A model for the spatiotemporal organization of DNA replication in Saccharomyces cerevisiae

Abstract

DNA replication in eukaryotes is considered to proceed according to a precise program in which each chromosomal region is duplicated in a defined temporal order. However, recent studies reveal an intrinsic temporal disorder in the replication of yeast chromosome VI. Here we provide a model of the chromosomal duplication to study the temporal sequence of origin activation in budding yeast. The model comprises four parameters that influence the DNA replication system: the lengths of the chromosomes, the explicit chromosomal positions for all replication origins as well as their distinct initiation times and the replication fork migration rate. The designed model is able to reproduce the available experimental data in form of replication profiles. The dynamics of DNA replication was monitored during simulations of wild type and randomly perturbed replication conditions. Severe loss of origin function showed only little influence on the replication dynamics, so systematic deletions of origins (or loss of efficiency) were simulated to provide predictions to be tested experimentally. The simulations provide new insights into the complex system of DNA replication, showing that the system is robust to perturbation, and giving hints about the influence of a possible disordered firing.

Fig. 1

Scheme of the chromosomal duplication model and its parametrization. The features and the algorithm are explained in the main text

Fig. 2

Replication profiles of chromosome II. The smooth curve is recalculated according to the microarray-based heavy:light data from Raghuraman et al. , whereas the straight curve represents the simulated profile obtained with the spatiotemporal model. The replication time in seconds is plotted as a function of chromosome coordinate in base pairs (bp)

Fig. 3

Replication profiles of chromosome II in a clb5Δ background. The dotted line represents the simulated profile for wild type cells, whereas the straight one represents the computed profile for the clb5Δ mutant

Fig. 4

Simulated replication kinetics of chromosome II. The simulations are performed for wild type (a) and perturbed conditions (b). In the case of perturbed conditions, the simulation has been performed considering 30 reduced sets of replication origins derived from the random deletion of 50% of the original origins

Fig. 5

Mean replication time (in seconds) for chromosomes II (a) and XVI (b). Solid line represents the curve for descending percentage of the considered replication origins (from 90 to 10%). Error bars show the standard deviation of 10,000 simulations. Dashed line indicates the experimental replication time for each chromosome, according to Raghuraman et al.

Fig. 6

Average delay in chromosomal duplication time (in minutes) plotted over the length (a) and the origin density of the chromosomes (b). The average delay is calculated after 10,000 simulations of DNA replication under perturbed conditions (50% origin deletion). The origin density is the ratio of the number of origins on a chromosome and the chromosome size