Fig. 1.

Dnmt3a deficiency results in focal, canonical CpG methylation loss in murine epidermal cells. (A) WGBS of isolated murine epidermal cells, comparing independent samples from 11 Dnmt3a^WT vs. 5 Dnmt3a^KO vs. 3 Dnmt3a^HET mice. Dot plots represent average methylation values over annotated regions for all CpGs (Top) and for DMRs within each annotated region (Bottom). Significance was determined by Student’s t test with denotation of “ns” for not significant and levels of significance as * adjusted P < 0.05, **P < 0.01, ***P < 0.001. (B) Methylation density plots for the indicated genotypes across all genomic CpGs (Top) and at DMRs (Bottom). (C) Targeted deficiency of Dnmt3a (Krt14-Cre⁺ × Dnmt3a^fl/fl, Dnmt3a^KO) results in 23,983 DMRs in epidermal cells compared to wild-type control, Dnmt3a^WT. Heatmap representation of WGBS data demonstrates DMRs defined by differences between Dnmt3a^WT vs. Dnmt3a^KO epidermal cells. Heterozygosity for Dnmt3a (Krt14-Cre⁺ × Dnmt3a^fl/+, Dnmt3a^HET) results in an intermediate phenotype. Each column represents an independent mouse. (D) Annotated regions associated with DMRs. *Of 16,315 DMRs involving gene bodies, 3,612 unique genes are involved. (E) Integrated genome viewer (IGV) view of the G0s2 gene CpG methylation of Dnmt3a^WT versus Dnmt3a^KO epidermal cells. Normalized methylated CpG reads are represented in bars (scale 0 to 1.0 for each row). Differentially methylated regions are indicated in the bottom track and highlighted in yellow.