Fig. 1: DNA methylation is eliminated in the mddcc mutant.

a Diagrams of the MET1 gene showing the mutation sites in met1-8 (upper) and met1-9 (lower) mutants. Purple bars indicate the position of the sgRNAs used. b Genome-wide distribution of DNA methylation in all three sequence contexts in the indicated mutants. Wireframes are zoom-in of the indicated regions. Biological replicates were combined as one sample. Independent biological replicates are shown in Supplementary Fig. 2a. It should be noted that the lines of the WT overlap with those of ddcc in the mCG row. c Screenshot of DNA methylation levels over one representative locus in the indicated mutants. Orange and blue bars indicate TEs and genes, respectively. TEs and genes oriented 5′–3′ and 3′–5′ are shown above and below the line, respectively. Biological replicates were combined as one sample. Independent biological replicates are shown in Supplementary Fig. 2b. d Comparison of the DNA methylation levels between nuclear and chloroplast genomes in the indicated genotypes. Biological replicates were combined as one sample. Independent biological replicates are shown in Supplementary Fig. 2c. The horizontal line within the box represents the median; the whiskers represent minimum and maximum values; and the lower and upper boundaries of the box represent the 25th and 75th percentiles, respectively.