Fig. 2: DNA methylation regulates genes expression in a dose-dependent manner.

a Numbers of differentially expressed genes (DEGs) in the indicated mutants relative to WT. b, c Venn diagrams showing the overlap among up-regulated genes (b) or down-regulated genes (c) in ddcc, met1-9, and mddcc mutants. d Flow diagram indicating the criteria for gene classification according to the DNA methylation status in the WT background. Genes with no detectable expression (FPKM < 0.5) in any genotype were excluded. FPKM: fragments per kilobase of exon model per million mapped fragments. e Heat maps showing the expression and DNA methylation patterns of the indicated groups of up-regulated in DNA methyltransferase-deficient mutants. Based on their expression pattern, DEGs methylated in the WT were classified in the following categories: Redundancy (expression increased only in mddcc); Dosage I (expression mildly increased upon loss of CG methylation (in met1-9), and further increased upon loss of non-CG methylation (in mddcc)); Dosage II (expression mildly increased upon loss of non-CG methylation (in ddcc), and further increased upon loss of CG methylation (in mddcc)); and Dosage III (expression weakly increased upon loss of either CG or non-CG methylation (in both met1-9 and ddcc) and further increased upon complete loss of DNA methylation (in mddcc)). f Proportion of DEGs in the gbM, teM, pM, dM, or UM categories in the indicated genotypes. Down: down-regulated; up: up-regulated. Numbers over the bars indicate the total number of genes in each category. Bottom, we randomly selected the same numbers of genes to perform the overlap analysis. g Relative proportion of different categories of methylated genes. The number of genes in each category is indicated. h Proportion of gene types in the indicated DEG subsets. Numbers above the bars indicate the total number of DEGs. i Snapshots of expression and DNA methylation levels over two Intron-teM genes in the indicated mutants. Structure of genes are shown in the bottom. + and − indicate forward and reverse strands in the genome, respectively. Source data are provided as a Source Data file.