DNA methylation is an important epigenetic modification that is essential for various developmental processes through regulating gene expression, genomic imprinting, and epigenetic inheritance1,2,3,4,5. Mammalian genomic DNA methylation is established during embryogenesis by de novo DNA methyltransferases, DNMT3A and DNMT3B6,7,8, and the methylation patterns vary with developmental stages and cell types9,10,11,12. DNA methyltransferase 3-like protein (DNMT3L) is a catalytically inactive paralogue of DNMT3 enzymes, which stimulates the enzymatic activity of Dnmt3a13. Recent studies have established a connection between DNA methylation and histone modifications, and revealed a histone-guided mechanism for the establishment of DNA methylation14. The ATRX–DNMT3–DNMT3L (ADD) domain of Dnmt3a recognizes unmethylated histone H3 (H3K4me0)15,16,17. The histone H3 tail stimulates the enzymatic activity of Dnmt3a in vitro17,18, 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 genome9,10,19,20. 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.
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We thank staff of beamline BL17U at Shanghai Synchrotron Radiation Facility, China, for their assistance in data collection, and H. Wang for help on electron microscopy analyses. We thank staff of the Biomedical Core Facility, Fudan University, for their help on biochemical analyses, and A. D. Riggs for providing the complementary DNAs of DNMT3A and DNMT3L. This work was supported by grants from the National Basic Research Program of China (2011CB965300, 2009CB918600, 2013CB910401), the National Science & Technology Major Project ‘Key New Drug Creation and Manufacturing Program’ of China (2014ZX09507-002, 2011ZX09506-001), the National Natural Science Foundation of China (31270779, 91419301, 31030019, U1432242, 31270771, 31222016, 31300685, U1332138), the Basic Research Project of Shanghai Science and Technology Commission (12JC1402700, 13JC1406300), the Fok Ying Tung Education Foundation (20090071220012), and the Chinese Academy of Sciences Pilot Strategic Science and Technology Projects B (numbers XDB08030201, XDB08030302). Y.C. is a scholar of the Hundred Talents Program of the Chinese Academy of Sciences.
This video illustrates the conformational changes of DNMT3A induced by histone H3 tail. DNMT3A exists in an autoinhibitory form, in which the ADD domain (green) binds to and inhibits the DNA-binding affinity of the CD domain (purple). Histone H3 (yellow) disrupts ADD-CD interaction, induces a large movement of the ADD domain, and releases the autoinhibition of DNMT3A. In the active form of DNMT3A, the ADD domain has no steric hindrance for DNA recognition by the CD domain. As pointed out in the main text, residues R790, R792, D529, and D531 of DNMT3A and H3K4 are shown as sticks.
About this article
Molecular Neurobiology (2018)