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Fig. 4 | Epigenetics & Chromatin

Fig. 4

From: Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA

Fig. 4

Comparative evaluation of HM450K Bis/OxBis and whole-genome Bis-/OxBis-seq for 5hmC profiling. a Scatter plots showing the correlation of 5modC (Bis, left), 5mC (OxBis, middle) and 5hmC (Bis-OxBis, right) between WG and HM450K Bis/OxBis across CpG sites (n = 42,537) considered as significantly hydroxymethylated by both approaches. Spearman’s correlation is indicated on each scatter plot. b The agreement in 5modC, 5mC and 5hmC levels detected by WG and HM450K Bis/OxBis as a function of WG sequencing coverage. The difference in methylation calling is plotted along the y-axis for each bin with defined sequencing coverage indicated (>10×, >20×, >30×–>60×). Green lines indicate ± 5% difference in methylation value detected between approaches (WG-HM450K). c Venn diagrams show the overlap of hydroxymethylated regions between WG and HM450K Bis/OxBis. Genomic regions with at least one CpG probe and at least 10× WG sequencing coverage were chosen for this analysis (11,625 of 25,235 total TssA; 14,945 of 27,078 total TssA_Flnk; 22,249 of 26,707 total Tx; 47,082 of 73,063 total Enh). Of those, the number of regions with at least one hydroxymethylated CpG according to HM450K only, WG only or both approaches was calculated and overlap was plotted. d The distribution of maximal hydroxymethylation values at the regions identified as hydroxymethylated according to the HM450K only (yellow) and according to the both WG and HM450K (green). For the active promoters (TssA), the median of the max(5hmC) distribution is 0.067 for the yellow group and 0.147 for the green group. For the regions flanking active promoters (TssA Flank), the median of the max(5hmC) distribution is 0.105 for the yellow group and 0.167 for the green group. The difference between the distributions of maximal 5hmC values between yellow and green groups of regions is statistically significant as determined by Kruskal–Wallis nonparametric test (p < 0.01)

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