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.为在营养匮乏条件下存活，细胞必须退出细胞周期，进入一种可逆的非复制状态，即静息态（quiescence）。酵母细胞在进入静息态的过程中会重编程基因表达以沉默转录，但目前学界尚未明确静息态下新生转录组（nascent transcriptome）的变化规律。本研究通过对静息态酵母细胞的新生转录组展开分析，发现非编码转录在静息态转录组中的占比高于G1期。为保障新生转录组分析工作的顺利开展，我们对静息态与G1期的千余种非编码RNA（ncRNAs）进行了注释。研究结果显示，相较于G1期，静息态下信使RNA（mRNA）与非编码RNA均受到了更为严格的转录后调控。我们发现，核外切体-NNS通路（nuclear exosome-NNS pathway）在静息态中除调控经典非编码RNA外，还可抑制千余种信使RNA的表达。静息态下，受NNS-核外切体通路调控的信使RNA中，仅有少数与葡萄糖剥夺条件下鉴定得到的靶标一致，这表明该通路存在此前未被发现的功能。通过对二次生长转换（diauxic shift）过程的RNA测序分析，我们发现核外切体至少在两个不同时间点调控参与蛋白质合成、细胞结构组织与代谢过程的信使RNA丰度，以实现最优的静息态进入效率。静息态下，转录与转录后调控均发生了显著重编程，改变了非编码与编码转录本的表达平衡。核外切体与NNS通路，对于静息态及静息态进入过程中，信使RNA与非编码RNA的精准调控均至关重要。