Chromatin modification effects on DNA replication

DNA replication is a heavily regulated process that occurs in all living cells. In eukaryotes, replication is highly ordered with different genomic regions reproducibly replicated at different times in S-phase. Replication initiates at origins of replication, where the replication machinery assembles. Following initiation, this machinery progresses bi-directionality defining the replication fork. A large number of proteins is involved in this process. Additionally, nucleosomes may be involved in this regulation: indeed, nucleosomes need to be displaced and re-positioned as the fork progresses, making the chromatin environment an integral part of replication.

Here, we focus on the regulation of replication timing in budding yeast. Specifically, we ask how chromatin modifications affect the timing of origin firing and the velocity by which the replication fork progresses along the DNA. We analyze replication in mutants deleted of chromatin modifiers, as well as histone tail point mutants that mimic various histone modifications. Replication profiles of these mutants are defined using whole genome sequencing applied to unsynchronized cultures or to cultures that progress synchronously through S-phase.

We find that deletion of Rtt109, a replication-specific histone acetyltransferase, increases replication velocity, and that this function of Rtt109 depends on specific modifications in the histone H3 tail. By contrast, components of the SAGA complex, which acetylate overlapping residues but do so throughout the cell cycle, are needed for proper timing of origin firing, but show limited impact on the replication velocity. Our study reveals distinct contributions of histone modification on DNA replication dynamics, through both direct and indirect pathways.