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Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation

Abstract

Genetic imprinting, found in flowering plants and placental mammals, uses DNA methylation to yield gene expression that is dependent on the parent of origin1. DNA methyltransferase 3a (Dnmt3a) and its regulatory factor, DNA methyltransferase 3-like protein (Dnmt3L), are both required for the de novo DNA methylation of imprinted genes in mammalian germ cells. Dnmt3L interacts specifically with unmethylated lysine 4 of histone H3 through its amino-terminal PHD (plant homeodomain)-like domain2. Here we show, with the use of crystallography, that the carboxy-terminal domain of human Dnmt3L interacts with the catalytic domain of Dnmt3a, demonstrating that Dnmt3L has dual functions of binding the unmethylated histone tail and activating DNA methyltransferase. The complexed C-terminal domains of Dnmt3a and Dnmt3L showed further dimerization through Dnmt3a–Dnmt3a interaction, forming a tetrameric complex with two active sites. Substitution of key non-catalytic residues at the Dnmt3a–Dnmt3L interface or the Dnmt3a–Dnmt3a interface eliminated enzymatic activity. Molecular modelling of a DNA–Dnmt3a dimer indicated that the two active sites are separated by about one DNA helical turn. The C-terminal domain of Dnmt3a oligomerizes on DNA to form a nucleoprotein filament. A periodicity in the activity of Dnmt3a on long DNA revealed a correlation of methylated CpG sites at distances of eight to ten base pairs, indicating that oligomerization leads Dnmt3a to methylate DNA in a periodic pattern. A similar periodicity is observed for the frequency of CpG sites in the differentially methylated regions of 12 maternally imprinted mouse genes. These results suggest a basis for the recognition and methylation of differentially methylated regions in imprinted genes, involving the detection of both nucleosome modification and CpG spacing.

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Figure 1: Structure of the Dnmt3a–Dnmt3L (3a–3L) C-terminal domain complex.
Figure 2: Model of Dnmt3a–Dnmt3L tetramer with DNA.
Figure 3: Periodicity of Dnmt3a-C activity on long DNA substrates.
Figure 4: Periodicity of CpG sites in maternally imprinted DMRs17.

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Acknowledgements

We thank J. R. Horton for assistance with X-ray diffraction data collection; Z. Yang for assistance in solving the structure; H. Sasaki and R. Hirasawa for providing DMR sequences; S. Devine and R. Mills for help with DMR sequence analysis; A. Pingoud for providing an R.EcoRV expression clone used for calibration of the EMSA experiments; R. M. Blumenthal for critical editing of the manuscript; and E. Bernstein and R. E. Collins for comments on the manuscript. This work was supported by grants from the National Institutes of Health to X.C. and grants from the Deutsche Forschungsgemeinschaft and BMBF (Biofuture programme) to A.J.

The X-ray structure of Dnmt3a–Dnmt3L C-terminal tetramer complex is deposited in the Protein Data Bank under ID code 2QRV.

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Correspondence to Albert Jeltsch or Xiaodong Cheng.

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The X-ray structure of Dnmt3a–Dnmt3L C-terminal tetramer complex is deposited in the Protein Data Bank under ID code 2QRV. Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Figures and Table 1

This file contains Supplementary Figures S1-S9 with Legends and Supplementary Table 1. (PDF 7394 kb)

Supplementary Sequences and Figure S8

This file contains Supplementary Sequences detailing DNA sequences used in the analysis of Figure 4 and Supplementary Figure S8 (PDF 157 kb)

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Jia, D., Jurkowska, R., Zhang, X. et al. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 449, 248–251 (2007). https://doi.org/10.1038/nature06146

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