Fig. 3

Transposon-like methylation (TEM-like) and gene body-like methylation (GBM-like) patterns in ddm1 plants. A Violin plots of DNA methylation levels of TEM-like regions in Col-0 and ddm1 plants. B Violin plots of CG methylation levels of GBM-like regions in Col-0 and ddm1 plants. C Scatter plot of CG methylation level of GBM-like regions in Col-0 (x-axis) and ddm1 (y-axis) plants. Each dot represents a gene body methylation locus. Orange dots indicates GBM-like^ddm1, and blue dots indicate GBM-like^weak. GBM-like^ddm1; strongly demethylated GBM-like regions in ddm1. GBM-like^weak; GBM-like regions that their methylation levels are weakly affected or not affected in ddm1. D Histone H1.1 and H1.2 level at GBM-like^ddm1 and GBM-like^weak. p-values from Student’s t test. E, F Gene body CG DNA methylation level at GBM-like^ddm1 (E) and GBM-like.^weak (F) in Col-0, h1, ddm1, and h1ddm1 plants. G Scatter plots of CG methylation change at TEM-like regions in relation to histone H1 and H2A.Z change in ddm1. Magenta box indicates highly demethylated TEM-like regions with increased DNA accessibility in ddm1. H Scatter plots of CG methylation change at GBM-like regions in relation to histone H1 and H2A.Z change in ddm1. G, H Dot color shows log₂ ratio of DNA accessibility in Col-0 to ddm1