ABSTRACT
Histone acetylation is a known regulator of DNA replication dynamics. In the yeast Saccharomyces cerevisiae, newly synthesized histone H3 deposited behind DNA replication forks are acetylated on lysine 56 (H3 K56ac) by the Rtt109 histone acetyltransferase. Two enzymes of the sirtuin family of deacetylases, Hst3 and Hst4, act redundantly to deacetylate this residue throughout chromosomes following S phase. Cells lacking Hst3 and Hst4 present constitutively acetylated H3 K56, which causes sensitivity to replication-blocking genotoxins and slow growth via mechanisms that remain poorly understood. Here, we present the results of a genome-wide screen aimed at identifying haploinsufficient genes that promote cell fitness in response to inhibition of sirtuins by nicotinamide (NAM). We find that heterozygous deletion alleles of genes involved in the regulation of DNA replication origins sensitize cells to NAM. Consistently, haploid cells harboring the hypomorphic temperature sensitive allele cdc7-4 present striking NAM-induced S phase progression defects at their semi-permissive temperature. We further show i) that Rap1-interacting factor 1 (Rif1), an inhibitor of Cdc7-dependent activation of replication origins, causes DNA damage and replication defects in cells exposed to NAM and in hst3Δ hst4Δ mutants, and ii) that cdc7-4 hst3Δ hst4Δ triple mutant cells present strong synthetic temperature sensitivity associated with defective activation of replication origin and delayed S phase progression. Our data further demonstrate that such replication defects are not due to intra-S phase checkpoint activation leading to inhibition of origin activity. We finally show that Rtt109-dependent acetylation of histone H3 lysine 56 and its associated Rtt101-Mms1 ubiquitin ligase complex cause the DNA replication defects observed in cdc7-4 hst3Δ hst4Δ cells. Overall, these results argue that abnormal regulation of nascent chromatin structure negatively influences DNA replication initiation in cells presenting reduced Dbf4-dependent kinase activity including those experiencing replicative stress.
Competing Interest Statement
The authors have declared no competing interest.