Fig. 5: Correlation of genomic DNA modification patterns with flanking sequence preferences of TET1 and TET2.

a Preferences of TET1 and TET2 for bases at the −1 and +1 flank site compared with the enrichment or depletion of bases at these flanking positions in genomic 5hmC pattern¹⁰ and at sites associated with gain of genomic 5mC content after TET1 or TET2 knock-out (KO) in mouse ES cells³⁴. b Average genomic 5hmC levels were determined for all NNCGNN sites and compared with average genomic 5mC pattern at the same sites^28,35. Shown are Weblogos of the sites with the highest and lowest ratios of 5hmC and 5mC contents. c Heatmaps of averaged genomic 5hmC levels (5hmC), genomic 5mC levels (5mC), averaged TET flanking sequence preferences (TET), and the prediction of 5hmC levels based on the combination of 5mC levels and TET flanking preferences (Pred). d Scatter plot of genomic 5hmC levels and its prediction from panel c. e The Pearson R-value was determined for the correlation of genomic 5hmC levels and average TET1 and TET2 NNCGNN preferences for regions of 18 consecutive CpG sites sliding over the genome. Frequency plot of the distribution of R-values among all regions. Positive R-values (dark blue bars) indicating a correlation of TET preferences and 5hmC patterns were observed much more frequently than negative R-values (dark red bars). f Ratio of the fractions of regions with positive and negative R-values shown in panel e in the different R-value ranges. g Example regions selected from arbitrary parts of different chromosomes showing the correlation of local 5hmC levels and average TET1 and TET2 NNCGNN preferences. 5hmC level and TET preferences were normalized to the highest and lowest values.