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Mammalian (cytosine-5) methyltransferases cause genomic DNA methylation and lethality in Drosophila

Nature Genetics volume 23, pages 363–366 (1999)Cite this article

Abstract

CpG methylation is essential for mouse development1 as well as gene regulation and genome stability2,3,4,5. Many features of mammalian DNA methylation are consistent with the action of a de novo methyltransferase that establishes methylation patterns during early development and the post-replicative maintenance of these patterns by a maintenance methyltransferase6. The mouse methyltransferase Dnmt1 (encoded by Dnmt) shows a preference for hemimethylated substrates in vitro , making the enzyme a candidate for a maintenance methyltransferase7,8. Dnmt1 also has de novo methylation activity in vitro 9, but the significance of this finding is unclear, because mouse embryonic stem (ES) cells contain a de novo methylating activity unrelated to Dnmt1 (ref. 10). Recently, the Dnmt3 family of methyltransferases has been identified and shown in vitro to catalyse de novo methylation11. To analyse the function of these enzymes, we expressed Dnmt and Dnmt3a in transgenic Drosophila melanogaster. The absence of endogenous methylation in Drosophila12,13 facilitates detection of experimentally induced methylation changes. In this system, Dnmt3a functioned as a de novo methyltransferase, whereas Dnmt1 had no detectable de novo methylation activity. When co-expressed, Dnmt1 and Dnmt3a cooperated to establish and maintain methylation patterns. Genomic DNA methylation impaired the viability of transgenic flies, suggesting that cytosine methylation has functional consequences for Drosophila development.

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Figure 1: Expression of mouse methyltransferases in Drosophila.
Figure 2: Expression of Dnmt3a, but not Dnmt, causes developmental defects in Drosophila.
Figure 3: Expression of Dnmt3a, but not Dnmt, causes CpG methylation of genomic DNA in Drosophila.
Figure 4: Dnmt functions as an enhancer of the Dnmt3a phenotype.

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References

  1. Li, E., Bestor, T.H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992).

    Article  CAS  PubMed  Google Scholar 

  2. Li, E., Beard, C. & Jaenisch, R. Role for DNA methylation in genomic imprinting. Nature 366, 362–365 ( 1993).

    Article  CAS  PubMed  Google Scholar 

  3. Panning, B. & Jaenisch, R. DNA hypomethylation can activate Xist expression and silence X-linked genes. Genes Dev. 10, 1991–2002 (1996).

    Article  CAS  PubMed  Google Scholar 

  4. Chen, R.Z., Pettersson, U., Beard, C., Jackson-Grusby, L. & Jaenisch, R. DNA hypomethylation leads to elevated mutation rates. Nature 395, 89– 93 (1998).

    Article  CAS  PubMed  Google Scholar 

  5. Walsh, C.P., Chaillet, J.R. & Bestor, T.H. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nature Genet. 20, 116–117 (1998).

    Article  CAS  PubMed  Google Scholar 

  6. Jaenisch, R. DNA methylation and imprinting: why bother? Trends Genet. 13, 323–329 (1997).

    Article  CAS  PubMed  Google Scholar 

  7. Gruenbaum, Y., Cedar, H. & Razin, A. Substrate and sequence specificity of a eukaryotic DNA methylase. Nature 295, 620– 622 (1982).

    Article  CAS  PubMed  Google Scholar 

  8. Bestor, T.H. & Ingram, V.M. Two DNA methyltransferases from murine erythroleukemia cells: purification, sequence specificity, and mode of interaction with DNA. Proc. Natl Acad. Sci. USA 80, 5559–5563 (1983).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Yoder, J.A., Soman, N.S., Verdine, G.L. & Bestor, T.H. DNA (cytosine-5)-methyltransferases in mouse cells and tissues. Studies with a mechanism-based probe. J. Mol. Biol. 270, 385–395 (1997).

    Article  CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  11. Okano, M., Xie, S. & Li, E. Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases. Nature Genet. 19, 219 –220 (1998).

    Article  CAS  PubMed  Google Scholar 

  12. Urieli-Shoval, S., Gruenbaum, Y., Sedat, J. & Razin, A. The absence of detectable methylated bases in Drosophila melanogaster DNA. FEBS Lett. 146, 148–152 ( 1982).

    Article  CAS  PubMed  Google Scholar 

  13. Patel, C.V. & Gopinathan, K.P. Determination of trace amounts of 5-methylcytosine in DNA by reverse-phase high-performance liquid chromatography. Anal. Biochem. 164, 164– 169 (1987).

    Article  CAS  PubMed  Google Scholar 

  14. Brand, A.H., Manoukian, A.S. & Perrimon, N. Ectopic expression in Drosophila. Methods Cell Biol. 44, 635–654 (1994).

    Article  CAS  PubMed  Google Scholar 

  15. Sutherland, E., Coe, L. & Raleigh, E.A. McrBC: a multisubunit GTP-dependent restriction endonuclease. J. Mol. Biol. 225, 327– 348 (1992).

    Article  CAS  PubMed  Google Scholar 

  16. Danilevskaya, O., Slot, F., Pavlova, M. & Pardue, M.L. Structure of the Drosophila HeT-A transposon: a retrotransposon-like element forming telomeres. Chromosoma 103, 215– 224 (1994).

    Article  CAS  PubMed  Google Scholar 

  17. Bestor, T.H. Activation of mammalian DNA methyltransferase by cleavage of a Zn binding regulatory domain. EMBO J. 11, 2611– 2617 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Holliday, R. & Pugh, J.E. DNA modification mechanisms and gene activity during development. Science 187, 226–232 (1975).

    Article  CAS  PubMed  Google Scholar 

  19. Riggs, A.D. X inactivation, differentiation, and DNA methylation. Cytogenet. Cell Genet. 14, 9–25 ( 1975).

    Article  CAS  PubMed  Google Scholar 

  20. Tucker, K.L. et al. Germ-line passage is required for establishment of methylation and expression patterns of imprinted but not of nonimprinted genes. Genes Dev. 10, 1008–1020 (1996).

    Article  CAS  PubMed  Google Scholar 

  21. Wines, D.R., Talbert, P.B., Clark, D.V. & Henikoff, S. Introduction of a DNA methyltransferase into Drosophila to probe chromatin structure in vivo. Chromosoma 104, 332–340 (1996).

    Article  CAS  PubMed  Google Scholar 

  22. Becker, P.B., Ruppert, S. & Schütz, G. Genomic footprinting reveals cell type-specific DNA binding of ubiquitous factors. Cell 51, 435–443 (1987).

    Article  CAS  PubMed  Google Scholar 

  23. Iguchi-Ariga, S.M. & Schaffner, W. CpG methylation of the cAMP-responsive enhancer/promoter sequence TGACGTCA abolishes specific factor binding as well as transcriptional activation. Genes Dev. 3, 612–619 ( 1989).

    Article  CAS  PubMed  Google Scholar 

  24. Ng, H.H. & Bird, A. DNA methylation and chromatin modification. Curr. Opin. Genet. Dev. 9, 158– 163 (1999).

    Article  CAS  PubMed  Google Scholar 

  25. Kudo, S. Methyl-CpG-binding protein MeCP2 represses Sp-1 activated transcription of the human leukosialin gene when the promoter is methylated. Mol. Cell. Biol. 18, 5492–5499 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Wade, P.A. et al. Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nature Genet. 23, 62–66 (1999).

    Article  CAS  PubMed  Google Scholar 

  27. Spradling, A.L. & Rubin, G.M. Transformation of cloned P elements into Drosophila germ line chromosomes. Science 218, 341–347 ( 1982).

    Article  CAS  PubMed  Google Scholar 

  28. Zink, D. & Paro, R. Drosophila Polycomb-group regulated chromatin inhibits the accessibility of a trans-activator to its target DNA. EMBO J. 14, 5660–5671 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Ashburner, M. Drosophila: A Laboratory Manual (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1989).

    Google Scholar 

  30. Kumar, S., Cheng, X., Pflugrath, J.W. & Roberts, R.J. Purification, crystallization, and preliminary X-ray diffraction analysis of an M.HhaI-AdoMet complex. Biochemistry 31, 8648–8653 (1992).

    Article  CAS  PubMed  Google Scholar 

  31. Gruenbaum, Y., Stein, R., Cedar, H. & Razin, A. Methylation of CpG sequences in eukaryotic DNA. FEBS Lett. 124, 67–71 (1981).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank D. Biniszkiewicz for Dnmt cDNA; D. Schneider and M. Voas for help with pictures; I. Rebay for fly strains; and H. LeBlanc for helpful discussions. This work was supported by NIH grants GM39341 (to T.O.-W.) and 5-R35-CA44339 (to R.J). F.L. received a research fellowship from the Deutsche Forschungsgemeinschaft.

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Authors and Affiliations

  1. Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA

    Frank Lyko, Helena Kashevsky, Matthew Tudor, Mary-Ann Mastrangelo, Terry L. Orr-Weaver & Rudolf Jaenisch

  2. Department of Haematology, University of Wales College of Medicine, Heath Park, Cardiff, UK

    Bernard H. Ramsahoye

  3. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Terry L. Orr-Weaver & Rudolf Jaenisch

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Correspondence to Rudolf Jaenisch.

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Lyko, F., Ramsahoye, B., Kashevsky, H. et al. Mammalian (cytosine-5) methyltransferases cause genomic DNA methylation and lethality in Drosophila. Nat Genet 23, 363–366 (1999). https://doi.org/10.1038/15551

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