Antisense transcriptional interference mediates condition-specific gene repression in budding yeast

Pervasive transcription generates many unstable non-coding transcripts. Although a few examples of pervasive antisense have been shown to mediate gene regulation by transcriptional interference, whether pervasive transcription has a general functional role or merely represents transcriptional noise remains unclear. In a mutant context that stabilised pervasive transcripts, we characterized more than 800 antisense RNAs genome wide and analysed the corresponding sense mRNA behaviour. We observed that antisense non-coding transcription was associated with genes tightly repressed during exponential growth compared to quiescence and with an opposite level of variation between the mRNA and the associated antisense. This suggested that antisense transcription might participate to gene repression during the exponential phase. We thus specifically interrupted the antisense transcription of a subset of genes, and found that it resulted in a de-repression of the corresponding mRNAs. Antisense-mediated repression involved a cis-acting mechanism and was dependent on several chromatin modification factors. Our data convey that transcriptional interference by pervasive antisense transcription is a general mechanism of gene repression between cellular states.