Regions of replication delay in haploid cells are correlated with the level of X Chromosome activity. (A) Haploid-delayed variants significantly overlap XaXa variant regions compared to matched permutations. Same as in Figure 4A; dark blue: permutations of haploid-dealyed regions, light blue: permutations of XaXa variant regions. (B) Haploid-advanced variants significantly overlap XaXa variant regions. Same as A, for haploid-advanced variants. (C) Replication timing differences between XaXa females and other ESCs (x-axis) compared to haploid versus diploid replication timing variants (y-axis). For presentation purposes, data was downsampled to one window every 200 kb of uniquely alignable sequence. (D) X Chromosome replication timing profiles for haploid, recently diploidized, and diploid ESCs. Haploid and recently diploidized cell lines show comparable replication timing along the X Chromosome that is earlier than diploid cells. This trend is more pronounced in experiment 2 (left) than in experiment 3 (right). (E) Replication timing in recently diploidized ESCs resembles haploids more than it resembles diploids, thus tracking X Chromosome status rather than ploidy. For experiment 2, P-values (t-test) are shown for each cell line compared to the single diploid cell line in that experiment; for experiment 3, a single P-value (ANOVA) is shown for the joint comparison of the two haploid cell lines with the two diploid cell lines. See Supplemental Table S2 for statistics at other haploid-delayed variants.
