Extended Data Fig. 10: Features of tissue-specific CTCF occupancy at gene promoters.

a, Histogram showing frequencies of genomic regions with 2 or more CBSs in all analyzed 9 tissues, classified based on GC content levels. Black line shows fold change between the two groups. Total numbers of genomic regions analyzed in each group are indicated on the bottom. *** p value < 0.001, two-tailed t-test. b, Histogram showing frequencies of CTCF motif sequences and their PhastCons conservation scores. c, Histogram showing the fractions of genes whose promoter-proximal CTCF binding motifs were the same direction as the orientation of transcription. The fractions in CTCF-dependent down-and up-regulated genes and CTCF-independent genes in ESCs and NPCs are shown. The numbers of genes analyzed in each group are indicated on the bottom. * p value < 0.05, ** p value < 0.01, *** p value < 0.001, Pearson’s Chi-squared test. d, Heatmap showing lineage-specific DNA methylation levels at CBSs (motif sequences ±100 bp) in promoter of genes shown in Fig. 5c. The DNA methylation levels at multiple CBSs in the same promoter region (TSS±10 kb) were averaged. Lineage-specificity of DNA methylation levels shown in the heatmap are calculated by log₂(DNA methylation level/average methylation level of all tissues). The heatmap was sorted by correlation coefficient between CTCF ChIP-seq signal levels and DNA methylation levels across multiple tissues in each group. Each correlation coefficient is shown in the scatter plots (right) (r<−0.5, highlighted in blue). e, Boxplots showing length of lineage-specific genes with CTCF occupied promoter that had high correlation coefficient (> 0.6) in Fig. 5b, c. Forebrain-specific genes and other lineage-specific genes are shown at right and middle, respectively. All genes whose RNA-seq RPKM value is more than 1 in at least one tissue sample were used as control (left). The numbers of genes analyzed in each group are indicated on the bottom. NS not significant, *** p value < 0.001, two-tailed t-test. f, Boxplots showing gene length of CTCF-dependent down-regulated, up-regulated and CTCF-independent genes in ESCs and NPCs. The numbers of genes analyzed in each group are indicated on the bottom. NS not significant, *** p value < 0.001, two-tailed t-test. g, Volcano plots showing the gene expression changes of the forebrain-specific CTCF-occupied genes between control cells and CTCF-depleted cells in ESCs (left) and NPCs (right). h, Volcano plots showing gene expression changes of heart-tissue-specific CTCF-occupied genes between control heart tissue and CTCF knockout heart tissue.