Abstract
DNA methyltransferase DNMT3A is essential for establishment of mammalian DNA methylation during development. The R882H DNMT3A is a hotspot mutation in acute myeloid leukemia (AML) causing aberrant DNA methylation. However, how this mutation affects the structure and function of DNMT3A remains unclear. Here we report structural characterization of wild-type and R882H-mutated DNMT3A in complex with DNA substrates with different sequence contexts. A loop from the target recognition domain (TRD loop) recognizes the CpG dinucleotides in a +1 flanking site-dependent manner. The R882H mutation reduces the DNA binding at the homodimeric interface, as well as the molecular link between the homodimeric interface and TRD loop, leading to enhanced dynamics of TRD loop. Consistently, in vitro methylation analyses indicate that the R882H mutation compromises the enzymatic activity, CpG specificity and flanking sequence preference of DNMT3A. Together, this study uncovers multiple defects of DNMT3A caused by the R882H mutation in AML.
Highlights
DNA methyltransferase DNMT3A is essential for establishment of mammalian DNA methylation during development
Recent studies have suggested that the R882H mutation may affect the relative enzymatic preference of DNMT3A toward different CpGflanking sequences: in comparison with wild-type DNMT3A, the R882H mutant shows stronger preference for the CG(G/A) motif over the CG(T/C) motif as substrate[25], which correlates with the aberrant DNA methylation and gene expression in acute myeloid leukemia (AML), suggesting an off-targeting effect of the DNMT3A R882H mutation that may contribute to AML pathogenesis[21]
Our study reveals that the TRD loop in the DNMT3AWT–DNMT3-like protein (DNMT3L)–CGA and DNMT3AR882H–DNMT3L–CGA (CGA DNA) complex recognizes the CpG site in a different mechanism than that in the previously reported DNMT3AWT–DNMT3L–CGT DNA complex[24], uncovering the inherent conformational dynamics of the TRD loop
Summary
DNA methyltransferase DNMT3A is essential for establishment of mammalian DNA methylation during development. The R882H DNMT3A is a hotspot mutation in acute myeloid leukemia (AML) causing aberrant DNA methylation. How this mutation affects the structure and function of DNMT3A remains unclear. Recent studies have suggested that the R882H mutation may affect the relative enzymatic preference of DNMT3A toward different CpGflanking sequences: in comparison with wild-type DNMT3A, the R882H mutant shows stronger preference for the CG(G/A) motif over the CG(T/C) motif as substrate[25], which correlates with the aberrant DNA methylation and gene expression in AML, suggesting an off-targeting effect of the DNMT3A R882H mutation that may contribute to AML pathogenesis[21]. An intramolecular hydrogen bond is formed between residues
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