Fig. 6: Persistent H3K56ac in hst3∆hst4∆ cells results in increased nucleosome repeat length, contributing to genome instability.

a A model depicting that H3K56ac, a mark on newly synthesized H3, could be detected on both parental and newly synthesized H3 in mcm2-3A hst3∆ hst4∆ cells. b and c Average bias of H3K56ac (b) and H3K4me3 (c) eSPAN bias within 4 kb of 134 early-firing replication in indicated yeast strains. d Average BrdU-IP-ssSeq bias of di-nucleosomes within 4 kb of 134 early-firing replication origins at indicated yeast strains. e Bar plot quantification of the NRL at leading and lagging strands in WT, hst3∆ hst4∆, mcm2-3A, and mcm2-3A hst3∆ hst4∆ cells. The number of independent repeats of BrdU-IP-ssSeq for WT, hst3∆ hst4∆, mcm2-3A, and mcm2-3A hst3∆ hst4∆ is 3, 3, 3, and 2, respectively. P values were calculated with two-sided Student’s t-test was performed. Data were presented as mean values ± standard deviation; error bars represent standard deviation. f Box plots of di-nucleosome density across the early replicated genes shared by three yeast strains (replicated genes = 1398). Density is normalized by mono-nucleosome levels. Box plots show the median, 25% and 75% quartiles and minimal and maximal values. P values were calculated using two-sided Mann-Whitney-Wilcoxon tests. g Depletion of ISW1 and CHD1 partially suppresses DNA damage sensitivity of hst3Δ hst4Δ mutant cells. Ten-fold diluted yeast cells of the indicated genotype on the left were spotted onto YPD medium alone or YPD medium supplemented with hydroxyurea (HU), dimethyl sulfoxide (DMSO), or camptothecin (CPT). For e and f, source data are provided as a Source Data file. Schematic in a was created in BioRender. Zhou, H. (2024) https://BioRender.com/d28x330.