Replication fork stalling elicits chromatin compaction for the stability of stalling replication forks

Abstract

DNA replication forks in eukaryotic cells stall at a variety of replication barriers. Stalling forks require strict cellular regulations to prevent fork collapse. However, the mechanism underlying these cellular regulations is poorly understood. In this study, a cellular mechanism was uncovered that regulates chromatin structures to stabilize stalling forks. When replication forks stall, H2BK33, a newly identified acetylation site, is deacetylated and H3K9 trimethylated in the nucleosomes surrounding stalling forks, which results in chromatin compaction around forks. Acetylation-mimic H2BK33Q and its deacetylase clr6-1 mutations compromise this fork stalling-induced chromatin compaction, cause physical separation of replicative helicase and DNA polymerases, and significantly increase the frequency of stalling fork collapse. Furthermore, this fork stalling-induced H2BK33 deacetylation is independent of checkpoint. In summary, these results suggest that eukaryotic cells have developed a cellular mechanism that stabilizes stalling forks by targeting nucleosomes and inducing chromatin compaction around stalling forks. This mechanism is named the “Chromsfork” control: Chromatin Compaction Stabilizes Stalling Replication Forks.

Mrc1-Dependent Chromatin Compaction Represses DNA Double-Stranded Break Repair by Homologous Recombination Upon Replication Stress

“…Notably, we observed that HU treatment induces global chromatin compaction that partially depends on Mrc1, leading to the blockage of the access of chromatin remodeling factors and resection machinery ( Figures 7A,B ). This is consistent with the observation that replication stress also triggers chromatin compaction in fission yeast (Feng et al, 2019 ). It was reported that replication stress induces the deacetylation of histone H2B-K33ac by Clr6 and the enrichment of H3K9 tri-methylation at stalled forks, which contributes to the formation of a compacted chromatin environment (Feng et al, 2019 ).…”

“…This is consistent with the observation that replication stress also triggers chromatin compaction in fission yeast (Feng et al, 2019 ). It was reported that replication stress induces the deacetylation of histone H2B-K33ac by Clr6 and the enrichment of H3K9 tri-methylation at stalled forks, which contributes to the formation of a compacted chromatin environment (Feng et al, 2019 ). Constitutive mimic acetylation of H2B-K33ac leads to uncoupling of replicative helicase and DNA polymerases and replication fork instability (Feng et al, 2019 ).…”

“…In fission yeast, it was recently reported that replication stress induces the deacetylation of H2B-K33Ac and tri-methylation on H3K79, thereby triggering chromatin compaction (Feng et al, 2019 ). We compared the chromatin structure of WT cells in the presence or absence of HU treatment using the MNase digestion.…”

“…It was reported that replication stress induces the deacetylation of histone H2B-K33ac by Clr6 and the enrichment of H3K9 tri-methylation at stalled forks, which contributes to the formation of a compacted chromatin environment (Feng et al, 2019 ). Constitutive mimic acetylation of H2B-K33ac leads to uncoupling of replicative helicase and DNA polymerases and replication fork instability (Feng et al, 2019 ). Thus, replication stress-triggered chromatin compaction is likely a conserved cellular response.…”

The epigenetic regulator LSH maintains fork protection and genomic stability via MacroH2A deposition and RAD51 filament formation

“…Meanwhile macroH2A is associated with compact chromatin, and it is a possibility that reduced macroH2A at the fork leads to greater accessibility. A recent report studying S. pombe cells found that chromatin compaction at the stalled fork protects, whereas chromatin relaxation is associated with greater fork instability 70 . Our model suggests that LSH acts globally on macroH2A deposition, but that an unfavorable pre-lesion chromatin environment at the replication fork promotes fork degradation.…”