Fig. 6

Model of the major determinants of human replication initiation site distribution. Two example genomic locations are shown, one replicating in early S-phase (left) and the other in late S-phase (right). (panels i–iii) A model to illustrate how the transcriptional (i) and chromatin (ii) landscape may influence sites and zones of DNA replication initiation (iii). (panels iv–v) Illustration of the types of replication initiation events that can be detected by population versus single-molecule genomic assays. In panel (i), the rectangles indicate high (black with triple arrowhead), medium (gray with double arrowhead), and low (light gray with single arrowhead) levels of transcription. In panel (ii) the peaks indicate regions of accessible chromatin, for example the signal from DNase I hypersensitive site sequencing. Panel (iii) illustrates sites of replication initiation (black circles) in a population of 5 example cells. Note, dormant origins are not marked. Open boxes illustrate zones of focused initiation sites within which multiple cells within the population initiate DNA replication. Gray-shaded rectangles indicate genome fragments detected by single-molecule sequencing in panel (v). Panel (iv) illustrates the nature of replication initiation signal from a population of cells (for example, Ok-seq), with gray-shaded rectangles highlighting two initiation zones. The dashed horizontal line illustrates the significance threshold for identifying initiation zones. Panel (v) illustrates five example single-molecule DNAscent replication profiles from the example cells in panel (iii). In each molecule, the white-black gradient illustrates low–high BrdU incorporation with replication fork direction indicated by arrows. Single-molecule replication initiation events are visualized by filled circles between diverging arrows with equal sensitivity to detect focused and dispersed initiation events in early and late S phase