DNA Damage-Induced Nucleosome Depletion Enhances Homology Search Independently of Local Break Movement

• Published in: Molecular cell 2020-10, Vol.80 (2), p.311-326.e4
• Main Authors: Cheblal, Anaïs, Challa, Kiran, Seeber, Andrew, Shimada, Kenji, Yoshida, Haruka, Ferreira, Helder C., Amitai, Assaf, Gasser, Susan M.
• Format: Article
• Language: English
• Subjects: Bleomycin - pharmacology; Cell Cycle; Cell Cycle Proteins - metabolism; Centromere - metabolism; Cep3; Chromatin - metabolism; Chromatin Assembly and Disassembly; chromatin movement; Chromosomal Proteins, Non-Histone - metabolism; Cohesin; Cohesins; DNA Breaks, Double-Stranded; DNA damage; DNA, Fungal - metabolism; double-strand break; histone eviction; Histones - metabolism; homologous recombination; kinetochore; Models, Biological; MRX; Nucleosomes - metabolism; Phosphorylation; Saccharomyces cerevisiae - cytology; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - metabolism; Spindle Pole Bodies - metabolism; Uls1
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2020.09.002

To determine whether double-strand break (DSB) mobility enhances the physical search for an ectopic template during homology-directed repair (HDR), we tested the effects of factors that control chromatin dynamics, including cohesin loading and kinetochore anchoring. The former but not the latter is altered in response to DSBs. Loss of the nonhistone high-mobility group protein Nhp6 reduces histone occupancy and increases chromatin movement, decompaction, and ectopic HDR. The loss of nucleosome remodeler INO80-C did the opposite. To see whether enhanced HDR depends on DSB mobility or the global chromatin response, we tested the ubiquitin ligase mutant uls1Δ, which selectively impairs local but not global movement in response to a DSB. Strand invasion occurs in uls1Δ cells with wild-type kinetics, arguing that global histone depletion rather than DSB movement is rate limiting for HDR. Impaired break movement in uls1Δ correlates with elevated MRX and cohesin loading, despite normal resection and checkpoint activation. [Display omitted] •Intrinsic and break-induced chromatin dynamics show cell-cycle dependence•Uls1 STUbL regulates local DSB dynamics through MRX and cohesin turnover•Chromatin expansion and ectopic movement are critical for DSB repair by HR•Loss of centromere tethering is not a major DNA damage response Cheblal et al. show that DNA damage checkpoint-induced histone depletion enhances the homology search for a resected chromosome break for its homologous donor. This is achieved through chromatin expansion and ectopic locus mobility, but it is independent of local DSB movement. Local DSB dynamics are cell-cycle dependent and are regulated by cohesin turnover at the break, under control of a SUMO-dependent ubiquitin ligase.