The budding yeast Saccharomyces cerevisiae (S. cerevisiae) has relatively short lifespan and is genetically tractable, making it a widely used model organism in aging research. Here, 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.
The chronological biography or ‘Nianpu’ is a special style of Chinese historical writing formed by a person’s life events in time order. It provides significant records for the research of historical events. However, from syntactic collation, structural, and semantic aspects, the heterogeneousness of Nianpu materials caused the lack of systematical information collation, which could hinder the research of historical events. The article presents a semantic WebGIS platform based on an entity-oriented search and visualization system to reorganize unstructured information. It delivers: (1) a Chinese historical event database to store and manage Chinese historical information derived from the chronological biography; (2) an ontology to integrate different historical datasets; and (3) a web geographic information system to visualize and analyze information of historical events. This platform achieves the reorganization of historical event information at spatial and temporal levels by the Web. It enables humanities researchers to explore the relationships of historical entities and their evolution visually and interactively. The platform is available at https://nianpu.pkudh.org/.
The budding yeast Saccharomyces cerevisiae has relatively short lifespan and is genetically tractable, making it a widely used model organism in ageing research. Here, we carried out a systematic and quantitative investigation of yeast ageing 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 ageing. 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 ageing in yeast. Remarkably, we uncovered a molecular marker, FIT3, that was linked to mitochondrial DNA loss and indicated the early heterogeneity during ageing 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 ageing in yeast. Overall, our data profoundly reveal early heterogeneity during ageing in yeast and shed light on the ageing dynamics at the single cell level.
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