Fig. 2

DNA methylation changes in mice carrying Dnmt3a^D329A allele. a Beanplots indicating whole genome methylation levels in hypothalamus of adult (14 week, male) mice carrying the alleles shown. Boxplot shows median value and 25–75th percentiles, whiskers show lowest and highest observation, excluding outliers. Raw data are provided in Source Data. b Scatterplot showing correlation of methylation levels of individual tiles between Dnmt3a^+/+ and Dnmt3a^Δ/D329A mice. Differentially methylated probes were determined using the EdgeR proportion statistic in SeqMonk (p < 0.01 corrected for multiple comparisons using Benjamini–Hochberg, methylation difference ≥ 20%). Pie-chart indicates how many of DMRs are hyper-methylated or hypo-methylated in Dnmt3a^Δ/D329A. n = 3 for each genotype. c, d Beanplots indicating DNA methylation levels over hypermethylated (c) and hypomethylated (d) DMRs. Boxplot shows median value and 25–75th percentiles, whiskers show lowest and highest observation, excluding outliers. Source data are listed in Supplementary Data 3. e Representative genome browser region showing the Hoxd hypermethylated domain. De-repressed gene Hoxd8 promoter region is shaded. For gene and mRNA tracks, the colour indicates direction, where red is a forward strand and blue is a reverse strand. Colour-coded blocks are tiles of 100-CpG positions. Error bars indicate standard deviation. f, g Scatterplots showing correlation between methylation levels of 100-CpG tiles in 14-week adult male hypothalamus of f Dnmt3a^Δ/+ and Dnmt3a^Δ/D329A, and g Dnmt3a^+/+ and Dnmt3a^Δ/+. Differentially methylated tiles were determined using the EdgeR proportion statistic in SeqMonk (p < 0.01 corrected for multiple comparisons using Benjamini-Hochberg, methylation difference ≥ 20%). The pie-chart indicates the number of DMRs identified. In a–g, Hypo: hypomethylated, hyper: hypermethylated. Tiles of 100-CpG positions. n(+/+, Δ/+, Δ/D329A) = 3, n(+/D329A) = 2. CGI: CpG island, DMR: differentially methylated region