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.
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References
Fazzari, M. J., Greally, J. M. (2004) Epigenomics: beyond CpG islands. Nat Rev Genet 5, 446–455.
Weber, M. Schübeler, D. (2007) Genomic patterns of DNA methylation: targets and function of an epigenetic mark. Curr Opin Cell Biol 19, 273–280.
Zilberman, D., Henikoff, S. (2007) Genome-wide analysis of DNA methylation patterns. Development 134, 3959–3965.
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.
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.
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.
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.
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.
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.)
Acknowledgements
The authors would like to thank the members of the Schübeler lab for helpful comments on the protocol.
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© 2009 Humana Press, a part of Springer Science+Business Media, LLC
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Mohn, F., Weber, M., Schübeler, D., Roloff, TC. (2009). Methylated DNA Immunoprecipitation (MeDIP). In: Tost, J. (eds) DNA Methylation. Methods in Molecular Biology, vol 507. Humana Press. https://doi.org/10.1007/978-1-59745-522-0_5
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DOI: https://doi.org/10.1007/978-1-59745-522-0_5
Publisher Name: Humana Press
Print ISBN: 978-1-934115-61-9
Online ISBN: 978-1-59745-522-0
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