Extended Data Figure 1. Clustering of early replication-timing borders and TAD boundary alignment at TTRs and A/B compartment transitions.

a, Cumulative density plot showing clustering of timing values at the early and late side of timing transition regions. For each genomic orientation (forward and reverse are shown in right and left columns), timing values are more tightly distributed at the early border than the later border. b, Directionality index data for individual IMR90 TTRs aligned at their early (left) or late (right) borders and arranged by TTR size. Solid black lines indicate the positions of early and late borders in each plot. c, Percentages of ESC TTR borders or random positions that align to TAD boundaries as a function of distance from the TTR centre. Boxplots indicate the positions of TTR borders. d, Percentages of mESC compartment A/B transitions that align to TAD boundaries as a function of distance from the A/B compartment threshold (eigenvector crosses zero). As observed for early TTR borders, more A/B transitions align with TAD boundaries on their compartment A side than on their compartment B side, which aligns with TAD boundaries at near random frequency.