The Temporal Program of Chromosome Replication: Genomewide Replication inclb5ΔSaccharomyces cerevisiae

Abstract

Temporal regulation of origin activation is widely thought to explain the pattern of early-and latereplicating 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 an underlying temporal order. To distinguish between these possibilities, we examined a clb5D 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 firing) or if only some origins (''late'' origins) are affected. Approximately half the origins in the mutant genome show delayed replication while the remainder replicate largely on time. The delayed regions can 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 firing for both early and late origins. Our results are consistent with a temporal model in which origins can show some heterogeneity in both time and probability of origin firing, but clustering of temporally like origins nevertheless yields a genome that is organized into blocks showing different replication times.

Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle

“…The read coverage of raw Hi‐C libraries reflects the replication progression throughout S phase, plotted along the 16 chromosomes of the yeast genome (top axis; blue curve). The replication timing obtained in this study is highly similar to the one from McCune et al (2008) (yellow curve).…”

Rif1 controls DNA replication by directing Protein Phosphatase 1 to reverse Cdc7-mediated phosphorylation of the MCM complex

“…The Y-axis shows the percent replication. (Bottom panel) The gray curve shows the DNA replication profile of chromosome IV in wildtype cells in early S phase 40 min after release from a-factor (redrawn from McCune et al 2008). Early initiating replication origins ARS418, ARS428, and ARS432.5 are indicated.…”

“…1D, bottom panel; McCune et al 2008). This replication pattern indicates that the sites most prone to replication initiation at 37°C in cdc7-1 rif1D are likely to correspond to normally early initiating origins; for example, origins ARS418, ARS428, and ARS432.5 (arrowheads in Fig.…”

Conservation of replication timing reveals global and local regulation of replication origin activity

“…Genome-wide measurements of S. cerevisiae replication dynamics suggest that there are broad chromosomal zones replicated from origins with similar activity; for example, clusters of lateactivating origins (Raghuraman et al 2001;Yabuki et al 2002;McCune et al 2008). Particular chromosomal regions have characteristic replication times: centromere proximal regions replicate early and telomere proximal regions replicate late.…”