HowXenopus laevisembryos replicate reliably: Investigating the random-completion problem

Abstract

DNA synthesis in Xenopus frog embryos initiates stochastically in time at many sites (origins) along the chromosome. Stochastic initiation implies fluctuations in the time to complete and may lead to cell death if replication takes longer than the cell cycle time (≈ 25 min). Surprisingly, although the typical replication time is about 20 min, in vivo experiments show that replication fails to complete only about 1 in 300 times. How is replication timing accurately controlled despite the stochasticity? Biologists have proposed two solutions to this "random-completion problem." The first solution uses randomly located origins but increases their rate of initiation as S phase proceeds, while the second uses regularly spaced origins. In this paper, we investigate the randomcompletion problem using a type of model first developed to describe the kinetics of first-order phase transitions. Using methods from the field of extreme-value statistics, we derive the distribution of replication-completion times for a finite genome. We then argue that the biologists' first solution to the problem is not only consistent with experiment but also nearly optimizes the use of replicative proteins. We also show that spatial regularity in origin placement does not alter significantly the distribution of replication times and, thus, is not needed for the control of replication timing.

Optimal Placement of Origins for DNA Replication

“…We also find that 8 groups of 8 pMcms gives the advantage of a 1.1 min quicker T rep than using random loci; even when the number of pMcms at these 8 groups varies, a quicker T rep is achieved (data not shown). Grouping pMcms also protects the overall replication process against fluctuations from one round of the cell cycle to another; a similar problem is discussed in [14]. This is because one initiation event at an origin is sufficient to activate replication forks.…”

“…There is also experimental evidence for grouping in X. laevis, where origins seem to be distributed with groups of 5 to 10 pMcms [8][9][10]. Most of the existing models of replication in X. laevis [9,[11][12][13][14][15]] -an exception is [16] -assume the origins to be random and independent of each other, and so they cannot explain pMcm grouping or the observed maximum-spacing of 25 kilobases (kb) between adjacent origins [9]. …”

Model-based analysis of DNA replication profiles: predicting replication fork velocity and initiation rate by profiling free-cycling cells

“…We note that previous studies considered a distribution of end-times p(t * ) (Yang and Bechhoefer 2008), while we consider a specific value t * (given our resolution ε) The reason for this difference is the biological properties of the systems investigated. Thus, this previous work considered origins which are not located in fixed positions.…”

“…It is less well suited for characterizing wild-type cells, primarily because the SVD projections are not intuitive and do not provide explicit information about the parameters controlling replication. Curve-fitting methods that attempt to more directly model the full replication profile are better suited for characterizing the wild-type profiles and were indeed applied to multiple systems ranging from a Xenopus embryo (Goldar et al 2008;Yang and Bechhoefer 2008;Gauthier and Bechhoefer 2009), budding yeast (Brümmer et al 2010;de Moura et al 2010;Yang et al 2010;Retkute et al 2011), regions of human cells (Gindin et al 2014), and others (Hyrien and Goldar 2010;Koutroumpas and Lygeros 2011;Retkute et al 2012;Baker and Bechhoefer 2014). These methods are labor-intensive and require an expert user to set up.…”

Checkpoint-independent scaling of the Saccharomyces cerevisiae DNA replication program

“…The locations of those origins and their relative activation times during S phase are largely conserved between individual cells defining the DNA replication program [1][2][3][4]. In recent years, the DNA replication program was mapped in different organisms [5][6][7][8][9]. Early replication was found to correlate with low mutation rate [10], high gene expression, open chromatin and a reduced nucleosome abundance [2,8,11,12].…”