Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
Faculty of Natural Sciences, University of Basel, Basel, Switzerland.
Nat Struct Mol Biol. 2017 Feb;24(2):99-107. doi: 10.1038/nsmb.3347. Epub 2017 Jan 9.
Nucleosomes are essential for proper chromatin organization and the maintenance of genome integrity. Histones are post-translationally modified and often evicted at sites of DNA breaks, facilitating the recruitment of repair factors. Whether such chromatin changes are localized or genome-wide is debated. Here we show that cellular levels of histones drop 20-40% in response to DNA damage. This histone loss occurs from chromatin, is proteasome-mediated and requires both the DNA damage checkpoint and the INO80 nucleosome remodeler. We confirmed reductions in histone levels by stable isotope labeling of amino acids in cell culture (SILAC)-based mass spectrometry, genome-wide nucleosome mapping and fluorescence microscopy. Chromatin decompaction and increased fiber flexibility accompanied histone degradation, both in response to DNA damage and after artificial reduction of histone levels. As a result, recombination rates and DNA-repair focus turnover were enhanced. Thus, we propose that a generalized reduction in nucleosome occupancy is an integral part of the DNA damage response in yeast that provides mechanisms for enhanced chromatin mobility and homology search.
核小体对于染色质的正确组织和基因组完整性的维持至关重要。组蛋白在翻译后会发生修饰，并且经常在 DNA 断裂部位被逐出，从而促进修复因子的招募。这种染色质变化是局部的还是全基因组范围的，这一点存在争议。在这里，我们表明，细胞内的组蛋白水平在 DNA 损伤后下降了 20-40%。这种组蛋白的丢失来自染色质，是蛋白酶体介导的，需要 DNA 损伤检查点和 INO80 核小体重塑酶。我们通过基于稳定同位素标记的氨基酸细胞培养（SILAC）-质谱、全基因组核小体作图和荧光显微镜确认了组蛋白水平的降低。染色质解压缩和纤维柔韧性增加伴随着组蛋白的降解，这既发生在 DNA 损伤后，也发生在人为降低组蛋白水平后。结果，重组率和 DNA 修复焦点周转率提高。因此，我们提出，核小体占有率的普遍降低是酵母中 DNA 损伤反应的一个组成部分，它为增强染色质的流动性和同源搜索提供了机制。
