Fig. 1

Complete loss of DNA methylation causes upheaval of the histone modification landscape. a Wild type (Col-0), ddcc (drm1 drm2 cmt2 cmt3), met1, and mddcc (met1 drm1 drm2 cmt2 cmt3) mutant plants and data generation in this study. Five-week-old plants are shown. Bar, 2 cm. b Changes of histone modifications in mddcc compared to the wild type. Six representative histone marks (H3K4me3, H3K9ac, H3K27ac, H3K4me1, H3K27me3, and H3K9me2) were investigated. These marks occupied 71% of the wild type and/or mddcc genome (left panel) and were divided into three categories based on their behavior in the mutant: loss/gain, up/downregulated, and stable/unchanged (right panel). c Peak changes of the indicated histone marks in mddcc compared with the wild type. d Distribution of DNA (CG) methylation levels in the wild type for the three categories of histone modification regions in (b). e Genomic distribution of the indicated categories in (d). The loss/gain category was divided into two sub-categories based on DNA methylation levels