Fig. 7: LPS-stimulated expression of pro-inflammatory cytokines was diminished in CTCF-deficient BMDCs.

a Number of the high-confidence RelA-mediated chromatin interactions in WTL. The number of RelA HiChIP loops overlapped with RelA ChIP-seq peaks at either one or both anchors was indicated in the bar. b Scatter plot showing Log2-fold changes in RNA expression levels of RelA direct target genes shown in Supplementary Fig. 9c. The number of genes exhibiting >2-fold changes in WTL versus WT and 1.5-fold changes in KOL versus WTL with a false discovery rate <0.05 is indicated at each quartile. c Bar plot of –Log10 P-value showing enrichment of gene ontology terms (biological process) associated with RelA direct target genes whose expressions were upregulated by LPS stimulation and downregulated by CTCF depletion. Significance was calculated by one-sided Fisher’s Exact test. d Changes in RNA expression of the genes associated with the pathway term of “cytokine production”. Error bars represent mean ± standard error of the mean (s.e.m). n = 3 biologically independent samples. e, f Snapshot showing virtual 4C plots, ChIP-seq signal tracks, and significant RelA loops (from top to bottom) at the Il6 (e) and Il12a (f) loci. Sky blue, orange, purple, and green represent unstimulated wild-type BMDCs (WT), LPS-stimulated wild-type BMDCs (WTL), unstimulated CTCF knockout BMDCs (KO), and LPS-stimulated CTCF knockout BMDCs (KOL), respectively. Virtual 4C plots (V4C) shows normalized H3K27ac HiChIP loop strength (represented as −Log10(Q)) with the TSSs of Il6 and Il12a genes as the viewpoint. IGV browser shows ChIP-seq signal tracks for CTCF, SMC1, RelA, H3K27ac. The location of super-enhancers (SE), if any, were shown under H3K27ac ChIP-seq signal tracks. RelA loops shows significant interactions with –Log10(Q) ≥ 2. Gray vertical bars highlight the location of viewpoints. g, h 3D cliques for Il6 (g) and Il12a (h) loci where each node represented a promoter or an enhancer and each edge represented a significant chromatin interaction of H3K27ac HiChIP loop with –Log10(Q) ≥ 5. The size of each node indicates the H3K27ac levels and the color of each edge indicates the loop strength (-Log10(Q)). Source data are provided as a Source Data file.