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Tools and Strategies for Analysis of Genome-Wide and Gene-Specific DNA Methylation Patterns

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Oral Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1537))

Abstract

DNA methylation is a stable epigenetic mechanism that has important roles in the normal function of a cell and therefore also in disease etiology. Accurate measurements of normal and altered DNA methylation patterns are important to understand its role in regulating gene expression and cell phenotype. Remarkable progress has been made over the last decade in developing methodologies to investigate DNA methylation. The availability of next-generation sequencing has enabled the profiling of methylation marks at an unprecedented scale. Several methods that were previously used to profile locus-specific methylation have now been upgraded to a genome-wide scale using high-throughput sequencing or array platforms. However, because there are so many techniques available, researchers are faced with the challenge of assessing the potential merits or limitations of each technique and selecting the appropriate method for their analysis. In this review we discuss the strengths and weaknesses of genome-wide and gene-specific analysis tools for interrogating DNA methylation. We particularly focus on the design and analysis strategies involved. This review will provide a guideline for selecting the appropriate methods and tools for large-scale and locus-specific DNA methylation analysis.

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Acknowledgments

AC and MRE would like to thank New Zealand Institute for Cancer Research Trust, and IM would like to thank Gravida (formerly NRCGD) for their support. We would like to apologize to other research groups whose work we could not cite due to context and space limitations.

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Authors and Affiliations

  1. Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand

    Aniruddha Chatterjee, Euan J. Rodger, Ian M. Morison & Michael R. Eccles

  2. Gravida: National Centre for Growth and Development, University of Auckland, 85 Park Road, Grafton, Auckland, New Zealand

    Aniruddha Chatterjee & Ian M. Morison

  3. Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin, 9054, New Zealand

    Peter A. Stockwell

  4. Maurice Wilkins Centre forMolecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand

    Michael R. Eccles

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  1. Aniruddha Chatterjee
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  2. Euan J. Rodger
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Correspondence to Aniruddha Chatterjee .

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  1. University of Otago Fac. Dentistry, Dunedin, New Zealand

    Gregory J. Seymour

  2. Department of Oral Sciences, University of Otago Faculty of Dentistry, Dunedin, New Zealand

    Mary P. Cullinan

  3. Sir John Walsh Research Institute, University of Otago Faculty of Dentistry, Dunedin, New Zealand

    Nicholas C.K. Heng

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Chatterjee, A., Rodger, E.J., Morison, I.M., Eccles, M.R., Stockwell, P.A. (2017). Tools and Strategies for Analysis of Genome-Wide and Gene-Specific DNA Methylation Patterns. In: Seymour, G., Cullinan, M., Heng, N. (eds) Oral Biology. Methods in Molecular Biology, vol 1537. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6685-1_15

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  • DOI: https://doi.org/10.1007/978-1-4939-6685-1_15

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6683-7

  • Online ISBN: 978-1-4939-6685-1

  • eBook Packages: Springer Protocols

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