No abstract

DNA replication is a complex process that ensures the maintenance of genetic information. Recently, advancements in chromatin conformation capture techniques have enabled the modeling of DNA replication as a spatio-temporal process. Here, we present a stochastic hybrid model for DNA replication that incorporates protein mobility dynamics and 3D chromatin structure. Performing simulations for three model variations and a broad range of parameter values, we collected about 300,000 in silico replication profiles for fission yeast and conducted a parameter sensitivity analysis. We find that the number of firing factors initiating replication is rate-limiting and dominates the time until completion of DNA replication. In support of recent work, we also find that explicitly modeling the recruitment of firing factors by the spindle pole body (SPB) best recapitulates published origin efficiencies, and independently validate these findings in vivo. Accounting for probabilistic effects in molecular interactions, we further investigated the replication kinetics inherent to the model and were able to capture known properties of DNA replication. Importantly, we confirm earlier observations that, without further assumptions, the characteristic shape of a function commonly used to describe replication kinetics arises from a rate-limiting number of firing factors in conjunction with their recycling upon replication fork collision. While the model faithfully recapitulates global spatial patterns of replication initiation, additional analysis of spatial concurrence and competition suggests that a uniform binding probability is too simplistic to capture local neighborhood effects in origin firing. In summary, our model provides a framework to realistically simulate DNA replication for a complete eukaryotic genome, and to investigate the relationship between three-dimensional chromatin conformation and DNA replication timing.Recent advancements in chromosome conformation capture techniques (e.g., 3C, Hi-C) have enabled the determination of DNA structure and nuclear organization. As a consequence, studies on various organisms have observed that DNA replication timing is highly correlated with chromatin folding and global nuclear architecture [34][35][36]. In mammalian cells, chromatin conformation maps agree with replication timing profiles

DNA replication is a complex and remarkably robust process: despite its inherent uncertainty, manifested through stochastic replication timing at a single-cell level, multiple control mechanisms ensure its accurate and timely completion across a population. Disruptions in these mechanisms lead to DNA re-replication, closely connected to genomic instability and oncogenesis. Here, we present a stochastic hybrid model of DNA re-replication that accurately portrays the interplay between discrete dynamics, continuous dynamics and uncertainty. Using experimental data on the fission yeast genome, model simulations show how different regions respond to re-replication and permit insight into the key mechanisms affecting re-replication dynamics. Simulated and experimental population-level profiles exhibit a good correlation along the genome, robust to model parameters, validating our approach. At a single-cell level, copy numbers of individual loci are affected by intrinsic properties of each locus, in cis effects from adjoining loci and in trans effects from distant loci. In silico analysis and single-cell imaging reveal that cell-to-cell heterogeneity is inherent in re-replication and can lead to genome plasticity and a plethora of genotypic variations.

DNA replication is a complex and remarkably robust process: despite its inherent uncertainty, manifested through stochastic replication timing at a single-cell level, multiple control mechanisms ensure its accurate and timely completion across a population. Disruptions in these mechanisms lead to DNA re-replication, closely connected to genomic instability and oncogenesis. We present a stochastic hybrid model of DNA re-replication that accurately portrays the interplay between discrete dynamics, continuous dynamics, and uncertainty. Using experimental data on the fission yeast genome, model simulations show how different regions respond to re-replication, and permit insight into the key mechanisms affecting re-replication dynamics. Simulated and experimental population-level profiles exhibit good correlation along the genome, which is robust to model parameters, validating our approach. At a single-cell level, copy numbers of individual loci are affected by intrinsic properties of each locus, in cis effects from adjoining loci and in trans effects from distant loci. In silico analysis and single-cell imaging reveal that cell-to-cell heterogeneity is inherent in re-replication and can lead to a 2 plethora of genotypic variations. Our thorough in silico analysis of DNA re-replication across a complete genome reveals that heterogeneity at the single cell level and robustness at the population level are emerging and co-existing principles of DNA re-replication. Our results indicate that re-replication can promote genome plasticity by generating many diverse genotypes within a population, potentially offering an evolutionary advantage in cells with aberrations in replication control mechanisms.

Copy Number Gains (CNGs) lead to genetic heterogeneity, driving evolution and carcinogenesis. The mechanisms promoting CNG formation however remain poorly characterized. We show that abnormal expression of the replication licensing factor Cdc18 in fission yeast, which leads to genome-wide re-replication, drives the formation of CNGs at different genomic loci, promoting the acquisition of new selectable traits. Whole genome sequencing reveals Mb long, primarily extrachromosomal amplicons. Genetic analysis shows that homology-mediated repair is required to resolve re-replication intermediates into heritable CNGs. Consistently, we show that in mammalian cells overexpression of CDC6 and/or CDT1 leads to CNGs and promotes drug resistance. In human cells, multiple repair pathways are activated upon rereplication and act antagonistically, with RAD52 promoting and 53BP1 inhibiting CNG formation. In tumours, CDT1 and/or CDC6 overexpression correlates with copy number gains genome-wide. We propose re-replication as an evolutionary-conserved driver of CNGs, highlighting a link between aberrant licensing, CNGs and cancer.