Figure 1

H3K27me3 and H3K4me3 mapping at gene promoters in DNA hypomethylated somatic cells. (A) Global quantification of the 5 mC base by HPLC. Values are 5 mC as a percentage of total C in Dnmt1^+/+ and Dnmt1^-/- MEFs. Error bars represent standard error of the mean. **P <0.001 by t-test. (B) Density plots showing CpG methylation levels in Dnmt1^+/+ and Dnmt1^-/- MEFs as measured by RRBS. (C, D) Volcano plots of all promoter H3K27me3 (C) and H3K4me3 (D) ChIP data measured by promoter microarray (ChIP-chip). Difference in normalized average promoter values between Dnmt1^+/+ and Dnmt1^-/- MEFs (Δlog2(IP/INP)) is plotted against q-value (P-value (two-tailed t-test) corrected for multiple testing by Benjamini-Hochberg method). Promoters that have a difference of <-0.5 or >0.5 and a q-value <0.05 are defined as significantly different. Red points indicate promoters with reduced H3K27me3/H3K4me3 in Dnmt1^-/- MEFs (H3K27me3/H3K4me3 down) and blue indicate promoters with increased H3K27me3/H3K4me3 in Dnmt1^-/- MEFs (H3K27me3/H3K4me3 up). (E, F) Western blot for histone modifications (E) and core PRC2 components (F) in Dnmt1^+/+ and Dnmt1^-/- MEFs. mC, methyl-cytosine. KO, knock-out, Dnmt1^-/- MEFs. WT, wild-type, Dnmt1^+/+ MEFs.