Letter | Published:

Structural basis for DNMT3A-mediated de novo DNA methylation

Nature volume 554, pages 387391 (15 February 2018) | Download Citation


DNA methylation by de novo DNA methyltransferases 3A (DNMT3A) and 3B (DNMT3B) at cytosines is essential for genome regulation and development1,2. Dysregulation of this process is implicated in various diseases, notably cancer. However, the mechanisms underlying DNMT3 substrate recognition and enzymatic specificity remain elusive. Here we report a 2.65-ångström crystal structure of the DNMT3A–DNMT3L–DNA complex in which two DNMT3A monomers simultaneously attack two cytosine–phosphate–guanine (CpG) dinucleotides, with the target sites separated by 14 base pairs within the same DNA duplex. The DNMT3A–DNA interaction involves a target recognition domain, a catalytic loop, and DNMT3A homodimeric interface. Arg836 of the target recognition domain makes crucial contacts with CpG, ensuring DNMT3A enzymatic preference towards CpG sites in cells. Haematological cancer-associated somatic mutations of the substrate-binding residues decrease DNMT3A activity, induce CpG hypomethylation, and promote transformation of haematopoietic cells. Together, our study reveals the mechanistic basis for DNMT3A-mediated DNA methylation and establishes its aetiological link to human disease.

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We thank X. Cheng for comments on the manuscript, M. Okano, J. Wang, and J.-A. Losman for providing reagents used in the study, and staff members at the Advanced Light Source, Lawrence Berkeley National Laboratory, and at the Advanced Photo Source, Argonne National Laboratory, for access to X-ray beamlines. We are also grateful for the support of University of North Carolina facilities including Genomics Core, which are partly supported by UNC Cancer Center Core Support Grant P30-CA016086. This work was supported by Kimmel Scholar Awards (to J.S. and G.G.W.), the March of Dimes Foundation (1-FY15-345 to J.S.), the DoD Peer-reviewed Cancer Research Program (W81XWH-14-1-0232 to G.G.W.), Gabrielle’s Angel Foundation for Cancer Research (to G.G.W.), Gilead Sciences Research Scholars Program in haematology/oncology (to G.G.W.), University Cancer Research Fund of the N.C. state (to G.G.W.), and the National Institutes of Health (1R35GM119721 to J.S.; R35GM124736 to S.B.R.; 5R21ES025392 to Y.W.; and 1R01CA215284, 1R01CA218600, and 1R01CA211336 to G.G.W.). G.G.W. is a Research Scholar of American Cancer Society and a Junior Faculty Scholar of American Society of Haematology. R.L. was supported by a Lymphoma Research Foundation postdoctoral fellowship.

Author information

Author notes

    • Zhi-Min Zhang

    Present address: School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.

    • Zhi-Min Zhang
    •  & Rui Lu

    These authors contributed equally to this work.

    • Gang Greg Wang
    •  & Jikui Song

    These authors jointly supervised this work.


  1. Department of Biochemistry, University of California, Riverside, California 92521, USA

    • Zhi-Min Zhang
    •  & Jikui Song
  2. The Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, USA

    • Rui Lu
    • , Dongliang Chen
    •  & Gang Greg Wang
  3. Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, USA

    • Rui Lu
    • , Dongliang Chen
    • , Scott B Rothbart
    •  & Gang Greg Wang
  4. Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, USA

    • Pengcheng Wang
    • , Yang Yu
    • , Linfeng Gao
    • , Shuo Liu
    • , Yinsheng Wang
    •  & Jikui Song
  5. Department of Chemistry, University of California, Riverside, California 92521, USA

    • Debin Ji
    •  & Yinsheng Wang
  6. Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA

    • Scott B Rothbart


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Z.-M.Z., R.L., P.W., Y.Y., D.C., L.G., S.L., D.J., and J.S. performed experiments. S.B.R. provided technical support. Y.W., G.G.W., and J.S. conceived and organized the study. Z.-M.Z., R.L., G.G.W., and J.S. prepared the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Gang Greg Wang or Jikui Song.

Reviewer Information Nature thanks A. Jeltsch, R. Xu and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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    This file contains the uncropped western blots from the main and supplementary figures.

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