Fig. 3

High levels of DNA methylation repel active marks, H3K27me3, and H3K4me1. a Association of DNA methylation surrounding the indicated histone modifications in the wild type. In our simulation, un-modified regions were uniformly sampled as simulated peaks, and the lengths of the simulated peaks follow the similar length distribution of the real peaks. b Heatmap of the indicated histone modification categories and DNA methylation changes in the wild type and mddcc. c, d Epigenetic patterns of H3K4me1 loci gained in mddcc and representative examples. These H3K4me1 loci were classified into three clusters: cluster 1, H3K4me1-H3K9ac/active cluster; class 2, H3K4me1-H3K27me3 bivalent cluster; class 3, H3K4me1 only cluster. e Expression levels of genes/TEs marked by different histone modifications in mddcc. “-” indicates absence. Each histone modification combination is divided into two groups: stable between mddcc and the wild type and gain in mddcc. The numbers indicate the sample size used in the analysis. Boxplots include a median with quartiles and outliers above the top whisker. The statistical analysis was performed using two-side Wilcoxon test. **p < 2.2e−16 from Wilcoxon test