Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

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

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.

This is a preview of subscription content

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

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.

References

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

    ADS  CAS  Article  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)

    ADS  CAS  Article  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)

    ADS  CAS  Article  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)

    CAS  Article  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)

    CAS  Article  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)

    CAS  Article  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)

    ADS  CAS  Article  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)

    CAS  Article  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)

    CAS  Article  Google Scholar 

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

    CAS  Article  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)

    CAS  Article  Google Scholar 

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

    CAS  Article  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)

    CAS  Article  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)

    ADS  CAS  Article  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)

    CAS  Article  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)

    CAS  Article  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)

    CAS  Article  Google Scholar 

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

    CAS  Article  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)

    CAS  Article  Google Scholar 

Download references

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.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Xiaodong Cheng or Timothy H. Bestor.

Ethics declarations

Competing interests

Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures S1-S2 and Supplementary Table S1 with Legends and additional references (PDF 1023 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature05987

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing