Targeted DNA Methylation Analysis Methods

  • David Cheishvili
  • Sophie Petropoulos
  • Steffan Christiansen
  • Moshe Szyf
Part of the Methods in Pharmacology and Toxicology book series (MIPT)


DNA methylation is an important enzymatic covalent modification of DNA that plays an important role in genome regulation. DNA methylation patterns are fashioned during development and could be altered in response to experience and exposure. Aberrations in DNA methylation patterns are noted in cancer and other diseases. It is therefore extremely important to accurately quantify DNA methylation states for studying physiology and disease as well as for using DNA methylation markers in diagnosis. Here, we review the most commonly used methods for quantifying DNA methylation states of single genes: Pyrosequencing, Quantitative Methylated DNA Immunoprecipitation (qMeDIP), and methylation-sensitive high resolution melting (MS-HRM). Each method is described and required steps are detailed. We also discuss the advantages and disadvantages of the different methods.

Key words

DNA methylation Sodium bisulfite Quantitative Methylated DNA Immunoprecipitation (qMeDIP) Methylation-sensitive high resolution melting (MS-HRM) Pyrosequencing 



double-stranded DNA


Formalin-fixed paraffin-embedded tissue


Genome-Wide Association Study


methylated DNA immunoprecipitation


Reduced representation bisulfite sequencing



D.C. is supported by fellowship from the Israel Cancer Research Foundation. S.P. is supported by the Mats Sundin Fellowship in Developmental Health.


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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • David Cheishvili
    • 1
  • Sophie Petropoulos
    • 2
  • Steffan Christiansen
    • 3
  • Moshe Szyf
    • 1
  1. 1.Department of Pharmacology and TherapeuticsMcGill University Medical SchoolMontrealCanada
  2. 2.Department of Clinical Science, Intervention and Technology (CLINTEC)Karolinska InstitutetStockholmSweden
  3. 3.Department of BiomedicineAarhus UniversityAarhusDenmark

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