A Dynamic Stochastic Model for DNA Replication Initiation in Early Embryos

Abstract

BackgroundEukaryotic cells seem unable to monitor replication completion during normal S phase, yet must ensure a reliable replication completion time. This is an acute problem in early Xenopus embryos since DNA replication origins are located and activated stochastically, leading to the random completion problem. DNA combing, kinetic modelling and other studies using Xenopus egg extracts have suggested that potential origins are much more abundant than actual initiation events and that the time-dependent rate of initiation, I(t), markedly increases through S phase to ensure the rapid completion of unreplicated gaps and a narrow distribution of completion times. However, the molecular mechanism that underlies this increase has remained obscure.Methodology/Principal FindingsUsing both previous and novel DNA combing data we have confirmed that I(t) increases through S phase but have also established that it progressively decreases before the end of S phase. To explore plausible biochemical scenarios that might explain these features, we have performed comparisons between numerical simulations and DNA combing data. Several simple models were tested: i) recycling of a limiting replication fork component from completed replicons; ii) time-dependent increase in origin efficiency; iii) time-dependent increase in availability of an initially limiting factor, e.g. by nuclear import. None of these potential mechanisms could on its own account for the data. We propose a model that combines time-dependent changes in availability of a replication factor and a fork-density dependent affinity of this factor for potential origins. This novel model quantitatively and robustly accounted for the observed changes in initiation rate and fork density.Conclusions/SignificanceThis work provides a refined temporal profile of replication initiation rates and a robust, dynamic model that quantitatively explains replication origin usage during early embryonic S phase. These results have significant implications for the organisation of replication origins in higher eukaryotes.

Optimal Placement of Origins for DNA Replication

“…Other authors have identified σ to be 6-10 min in X. laevis [13,21] as well as in S. cerevisiae [2,5,20,22]. Our results [ Fig.…”

Mathematical modelling of eukaryotic DNA replication

“…Two conditions were required to fit this expression to combing data. First, the number of searchers, N s (t), had to increase with time, as proposed by Goldar et al (2008). Second, the decreasing part of the data could be explained if α< 1, i.e.…”

“…Recently, the I(t) profile was determined without relying on a numerical inversion procedure but by counting individual initiation events on combed DNA fibres at different f(t) (Goldar et al 2008). This analysis showed that the decreasing part of I(t), which was not initially taken into account, is not a statistical artefact but a real feature of chromosome replication.…”

“…Two models to explain the observed shape of I(t) in terms of protein-DNA interactions have been proposed. Goldar et al (2008) have performed simulations wherein the encounter of a limiting, recyclable replication fork factor with potential origins results in productive initiation with probability P. When forks meet, the factor is released and made available again for initiation. The total number of factor molecules N T and the probability P were either held constant or allowed to change with time.…”

“…However, simulations have shown that recycling is not efficient when the number of unfired origins decreases as S phase progresses, even if the affinity of potential origins for the factor is very high (Figure 2A in Goldar et al (2008)). Furthermore, the spatially averaged profile of I(t), which is equivalent to the mean firing propensity, was recently extracted (Goldar et al 2009) from the published S. pombe replication timing profiles (Heichinger et al 2006;Eshaghi et al 2007).…”