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

Fig. 2.

Fig. 2.

Subsets of endogenous retroviruses and ERML show significant mCG reduction in Setdb1 KO mESCs. (A) Pie charts demonstrating the distribution of repetitive element classes among all mappable repeats (n = 4,989,421) in the mouse mm9 reference genome [short interspersed nuclear elements (SINEs) = 30.5%, long interspersed nuclear elements (LINEs) = 19.4%, simple repeats = 21.3%, LTR = 17%, DNA transposons = 3.1%, and others = 8.4%] (Left) and significantly hypomethylated elements (n = 2,395) in Setdb1 KO mESCs (SINE = 14.7%, LINE = 8.4%, simple repeats = 1.6%, LTR = 73%, DNA transposons = 0.5%, and others = 1.7%) (Right). (B) Pie charts demonstrating the distribution of the three ERV classes among all mappable ERVs (n = 849,327) (Left) and significantly hypomethylated elements (n = 1,748) in Setdb1 KO mESCs. (C) Screen capture illustrating the overlap of ERML and an IAP-EY endogenous retroviral element. MethlyC-seq reads from WT (predeletion) and Setdb1 KO mESCs are mapped and divided into 100-bp bins, showing mCG ratios with bar heights between 0 and 1. Log P values (Fisher’s exact test) are shown for bins with significant difference in mCG ratio between WT and Setdb1 KO (P value cutoff of 0.001 or log = −3). RNA-seq (20) confirms substantial reactivation of this element in Setdb1 KO mESCs. Mappability or uniqueness of reference genome from the ENCODE project for 50-bp segments is shown with the score between 0 and 1.