A general topoisomerase I-dependent transcriptional repression in the stationary phase in yeast.

This paper shows that in the yeast Saccharomyces cerevisiae the levels of most mRNAs decrease, in a temporally orchestrated manner, as cells approach and enter the stationary phase. The decreased level of mRNAs is primarily due to transcriptional repression because the overall rate of in vivo transcription by RNA polymerase II is similarly reduced in the stationary phase. The reduction in mRNA levels and the general transcriptional repression are both dependent on topoisomerase I (encoded by TOP1). Specifically, these two processes are much slower in top1 mutants, as their mRNA levels and transcriptional rate remain unchanged for a longer period of time in the stationary phase before they start to decrease. In contrast, the mRNA levels in the stationary phase are not affected by perturbation of topoisomerase II activity. TOP1-dependent repression operates even on HSP26 and SSA3, which have been shown previously to be transcriptionally induced in early stationary phase. Thus, their mRNA levels are high upon the entry of the cells into the stationary phase but gradually decrease, by a TOP1-dependent mechanism, later in the stationary phase. A minor population of mRNAs is not subjected to the TOP1-dependent regulation, as their levels do not change in stationary phase. The possible role of topoisomerase I in the general transcriptional repression is discussed.