Prajapati Hemant K, Eriksson Peter R, Elizalde Paul A, Coey Christopher T, Xu Zhuwei, Clark David J
Division of Developmental Biology, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
NIH-JHU Graduate Partnership Program, Johns Hopkins University, Baltimore, MD, USA.
Nat Struct Mol Biol. 2025 Feb;32(2):247-256. doi: 10.1038/s41594-024-01318-2. Epub 2024 Nov 25.
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.
真核生物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细丝组成，类似于串珠。核小体包含约147个碱基对的DNA，几乎绕着一个中央核心组蛋白八聚体缠绕两圈。将DNA包装成染色质对转录因子和其他需要接近其结合位点的蛋白质构成了挑战。因此，DNA可及性的控制被认为在基因调控中起关键作用。在这里，我们通过诱导表达DNA甲基转移酶，在活的芽殖酵母细胞中全基因组范围内测量DNA可及性。我们发现，与分离的细胞核中DNA可及性受到严重限制不同，活细胞中的基因组在整体上是可及的。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，沉默位点和着丝粒受到强烈保护。当细胞中依赖ATP的染色质重塑因子耗尽时，核小体位置会发生全局变化，这表明核小体动态是由这些酶之间的竞争导致的。我们得出结论，染色质在活细胞中处于持续变化的状态，但在细胞核中是静态的，这表明酵母中的DNA包装通常不是抑制性的。
