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. 2020 Jul 9;11:3419. doi: 10.1038/s41467-020-17065-z

Fig. 4. Chd4 coordinates intra-domain loop strength and gene expression.

Fig. 4

a (Top) Hi-C contact matrix of a loop domain on chromosome 4 and the flanking region, with an intra-domain enhancer-promoter (E–P) loop highlighted by a white box. (Bottom) Genome-browser snapshot of the region corresponding to the Hi-C contact matrix displaying the ChIP-seq profiles of H3K27ac, Smc1, and Ctcf as well as DNaseI-seq from the control and Chd4 cKO cerebellum. Blue denotes the the loop anchors and regions of the insets. Numbers indicate the Log2 change in signal in the Chd4 cKO cerebellum, including that of mRNA for Jun. b, c Hi-C contacts at intra-domain (b) or intra-domain E–P (c) loops among domains with increased (n = 938 intra-domain; n = 116 intra-domain E–P), unchanged (n = 4928 intra-domain; n = 953 intra-domain E–P), or decreased (n = 133 intra-domain; n = 26 intra-domain E–P) accessibility in the Chd4 cKO. Two-sided Kruskal–Wallis H-test for independent samples with Dunn’s post hoc T-test and corrected for multiple comparisons by the Bonferroni–Hochberg procedure. ***p < 0.001. d Aggregate peak analysis of enhancer-promoter loops in domains with increased accessibility in the Chd4 cKO cerebellum. P2LL, peak-to-lower-left. e Change in (left) H3K27ac and (right) Smc1 at enhancers underlying intra-domain E–P loops among domains with increased (n = 183), unchanged (n = 1682), or decreased (n = 45) accessibility. Two-sided Kruskal–Wallis H-test for independent samples with Dunn’s post hoc T-test and corrected for multiple comparisons by the Bonferroni–Hochberg procedure. ***p < 0.001. f Change in mRNA of genes in domains with increased (n = 3,202), unchanged (n = 12,649), or decreased (n = 311) accessibility in the Chd4 cKO. Two-sided Kruskal–Wallis H-test for independent samples with Dunn’s post hoc T-test and corrected for multiple comparisons by the Bonferroni–Hochberg procedure. ***p < 0.001. g Change in mRNA of genes at intra-domain E–P loops (green, n = 145) or underlying no detectable loop (brown, n = 3057) in domains with increased accessibility in the Chd4 cKO. Two-sided Mann–Whitney U. ***p < 0.001.