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DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA

Nature volume 448, pages 714–717 (2007)Cite this article

Abstract

Mammals use DNA methylation for the heritable silencing of retrotransposons and imprinted genes and for the inactivation of the X chromosome in females. The establishment of patterns of DNA methylation during gametogenesis depends in part on DNMT3L, an enzymatically inactive regulatory factor that is related in sequence to the DNA methyltransferases DNMT3A and DNMT3B1,2. The main proteins that interact in vivo with the product of an epitope-tagged allele of the endogenous Dnmt3L gene were identified by mass spectrometry as DNMT3A2, DNMT3B and the four core histones. Peptide interaction assays showed that DNMT3L specifically interacts with the extreme amino terminus of histone H3; this interaction was strongly inhibited by methylation at lysine 4 of histone H3 but was insensitive to modifications at other positions. Crystallographic studies of human DNMT3L showed that the protein has a carboxy-terminal methyltransferase-like domain and an N-terminal cysteine-rich domain. Cocrystallization of DNMT3L with the tail of histone H3 revealed that the tail bound to the cysteine-rich domain of DNMT3L, and substitution of key residues in the binding site eliminated the H3 tail–DNMT3L interaction. These data indicate that DNMT3L recognizes histone H3 tails that are unmethylated at lysine 4 and induces de novo DNA methylation by recruitment or activation of DNMT3A2.

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Figure 1: Generation of epitope-tagged Dnmt3L locus and DNMT3L protein interaction screen in ES cells.
Figure 2: Interaction of DNMT3L with the N terminus of histone H3 is abolished by methylation of H3 lysine 4.
Figure 3: Structure of DNMT3L and mode of recognition of histone H3 unmethylated at lysine 4.

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References

  1. Bourc'his, D. & Bestor, T. H. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431, 96–99 (2004)

    Article  ADS  CAS  Google Scholar 

  2. Bourc'his, D., Xu, G. L., Lin, C. S., Bollman, B. & Bestor, T. H. Dnmt3L and the establishment of maternal genomic imprints. Science 294, 2536–2539 (2001)

    Article  ADS  CAS  Google Scholar 

  3. Webster, K. E. et al. Meiotic and epigenetic defects in Dnmt3L-knockout mouse spermatogenesis. Proc. Natl Acad. Sci. USA 102, 4068–4073 (2005)

    Article  ADS  CAS  Google Scholar 

  4. Chen, T, Ueda, Y, Xie, S & Li, E . A novel Dnmt3a isoform produced from an alternative promoter localizes to euchromatin and its expression correlates with active de novo methylation. J.Biol. Chem 277, 38746–38754 (2002)

    Article  CAS  Google Scholar 

  5. Suetake, I., Shinozaki, F., Miyagawa, J., Takeshima, H. & Tajima, S. DNMT3L stimulates the DNA methylation activity of Dnmt3a and Dnmt3b through a direct interaction. J. Biol. Chem. 279, 27816–27823 (2004)

    Article  CAS  Google Scholar 

  6. Kareta, M. S., Botello, Z. M., Ennis, J. J., Chou, C. & Chedin, F. Reconstitution and mechanism of the stimulation of de novo methylation by human DNMT3L. J. Biol. Chem. 281, 25893–25902 (2006)

    Article  CAS  Google Scholar 

  7. Kaneda, M. et al. Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting. Nature 429, 900–903 (2004)

    Article  ADS  CAS  Google Scholar 

  8. Lei, H. et al. De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells. Development 122, 3195–3205 (1996)

    CAS  Google Scholar 

  9. Humpherys, D. et al. Epigenetic instability in ES cells and cloned mice. Science 293, 95–97 (2001)

    Article  CAS  Google Scholar 

  10. Chen, Z. X., Mann, J. R., Hsieh, C. L., Riggs, A. D. & Chedin, F. Physical and functional interactions between the human DNMT3L protein and members of the de novo methyltransferase family. J. Cell. Biochem. 95, 902–917 (2005)

    Article  CAS  Google Scholar 

  11. Goll, M. G. & Bestor, T. H. Eukaryotic cytosine methyltransferases. Annu. Rev. Biochem. 74, 481–514 (2005)

    Article  CAS  Google Scholar 

  12. Klimasauskas, S., Kumar, S., Roberts, R. J. & Cheng, X. HhaI methyltransferase flips its target base out of the DNA helix. Cell 76, 357–369 (1994)

    Article  CAS  Google Scholar 

  13. Shi, Y. et al. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119, 941–953 (2004)

    Article  CAS  Google Scholar 

  14. Lan, F. F. et al. Recognition of un-methylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature doi:10.1038/nature06034 (this issue).

  15. Tamaru, H. et al. Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nature Genet. 34, 75–79 (2003)

    Article  CAS  Google Scholar 

  16. Jackson, J. P., Lindroth, A. M., Cao, X. & Jacobsen, S. E. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416, 556–560 (2002)

    Article  ADS  CAS  Google Scholar 

  17. Lehnertz, B. et al. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr. Biol. 13, 1192–1200 (2003)

    Article  CAS  Google Scholar 

  18. Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature Genet. 39, 457–466 (2007)

    Article  CAS  Google Scholar 

  19. Appanah, R., Dickerson, D. R., Goyal, P., Groudine, M. & Lorincz, M. C. An unmethylated 3′ promoter-proximal region is required for efficient transcription initiation. PLoS Genet. 3, e27 (2007)

    Article  Google Scholar 

  20. Wysocka, J. et al. WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 121, 859–872 (2005)

    Article  CAS  Google Scholar 

  21. Sebastiaan Winkler, G. et al. Isolation and mass spectrometry of transcription factor complexes. Methods 26, 260–269 (2002)

    Article  CAS  Google Scholar 

  22. Erdjument-Bromage, H. et al. Examination of micro-tip reversed-phase liquid chromatographic extraction of peptide pools for mass spectrometric analysis. J. Chromatogr. A. 826, 167–181 (1998)

    Article  CAS  Google Scholar 

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Acknowledgements

We thank C.S. Lin for advice and assistance, D. Bourc’his, M. Damelin, C. Schaefer, X. Zhang and R. E. Collins for helpful discussions, J. R. Horton for collection of X-ray diffraction data, A. Ruthenberg for recombinant WDR5 protein, and K. Anderson, D. Bourc’his and C. Schaefer for criticism of the manuscript. This work was supported by grants from the National Institutes of Health to C. D. A., X. C., P. T. and T. H. B. and by a fellowship from the European Molecular Biology Organisation to S.K.T.O.

The X-ray structures of DNMT3L and the DNMT3L-H3 tail complex have been submitted to PDB as 2PV0 and 2PVC, respectively.

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Author notes

  1. Steen K. T. Ooi, Chen Qiu, Emily Bernstein and Keqin Li: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Genetics and Development, College of Physicians and Surgeons of Columbia University, New York, New York 10032, USA,

    Steen K. T. Ooi & Timothy H. Bestor

  2. Department of Biochemistry, Emory University, Atlanta, Georgia 30322, USA,

    Chen Qiu, Keqin Li, Da Jia, Zhe Yang & Xiaodong Cheng

  3. Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA,

    Emily Bernstein & C. David Allis

  4. Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA,

    Hediye Erdjument-Bromage & Paul Tempst

  5. Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan,

    Shau-Ping Lin

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Correspondence to Xiaodong Cheng or Timothy H. Bestor.

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Ooi, S., Qiu, C., Bernstein, E. et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714–717 (2007). https://doi.org/10.1038/nature05987

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