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


CONCLUSIONS
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.
Vallon-Christersson
Johan
J
Department of Oncology, Institute of Clinical Sciences, and SWEGENE DNA microarray resource center, Lund University, Barngatan 2:1, SE-221 85 Lund, Sweden. johan.vallon-christersson@med.lu.se
Staaf
Johan
J
Kvist
Anders
A
Medstrand
Patrik
P
Borg
Ake
A
Rovira
Carlos
C
D002478:Cells, Cultured; D016373:DNA, Antisense / Q000032:analysis*; D003951:Diagnostic Errors; D020869:Gene Expression Profiling / Q000592:standards*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D014018:Tissue Distribution; D014158:Transcription, Genetic
D016373:DNA, Antisense