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.

  • Article
  • Published:

CpNpG methylation in mammalian cells

Abstract

In vertebrate DMA, 3% to 5% of cytosine residues are present as 5–methylcytosine, and it is generally accepted that essentially all of this methylation occurs at cytosines which are contained in the symmetrical dinucleotide CpG. In this report we demonstrate, using bisulphite genomic sequencing, that the methylation machinery of mammalian cells is capable of both maintenance and de novo methylation at CpNpG sites. The existence of inherited CpNpG methylation in mammalian cells has important implications in gene regulation and in the aetiology of disease

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Similar content being viewed by others

References

  1. Bestor, T., Laudano, A., Mattaliano, R. & Ingram, V. Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. J. molec. Biol. 203, 971–983 (1988).

    Article  CAS  Google Scholar 

  2. Yen, R.-W. et al. Isolation and characterisation of the cDNA encoding human DNA methyltransferase. Nucl. Acids Res. 20, 2287–2291 (1992).

    Article  CAS  Google Scholar 

  3. Bestor, T.H. & Ingram, V.M. Two DNA methyltransferases from murine erythroleukaemia cells: purification, sequence specificity, and mode of interaction with DNA. Proc. natn. Acad. Sci. U.S.A. 80, 5559–5563 (1983).

    Article  CAS  Google Scholar 

  4. Gruenbaum, Y., Cedar, H. & Razin, A. Substrate and sequence specificity of a eukaryotic DNA methylase. Nature 295, 620–625 (1982).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  6. Monk, M., Adams, R.L.P. & Rinald, A. Decrease in DNA methylase activity during preimplantation development in the mouse. Development 112, 189–192 (1991).

    CAS  PubMed  Google Scholar 

  7. 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  Google Scholar 

  8. Graessmann, M. & Graessmann, A. DNA methylation, chromatin structure and the regulation of gene expression. In DNA Methylation: Molecular Biology and Biological Significance (eds Jost, J.P. & Saluz, H.P.) 404–424 (Birkhauser Verlag, Basel, 1993).

    Chapter  Google Scholar 

  9. Sasaki, H., Alien, N.D. & Surani, M.A. DNA methylation and genomic imprinting in mammals. In DNA Methylation: Molecular Biology and Biological Significance (eds Jost, J.P. & Saluz, H.P.) 469–486 (Birkhauser Verlag, Basel, 1993).

    Chapter  Google Scholar 

  10. Spruck III, C. H., Rideout III, W.M. & Jones, P.A. DNA methylation and cancer. In DNA Methylation: Molecular Biology and Biological Significance (eds. Jost, J.P. & Saluz, H.P.) 487–509 (Birkhauser Verlag, Basel, 1993).

    Chapter  Google Scholar 

  11. Bates, G. & Lehrach, H. Trinucleotide repeat expansions and human genetic disease. BioEssays 16, 277–284 (1994).

    Article  CAS  Google Scholar 

  12. Gruenbaum, Y., Naveh-Many, T., Cedar, H. & Razin, A. Sequence specificity of methylation in higher plant DNA. Nature 292, 860–862 (1981).

    Article  CAS  Google Scholar 

  13. Finnegan, E.J. & Dennis, E.S. Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana. Nucl. Acids Res. 21, 2383–2388 (1993).

    Article  CAS  Google Scholar 

  14. Scheldt, G., Weber, H., Graessmann, M. & Graessmann, A. Are there two DNA methyltransferase gene families in plant cells? Nucl. Acids Res. 22, 953–958 (1994).

    Article  Google Scholar 

  15. Bird, A.P. & Southern, E.M. Use of restriction enzymes to study eukaryotic DNA methylation. J. molec. Biol. 118, 27–47 (1978).

    Article  CAS  Google Scholar 

  16. Church, G.M. & Gilbert, W. Genomic sequencing. Proc. natn. Acad. Sci. U.S.A. 81, 1991–1995 (1984).

    Article  CAS  Google Scholar 

  17. Saluz, H.P. & Jost, J.P. Genomic footprinting with Taq polymerase. Proc. natn. Acad. Sci. U.S.A. 86, 2602–2606 (1989).

    Article  CAS  Google Scholar 

  18. Pfeifer, G.P., Steigerwald, S.D., Mueller, P.R., Wold, B. & Riggs, A.D. Genomic sequencing and methylation analysis by ligation mediated PCR. Science 246, 810–813 (1989).

    Article  CAS  Google Scholar 

  19. Woodcock, D.M., Crowther, P.J. & Diver, W.P. The majority of methylated deoxycytidines in human DNA are not in the CpG dinucleotide. Biochem. Biophys. Res. Comm. 145, 888–894 (1987).

    Article  CAS  Google Scholar 

  20. Toth, M., Muller, U. & Doerfler, W. Establishment of de novo DNA methylation patterns. J. molec. Biol. 214, 673–683 (1990).

    Article  CAS  Google Scholar 

  21. Tommasi, S., LeBon, J.M., Riggs, A.D. & Singer-Sam, J. Methylation analysis by genomic sequencing of 5′ region of mouse Pgk-1 gene and a cautionary note concerning the method. Somat. Cell molec. Genet. 19, 529–541 (1993).

    Article  CAS  Google Scholar 

  22. Frommer, M. et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. natn. Acad. Sci. U.S.A. 89, 1827–1831 (1992).

    Article  CAS  Google Scholar 

  23. Clark, S.J., Harrison, J., Paul, C.L. & Frommer, M. High sensitivity mapping of methylated cytosines. Nucl. Acids Res. 22, 2990–2997 (1994).

    Article  CAS  Google Scholar 

  24. Leonhardt, H. & Bestor, T.H., Structure, function and regulation of mammalian DNA methyltransferase. In DNA Methylation: Molecular Biology and Biological Significance (eds Jost, J.P. & Saluz, H.P.) 109–119 (Birkhauser Verlag, Basel, 1993).

    Chapter  Google Scholar 

  25. Bestor, T.H. DNA methylation: evolution of a bacterial immune function into a regulator of gene expression and genome structure in higher eukaryotes. Phil. Trans. Roy. Soc. (Lond.) 326, 179–187 (1990).

    Article  CAS  Google Scholar 

  26. Walter, J., Trautner, T.A. & Noyer-Weidner, M. High plasticity of multispecific DNA methyltransferases in the region carrying DNA target recognising enzyme modules. EMBO J. 11, 4445–4450 (1992).

    Article  CAS  Google Scholar 

  27. Simon, D., Stuhlmann, H., Jahner, D., Wagner, H., Werner, E. & Jaenisch, R. Retrovirus genomes methylated by mammalian but not bacterial methylase are non-infectious. Nature 304, 275–277 (1983).

    Article  CAS  Google Scholar 

  28. Tasheva, E.S. & Roufa, D.J. Densely methylated DNA islands in mammalian chromosomal replication origins. Molec. cell. Biol. 14, 5636–5644 (1994).

    Article  CAS  Google Scholar 

  29. Selker, E.U. Control of DNA methylation in fungi. In DNA Methylation: Molecular Biology and Biological Significance (eds Jost, J.P. & Saluz, H.P.) 212–217 (Birkhauser Verlag, Basel, 1993).

    Chapter  Google Scholar 

  30. Meyer, P., Niedenof, I. & ten Lohuis, M. Evidence for cytosine methylation of non-symmetrical sequences in transgenic Petunia hybrida. EMBO J. 13, 2084–2088 (1994).

    Article  CAS  Google Scholar 

  31. Noyer-Weidner, M. & Trautner, T.A. Methylation of DNA in prokaryotes. In DNA Methylation: Molecular Biology and Biological Significance (eds Jost, J.P. & Saluz, H.P.) 39–108 (Birkhauser Verlag, Basel, 1993).

    Chapter  Google Scholar 

  32. Rosenstraus, M.J. & Levine, A. Alterations in the developmental potential of embryonal carcinoma cells in mixed aggregates of nullipotent and pluripotent cells. Cell 17, 337–346 (1979).

    Article  CAS  Google Scholar 

  33. Harrison, J., Molloy, P.L. & Clark, S.J. Direct cloning of polymerase chain reaction products in an Xcml T-vector. Analyti. Biochem. 216, 235–236 (1994).

    Article  CAS  Google Scholar 

  34. Sambrook, J., Fritsch, E.F. & Maniatis, T. in Molecular Cloning; a laboratory manual. 2nd edn (Cold Spring Harbor Press.Cold Spring Harbor, 1989).

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Clark, S., Harrison, J. & Frommer, M. CpNpG methylation in mammalian cells. Nat Genet 10, 20–27 (1995). https://doi.org/10.1038/ng0595-20

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng0595-20

This article is cited by

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