The Temporal Program of Chromosome Replication: Genomewide Replication in clb5Δ Saccharomyces cerevisiae

Temporal regulation of origin activation is widely thought to explain the pattern of early- and late-replicating domains in the Saccharomyces cerevisiae genome. Recently, single-molecule analysis of replication suggested that stochastic processes acting on origins with different probabilities of activation Could generate the observed kinetics of replication Without requiring all Underlying temporal order. To distinguish between these possibilities, we examined a clb5 Delta strain, where origin firing is largely limited to the first half of S phase, to ask whether all origins nonspecifically show decreased firing (as expected for disordered filing) of if only some origins ("late" origins) are affected. Approximately half the origins in the mutant genome show delayed replication while tire remainder replicate largely on time. The delayed regions call encompass hundreds of kilobases and generally correspond to regions that replicate late in wild-type cells. Kinetic analysis of replication in wild-type cells reveals broad windows of origin filing for both early and late origins. Our results are consistent with a temporal model in which origins call show some heterogeneity in both Lime and probability Of Origin firing, but clustering of temporally like origins nevertheless yields a genome that is organized into blocks showing different replication times.