Fig. 2: Developmental genes and clusters of CTCF sites are sequentially organized near mouse TAD boundaries. | Nature Communications

Fig. 2: Developmental genes and clusters of CTCF sites are sequentially organized near mouse TAD boundaries.

From: Cooperative insulation of regulatory domains by CTCF-dependent physical insulation and promoter competition

Fig. 2

TAD maps, Hi-C data and CTCF ChIP-seq profiles previously generated in mESC (A) or hESC (B) were used to investigate the insulation scores, boundary strength, number of CTCF peaks and CTCF peaks aggregated signal at developmental TAD boundaries, all other TAD boundaries or random regions. Developmental boundaries were defined as those having a nearby developmental gene located within bin 1 (Fig. 1B). P-values were calculated using unpaired two-sided Wilcoxon tests with false discovery rate correction for multiple testing; Cliff’s delta (Cd) effect sizes are shown as coloured numbers (green: large effect size; blue: medium effect size; orange: small effect size; red: negligible effect size). In (A-B) box plots, the upper and lower parts of the box are the upper and lower quartiles, respectively, the horizontal line that splits the box in two is the median and the upper and lower whiskers indicate the maximum and minimum, respectively. C To investigate the distribution of CTCF peaks around different types of genes located close to TAD boundaries (Bin1 genes), we considered the TSS of each gene as a reference point and a window of ±100 Kb to calculate: ΔCTCFpeaks@Bdry as the difference between the number of CTCF peaks located towards the TAD center and those located towards the TAD boundary (negative values: CTCF peaks more abundant towards the TAD boundary; positive values: CTCF peaks more abundant towards the TAD center); ΔCTCFsignal@Bdry as the difference between the aggregated signal of the CTCF peaks located towards the TAD center and the aggregated signal of the CTCF peaks located towards the TAD boundary (negative values: CTCF signals higher towards the TAD boundary; positive values: CTCF signals higher towards the TAD center). D Histogram showing the distribution of ΔCTCFpeaks@Bdry values in mESC for different types of genes (developmental, housekeeping, all) located close to TAD boundaries (bin 1 in Fig. 1B). E Cumulative distribution plots for ΔCTCFpeaks@Bdry (left) and ΔCTCFsignal@Bdry (right) values in mESC. P-values were calculated using unpaired two-sided Wilcoxon tests with false discovery rate correction for multiple testing.

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