title: Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana.
abstract: BACKGROUND
  Natural antisense transcripts (NAT) are a class of endogenous coding or non-protein-coding RNAs with sequence complementarity to other transcripts. Several lines of evidence have shown that cis- and trans-NATs may participate in a broad range of gene regulatory events. Genome-wide identification of cis-NATs in human, mouse and rice has revealed their widespread occurrence in eukaryotes. However, little is known about cis-NATs in the model plant Arabidopsis thaliana.
  
  
  RESULTS
  We developed a new computational method to predict and identify cis-encoded NATs in Arabidopsis and found 1,340 potential NAT pairs. The expression of both sense and antisense transcripts of 957 NAT pairs was confirmed using Arabidopsis full-length cDNAs and public massively parallel signature sequencing (MPSS) data. Three known or putative Arabidopsis imprinted genes have cis-antisense transcripts. Sequences and the genomic arrangement of two Arabidopsis NAT pairs are conserved in rice.
  
  
  CONCLUSIONS
  We combined information from full-length cDNAs and Arabidopsis genome annotation in our NAT prediction work and reported cis-NAT pairs that could not otherwise be identified by using one of the two datasets only. Analysis of MPSS data suggested that for most Arabidopsis cis-NAT pairs, there is predominant expression of one of the two transcripts in a tissue-specific manner.
authors.affiliation: Laboratory of Computational Genomics, The Rockefeller University, New York, NY 10021, USA. wangx@rockefeller.edu
authors.forename: Xiu-Jie
authors.initials: XJ
authors.lastname: Wang
authors.forename: Terry
authors.initials: T
authors.lastname: Gaasterland
authors.forename: Nam-Hai
authors.initials: NH
authors.lastname: Chua
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D030561:Databases, Nucleic Acid; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D012275:Oryza / Q000235:genetics; D016372:RNA, Antisense / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics
chemical_list: D018076:DNA, Complementary; D016372:RNA, Antisense; D018749:RNA, Plant; D034741:RNA, Small Interfering