The Design and Optimization of DNA Methylation Pyrosequencing Assays Targeting Region-Specific Repeat Elements

  • Gwen Hoad
  • Kristina HarrisonEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1589)


Epigenetic modifications, such as DNA methylation, can contribute to gene regulation and chromosomal stability. There are several methods and techniques available for methylation analysis, ranging from global methylation to gene-specific targeted regions. Bisulfite conversion enables numerous methodologies to be used for downstream applications, including pyrosequencing which measures DNA methylation at an individual CpG site level. This allows specific regions of interest to be targeted for DNA methylation analysis. Designing and optimizing pyrosequencing assays correctly is vital for the interpretation of results.

Dysregulation of DNA methylation has been implicated in human diseases, with regions such as repeat elements commonly altered. Human population studies investigating these tend to use consensus sequences to target repeat elements. However, these elements have high mutational rates, particularly Alu sequences, which could lead to assay bias and masking of changes at a regional level. Therefore, it may be more beneficial to target specific repeat elements depending upon their chromosomal location, rather than analyzing overall methylation levels.


DNA methylation Epigenetics Pyrosequencing Bisulfite conversion CpGs Bisulfite sequencing 


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Natural Products Group, Rowett Institute of Nutrition and HealthUniversity of AberdeenAberdeenUK

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