An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and independent dynamics of H3K36 methylation

Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification associated with transcription and DNA repair. Although the effects of H3K36 methylation have been studied, the genome-wide dynamics of H3K36me deposition and removal are not known. We established rapid and reversible optogenetic control for Set2, the sole H3K36 methyltransferase in yeast, by fusing the enzyme with the light activated nuclear shuttle (LANS) domain. Early H3K36me3 dynamics identified methylation in vivo, with total H3K36me3 levels correlating with RNA abundance. Although genes exhibited disparate levels of H3K36 methylation, relative rates of H3K36me3 accumulation were largely linear and consistent across genes, suggesting that H3K36me3 deposition occurs uniformly across all genes in a directed fashion regardless of transcription frequency. Removal of H3K36me3 was highly dependent on the demethylase Rph1. However, the per-gene rate of H3K36me3 loss weakly correlated with RNA abundance and followed exponential decay, suggesting H3K36 demethylases act in a global, stochastic manner. Altogether, these data provide a detailed temporal view of H3K36 methylation and demethylation that suggest transcription-dependent and independent mechanisms for H3K36me deposition and removal, respectively.

组蛋白H3赖氨酸36甲基化（H3K36me）是一种与转录及DNA修复相关的保守组蛋白修饰。尽管学界已对H3K36甲基化的效应开展研究，但H3K36me在全基因组范围内的沉积与去除动态过程仍未明确。本研究将酵母中唯一的H3K36甲基转移酶Set2与光激活核穿梭（LANS）结构域融合，建立了快速且可逆的光遗传调控体系。对早期H3K36me3动态的观测证实了体内甲基化过程，且总H3K36me3水平与RNA丰度呈正相关。尽管不同基因的H3K36甲基化水平存在差异，但H3K36me3的相对积累速率整体呈线性特征，且在各基因间保持一致，这提示H3K36me3的沉积以定向方式均匀发生于所有基因，不受转录频率影响。H3K36me3的去除高度依赖去甲基化酶Rph1。然而，单基因水平的H3K36me3丢失速率仅与RNA丰度呈弱相关，且遵循指数衰减模式，这表明H3K36去甲基化酶以全局随机的方式发挥作用。综上，本研究的数据详细呈现了H3K36甲基化与去甲基化的时序动态，分别揭示了H3K36me沉积与去除依赖转录、不依赖转录的潜在机制。