Fig. 1

a Pictures of wild-type (WT), ctcf^+/− and ctcf^−/− zebrafish embryos at 48 h post fertilization (hpf) showing homozygous mutant phenotypes, including the reduced size of head and eyes, heart edema, and defective pigmentation (arrow heads). Scale bars represent 250 μm. b Whole-mount embryo immunofluorescence of CTCF (red) and dapi (blue) in WT, ctcf^+/− and ctcf^−/− zebrafish embryos at the stages of 1000 cells (1 K cells), 30% of epiboly (30% epib.), 80% of epiboly (80% epib.), 18 somites (18 som.) and 24 hpf showing the maternal contribution of CTCF protein. Relative quantification of CTCF/dapi signal with average values ± standard error is shown. Statistical significance was measured using a two-sided Student’s t test. The number of embryos for WT, ctcf^+/− and ctcf^−/− used for quantification are as follows: 1 K cells (n = 3, n = 12, n = 3); 30% epib. (n = 4, n = 8, n = 5); 80% epib. (n = 3, n = 10, n = 5); 18 som. (n = 5, n = 5, n = 7) and 24 hpf (n = 5, n = 17, n = 5). Source data are provided as a Source Data file. c HiC normalized contact maps at 10-kb resolution from WT and ctcf^−/− zebrafish embryos at 24 and 48 hpf. A 3-Mb genomic region in chr11 is plotted, aligned with the insulation scores and the called topologically associating domain (TAD) boundaries. d Average insulation score profiles of WT and ctcf^−/− zebrafish embryos at 24 and 48 hpf around the TAD boundaries called in the WT. e Average CTCF ChIP-seq signal around TAD boundaries (green) and a shuffle control (brown) in WT embryos at 24 and 48 hpf.