Extended Data Fig. 9: Distinct DNA methylation and gene expression patterns in PKO and R-PKO mESCs.

a, A UCSC genome browser snapshot showing the DNA methylation levels in PKO, Dnmt3a/3b DKO, R-PKO and R-PKO;Dnmt3b^TOE mESCs. b, Violin plots showing the global DNA methylation levels of PKO, Dnmt3a/3b DKO, R-PKO and R-PKO;Dnmt3b^TOE mESCs (n = 1). The median is indicated by the white dots. The edges of thick and thin black lines represent the 25th/75th percentiles and 1.5 times of the IQR, respectively. c, Bar charts showing the average DNA methylation levels at various types of DNA elements in WT, TKO, PKO, and R-PKO. DMV, DNA methylation valley¹⁸. d, Boxplots showing the gene expression and promoter DNA methylation levels for differentially expressed genes (R-PKO vs. PKO) in WT, TKO, PKO, R-PKO, and Dnmt TKO mESCs⁵². The median is indicated by the center lines. The bottom, top edges and whiskers represent the 25th/75th percentiles and 1.5 times of the IQR, respectively. e, Schematic showing generation of R-PKO with transient expression of Dnmt3b (R-PKO;Dnmt3b^TOE) (Methods). f, Bar charts showing the relative ratios of fully and hemi-methylated CGs in SKO, PKO and R-PKO cells at hypomethylated and hypermethylated CGI. For R-PKO, the ratios for RMRs and non-RMRs are also shown. Un-methylated CG dyads are excluded from this analysis which would otherwise dominate the bar charts due to their large numbers.