title: A variable fork rate affects timing of origin firing and S phase dynamics in Saccharomyces cerevisiae.
abstract: Activation (in the following referred to as firing) of replication origins is a continuous and irreversible process regulated by availability of DNA replication molecules and cyclin-dependent kinase activities, which are often altered in human cancers. The temporal, progressive origin firing throughout S phase appears as a characteristic replication profile, and computational models have been developed to describe this process. Although evidence from yeast to human indicates that a range of replication fork rates is observed experimentally in order to complete a timely S phase, those models incorporate velocities that are uniform across the genome. Taking advantage of the availability of replication profiles, chromosomal position and replication timing, here we investigated how fork rate may affect origin firing in budding yeast. Our analysis suggested that patterns of origin firing can be observed from a modulation of the fork rate that strongly correlates with origin density. Replication profiles of chromosomes with a low origin density were fitted with a variable fork rate, whereas for the ones with a high origin density a constant fork rate was appropriate. This indeed supports the previously reported correlation between inter-origin distance and fork rate changes. Intriguingly, the calculated correlation between fork rate and timing of origin firing allowed the estimation of firing efficiencies for the replication origins. This approach correctly retrieved origin efficiencies previously determined for chromosome VI and provided testable prediction for other chromosomal origins. Our results gain deeper insights into the temporal coordination of genome duplication, indicating that control of the replication fork rate is required for the timely origin firing during S phase.
authors.affiliation: Institute for Biology, Theoretical Biophysics, Humboldt University Berlin, Invalidenstraβe 42, 10115 Berlin, Germany.
authors.forename: Adriana
authors.initials: A
authors.lastname: Supady
authors.forename: Edda
authors.initials: E
authors.lastname: Klipp
authors.forename: Matteo
authors.initials: M
authors.lastname: Barberis
mesh_terms: D015825:Chromosomes, Fungal; D042522:DNA Replication Timing; D004271:DNA, Fungal / Q000378:metabolism*; D016681:Genome, Fungal; D008957:Models, Genetic; D056004:Molecular Dynamics Simulation; D018741:Replication Origin / Q000235:genetics*; D016196:S Phase; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism
chemical_list: D004271:DNA, Fungal
keywords: Budding yeast; DNA replication; Firing efficiency; Origin firing; Replication fork rate; Replication timing