Supplementary Figure 1: Effect of DNA methylation on the base editing efficiency induced by BE3.

(a) DNMT3-induced DNA methylation leads to the decreased base editing efficiency induced by BE3. Top panels, DNA methylation status of indicated genomic regions from NT or dCas9-DNMT3-transfected HEK293T cells are shown. Bottom panels, BE3-induced C-to-T editing frequencies at indicated cytosines were individually determined under different conditions. (b) TET1-induced DNA demethylation increased the efficiency of BE3-mediated base editing. Top panels, DNA methylation status of indicated genomic regions from NT or dCas9-TET1-transfected HEK293T cells are shown. Bottom panels, BE3 induced C-to-T editing frequencies at indicated cytosines were individually determined under different conditions. (a,b) Target site sequences are shown with the editing window (position 4-8, setting the base distal to the protospacer adjacent motif (PAM) as position 1) in lavender, PAM in cyan and CpG site in capital. NT, native HEK293T cells with no treatment. M, methylable regions. (c) Normalized C-to-T editing frequencies at CpG sites shown in (a) and (b), setting the ones induced at low-methylation levels as 100%. (d) Statistical analysis of normalized C-to-T editing frequencies at CpG and non-CpG sites, setting the ones induced at low-methylation levels as 100%. The data analyzed are from panels (a) and (b). Left, n = 36 samples from three independent experiments; right, n = 18 samples from three independent experiments. P value, one-tailed Student’s t test. The median and interquartile range (IQR) are shown.

(a-c) Means ± s.d. were from three independent experiments.