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 genome is globally accessible in living cells, unlike in isolated nuclei, where DNA accessibility is severely restricted. Gene bodies are methylated at only slightly slower rates than promoters, indicating that yeast chromatin is highly dynamic in vivo. In contrast, silenced loci and centromeres are strongly protected. Global shifts in nucleosome positions occur in cells as they are depleted of ATP-dependent chromatin remodelers, suggesting that nucleosome dynamics result from competition among these enzymes. We conclude that chromatin is in a state of continuous flux in living cells, but static in nuclei, suggesting that DNA packaging in yeast is not generally repressive.

真核基因组被包装成染色质，染色质由规则间隔的核小体的浓缩丝组成，类似于绳子上的珠子。核小体含有 ~147 bp 的 DNA，几乎两倍地包裹在中央核心组蛋白八聚体周围。将 DNA 包装到染色质中对转录因子和其他需要进入其结合位点的蛋白质来说是一个挑战。因此，对 DNA 可及性的控制被认为在基因调控中起着关键作用。在这里，我们通过诱导 DNA 甲基转移酶的表达来测量活的出芽酵母细胞中全基因组的 DNA 可及性。我们发现，基因组在活细胞中是全局可及的，这与在离体细胞核中不同，在离体细胞核中，DNA 可及性受到严重限制。基因体的甲基化速率仅比启动子略慢，这表明酵母染色质在体内具有高度动态性。相比之下，沉默基因座和着丝粒受到强烈保护。核小体位置的整体变化发生在细胞中，因为它们耗尽了 ATP 依赖性染色质重塑剂，这表明核小体动力学是这些酶之间竞争的结果。我们得出结论，染色质在活细胞中处于连续通量状态，但在细胞核中处于静态状态，这表明酵母中的 DNA 包装通常不具有抑制性。