The yeast genome is globally accessible in living cells [OxfordNanopore]

Eukaryotic genomes are packaged into chromatin, which is composed of condensed filaments of regularly spaced nucleosomes, resembling beads on a string. The nucleosome contains ~147 bp of DNA wrapped almost twice around a central core histone octamer. The packaging of DNA into chromatin represents a challenge to transcription factors and other proteins requiring access to their binding sites. Consequently, control of DNA accessibility is thought to play a key role in gene regulation. Here, we measure DNA accessibility genome-wide in living budding yeast cells by inducible expression of DNA methyltransferases. We find that the yeast genome is globally accessible to the methylase in living cells, unlike in nuclei, where DNA accessibility is severely limited. Gene bodies are methylated at only slightly slower rates than promoters, indicating that yeast chromatin is highly dynamic in vivo. In contrast, centromeres are strongly protected in vivo. Global shifts in nucleosome positions occur in cells as they are depleted of RSC, or ISW1 and CHD1, indicating that global nucleosome dynamics are at least partly attributable to ATP-dependent chromatin remodelers. We propose that virtually all yeast chromatin is in a state of continuous flux in living cells, but static in nuclei, suggesting that chromatin packaging is not generally repressive.真核生物基因组被包装为染色质（chromatin），其由规则排布的核小体（nucleosome）浓缩丝束构成，形态类似串珠。每个核小体包含约147 bp的DNA，在核心组蛋白八聚体上缠绕近两圈。DNA被包装为染色质的过程，会给转录因子及其他需要结合其靶位点的蛋白质带来结合障碍。因此，学界普遍认为DNA可及性的调控在基因调控中发挥核心作用。本研究通过诱导表达DNA甲基转移酶（DNA methyltransferase），在活酿酒酵母（budding yeast）细胞中实现了全基因组范围的DNA可及性检测。研究发现，活细胞内酵母基因组对甲基化酶整体呈现可及状态，而在分离的细胞核中，DNA可及性则受到严重限制。基因体（gene body）的甲基化速率仅略低于启动子（promoter），这表明活体内酵母染色质具有高度动态性。与之相反，着丝粒（centromere）在活体内受到强烈的保护。当细胞缺失RSC、ISW1及CHD1时，核小体位置会发生全局偏移，这说明全局核小体动态变化至少部分归因于ATP依赖型染色质重塑因子（ATP-dependent chromatin remodeler）。我们提出，酿酒酵母的几乎所有染色质在活体内都处于持续动态变化的状态，而在分离的细胞核中则呈静态，这表明染色质包装通常并不具备转录抑制性。