Structural insight into autoinhibition and histone H3-induced activation of DNMT3A

Abstract

DNA methylation is an important epigenetic modification that is essential for various developmental processes through regulating gene expression, genomic imprinting, and epigenetic inheritance. Mammalian genomic DNA methylation is established during embryogenesis by de novo DNA methyltransferases, DNMT3A and DNMT3B, and the methylation patterns vary with developmental stages and cell types. DNA methyltransferase 3-like protein (DNMT3L) is a catalytically inactive paralogue of DNMT3 enzymes, which stimulates the enzymatic activity of Dnmt3a. Recent studies have established a connection between DNA methylation and histone modifications, and revealed a histone-guided mechanism for the establishment of DNA methylation. The ATRX-DNMT3-DNMT3L (ADD) domain of Dnmt3a recognizes unmethylated histone H3 (H3K4me0). The histone H3 tail stimulates the enzymatic activity of Dnmt3a in vitro, whereas the molecular mechanism remains elusive. Here we show that DNMT3A exists in an autoinhibitory form and that the histone H3 tail stimulates its activity in a DNMT3L-independent manner. We determine the crystal structures of DNMT3A-DNMT3L (autoinhibitory form) and DNMT3A-DNMT3L-H3 (active form) complexes at 3.82 and 2.90 Å resolution, respectively. Structural and biochemical analyses indicate that the ADD domain of DNMT3A interacts with and inhibits enzymatic activity of the catalytic domain (CD) through blocking its DNA-binding affinity. Histone H3 (but not H3K4me3) disrupts ADD-CD interaction, induces a large movement of the ADD domain, and thus releases the autoinhibition of DNMT3A. The finding adds another layer of regulation of DNA methylation to ensure that the enzyme is mainly activated at proper targeting loci when unmethylated H3K4 is present, and strongly supports a negative correlation between H3K4me3 and DNA methylation across the mammalian genome. Our study provides a new insight into an unexpected autoinhibition and histone H3-induced activation of the de novo DNA methyltransferase after its initial genomic positioning.

MBD3L2 promotes Tet2 enzymatic activity for mediating 5-methylcytosine oxidation

“…The Tet2 protein we used is purified from HEK293T cell and the amount of Tet2 protein is limited. In addition, the newly published data (Guo et al, 2015) indicate that Tet proteins are evolutionarily tuned to be less reactive towards 5hmC, therefore the generation of 5fC and 5caC is far less than 5hmC. When we increase the amount of Tet2 protein in enzymatic activity, we found that 5fC and 5caC can be detected, moreover, the amount of 5fC and 5caC increased with the addition of MBD3L2 in vitro.…”

SETD2andDNMT3Ascreen in the Sotos-like syndrome French cohort

“…DNMT3A contains three functional domains: a PWWP domain, an ADD domain and a C-terminal DNA methyltransferase (MTase) domain 16. Mutants were mapped onto the active and autoinhibited form of the DNMT3A-DNMT3L complex (Protein Data Bank (PDB) 4U7T and 4U7P).…”

DOT1L as a therapeutic target for the treatment of DNMT3A-mutant acute myeloid leukemia

“…Given the known functional interaction between DNA methylation and histone modifications, these alterations were intriguing. [13][14][15][16] The observed overexpression of the histone 3, lysine 79 (H3K79) methyltransferase, Dot1l (disrupter of telomere silencing 1-like), was especially interesting because it plays a critical role in leukemia with MLL rearrangements. [17][18][19][20] Pharmacologic inhibition of DOT1L has shown promising preclinical activity in MLL-rearranged leukemia and is now being tested in adult and pediatric clinical trials.…”