Bre1-mediated Set2 protein degradation promotes chronological aging in budding yeast [ChIP-seq]

Histone modification affects life span in various organisms. The loss of Histone H3K36 methylation can shorten replicative life span in Saccharomyces cerevisiae. However, budding yeast, as a model organism for aging research, has replicative life span (RLS) and chronological life span (CLS). In this study, we showed that the loss of Histone H3K36 methylation can shorten CLS in Saccharomyces cerevisiae. We identified Ubc3/Bre1 mediates polyubiquitination of Set2 K25 and K530 at log phase and stationary phase, and Bre1 interacts with Ubc3 and Rad6 simultaneously. BRE1 knockout can stabilize Set2 protein to maintain H3K36me3 and regulate the transcription of aging related genes, such as DSE1/DSE2/SUN4/EGT2/SCW11. We also proved that Gcn5-mediated Set2 acetylation regulates Set2 protein stability and chronological aging. Altogether, our study showed that knockout of BRE1 and GCN5 regulate Set2 protein level by mediating the polyubiquitination of Set2 to influence the level of H3K36me3 and the transcription level of aging related genes enriched by H3K36me3, thereby extending the chronological life span. ChIP-seq analysis of H3K36me3 binding in WT and bre1-delta cells Saccharomyces cerevisiae during chronological aging (Day4 vs Day1)

组蛋白修饰(Histone modification)可调控多种生物的寿命。组蛋白H3K36甲基化(Histone H3K36 methylation)的缺失会缩短酿酒酵母(Saccharomyces cerevisiae)的复制型寿命(Replicative Life Span, RLS)。而作为衰老研究的经典模式生物，酿酒酵母存在两种寿命评价体系：复制型寿命(RLS)与时序寿命(Chronological Life Span, CLS)。本研究证实，酿酒酵母中组蛋白H3K36甲基化的缺失同样会缩短其时序寿命CLS。本研究鉴定发现，Ubc3/Bre1可分别在对数生长期与稳定期介导Set2蛋白K25与K530位点的多泛素化(polyubiquitination)，且Bre1可同时与Ubc3及Rad6发生相互作用。BRE1基因敲除可稳定Set2蛋白，以维持H3K36me3的修饰水平，并调控DSE1、DSE2、SUN4、EGT2、SCW11等衰老相关基因的转录。本研究同时证实，Gcn5介导的Set2乙酰化(acetylation)可调控Set2蛋白稳定性与时序衰老进程。综上，本研究表明：通过介导Set2的多泛素化，BRE1与GCN5基因敲除可调节Set2蛋白水平，进而影响H3K36me3的丰度以及受H3K36me3富集调控的衰老相关基因的转录水平，最终延长酿酒酵母的时序寿命CLS。本研究还针对酿酒酵母时序衰老过程中（第4天与第1天对比）野生型(WT)与bre1Δ敲除细胞内H3K36me3的结合情况开展了染色质免疫共沉淀测序(ChIP-seq)分析。