A variable fork rate affects timing of origin firing and S phase dynamics in Saccharomyces cerevisiae

Stochasticity of replication forks' speeds plays a key role in the dynamics of DNA replication

Eukaryotic DNA replication is elaborately orchestrated to duplicate the genome timely and faithfully. Replication initiates at multiple origins from which replication forks emanate and travel bi-directionally. The complex spatio-temporal regulation of DNA replication remains incompletely understood. To study it, computational models of DNA replication have been developed in S. cerevisiae. However, in spite of the experimental evidence of forks’ speed stochasticity, all models assumed that forks’ speeds are the same. Here, we present the first model of DNA replication assuming that speeds vary stochastically between forks. Utilizing data from both wild-type and hydroxyurea-treated yeast cells, we show that our model is more accurate than models assuming constant forks’ speed and reconstructs dynamics of DNA replication faithfully starting both from population-wide data and data reflecting fork movement in individual cells. Completion of replication in a timely manner is a challenge due to its stochasticity; we propose an empirically derived modification to replication speed based on the distance to the approaching fork, which promotes timely completion of replication. In summary, our work discovers a key role that stochasticity of the forks’ speed plays in the dynamics of DNA replication. We show that without including stochasticity of forks’ speed it is not possible to accurately reconstruct movement of individual replication forks, measured by DNA combing.

DNA replication in eukaryotes starts from multiple sites termed replication origins. Replication timing at individual sites is stochastic, but reproducible population-wide. Complex and not yet completely understood mechanisms ensure that genome is replicated exactly once and that replication is finished in time. This complex spatio-temporal organization of DNA replication makes computational modeling a useful tool to study replication mechanisms. For simplicity, all previous models assumed constant replication forks’ speed. Here, we show that such models are incapable of accurately reconstructing distances travelled by individual replication forks. Therefore, we propose a model assuming that replication speed varies stochastically between forks. We show that such model reproduces faithfully distances travelled by individual replication forks. Moreover, our model is simpler than previous model and thus avoids over-learning (fitting noise). We also discover how replication speed may be attuned to timely complete replication. We propose that forks’ speed increases with diminishing distance to the approaching fork, which we show promotes timely completion of replication. Such speed up can be e.g. explained by a synergy effect of chromatin unwinding by both forks. Our model can be used to simulate phenomena beyond replication, e.g. DNA double-strand breaks resulting from broken replication forks.