Variance in Initiation Factors Does Not Strongly Affect the Replication Profile of Budding Yeast DNA

DNA replication starts at many sites (origins) throughout eukaryotic DNA. To fully understand the replication program in higher organisms, one needs to understand the behaviour of these origins. In Saccharomyces cerevisiae (budding yeast), the spatial organization of the origins is simple: The origins are confined to known specific sites on the genome. The temporal behaviour of origins in budding yeast is more complex: They fire stochastically with a broad distribution of firing times. Several key proteins take part in the DNA replication process. The MCM2-7 hexamer in particular forms a helicase that unwinds DNA locally, allowing access for other proteins to replicate the separated DNA. Past analysis of the budding yeast replication program suggested the Multiple Initiator Model (MIM), which hypothesizes that the number of these MCMs loaded at an origin predicts the firing time of that origin. Part of the MIM formalism assumes that the number of loaded MCMs is large; in this case the relative fluctuations between cells will be small and are ignored. However, a recent experiment measuring the number of loaded MCMs has revealed that the number is low, and thus, cell-to-cell fluctuations may be larger than expected. The purpose of this thesis is to investigate the impact of large relative fluctuations in the number of MCMs on the MIM. To measure this effect, we built the "MIM simulator," a modular program that simulates the replication process. Although a naive argument suggests that the MIM should fail when the number of MCMs is low, the impact of these fluctuations is mitigated by the contributions from neighbouring origins. We conclude that inferences made with the MIM remain accurate in the case that the number of MCMs is lower than first assumed.