A pair of partially overlapping Arabidopsis genes with antagonistic circadian expression.

A large number of plant genes are aligned with partially overlapping genes in antisense orientation. Transcription of both genes would therefore favour the formation of double-stranded RNA, providing a substrate for the RNAi machinery, and enhanced antisense transcription should therefore reduce sense transcript levels. We have identified a gene pair that resembles a model for antisense-based gene regulation as a T-DNA insertion into the antisense gene causes a reduction in antisense transcript levels and an increase in sense transcript levels. The same effect was, however, also observed when the two genes were inserted as transgenes into different chromosomal locations, independent of the sense and antisense gene being expressed individually or jointly. Our results therefore indicate that antagonistic changes in sense/antisense transcript levels do not necessarily reflect antisense-mediated regulation. More likely, the partial overlap of the two genes may have favoured the evolution of antagonistic expression patterns preventing RNAi effects.