Oral Biology pp 249-277 | Cite as

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

  • Aniruddha ChatterjeeEmail author
  • Euan J. Rodger
  • Ian M. Morison
  • Michael R. Eccles
  • Peter A. Stockwell
Part of the Methods in Molecular Biology book series (MIMB, volume 1537)


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.

Key words

Epigenetics DNA methylation Bisulfite sequencing RRBS WGBS 450K Next-generation DNA sequencing CpG island Differential methylation Alignment 



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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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Aniruddha Chatterjee
    • 1
    • 2
    Email author
  • Euan J. Rodger
    • 1
  • Ian M. Morison
    • 1
    • 2
  • Michael R. Eccles
    • 1
    • 4
  • Peter A. Stockwell
    • 3
  1. 1.Department of Pathology, Dunedin School of MedicineUniversity of OtagoDunedinNew Zealand
  2. 2.Gravida: National Centre for Growth and DevelopmentUniversity of AucklandGraftonNew Zealand
  3. 3.Department of BiochemistryUniversity of OtagoDunedinNew Zealand
  4. 4.Maurice Wilkins Centre forMolecular BiodiscoveryAucklandNew Zealand

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