Transcriptional heterogeneity shapes stress-adaptive responses in yeast

In response to stress, cells activate signaling pathways that coordinate broad changes in gene expression to enhance cell survival. Remarkably, complex variations in gene expression occur even in isogenic populations and in response to similar signaling inputs. However, the molecular mechanisms underlying this variability and their influence on adaptive cell fate decisions are not fully understood. Here, we use scRNA-seq to longitudinally assess transcriptional dynamics during osmoadaptation in yeast. Our findings reveal highly heterogeneous expression of the osmoresponsive program, which organizes into combinatorial patterns that generate distinct cellular programs. The induction of these programs is favored by global transcriptome repression upon stress. Cells displaying basal expression of the osmoresponsive program are hyper-responsive and resistant to stress. Through a transcription-focused analysis of more than 300 RNA-barcoded deletion mutants, we identify genetic factors that shape the heterogeneity of the osmostress-induced transcriptome, define regulators of stress-related subpopulations and find a link between transcriptional heterogeneity and increased cell fitness. Our findings provide a regulatory map of the complex transcriptional phenotypes underlying osmoadaptation in yeast and highlight the importance of transcriptional heterogeneity in generating distinct adaptive strategies.细胞受到应激刺激时，会激活信号通路以协调广泛的基因表达变化，从而提升细胞存活能力。值得注意的是，即便在同源克隆的细胞群体中，当受到相似的信号刺激时，基因表达仍会出现复杂的差异。然而，这种表达差异背后的分子机制，以及其对适应性细胞命运决策的影响，仍未被完全阐明。本研究采用单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）技术，对酵母渗透压适应过程中的转录动态变化进行纵向时序分析。研究结果显示，渗透压应答程序的表达具有高度异质性，这些异质性会形成组合模式，进而产生不同的细胞功能程序。应激状态下的全局转录组抑制，会促进这类细胞程序的诱导激活。呈现渗透压应答程序基础表达的细胞，会表现出超敏反应特性且具备应激抗性。本研究通过对300余个RNA条形码标记的缺失突变体开展转录聚焦分析，鉴定出了调控渗透压应激诱导转录组异质性的遗传因子，明确了应激相关亚群的调控因子，并发现转录异质性与细胞适合度提升之间存在关联。本研究绘制了酵母渗透压适应过程中复杂转录表型的调控图谱，并凸显了转录异质性在形成不同适应性策略中的关键作用。