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. 2014 Apr 22;111(18):6690–6695. doi: 10.1073/pnas.1322273111

Fig. 4.

Fig. 4.

Germ-line–specific and imprinted genes show reduction of mCG and/or increase in 5hmC. (A) Analysis of DNA hypomethylated regions in Setdb1 KO mESCs yielded three of seven Gene Ontology terms relating to meiosis. The values plotted are transformed P value [−log10(P value)] of each term. (B) Boxplot demonstrating a significant difference between the median mCG ratios at the promoters of 30 germline genes, which are up-regulated in both Setdb1 KO and Dnmt TKO mESCs, as previously shown (20) (Left) and all RefSeq genes (Right). (C) The mCG ratios (Left) of four germ-line–specific genes are significantly reduced upon Setdb1 deletion, concomitant with transcriptional up-regulation (Right). (D) Significant reduction of mCG was also observed at the differentially methylated regions of four of the five analyzed imprinted genes (Left). Four of the five genes also show dramatic increase in 5hmC (Right). (*P < 0.05 and ***P < 0.001, respectively, as comparing WT versus Setdb1 KO with the Wilcoxon test).