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

Xiu-Jie Wang¹^,2 , Terry Gaasterland¹^,3 and Nam-Hai Chua⁴

¹Laboratory of Computational Genomics, The Rockefeller University, New York, NY 10021, USA

²Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

³Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA

⁴Laboratory of Plant Molecular Biology, The Rockefeller University, New York, NY 10021, USA

author email corresponding author email

Genome Biology 2005, 6:R30doi:10.1186/gb-2005-6-4-r30


Published:	15 March 2005

Subject areas: Bioinformatics, Genetics, Plant biology

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.

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.