Persistent acetylation of histone H3 lysine 56 compromises the activity of DNA replication origins

ABSTRACT In Saccharomyces cerevisiae , newly synthesized histone H3 are acetylated on lysine 56 (H3 K56ac) by the Rtt109 acetyltransferase prior to their deposition on nascent DNA behind replication forks. Two deacetylases of the sirtuin family, Hst3 and Hst4, remove H3 K56ac from chromatin following S phase. hst3 Δ hst4 Δ cells present constitutive H3 K56ac, which sensitizes cells to replicative stress via mechanisms that remain unclear. We performed a screen to identify genes that influence cell fitness upon nicotinamide (NAM)-induced inhibition of sirtuins. The screen revealed that DBF4 heterozygosity causes NAM sensitivity. DBF4 and CDC7 encode subunits of the Dbf4-dependent kinase, which activates origins of DNA replication. We show that i) cells harboring the dbf4-1 or cdc7-4 hypomorphic alleles are sensitive to NAM, ii) Rif1, an inhibitor of Cdc7-dependent activation of origins, causes DNA damage and replication defects in NAM-treated cells and hst3 Δ hst4 Δ mutants, and iii) cdc7-4 hst3 Δ hst4 Δ cells display synthetic temperature sensitivity associated with delayed initiation of DNA replication. Such replication defects are not due to activation of the intra-S phase checkpoint but require Rtt109-dependent H3 K56ac. Overall, these results suggest that persistent H3 K56ac sensitizes cells to replicative stress in part by negatively influencing replication origin activity.