DNA methylation is an important epigenetic modification regulating various 
biological phenomena, including genomic imprinting and transposon silencing. It 
is known that methylation of the differentially methylated regions (DMRs) 
associated with paternally imprinted genes and of some repetitive elements 
occurs during male germ cell development in the mouse. We have performed a 
detailed methylation analysis of the paternally methylated DMRs (H19, Dlk1/Gtl2 
and Rasgrf1), interspersed repeats [SineB1, intracisternal A particle (IAP) and 
Line1] and satellite repeats (major and minor) to determine the timing of this 
de novo methylation in male germ cells. Furthermore, we have examined the roles 
of the de novo methyltransferases (Dnmt3a and Dnmt3b) and related protein 
(Dnmt3L) in this process. We found that methylation of all DMRs and repeats 
occurred progressively in fetal prospermatogonia and was completed by the 
newborn stage. Analysis of newborn prospermatogonia from germline-specific 
Dnmt3a and Dnmt3b knockout mice revealed that Dnmt3a mainly methylates the H19 
and Dlk1/Gtl2 DMRs and a short interspersed repeat SineB1. Both Dnmt3a and 
Dnmt3b were involved in the methylation of Rasgrf1 DMR and long interspersed 
repeats IAP and Line1. Only Dnmt3b was required for the methylation of the 
satellite repeats. These results indicate both common and differential target 
specificities of Dnmt3a and Dnmt3b in vivo. Finally, all these sequences showed 
moderate to severe hypomethylation in Dnmt3L-deficient prospermatogonia, 
indicating the critical function and broad specificity of this factor in de novo 
methylation.