Fig. 4: SATB1 mediated the chromatin interactions of super-enhancers. | Nature Communications

Fig. 4: SATB1 mediated the chromatin interactions of super-enhancers.

From: Chromatin organizer SATB1 controls the cell identity of CD4+ CD8+ double-positive thymocytes by regulating the activity of super-enhancers

Fig. 4

a Boxplot showing the contact distance changes between two anchors of significantly changed contacts (50 kb bin) in Satb1-deficient DP thymocytes. Gained, significantly increased interactions; lost, significantly decreased interactions; maintained, no significant changed interactions. The interactions with 0 bp distance were deleted. (gained, n = 500, P = 2.2e-16; lost, n = 411, P = 2.22e-16; maintained, n = 765200, P = 2.22e-16). Box plots show median (center line), interquartile range (box), and fifth and 95th percentiles (whiskers). The one-tailed Wilcoxon signed-rank test was used. b Boxplot of ChIP-seq signals in anchors of differential chromatin interactions (50 kb bin). 648 gained SEs and 549 lost SEs, P = 2.22e-16. Box plots show median (center line), interquartile range (box), and fifth and 95th percentiles (whiskers). The one-tailed Wilcoxon signed-rank test was used. c Aggregate interactions of all loops, enhancer–promoter (E-P) loops, super-enhancer (SE) loops, and Satb1-SC loops identified from Hi-C data of Satb1WT thymocytes. Pile-up plots showing contacts of ± 250 kb regions around loops in WT or Satb1cKO Hi-C (10 kb resolution). The numbers in pile-up plots represent the value of the highest contacts in the heatmap. SE loops, loops with one or two anchors in WT-SE regions. d Boxplot of loop sizes of all loops (WT, 392,910 loops; KO, 386,029 loops, P = 0), E-P loops (WT, 34,119 loops; KO, 31,808 loops, P = 3.42e-165), SE loops (WT, 13,507 loops; KO, 12,758 loops; P = 5.40e-16) identified from Hi-C data of Satb1WT thymocytes. Box plots show median (center line), interquartile range (box) and 10th and 90th percentiles (whiskers). ****P value <0.0001 by two-sided Student’s t test. e Pearson’s correlation analysis of super-enhancer associated H3K27ac signals (up, P = 0.0037) or relative gene expression (down, P = 3.94e-05) with numbers of loops associated with WT super-enhancers. P values by two-sided F test. Source data are provided as a Source Data file.

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