De novo methylation of proviral DNA requires DNMT3L (DNA methyltransferase 3-like). (a) Retrovirus reporter construct with long terminal repeats (LTRs) modified to allow identification of reporter provirus against background of endogenous retroviruses. (b) Replacement of primer binding site relieved TRIM28-ZFP809 mediated silencing, and the primer binding site was changed to be complementary to glutamine (Q) transfer (t)RNA. (c) Embryonic stem (ES) cells lacking DNMT3L were unable to silence the retrovirus shown in (a). Green fluorescent protein (GFP)-expressing cells were isolated by flow sorting 3 days post-infection (dpi), and GFP expression was monitored by fluorescence-activated cell sorting over the time period indicated. (d) Lack of retrovirus silencing accompanied lack of LTR methylation. (e) Wild-type female ES cells were inefficient in de novo methylation, and methylation defect in female ES cells was seen in wild-type cells but was more severe in Dnmt3L-/- ES cells. (f) De novo methylation of Oct4 5' region was not affected by loss of DNMT3L. All P values were obtained by the non-parametric two-tailed Mann-Whitney test.