Eukaryotic cells package their genomes around histone octamers. In response to DNA damage, checkpoint activation in yeast induces core histone degradation resulting in 20%–40% reduction in nucleosome occupancy. To gain insight into this process, we developed a new approach to analyze the chromatin-associated proteome comprehensively before and after damage. This revealed extensive changes in protein composition after Zeocin-induced damage. First, core histones and the H1 homolog Hho1 were partially lost from chromatin along with replication, transcription, and chromatin remodeling machineries, while ubiquitin ligases and the proteasome were recruited. We found that the checkpoint- and INO80C-dependent recruitment of five ubiquitin-conjugating factors (Rad6, Bre1, Pep5, Ufd4, and Rsp5) contributes to core and linker histone depletion, reducing chromatin compaction and enhancing DNA locus mobility. Importantly, loss of Rad6/Bre1, Ufd4/TRIP12, and Pep5/VPS11 compromise DNA strand invasion kinetics during homology-driven repair. Thus we provide a comprehensive overview of a functionally relevant genome-wide chromatin response to DNA damage.

真核细胞将其基因组包裹在组蛋白八聚体周围。为了响应DNA损伤，酵母中的检查点激活会诱导核心组蛋白降解，从而导致核小体占有率降低20％至40％。为了深入了解这一过程，我们开发了一种新方法来分析损伤前后与染色质相关的蛋白质组。这揭示了Zeocin诱导的损伤后蛋白质组成的广泛变化。首先，核心组蛋白和H1同源物Hho1随复制，转录和染色质重塑机制从染色质中部分丢失，而招募了泛素连接酶和蛋白酶体。我们发现五个泛素结合因子（Rad6，Bre1，Pep5，Ufd4和Rsp5）的依赖检查点和依赖INO80C的募集有助于核心和接头组蛋白的消耗，减少染色质紧密度并增强DNA位点迁移率。重要的是，在同源性驱动的修复过程中，Rad6 / Bre1，Ufd4 / TRIP12和Pep5 / VPS11的丧失会破坏DNA链的入侵动力学。因此，我们提供了功能相关的全基因组染色质对DNA损伤的全面概述。