Single-cell RNA-seq reveals early heterogeneity during aging in yeast

we carried out a systematic and quantitative investigation of yeast aging with single-cell resolution through transcriptomic sequencing. We optimized a single-cell RNA sequencing (scRNA-seq) protocol to quantitatively study the whole transcriptome profiles of single yeast cells at different ages, finding increased cell-to-cell transcriptional variability during aging. The single-cell transcriptome analysis also highlighted key biological processes or cellular components, including oxidation-reduction process, oxidative stress response (OSR), translation, ribosome biogenesis and mitochondrion that underlie aging in yeast. We uncovered a molecular marker of FIT3, indicating the early heterogeneity during aging in yeast. We also analyzed the regulation of transcription factors and further characterized the distinctive temporal regulation of the OSR by YAP1 and proteasome activity by RPN4 during aging in yeast. Overall, our data profoundly reveal early heterogeneity during aging in yeast and shed light on the aging dynamics at the single cell level. Overall design: We selected relatively young and small sized cells from the yeast colonies and aligned them on the same agar plate and dissected daughter cells per 1.5 hours. After 2/16/36 hours, we isolated yeast mother cell and conducted scRNA-seq process. The data analysis reveal transcriptional change during aging.

本研究通过转录组测序技术，以单细胞分辨率对酵母衰老过程开展了系统性定量研究。我们优化了单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）实验方案，以定量分析不同衰老阶段酵母单细胞的完整转录组特征，发现衰老过程中细胞间的转录异质性显著升高。单细胞转录组分析还筛选出了酵母衰老相关的关键生物学过程与细胞组分，包括氧化还原过程、氧化应激应答（oxidative stress response, OSR）、翻译过程、核糖体生物发生以及线粒体。我们发现了FIT3分子标记物，可用于指示酵母衰老早期的细胞异质性。此外，本研究还分析了转录因子的调控机制，并进一步解析了酵母衰老过程中YAP1对氧化应激应答的独特时序调控，以及RPN4对蛋白酶体活性的调控特征。综上，本研究数据深刻揭示了酵母衰老早期的细胞异质性，阐明了单细胞层面的衰老动态变化规律。实验设计：我们从酵母菌落中挑选出体积较小的年轻细胞，将其接种于同一琼脂平板上，每隔1.5小时分离子代细胞；分别在培养2、16、36小时后，分离酵母母细胞并进行单细胞RNA测序（scRNA-seq）。后续数据分析揭示了衰老过程中的转录组变化。