Strand-specific RNA sequencing reveals extensiveregulated long antisense transcripts that areconserved across yeast species

摘要

Background: Recent studies in budding yeast have shown that antisense transcription occurs at many loci.However, the functional role of antisense transcripts has been demonstrated only in a few cases and it has beensuggested that most antisense transcripts may result from promiscuous bi-directional transcription in a densegenome. Results: Here, we use strand-specific RNA sequencing to study anti-sense transcription in Saccharomyces cerevisiae.We detect 1,103 putative antisense transcripts expressed in mid-log phase growth, ranging from 39 shorttranscripts covering only the 3’ UTR of sense genes to 145 long transcripts covering the entire sense open readingframe. Many of these antisense transcripts overlap sense genes that are repressed in mid-log phase and areimportant in stationary phase, stress response, or meiosis. We validate the differential regulation of 67 antisensetranscripts and their sense targets in relevant conditions, including nutrient limitation and environmental stresses.Moreover, we show that several antisense transcripts and, in some cases, their differential expression have beenconserved across five species of yeast spanning 150 million years of evolution. Divergence in the regulation ofantisense transcripts to two respiratory genes coincides with the evolution of respiro-fermentation. Conclusions: Our work provides support for a global and conserved role for antisense transcription in yeast generegulation.