CTCF-mediated Chromatin Structures Dictate the Spatio-temporal Propagation of Replication Foci

Mammalian DNA replicationis initiated at numerous replicationorigins, which are clustered into thousands of replicationdomains (RDs) across the genome. However, it remains unclear whether the replicationorigins within each RD are activated stochastically. To understand how replicationis regulated at the sub-RD level, we directly visualized the spatio-temporal organization, morphology, and in situ epigenetic signatures of individual replicationfoci (RFi) across S-phaseusing super-resolution stochastic optical reconstruction microscopy (STORM). Importantly, we revealed a hierarchical radial pattern of RFi propagation that reverses its directionality from early to late S-phase, and is diminished upon caffeine treatment or CTCFknockdown. Together with simulation and bioinformatic analyses, our findings point to a " CTCF-organized REplicationPropagation" (CoREP) model. The CoREP model suggests a non-random selection mechanism for replicationactivation mediated by CTCFat the sub-RD level, as well as the critical involvement of local chromatin environment in regulating replicationin space and time.