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Targeted DNA Methylation Analysis Methods

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Epigenetics and Gene Expression in Cancer, Inflammatory and Immune Diseases

Part of the book series: Methods in Pharmacology and Toxicology ((MIPT))

Abstract

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.

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Abbreviations

dsDNA:

double-stranded DNA

FFPE :

Formalin-fixed paraffin-embedded tissue

GWAS:

Genome-Wide Association Study

MeDIP:

methylated DNA immunoprecipitation

RRBS:

Reduced representation bisulfite sequencing

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Acknowledgments

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

Author information

Authors and Affiliations

  1. Department of Pharmacology and Therapeutics, McGill University Medical School, McIntyre Medical Building, 3655 Prom. Sir-William-Osler, Montreal, QC, Canada, H3G 1Y6

    David Cheishvili & Moshe Szyf

  2. Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden

    Sophie Petropoulos

  3. Department of Biomedicine, Aarhus University, Aarhus, Denmark

    Steffan Christiansen

Authors
  1. David Cheishvili
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  2. Sophie Petropoulos
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  3. Steffan Christiansen
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  4. Moshe Szyf
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Editor information

Editors and Affiliations

  1. Department of Nutrition Science, Purdue University, West Lafayette, Indiana, USA

    Barbara Stefanska

  2. Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine University of Liverpool, Liverpool, United Kingdom

    David J. MacEwan

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Cheishvili, D., Petropoulos, S., Christiansen, S., Szyf, M. (2017). Targeted DNA Methylation Analysis Methods. In: Stefanska, B., MacEwan, D. (eds) Epigenetics and Gene Expression in Cancer, Inflammatory and Immune Diseases. Methods in Pharmacology and Toxicology. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6743-8_3

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  • DOI: https://doi.org/10.1007/978-1-4939-6743-8_3

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6741-4

  • Online ISBN: 978-1-4939-6743-8

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