Supplementary Figure 5 from Chromatin Helicase CHD6 Establishes Proinflammatory Enhancers and Is a Synthetic Lethal Target in FH-Deficient Renal Cell Carcinoma

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Supplementary Figure 5. CHD6/SMARCA2/4-coordinated SEs-promoter looping boosts the transcription of NF-κB-related targets, related to Figure 6. A. 3C assay of the indicated genes in WT, CHD6-KO Caki-2 cells with or without DMF stimulation. “Pro” means the input-pro, while “3C” means the 3C primers targeting the indicated enhancer region. B. ChIP-qPCR of H3K27ac markers in promoters or enhancers of CCL2, ICAM1, or BCL3 gene in UOK-262 cells (n = 5). C. Immunoblotting analysis of p65 immunoprecipitates in UOK-262 cells with or without CHD6 depletion. D. ChIP-qPCR of SMARCA2/4 markers in the SEs of CCL2, ICAM1, or BCL3 gene (n = 5) in CHD6-KO UOK-262 cells with or without CHD6 restoration. E. RT-qPCR analysis of mRNA level for CCL2, ICAM1 and BCL3 genes (n = 5) in UOK-262 cells transfected with indicated siRNAs targeting cBAF, PBAF, or ncBAF. F. ChIP-qPCR of H3K27ac markers in indicated SEs of CCL2, ICAM1, or BCL3 gene (n = 5) in SMARCA2/4-KD UOK-262 cells with or without CHD6 overexpression. G. MA plot of differential H3K4me1 or H3K27ac ChIP-seq signals in UOK-262 cells treated with 12 h AU-15330 versus DMSO. Log2 fold changes of peaks are plotted on the y-axis. Significantly changed peaks (FDR< 0.05) are marked in grey. H. Gene set enrichment analysis (GSEA) revealed the inhibition of CHD6-signature by AU-15330. I. Plot of CHD6/p65 co-binding intensities in UOK-262 treated with control and AU-15330 (5 μM), respectively. P values were calculated using a two-tailed Student’s t-test (B, D-F). *p < 0.05, **p < 0.01, and ***p < 0.001. ns, no significance.

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