Application of Microarrays for DNA Methylation Profiling

  • Axel Schumacher
  • Andreas Weinhäusl
  • Arturas Petronis
Part of the Methods in Molecular Biology™ book series (MIMB, volume 439)


Comprehensive analyses of the human epigenome may be of critical importance in understanding the molecular mechanisms of complex diseases, development, aging, tissue specificity, parental origin effects, and sex differences, among other systemic aspects of human biology. However, traditional DNA methylation methods allowed for screening of only relatively short DNA fragments. The advent of microarrays has provided new possibilities in DNA methylation analysis, because this technology is able to interrogate a very large number of loci in a highly parallel fashion. There are several permutations of the microarray application in DNA methylation profiling, and such include microarray analysis of bisulfite modified DNA and also the enriched unmethylated or hypermethylated DNA fractions using methylation-sensitive restriction enzymes or antibodies against methylated cytosines. The method described in detail here is based on the analysis of the enriched unmethylated DNA fraction, using a series of treatments with methylation-sensitive restriction enzymes, adaptor ligation, PCR amplification, and quantitative mapping of unmethylated DNA sequences using microarrays. The key advantages of this approach are the ability to investigate DNA methylation patterns using very small DNA amounts and relatively high informativeness in comparison to the other restriction-enzyme- based strategies for DNA methylation profiling [1].


DNA methylation microarrays epigenetic profiling epigenetic biomarkers whole genome approach epigenetics 



We thank Professor Bernhard Horsthemke for providing DNA samples of Prader-Willi and Angelman syndrome patients and Dr. Jon Mill and Carolyn Ptak for their critical reading of the manuscript.


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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Axel Schumacher
    • 1
  • Andreas Weinhäusl
    • 2
  • Arturas Petronis
    • 3
  1. 1.Epigenetics Lab, Department of Medicine II, Klinikum rechts der IsarTechnical University MunichMunichGermany
  2. 2.Austrian Research CenterARCSSeibersdorfAustria
  3. 3.Centre for Addiction and Mental HealthThe Krembil Family Epigenetics LaboratoryToronto, OntarioCanada

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