Fig. 1: The Xi replicates rapidly and uniformly in late S during XCI.
From: Replication dynamics identifies the folding principles of the inactive X chromosome
a, Neural differentiation protocols of JB4/EI7HZ2 mESCs. b, Schematic diagram of BrdU-IP Repli-seq experiment. BrdU-labeled cells are sorted into early and late S-phase fractions (gating strategy is shown in Supplementary Fig. 1i), which are subject to immunoprecipitation (IP) using an anti-BrdU antibody. The ratio of early and late S-phase DNA is calculated to generate a genome-wide RT profile. c, Comparison of genome-wide RT profiles (sliding windows of 200 kb at 80-kb intervals, excluding the X) during differentiation of JB4/EI7HZ2 mESCs, CBMS1 mESCs30, EpiSCs and MEFs by hierarchical clustering. d, BrdU-IP RT profiles of the JF1-X and the B6-X during JB4/EI7HZ2 mESC differentiation (average of 2–3 replicates, 400-kb bins). RT classes represent four types of ESC-to-NSC RT regulation, which were described on the right. The blue line shows Dxz4 position. e, Binarized whole-S scRepli-seq profiles of the JF1-Xa and the B6-Xi from 94 NSCs throughout the S. The scRepli-seq profiles are ordered by their percentage replication scores (of the whole genome excluding the X). BrdU-IP RT of the NSCs is shown for comparison. The blue lines show Dxz4 position. f, Percentage replication scores of the JF1-Xa and the B6-Xi were plotted against those of the whole genome for each NSC (open circles). Cells were divided into 18 groups by their percentage replication scores and the average scores of the JF1-Xa and the B6-Xi in each group are shown by filled circles. To minimize errors during data fitting, we added two pseudo-percentage replication scores, 0 and 100%, at the earliest end and the latest end of the S-phase, respectively. We fitted a linear and a sigmoid model to the JF1-Xa and the B6-Xi, respectively, to calculate the T10–90% values (the time required to go from 10 to 90% replication, assuming a 10 h S). g, Cells were divided into ten groups by percentage replication scores and the boxplots show distributions of percentage replication scores of the JF1-Xa and the B6-Xi in each group. h, An exemplary latest RT region on the Xa, which advanced its RT on the Xi in NSCs. CBMS1 mESC data are shown for comparison30.
