Fig. 2: SmcHD1 is required for maintaining the uniformly late-replicating Xi but dispensable for the initiation of the RT switch.
From: Replication dynamics identifies the folding principles of the inactive X chromosome
a, BrdU-IP RT profiles of the B6-X during WT and SmcHD1-mutant (KO) mESC differentiation (average of 2–3 replicates). In addition to the ESC-to-NSC RT classes, those identified in SmcHD1-mutant cells are shown. The blue lines show Dxz4 position. b, Whole-S scRepli-seq plots of the B6-Xi from 94 WT NSCs and 85 SmcHD1-mutant NSCs, as in Fig. 1e. ESC-to-NSC RT classes as well as those identified in SmcHD1-mutant NSCs are shown. The blue lines show Dxz4 position. c, Single-cell RT (scRT) values were calculated for four RT classes identified by SmcHD1-mutant NSC analysis. Single-cell RT represents an estimated time when a given genomic bin replicates in S (assuming a 10 h S). P values were obtained from one-sided paired Wilcoxon signed-rank test. N, the number of bins in each RT class. d, Whole-S scRepli-seq plots in Fig. 2b were sorted by the BrdU-IP RT values of SmcHD1-mutant NSCs (from early to late RT). The red box corresponds mostly to the SD and CE classes and is magnified on the right. e, Comparison of percentage replication scores of the Xs in WT (black) and SmcHD1-mutant NSCs (red) with those of the whole genome, as in Fig. 1f.
