Kinetic model of DNA replication in eukaryotic organisms

Nucleation and growth in one dimension. I. The generalized Kolmogorov-Johnson-Mehl-Avrami model

Motivated by a recent application of the Kolmogorov-Johnson-Mehl-Avrami (KJMA) model to the study of DNA replication, we consider the one-dimensional (1D) version of this model. We generalize previous work to the case where the nucleation rate is an arbitrary function I (t) and obtain analytical results for the time-dependent distributions of various quantities (such as the island distribution). We also present improved computer simulation algorithms to study the 1D KJMA model. The analytical results and simulations are in excellent agreement.

Nucleation and growth in one dimension. II. Application to DNA replication kinetics

Inspired by recent experiments on DNA replication, we apply a one-dimensional nucleation-and-growth model to DNA-replication kinetics, focusing on how to extract the time-dependent nucleation rate I (t) and growth speed v from data. We discuss generic experimental problems: namely, spatial inhomogeneity, measurement noise, and finite-size effects. After evaluating how each of these affects the measurements of I (t) and v , we give guidelines for the design of experiments. These ideas are then discussed in the context of the DNA-replication experiments.

Dynamics of DNA replication in mammalian somatic cells: nucleotide pool modulates origin choice and interorigin spacing

Selection of active origins and regulation of interorigin spacing are poorly understood in mammalian cells. Using tricolor analysis of combed DNA molecules, we studied an amplified locus containing the known origin, oriGNAI3. We visualized replication firing events at this and other discrete regions and established a strict correlation between AT richness and initiation sites. We found that oriGNAI3 is the prominent origin of the domain, the firing of which correlates with silencing of neighboring sites and establishes large interorigin distances. We demonstrate that cells reversibly respond to a reduction in nucleotide availability by slowing the rate of replication fork progression; in addition, the efficiency of initiation at oriGNAI3 is lowered while other normally dormant origins in the region are activated, which results in an overall increase in the density of initiation events. Thus, nucleotide pools are involved in the specification of active origins, which in turn defines their density along chromosomes.