Oligomerization and Binding of the Dnmt3a DNA Methyltransferase to Parallel DNA Molecules

Abstract

Structural studies showed that Dnmt3a has two interfaces for protein-protein interaction in the heterotetrameric Dnmt3a/3L C-terminal domain complex: the RD interface (mediating the Dnmt3a-3a contact) and the FF interface (mediating the Dnmt3a-3L contact). Here, we demonstrate that Dnmt3a-C forms dimers via the FF interface as well, which further oligomerize via their RD interfaces. Each RD interface of the Dnmt3a-C oligomer creates an independent DNA binding site, which allows for binding of separate DNA molecules oriented in parallel. Because Dnmt3L does not have an RD interface, it prevents Dnmt3a oligomerization and binding of more than one DNA molecule. Both interfaces of Dnmt3a are necessary for the heterochromatic localization of the enzyme in cells. Overexpression of Dnmt3L in cells leads to the release of Dnmt3a from heterochromatic regions, which may increase its activity for methylation of euchromatic targets like the differentially methylated regions involved in imprinting.

Engineering of a Histone-Recognition Domain in Dnmt3a Alters the Epigenetic Landscape and Phenotypic Features of Mouse ESCs

“…Dnmt3L, a catalytically inactive Dnmt3, is abundantly expressed in TKO and the established ESC lines. Dnmt3L is known to interact with Dnmt3a/3b Jurkowska et al, 2011) as well as Dnmt3a2 (Ooi et al, 2007). Given that ADD 3l binding to the H3 N-terminus is disrupted by H3K4me3 (Ooi et al, 2007) (Figure 1C) and Dnmt3L incorporation stimulates Dnmt3a2 enzymatic activity (Gowher et al, 2005;Kareta et al, 2006), Dnmt3L itself may facilitate WT-, WWD-, R-Dnmt3a2 binding/activity to unmodified H3, limiting WWDDnmt3a2 access to H3K4 methylation.…”

Genetic and Epigenetic Mechanisms in Down Syndrome Brain

“…DNMT3L is localized on HSA21, and its triplication in DS suggests aberrant levels of expression. DNMT3L can form a heterotetramer with DNMT3A, and increased DNMT3L levels could potentially promote release of DNMT3A as well as increase its methylation activity [56]. DNMT3L can also stimulate DNMT3B activity directly [57,73].…”

“…DNMT2 is involved in RNA methylation. DNMT3L (DNA methyltransferase 3-like) does not have enzymatic activity but can stimulate DNMT3A and DNMT3B activation [55][56][57]. The addition of a methyl group to cytosine may physically impede the binding of transcriptional factors to the gene itself, or by recruiting protein complexes including methyl-CpG-binding protein 2 (MECP2), methyl-CpG-binding domain proteins (MBDs), HDACs and other chromatin remodeling proteins [58].…”

The de novo DNA methyltransferase DNMT3A in development and cancer

“…2). 67,68 Moreover, DNMT3A homodimer of the heterotetramer complex showed specific contacts with the DNA substrate and substitution of key non-catalytic residues at the Dnmt3a-Dnmt3l interface or the Dnmt3a-Dnmt3a interface eliminated enzymatic activity.…”