: Wang
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D020029:Base Pairing; D004251:DNA Transposable Elements / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D017343:Genes, Plant; D018745:Genome, Plant; D016372:RNA, Antisense / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D004251:DNA Transposable Elements; D018744:DNA, Plant; D016372:RNA, Antisense