Fig. 3
From: Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA
DNA methylation and hydroxymethylation profiling by HM450K Bis/OxBis. a Scatter plots showing the high correlation between HM450K Bis (left) and HM450K OxBis (right) replicates. Each dot (smoothed) reflects each probe 5modC (left) or 5mC (right) levels detected by two technical replicates (x- and y-axes). Spearman’s correlation 0.987406 (left) and 0.985664 (right), respectively. b, c 5hmC and 5modC MiSeq amplicon validation of candidate loci using Bis- and TAB-Seq. b Scatter plots showing the correlation of 5modC (left) and 5hmC (right) levels between HM450K and amplicon Bis- and TAB-seq. Each dot represents single CpG site/probe. The pink and blue regression lines show the intercept and slope of the plots. c HM450K screen shots of candidate regions, showing 450K_5hmC, 450K_Bis, 450K_OxBis. Amplicon validation of these genomic regions shows agreement in total methylation (5modC) and hydroxymethylation levels detected by HM450K Bis/OxBis and loci-specific Bis/TAB-seq, respectively. Red dots depict 5modC (top) and 5hmC (bottom) levels of each CpG site detected by loci-specific Bis-/TAB-seq, respectively. Green dots depict 5modC (top) and 5hmC (bottom) levels of HM450K CpG probes on the array. d The relationship between hydroxymethylation and different levels of total methylation detected by HM450K. CpG probes were binned into groups based on the total methylation levels, and the distribution of hydroxymethylation levels was calculated for each of these groups. e Bar plot showing observed over expected by chance enrichment of CpGs with different 5hmC levels (0–10, 10–20, 20–30, >30%) at multiple genomic locations; computationally derived chromatin segmentation (ChromHMM) of Brain Frontal Lobe genome, as well as CpG islands and CpG island shores. f Pie charts showing the proportion of genomic regions defined as hydroxymethylated by HM450K Bis/OxBis compared to the total number defined as hydroxymethylated according to the WG Bis/OxBis-seq. A region is considered hydroxymethylated if it contains >1 significantly hydroxymethylated CpG site