Fig. 3.

ERML gain 5hmC in Setdb1 KO mESCs. (A) Boxplot showing an increase of 5hmC enrichment (RPKM) at ERML, which become hypomethylated upon Setdb1 depletion (n = 288). An increase is also observed at mappable ETn (n = 11,207) and IAP elements (n = 22,962). Mappable ERVL elements (n = 9,704), which are not generally marked by Setdb1-deposited K9me3, show a subtle decrease of 5hmC enrichment in Setdb1 KO mESCs. (B) Heat maps showing the difference of K9me3 and 5hmC enrichment (RPKM) between Setdb1 KO and WT mESCs at ERML marked by K9me3 (n = 2,451) (Left) and size-matched shuffled control regions (Right). (C) Boxplots illustrate the increase of Tet1 enrichment (RPKM) at ERML marked by K9me3 (n = 2,451) but not at control regions (n = 2,451), in Setdb1 KO mESCs. (*P < 0.05 and ***P < 0.001, respectively, as comparing WT versus Setdb1 KO with the Wilcoxon test.)