Extended Data Figure 5: CHD1 collaborates with H3K4me3 to activate gene transcription.
From: Synthetic essentiality of chromatin remodelling factor CHD1 in PTEN-deficient cancer
a, Endogenous H3K4me3 was immunoprecipitated from BPH1 cells and CHD1 binding was detected by immunoblot. b, c, Immunoblots of H3K4me3 in CHD1-knockdown PC-3 cells or CHD1-knockout LNCaP cells. d, Heat maps showing the CHD1- and H3K4me3-binding features across gene promoters in shCHD1-treated versus control shRNA (Ctrl)-treated PC-3 cells (only CHD1/H3K4me3-overlap genes shown). Each panel represents 5 kb upstream and downstream of the transcription start site. e, Top ten hallmark pathways showing enrichment of CHD1-target genes identified by ChIP–seq. Fifty MSigDB hallmark pathways emerged following IPA core analysis. Graph displays category scores as –log10(P value) from Fisher’s exact test. f, Microarray analysis was performed in CHD1-knockdown and control PC-3 cells. Top ten hallmark pathways exhibiting enrichment of the downregulated genes in shCHD1 PC-3 cells (fold changes > 1.5). g, h, GSEA correlation of NF-κB signature with alternatively expressed genes in CHD1-knockout LNCaP cells (g) and wild-type and PTEN-knockout mouse prostate tissues (h). Normalized enrichment score (NES), nominal P-value and false discovery rate q value of correlation are shown. i, Heat map representation of 25 most downregulated NF-κB pathway genes in CHD1-knockdown PC-3 cells (from blue (low expression) to red (high expression)). j, Validation of CHD1-regulating genes in two individual CHD1-knockout LNCaP cells using qPCR. Data are mean ± s.d. of triplicate experiments.
