Fig. 8: NF-κB signaling controls enhancer activation and enhancer-promoter interactions for optimal expression of its target genes. | Nature Communications

Fig. 8: NF-κB signaling controls enhancer activation and enhancer-promoter interactions for optimal expression of its target genes.

From: CTCF controls three-dimensional enhancer network underlying the inflammatory response of bone marrow-derived dendritic cells

Fig. 8

a WT BMDCs were either untreated or treated with JSH-23 for 3 h and Western blot analysis was performed to assess LPS-induced RelA nuclear translocation. The data are representative of three independent experiments with similar results. b Densitometric analysis of the proteins in a was performed using ImageJ. Error bars represent mean ± standard error of the mean (s.e.m.). Significance was calculated using a two-way ANOVA with multiple comparisons of Bonferroni post-test. The sample sizes (n) were labeled in the figure. c Heatmaps of normalized ChIP-seq tag densities for H3K27ac at RelA binding sites called from LPS-stimulated WT BMDCs (WTL). Histogram showing the average tag density of ChIP-seq peaks are displayed at the right of the heatmaps. The data are representative of two independent experiments. d The effect of JSH-23 on the extent of changes in the chromatin interactions of either gained or lost RelA loops in response to LPS stimulation was analyzed by H3K27ac HiChIP. e The effect of JSH-23 on the transcript abundance of either upregulated or downregulated RelA target genes in response to LPS stimulation was analyzed by RNA-seq. DEG: differentially expressed gene. Box-plot in d, e with midline = median, box limits = Q1 (25th percentile)/Q3 (75th percentile), whiskers = minimum and maximum values. Significance in d, e was calculated using two-sided Wilcoxon rank sum test. The sample sizes (n) were labeled in the figure. f Snapshot showing virtual 4C plots (V4C), ChIP-seq signal tracks, and RNA-seq signal tracks (from top to bottom) at the Il6 (left) and Il12a (right) loci. Sky blue, blue, orange, and brown represent unstimulated WT BMDCs in the absence of JSH-23 (WT) or pretreated with JSH-23 (WT + JSH23), LPS-stimulated WT BMDCs in the absence of JSH-23 (WTL) or pretreated with JSH-23 (WTL + JSH23), respectively. V4C shows normalized H3K27ac HiChIP contact counts with the TSSs of Il6 and Il12a as the viewpoint. Source data are provided as a Source Data file.

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