Dnmt3a and Dnmt3b are transcriptional repressors that exhibit unique localization properties to heterochromatin

We demonstrate that the recently identified DNA methyltransferases, Dnmt3a and Dnmt3b, like DNMT1, repress transcription in a methylation-independent manner. Dnmt3a and Dnmt3b repress transcription primarily through a plant h omeodomain-like motif that is shared with the ATRX protein but is not prese nt in DNMT1. Unlike DNMT1, which localizes to replication foci during S-pha se in murine embryonic fibroblasts, Dnmt3a co-localizes with heterochromati n protein I a (HP1 alpha) and methyl-CpG binding proteins throughout the ce ll cycle to late-replicating pericentromeric heterochromatin. In contrast t o Dnmt3a, Dnmt3b remained diffuse in the nucleus of embryonic fibroblasts a t all cell cycle stages. However, Dnmt3a and Dnmt3b co-localize to these pe ricentromeric heterochromatin regions in murine embryonic stem cells. This finding is important to the fact that mutations in DNMT3B are found in the developmental syndrome, ICF (immunodeficiency, centromeric heterochromatin instability, and facial anomalies), which involves extensive loss of methyl ation from pericentromeric regions. The localization of Dnmt3a and Dnmt3b w as unaffected in Dnmt1 null embryonic stem cells, which lose the majority o f methylation at pericentromeric major satellite repeats, suggesting that t hese enzymes are not dependent upon preexisting methylation for their targe ting. DNMT1 is then positioned to reestablish transcriptionally repressive chromatin as cells replicate, while Dnmt3a and Dnmt3b may help to establish such chromatin in late S-phase and maintain this repressive heterochromati n throughout the cell cycle in a developmentally and/or cell type manner.