CHD6 eviction of promoter nucleosomes maintains housekeeping transcriptional program in prostate cancer

Abstract

CHD6, a member of the chromodomain helicase DNA-binding protein family, has been implicated in various diseases and tumors. However, its precise binding model of CHD6 on regulatory functional genes remains poorly understood. In this study, we discovered sharp peaks of CHD6, as the first member of CHD family for housekeeping process, binding only to the promoter region of genes in the C4-2 cell line. These genes, with conserved sharp CHD6 peaks across tumor cells, likely represent housekeeping genes ADNP and GOLGA5. Genes with sharp CHD6 peaks exhibit stable and low expression levels, sharing epigenetic features similar to housekeeping genes. Furthermore, this regulatory model also exists in both HEK293 cells and cardiomyocytes. Overall, the results of this study demonstrate that CHD6 binds to the promoter regions of housekeeping genes, regulating their histone modifications, chromatin structure, and gene expression.

Keywords: CHD6; MT: Bioinformatics; chromatin remodeling; epigenetics; histone modifications; housekeeping genes.

Graphical abstract

Figure 1

Sharp CHD6 peaks in the C4-2 cell line (A) Density of CHD6 in the housekeeping (HK) genes ANDP and GOLGA5 and the oncogenes (OGs) FGFR3 and CBX8. (B) Definition of genes with sharp and broad CHD6 peaks. (C) Heatmap of CHD6. Each row represents a gene region from −1 to +1 kb with respect to the gene. Top: the top 1,000 sharp CHD6 peaks; center: the top 1,000 broad CHD6 peaks; bottom: 1,000 random genes. (D) Average ChIP-seq signal value of CHD6 plotted around groups. (E) KEGG pathway enrichment of genes with sharp, broad, and control peaks. (F) Enrichment p values (y axis) of HK genes, OGs, and tumor suppressor genes (TSGs) in the different groups. (G) The percentage of gene expression. (H) Expression levels of the HK genes ANDP and GOLGA5 in tumor and normal cells. For (F), p values determined using Fisher's exact test. For (G), p values determined using one-tailed Wilcoxon test. ∗p < 0.05; ∗∗p <0.01; ∗∗∗p < 0.001.

Figure 2

Epigenetic features of genes with sharp CHD6 peaks (A) Average ChIP-seq signal value of H3K4me3 plotted around groups. (B) Average ChIP-seq signal value of RNA Pol II plotted around groups. (C) RNA Pol II pausing index plotted against sharp, broad, and control CHD6 peaks. (D) Boxplots showing gene expression levels (y axis) of the genes (n = 1,000 for each group), with the center line indicating the median. (E) Average ChIP-seq signal value of H3K27ac plotted around groups. (F) Boxplot showing CGI proportion (y axis) of groups. p values determined using one-tailed Wilcoxon test. ∗p < 0.05; ∗∗p < 0.01; ∗∗∗p < 0.001.

Figure 3

Expression levels of genes with sharp CHD6 peaks (A) Coefficient of variation around groups. (B) Average MNase-seq read density plotted around genes. (C) Average ChIP-seq signal value of H3K9me3 plotted around genes. (D) Average ChIP-seq signal value of H3K27me3 plotted around genes. (E) The logFC (y axis) change in the genes with sharp and broad CHD6 peaks after CHD6 knockdown. (F) Nucleosome density of genes with sharp CHD6 peaks in both the C4-2 control cells and the CHD6 knockdown cells. (G) Comparison of gene expression levels between normal and cancer cell lines. p values determined using one-tailed Wilcoxon test. ∗p < 0.05; ∗∗p < 0.01; ∗∗∗p < 0.001.

Figure 4

Characterization of sharp CHD6 peaks motifs and transcription factors (A) Volcano plots of motif enrichment scores (percentage enrichment/percentage background) of the sharp CHD6 peaks compared with the log10 (p value). (B) Volcano plots of motif enrichment scores of the broad CHD6 peaks compared with the log10 (p value). (C) Distribution of ETS1 binding sites. (D) Venn diagram showing the overlap between the sharp CHD6 peaks and ETS1 binding peaks.

Figure 5

Characterization of genes with sharp CHD6 peaks in normal cells (A) Average signal value of CHD6 peaks plotted around different genes in normal cells. (B) KEGG pathway enrichment of genes with sharp, broad, and control peaks in HEK293 and cardiomyocytes. (C) Enrichment p values (y axis) of the HK genes in HEK293 and cardiomyocytes. p values determined using Fisher's test exact test.