Fig. 2: CTCF loop domain boundaries in ES cell differentiation.

a Boundary-anchored virtual 4 C heatmap of the domain boundaries in HUES64 and its derivatives. The locations of domain boundaries were identified in HUES64 Hi-C data. The −log10 P-value (before adjusting for multiple comparisons) obtained from Fit-Hi-C software are shown. Each row represents the domain of one gene. The strongest domain (i.e., that with the lowest Hi-C interaction P-value between boundaries) per gene is shown if there are multiple domains for that gene. b Boundary-anchored virtual 4 C heatmap of the domain boundaries identified from HUES64 Hi-C data plotted by using the Hi-C data of HUES64 and its derivatives as the underlying contact maps. The normalized Hi-C interactions are shown. The ordering is the same as in a. c Boundary-anchored virtual 4 C average profile of the domain boundaries in HUES64 and its derivatives. The locations of domain boundaries were identified in HUES64 Hi-C data. The normalized Hi-C interactions are shown. The dotted line separates the left and right boundary regions, which represent the regions in the left and right heatmap in b. Average signals across all boundaries are shown with the shaded area indicating the standard error. Two-sided Wilcoxon test was used to determine significance level of boundary-to-boundary interactions between the two groups. Data are presented as mean values ± SE. d Hi-C signal fold-change of boundary-to-boundary interactions in HUES64 derivatives over HUES64 cells. Two-sided Wilcoxon test p-value is shown. Hi-C signals were normalized by library size in individual samples prior to the analysis. The box indicates the interquartile range (IQR), the line inside the box shows the median, and whiskers show the locations of either 1.5 × IQR above the third quartile or 1.5 × IQR below the first quartile, n = 3,310 boundary-to-boundary interactions for single-gene domain, n = 8,729 boundary-to-boundary interactions for multi-gene domain. e Boundary-anchored virtual 4 C average profile of the domain boundaries at the 2-cell, 8-cell, 8-cell treated with α-amanitin, morula, blastocyst stages, and 6-week embryos. The locations of domain boundaries were identified in HUES64 Hi-C data. CTCF expression is inhibited under α-amanitin treatment at the 8-cell stage. The normalized Hi-C interactions are shown. The dotted line separates the left and right boundary regions. Average signals across all boundaries are shown with the shaded area indicating the standard error. Two-sided Wilcoxon test was used to determine the significance level of boundary-to-boundary interactions between the two groups. Data are presented as mean values ± SE.