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Open Access Research article

Non-coding antisense transcription detected by conventional and single-stranded cDNA microarray

Johan Vallon-Christersson1, Johan Staaf1, Anders Kvist2, Patrik Medstrand2, Åke Borg13 and Carlos Rovira13*

Author Affiliations

1 Department of Oncology, Institute of Clinical Sciences, and SWEGENE DNA microarray resource center, Lund University, Barngatan 2:1, SE-221 85 Lund, Sweden

2 Genomics and Bioinformatics, Department of Experimental Medical Science, BMC C13, SE-221 84 Lund, Sweden

3 Lund Stem Cell Centre, University of Lund, BMC C13 SE-221 84 Lund, Sweden

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BMC Genomics 2007, 8:295  doi:10.1186/1471-2164-8-295

Published: 29 August 2007

Abstract

Background

Recent studies revealed that many mammalian protein-coding genes also transcribe their complementary strands. This phenomenon raises questions regarding the validity of data obtained from double-stranded cDNA microarrays since hybridization to both strands may occur. Here, we wanted to analyze experimentally the incidence of antisense transcription in human cells and to estimate their influence on protein coding expression patterns obtained by double-stranded microarrays. Therefore, we profiled transcription of sense and antisense independently by using strand-specific cDNA microarrays.

Results

Up to 88% of expressed protein coding loci displayed concurrent expression from the complementary strand. Antisense transcription is cell specific and showed a strong tendency to be positively correlated to the expression of the sense counterparts. Even if their expression is wide-spread, detected antisense signals seem to have a limited distorting effect on sense profiles obtained with double-stranded probes.

Conclusion

Antisense transcription in humans can be far more common than previously estimated. However, it has limited influence on expression profiles obtained with conventional cDNA probes. This can be explained by a biological phenomena and a bias of the technique: a) a co-ordinate sense and antisense expression variation and b) a bias for sense-hybridization to occur with more efficiency, presumably due to variable exonic overlap between antisense transcripts.