Origins Anywhere and Everywhere: Genome replication requires cooperative activation of thousands of origins in each cell

Our model of replication dynamics in a single eukaryotic cell supplants current population-based models. Long-read sequencing reveals cooperative activation of ∼8400 closely spaced origins in every S.cerevisiae cell. Origins with bidirectional forks of comparable velocities are evenly distributed across the genome. The probability of early origin activation directly correlates with the average density of ORC (Origin Recognition Complex) binding motifs in a 10-20kbp region. We propose that 3D chromosome folding creates genomic pockets that act as ORC traps to increase local concentrations of pre-RC (Replication Complexes) and favor origin activation. Our results indicate that efficient replication through chromatin requires the activation of thousands of origins spanning the entire genome. This is consistent with genome instability being caused by insufficient origin activation rather than by perturbations in the replication timing program.