An in silico mathematical model of the initiation of DNA replication

Authors: Rohan D. Gidvani, Brendan J. McConkey, Bernard P. Duncker and Brian P. Ingalls.

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Abstract:
Proper eukaryotic cell proliferation depends upon DNA replication, a closely regulated process mediated by the actions of a multitude of factors. The initiation of replication is regulated by the heterohexameric Origin Recognition Complex (ORC). At origins of replication, ORC recruits and/or associates with protein factors such as Cdt1, Cdc6, the MCM2-7 complex, Cdc45 and the Dbf4-Cdc7 kinase. The mechanisms controlling these associations are well documented, allowing the development of a mathematical model that allows us to explore the network's behaviour. Using budding yeast as a model organism, we have developed an ordinary differential equation (ODE)-based model of the protein-protein interaction network regulating replication initiation. Precise quantification of protein factors at various timepoints is critical to calibration of the model parameters. To this end, we have made use of genetic manipulations and quantitative protein expression analysis. Using chromatin extracts from synchronized cell cultures, we were able to monitor the fluctuation of a number of the aforementioned proteins. This information was used to infer qualities of the protein network and to calibrate a predictive mathematical model of the process of DNA replication initiation, which can be integrated into existing models of the entire budding yeast cell cycle.