Fig. 3: Deep enzymology analysis of the flanking sequence preferences of DNMT1.

a Relative base preferences of DNMT1 at the −10 to +10 flanking positions surrounding the CpG site. The numbers refer to the root mean squared deviations (RMSD) of the observed/expected base composition at each site among the methylated sequence reads, normalized to the highest effect observed at position −2. The bars show averages of two independent experiments. b Methylation levels were obtained from two experimental repeats (R1 and R2), averaged for all NNCGNN flanking sites and the Pearson correlation coefficients (r values) of the pairwise comparison of the data sets were determined. DNMT3A and DNMT3B data were taken from our previous study for comparison²⁵. c The methylation levels of NNCGNN sites of both repeats of the DNMT1 methylation reaction displayed as heatmap to show the strong correlation of both data sets (see also Supplementary Fig. 3b). d Heatmap of the methylation levels of NNCGNN flanking sites ordered by decreasing DNMT1 activity. The outlines show the 20 most favored or disfavored flanking sites. e Sequence logos of the 20 flanking sites most favored or disfavored by DNMT1. f Comparison of the NNCGNN methylation levels determined for the 44 CpG sites on the long substrate (long substrate) with the methylation levels determined for the corresponding NNCGNN sites in random flank library methylation experiment (random flank substrate—RFS). The image shows the methylation levels of individual NNCGNN sites as heatmap. The p value of the correlation is 1.25 × 10⁻⁴. The p value is based on the Pearson correlation coefficient (r-factor) and the Z-statistics of the distribution of r-factors determined after randomization of one of the data sets. See also Supplementary Fig. 4b for a box plot comparison. Source data are provided as a Source Data file.