Sir2 tempers an intrinsic imbalance in origin licensing efficiency between early and late replicating euchromatin

The replication of eukaryotic chromosomes proceeds through the temporal activation of spatially distributed chromosomal origins. The function of every origin depends on two distinct cell-cycle restricted reactions, loading of an inactive form of the replicative helicase, the MCM complex, in G1-phase, referred to as origin licensing, and activation of this MCM complex into two active helicases in S-phase. Recent progress in the model organism Saccharomyces cerevisiae establishes that the temporal distribution of origin activation is determined by the probability that a licensed origin will recruit the S-phase MCM complex-activation kinase. In contrast, the mechanisms that promote the spatial distribution of licensed origins across yeast chromosomes have not been addressed. Using quantitative analyses of high-resolution MCM ChIP-Seq and Sort-Seq experiments, we show that the Sir2 histone deacetylase, recently shown to act directly on nucleosomes adjacent to euchromatic origins, attenuated origin licensing at both early euchromatic and Sir2-heterochromatic telomeric X-origins. In SIR2 cells, early and late euchromatic origins as well as telomeric X-origins origins contained similar levels of MCM. However, in sir2 null cells MCM accumulated at early euchromatic and telomeric X-origins relative to late euchromatic origins. Sort-Seq experiments and direct 2-D origin mapping provided evidence that the enhanced levels of licensing observed by MCM ChIP-Seq in sir2 null cells caused the enhanced replication function of these origins at the expense of late euchromatic origin function, leading to substantial delays in completing the duplication of late replicating euchromatin. We conclude that Sir2 is required to balance the distribution of licensed origins across yeast chromosomes by directly attenuating the efficiency of MCM complex loading within some of the most active and receptive regions of euchromatin