Chromatin Targeting of de Novo DNA Methyltransferases by the PWWP Domain

Abstract

DNA methylation patterns of mammalian genomes are generated in gametogenesis and early embryonic development. Two de novo DNA methyltransferases, Dnmt3a and Dnmt3b, are responsible for the process. Both enzymes contain a long N-terminal regulatory region linked to a conserved C-terminal domain responsible for the catalytic activity. Although a PWWP domain in the N-terminal region has been shown to bind DNA in vitro, it is unclear how the DNA methyltransferases access their substrate in chromatin in vivo. We show here that the two proteins are associated with chromatin including mitotic chromosomes in mammalian cells, and the PWWP domain is essential for the chromatin targeting of the enzymes. The functional significance of PWWPmediated chromatin targeting is suggested by the fact that a missense mutation in this domain of human DNMT3B causes immunodeficiency, centromeric heterochromatin instability, facial anomalies (ICF) syndrome, which is characterized by loss of methylation in satellite DNA, pericentromeric instability, and immunodeficiency. We demonstrate that the mutant protein completely loses its chromatin targeting capacity. Our data establish the PWWP domain as a novel chromatin/ chromosome-targeting module and suggest that the PWWP-mediated chromatin association is essential for the function of the de novo methyltransferases during development.

Histone tails regulate DNA methylation by allosterically activating de novo methyltransferase

“…The PHD domain of Dnmt3a is able to bind histone tails in vitro [14,15], but is dispensable for the enzyme association with chromatin in vivo [19,20]. These observations suggest that recruitment of Dnmt3a to chromatin could be independent of the PHD domain-mediated binding to the H3 N-terminus.…”

“…As previous studies indicate that the Dnmt3a PHD domain is not required for its chromatin association [19,20], we reasoned that the binding of H3 peptide via the PHD domain might regulate the Dnmt3a function through allosteric enzymatic activation rather than chromatin recruitment. As the allosteric effect of H3 binding might be mediated by interaction between the PHD and catalytic domains, we sought to characterize crucial residues at the interaction interfaces, whose substitutions would block allosteric activation of enzymatic activity but have no effect on the H3 binding and the basal catalytic activities.…”

Role of hepatoma‐derived growth factor in promoting de novo lipogenesis and tumorigenesis in hepatocellular carcinoma

“…The S144I mutation in the PWWP domain of mismatch repair protein 6 leads to hereditary nonpolyposis colorectal cancer(Laguri et al ., 2008). A missense mutation in the PWWP domain of mammalian DNA methyltransferase 3B is closely related to immunodeficiency, centromeric heterochromatin instability, facial anomalies syndrome (Ge et al ., 2004). Our data indicate that the first amino acid mutation in the PWWP domain inhibits HCC cell proliferation and tumorigenesis, confirming the important role of the PWWP domain in biological processes.…”

Diverse Domains of (Cytosine-5)-DNA Methyltransferases: Structural and Functional Characterization

“…On the contrary, the PWWP domain of Dnmt3a is almost unable to bind DNA [121]. The PWWP domains of Dnmt3a and Dnmt3b are necessary for targeting these MTases to pericentromeric heterochromatin [121][122][123]. Deletions in the PWWP domain change the protein distribution in a nucleus and therefore result in its disability to methylate satellite repeats.…”