DNA methylation is involved in fundamental cellular processes such as silencing 
of genes and transposable elements, but the underlying mechanism of regulation 
of DNA methylation is largely unknown. DNA methyltransferase 3-like protein 
(Dnmt3L), a member of the Dnmt3 family of proteins, is required during the 
establishment of DNA methylation patterns in germ cells. Dnmt3L does not possess 
enzymatic activity. Rather, in vitro analysis indicates that Dnmt3L stimulates 
DNA methylation by both Dnmt3a and Dnmt3b through direct binding to these 
proteins. In the current study, we demonstrated that in vivo, Dnmt3L physically 
and functionally interacted with the Dnmt3 isoform Dnmt3a2. In wild-type 
embryonic stem (ES) cells, but not in cells lacking Dnmt3a, endogenous Dnmt3L 
was concentrated in chromatin foci. In ES cells deficient in both Dnmt3a and 
Dnmt3b, Dnmt3L was distributed diffusely throughout the nucleus and cytoplasm, 
and ectopic expression of Dnmt3a2, but not Dnmt3a or Dnmt3b, restored wild-type 
Dnmt3L localization. We showed that endogenous Dnmt3L physically interacted with 
Dnmt3a2, but not Dnmt3a or Dnmt3b, in ES cells and embryonic testes. We also 
found that specific CpG sites were demethylated upon depletion of either Dnmt3a 
or Dnmt3L, but not Dnmt3b, in ES cells. These results provide evidence for a 
physical and functional interaction between Dnmt3L and Dnmt3a2 in the nucleus. 
We propose that Dnmt3a2 recruits Dnmt3L to chromatin, and induces regional DNA 
methylation in germ cells.