Reconciling stochastic origin firing with defined replication timing

Abstract

Eukaryotic chromosomes replicate with defined timing patterns. However, the mechanism that regulates the timing of replication is unknown. In particular, there is an apparent conflict between population experiments, which show defined average replication times, and single-molecule experiments, which show that origins fire stochastically. Here, we provide a simple simulation that demonstrates that stochastic origin firing can produce defined average patterns of replication firing if two criteria are met. The first is that origins must have different relative firing probabilities, with origins that have relatively high firing probability being likely to fire in early S phase and origins with relatively low firing probability being unlikely to fire in early S phase. The second is that the firing probability of all origins must increase during S phase to ensure that origins with relatively low firing probability, which are unlikely to fire in early S phase, become likely to fire in late S phase. In addition, we propose biochemically plausible mechanisms for these criteria and point out how stochastic and defined origin firing can be experimentally distinguished in population experiments.

Fig. 1

Stochastic origin firing can produce defined replication timing patterns. a Three simulated replication profiles. Each simulation covers ten origins spaced every 20 kb. The five origins on the right fire early, those on the left fire late. In these simulations, all of the early region is on average replicated before any of the late origins fire. Model I: Origins fire with a defined average time and variance. The early origins fire at 37.5±6 min, and the late origins fire at 47±6 min. Model II: The origins fire stochastically, with a probability that increases during S phase. The early-firing origins have a higher relative probability, and the late-firing origins have a lower relative firing probability. In this incarnation of the increasing-probability model, the increase in firing probability follows a power law that increases the firing probability of a late origin by tenfold between early S phase and late S phase. However, other kinetic schemes with a similar increase in firing probability would work just as well. Model III: The origins fire stochastically with a constant firing probability. b The cumulative firing probability of a representative early- and late-firing origin from Model II. An origin with relatively high firing probability is likely to fire in early S phase. An origin with relatively low firing probability is unlikely to fire in early S phase, but as its firing probability increases, it becomes likely to fire in late S phase. c The firing kinetics of a representative early- and late-firing origin from Models I and II