Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana

Genome Biol. 2005;6(4):R30. doi: 10.1186/gb-2005-6-4-r30. Epub 2005 Mar 15.


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.

Conclusion: 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Alternative Splicing / genetics
  • Arabidopsis / genetics*
  • Chromosomes, Plant / genetics
  • Conserved Sequence / genetics
  • DNA, Complementary / genetics
  • Databases, Nucleic Acid
  • Gene Expression Regulation, Plant / genetics*
  • Genome, Plant / genetics*
  • Oryza / genetics
  • RNA, Antisense / genetics*
  • RNA, Plant / genetics*
  • RNA, Small Interfering / genetics


  • DNA, Complementary
  • RNA, Antisense
  • RNA, Plant
  • RNA, Small Interfering