Fig. 1: Deep enzymology flanking sequence analysis links intrinsic substrate preference of DNMT3B to SatII sequence recognition. | Nature Communications

Fig. 1: Deep enzymology flanking sequence analysis links intrinsic substrate preference of DNMT3B to SatII sequence recognition.

From: Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms

Fig. 1

a Relative base preferences at the −5 to +5 flanking positions of mouse DNMT3A (mDNMT3A) and DNMT3B (mDNMT3B) indicating the strength of sequence readout at each site. The numbers refer to the standard deviations of the observed/expected base composition at each site among the methylated sequence reads, normalized to the highest value for each enzyme. n = 3 replicates. Data are mean ± SD. b Correlation of the NNNCGNNN methylation profiles of mDNMT3A and mDNMT3B for two independent experiments (repetition R1 and R2). The numbers refer to the pairwise Pearson correlation coefficients of two data sets. c Weblogos of the 50–200 most preferred NNNCGNNN methylation sites by mDNMT3A and mDNMT3B. Quantitative enrichment and depletion plots and statistics are provided in Supplementary Fig. 2c, d. d Heatmap of the normalized DNMT3B/DNMT3A preferences for methylation of NNNCGNNN sites. The position of the SatII sequence (TCCATTCGATGATG) in the ranking is indicated (rank 131 of 4096) as well as the position of the mDNMT3B-disfavored reference substrate (AGGCGCCC) used in panel (c) (rank 4092 of 4096). e mDNMT3B/mDNMT3A preferences (B/A preference) were binned and averaged based on their similarity to the SatII sequence. The median preference of each bin is shown. The error bars indicate the first and third quartile. f Experimental validation of the SatII preference of DNMT3B by radioactive methylation assays. The methylation activity of each enzyme was normalized to the more active substrate. The figure shows average values and standard deviations based on two independent measurements (see also Supplementary Fig. 6a, b). g Ratio of the medians of the distributions of DNMT3A/DNMT3B preference among all CpG sites from human SatII repeats (n = 1), mouse minor satellite repeats (Genbank Z22168.1) (n = 9), major satellite repeats (Genbank EF028077.1) (n = 23), and IAP elements (Genbank AF303453.1) (n = 19). A high DNMT3A/DNMT3B rank ratio corresponds to preferred methylation by DNMT3B. Refer to Supplementary Fig. 6d and the text for details. Source data are provided as a Source Data file.

Back to article page