DNA replication timing: random thoughts about origin firing

Abstract

Regions of metazoan genomes replicate at defined times within S phase. This observation suggests that replication origins fire with a defined timing pattern that remains the same from cycle to cycle. However, an alterative model based on the stochastic firing of origins may also explain replication timing. This model assumes varying origin efficiency instead of a strict origin-timing programme. Here, we discuss the evidence for both models.Models for the organization of eukaryotic DNA replication have to account for two diametrically opposed conceptions of replication. On one side of the spectrum is the replicon paradigm, exemplified by the mechanism of bacterial replication, in which origins are welldefined sites that fire once in each cell cycle, leading to uniform replication that is identical in every cell 1 . At the opposite end of the spectrum is the mechanism of replication in frog and fly embryos, in which replication initiates asynchronously throughout S phase at indiscriminate sites, presumably leading to a different, random pattern of replication in each cell 2,3 . It is clear that neither of these extreme mechanisms reflect the reality of replication in most eukaryotic somatic cells, but it is also clear that both models contain a kernel of truth. So how do we reconcile these apparently competing views of replication? Recent work suggests a way to bridge the gap and to reconcile stochastic origin firing with defined patterns of genome replication.It is useful to first establish which parts of each model generally apply to eukaryotic replication. The replicon paradigm, which serves as the foundation for most textbook models of eukaryotic replication, describes eukaryotic replication reasonably well, with two major exceptions: first, most eukaryotes do not seem to have well-defined, sequence-specific origins4 , 5. Consequently, it has been difficult to identify metazoan replication origins, and in the few cases in which they have been identified, they seem to have no particular sequence specificity. However, too few metazoan origins have been defined to exclude the possibility of origin specific sequences. The question of what constitutes a eukaryotic replication origin remains an active field of research, and as knowledge of the exact location of origins is not necessary for the ideas presented here, we will not pursue it further. Second, eukaryotic origins are inefficient and fire in only a subset of S phases 6 -only a fraction of the origins established in G1 are fired in S phase and it is a different set in each cell. In fission yeast, most origins fire about 30% of the time, whereas in mammals, the well-studied dihydrofolate reductase (DHFR) origins fire approximately 20% of the time 7, 8.In terms of these two exceptions to the replicon paradigm, eukaryotic replication looks more like the example of frog and fly embryos. Frog embryos go to the extreme of establishing origins randomly across the genome, without regard to DNA sequence 2,9 . This is not the case for eukaryotes in general, whi...

Stochastic hybrid modeling of DNA replication across a complete genome

“…Additionally, the firing propensity of each origin along the genome has been determined based on the experimentally defined observed efficiencies in the presence of the drug hydroxyurea, which inhibits fork progression, thereby eliminating passive replication (24). In fission yeast, only a small number of origins genome-wide appear intrinsically late and do not fire during a long hydroxyurea block (24,27), while for the vast majority of origins, the timing of firing appears correlated to their firing propensities (24), suggesting that stochastic determination of firing times is the prevailing mechanism in the fission yeast (18). Fission yeast offers therefore a good opportunity to capture full genome replication based on experimental data coupled to an understanding of the underlining biology.…”

“…The model was modified to accommodate a specific biological hypothesis for the reason behind the probabilistic nature of the firing of origins: the presence of a limiting initiation factor, which is released following origin firing and binds again to origins still at the prereplicative state (18). Since the number of origins in the prereplicative state decreases as S-phase progresses, the probability of the limiting factor binding to a particular prereplicative origin (and therefore the firing probability of this origin) increases along S-phase (18). The firing propensity redistribution model was developed to code this hypothesis, assuming that the pool of available factor remains roughly constant during S-phase.…”

“…Stochasticity could be brought about by a limiting factor that allows firing of a fraction of putative origins. The redistribution of this factor after an origin fires or gets passively replicated would imply a gradual increase in firing propensity of origins still in the prereplicative state as S-phase progresses (18). This biological scenario can be captured in our model by keeping the total system firing propensity (given by the sum of the firing propensities of all origins) constant throughout S-phase.…”

“…Our analysis leads to two alternatives: Either S-phase duration in the presence of stochastic firing is longer than experimentally defined, or a further mechanism exists that succeeds in limiting S-phase duration circumventing the random gap problem. One proposed solution to the random gap problem is that the efficiency of unreplicated origins may increase during the course of S-phase (14,18). Stochasticity could be brought about by a limiting factor that allows firing of a fraction of putative origins.…”

“…This complication of stochastic DNA replication initiation is known as the random gap problem (14). Different solutions to this problem have been suggested, including a spacing mechanism for the generation of defined interorigin gaps (15,16), coordination of fork velocity with interorigin distance (17), and an increase in origin efficiency during S-phase (14,18).…”