Advertisement

Methylated DNA Immunoprecipitation (MeDIP)

  • Fabio Mohn
  • Michael Weber
  • Dirk Schübeler
  • Tim-Christoph Roloff
Part of the Methods in Molecular Biology book series (MIMB, volume 507)

Abstract

Methylated DNA immunoprecipitation (MeDIP) is a versatile immunocapturing approach for unbiased detection of methylated DNA. In brief, genomic DNA is randomly sheared by sonication and immunoprecipitated with a monoclonal antibody that specifically recognizes 5-methylcytidine. The resulting enrichment of methylated DNA in the immunoprecipitated fraction can be determined by PCR to assess the methylation state of individual regions. Alternatively, MeDIP can be combined with large-scale analysis using microarrays as a genome-wide experimental readout. This protocol has been applied to generate comprehensive DNA methylation profiles on a genome-wide scale in mammals and plants, and further to identify abnormally methylated genes in cancer cells.

Keywords

MeDIP methylated DNA DNA methylation genome-wide analysis epigenomics 5mC antibody CpG immunoprecipitation 

Notes

Acknowledgements

The authors would like to thank the members of the Schübeler lab for helpful comments on the protocol.

References

  1. 1.
    Fazzari, M. J., Greally, J. M. (2004) Epigenomics: beyond CpG islands. Nat Rev Genet 5, 446–455.CrossRefPubMedGoogle Scholar
  2. 2.
    Weber, M. Schübeler, D. (2007) Genomic patterns of DNA methylation: targets and function of an epigenetic mark. Curr Opin Cell Biol 19, 273–280.CrossRefPubMedGoogle Scholar
  3. 3.
    Zilberman, D., Henikoff, S. (2007) Genome-wide analysis of DNA methylation patterns. Development 134, 3959–3965.CrossRefPubMedGoogle Scholar
  4. 4.
    Reynaud, C., Bruno, C., Boullanger, P., et al. (1992) Monitoring of urinary excretion of modified nucleosides in cancer patients using a set of six monoclonal antibodies. Cancer Lett 61, 255–262.CrossRefPubMedGoogle Scholar
  5. 5.
    Weber, M., Davies, J. J., Wittig, D., et al. (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37, 853–862.CrossRefPubMedGoogle Scholar
  6. 6.
    Weber, M., Hellmann, I., Stadler, M. B., et al. (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39, 457–466.CrossRefPubMedGoogle Scholar
  7. 7.
    Zilberman, D., Gehring, M., Tran, R. K., et al. (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39, 61–69.CrossRefPubMedGoogle Scholar
  8. 8.
    Keshet, I., Schlesinger, Y., Farkash, S., et al. (2006) Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet 38, 149–153.CrossRefPubMedGoogle Scholar
  9. 9.
    The EPIGENOME Network of Excellence (2007) Whole genome amplification protocol for ChIP–chip (PROT30). (Accessed at http://www.epigenome-noe.net/ researchtools/pdfs/p30.pdf.)

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Fabio Mohn
    • 1
  • Michael Weber
    • 1
  • Dirk Schübeler
    • 1
  • Tim-Christoph Roloff
    • 1
  1. 1.Friedrich Miescher Institute for Biomedical ResearchSwitzerland

Personalised recommendations