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

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.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.Non-coding RNAs have recently been reported as more common, more diverse, and accredited more important functions than previously anticipated [1-3]. Among the most abundant non-coding transcripts, there is a group called natural antisense transcripts (NATs) that carries regions of perfect complementarity to protein coding (sense) RNAs [4-7]. In silico studies of available transcript sequence data have found that up to 24% of human protein coding loci also encode cis-NATs [8,9]. However, antisense transcripts tend to be poly(A) negative and nuclear localized [10]. If this is true, the abundance of NATs (cis and trans) may be higher yet, since nuclear non-polyadenylated transcripts are underrepresented in transcript sequence databases.This fact may have important implications for researchers, not only because of their potential biological function but they may also turn out to be influential on the interpretation of large experimental data sets. For instance, the cDNA microarray technique has been used in genome-wide expression studies to address basic questions about gene function and in the pursuit of a more prec