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Review
. 2016 Jan 6;5(1):3.
doi: 10.3390/biology5010003.

DNA Methylation Analysis: Choosing the Right Method

Sergey Kurdyukov  1 , Martyn Bullock  2
Affiliations
Review

DNA Methylation Analysis: Choosing the Right Method

Sergey Kurdyukov et al. Biology (Basel). .

Abstract

In the burgeoning field of epigenetics, there are several methods available to determine the methylation status of DNA samples. However, choosing the method that is best suited to answering a particular biological question still proves to be a difficult task. This review aims to provide biologists, particularly those new to the field of epigenetics, with a simple algorithm to help guide them in the selection of the most appropriate assay to meet their research needs. First of all, we have separated all methods into two categories: those that are used for: (1) the discovery of unknown epigenetic changes; and (2) the assessment of DNA methylation within particular regulatory regions/genes of interest. The techniques are then scrutinized and ranked according to their robustness, high throughput capabilities and cost. This review includes the majority of methods available to date, but with a particular focus on commercially available kits or other simple and straightforward solutions that have proven to be useful.

Keywords: 5-methylcytosine; CpG islands; DNA methylation; epigenetics; next generation sequencing.

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Figures

Figure 1
Figure 1
Algorithm for choosing a suitable method for DNA methylation analysis.
Figure 2
Figure 2
An example of how the algorithm can be applied.
Figure 3
Figure 3
Scheme of the methyl-sensitive cut counting technique for elucidation of DNA methylation status for a particular gene of interest.
Figure 4
Figure 4
Typical presentation of the results for DNA methylation after bisulfite sequencing. The PCR product is cloned, and several randomly-selected plasmids are sequenced.
See this image and copyright information in PMC

References

    1. Olkhov-Mitsel E., Bapat B. Strategies for discovery and validation of methylated and hydroxymethylated DNA biomarkers. Cancer Med. 2012;1:237–260. doi: 10.1002/cam4.22. - DOI - PMC - PubMed
    1. Sant K.E., Nahar M.S., Dolinoy D.C. DNA methylation screening and analysis. Methods Mol. Biol. 2012;889:385–406. - PMC - PubMed
    1. Hsu H.K., Weng Y.I., Hsu P.Y., Huang T.H., Huang Y.W. Detection of DNA methylation by medip and mbdcap assays: An overview of techniques. Methods Mol. Biol. 2014;1105:61–70. - PubMed
    1. Hernandez H.G., Tse M.Y., Pang S.C., Arboleda H., Forero D.A. Optimizing methodologies for pcr-based DNA methylation analysis. BioTechniques. 2013;55:181–197. - PubMed
    1. Sun Z., Cunningham J., Slager S., Kocher J.P. Base resolution methylome profiling: Considerations in platform selection, data preprocessing and analysis. Epigenomics. 2015;7:813–828. doi: 10.2217/epi.15.21. - DOI - PMC - PubMed