Methodology article

Genome-wide analysis of antisense transcription with Affymetrix exon array

Xijin Ge¹ , Wendy S Rubinstein^2,5 , Yong-chul Jung³ and Qingfa Wu⁴

¹Department of Mathematics and Statistics, South Dakota State University, Box 2220, Brookings, SD 57007, USA

²Center for Medical Genetics, Evanston Northwestern Healthcare, 1000 Central Street, Suite 620, Evanston, IL 60201, USA

³Center for Functional Genomics, ENH Research Institute, 1001 University Place, Evanston, IL 60201, USA

⁴Dept. of Plant Pathology & Microbiology, College of Natural and Agricultural Sciences, University of California Riverside, Riverside, CA 92521, USA

⁵Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA

author email corresponding author email

BMC Genomics 2008, 9:27doi:10.1186/1471-2164-9-27

Published:	22 January 2008

Abstract

Background

A large number of natural antisense transcripts have been identified in human and mouse genomes. Study of their potential functions clearly requires cost-efficient method for expression analysis.

Results

Here we show that Affymetrix Exon arrays, which were designed to detect conventional transcripts in the sense orientation, can be used to monitor antisense expression across all exonic loci in mammalian genomes. Through modification of the cDNA synthesis protocol, we labeled single-strand cDNA in the reverse orientation as in the standard protocol, thus enabling the detection of antisense transcripts using the same array. Applying this technique to human Jurkat cells, we identified antisense transcription at 2,088 exonic loci of 1,516 UniGene clusters. Many of these antisense transcripts were not observed previously and some were validated by orientation-specific RT-PCR.

Conclusion

Our results suggest that with a modified protocol Affymetrix human, mouse and rat Exon arrays can be used as a routine method for genome-wide analysis of antisense transcription in these genomes.