Fig. 2

DNA methylation and hydroxymethylation profiling by whole-genome Bis-seq/OxBis-seq. a Methylation density plot showing the distribution of 5hmC and 5modC levels. Both 5modC and 5hmC density plots include CpG sites showing significant hydroxymethylation. b The relationship between the hydroxymethylated fraction and total methylation levels at each CpG site. CpG sites were binned into groups based on the total methylation levels, and the distribution of hydroxymethylation levels was calculated for each of these groups. c Bar plot showing observed over expected by chance enrichment of CpGs with different 5hmC levels at multiple genomic locations. Genomic regions comprise of Brain Frontal Lobe ChromHMM features as well as CpG islands and CpG island shores. d The percentage of genomic regions harbouring no hydroxymethylated CpG sites (grey) and those harbouring at least one hydroxymethylated CpG site (blue). e The proportion of hydroxymethylated CpGs of the total number of CpGs per genomic region. For each region, the total number of CpGs and number of hydroxymethylated CpGs were calculated (Additional file 2: Figure S1D). From that, for each region, the percentage of hydroxymethylated CpGs of all CpGs was calculated and distribution of those percentages was plotted. f The distribution of the total number of CpG sites and the number of hydroxymethylated CpG sites per genomic region. g The relationship between average total methylation (5modC) (x-axis) and average hydroxymethylation (5hmC) (y-axis) at different genomic regions. Each dot represents a single region. Hydroxymethylation levels of CpG sites that did not pass the statistical significance criteria were assigned to zero. h The hydroxymethylation contribution to the average total methylation at different genomic regions. For each genomic region, the percentage of hydroxymethylation contribution to the total methylation was calculated; the numbers of regions with the corresponding 5hmC contribution were plotted