Post-transcriptional regulation shapes the transcriptome of quiescent yeast

To survive in nutrient-poor conditions, cells must exit the cell cycle and enter a reversible non-replicative state known as quiescence. Yeast cells reprogram their gene expression during quiescence entry to silence transcription, but how the nascent transcriptome changes in quiescence has not been determined. By investigating the nascent transcriptome in quiescent yeast cells, we found noncoding transcription represented a larger portion of the quiescent transcriptome than in G1. To enable our nascent transcriptome analyses, we annotated over a thousand noncoding RNAs (ncRNAs) in quiescence and G1. Our work revealed that both mRNA and ncRNA are subject to increased post-transcriptional regulation in quiescence compared to G1. We found that the nuclear exosome-NNS pathway suppresses over one thousand mRNAs, in addition to canonical noncoding RNAs, in quiescence. In quiescence, a minority of the mRNAs affected by the NNS-nuclear exosome pathway are the same as those identified when glucose was removed, demonstrating a previously unidentified role for the pathway. RNA sequencing through the diauxic shift revealed at least two distinct time points at which the nuclear exosome controls the abundance of mRNAs involved in protein production, cellular organization, and metabolism, for optimal quiescence entry. Both transcription and post-transcriptional regulation are dramatically reprogrammed in quiescence, shifting the balance of noncoding and coding transcripts. The nuclear exosome and NNS are crucial for proper regulation of both mRNAs and ncRNAs in quiescence and through quiescence entry. Overall design: To understand how the nascent transcriptome changes in quiescence, we measured both nascent and steady-state transcription in wild-type, RRP6-deleted, and Nab3-depleted yeast cells in both quiescent and G1 cell states. RNA-seq experiments were performed to obtain measures of steady-state transcription for the different cell states and genetic backgrounds. To obtain measures of both nascent and steady-state transcription, 4tU-seq experiments were conducted for the same cell states and genetic backgrounds. RNA-seq was performed for RRP6-deleted and wild-type control cells in the hours surrounding the diauxic shift. All experiments were performed with two biological replicates, and technical replicates were generated for some samples.