Efficiency of Methylated DNA Immunoprecipitation Bisulphite Sequencing for Whole-Genome DNA Methylation Analysis

Abstract

Aims: We compared four common methods for measuring DNA methylation levels and recommended the most efficient method in terms of cost and coverage. Materials & methods: The DNA methylation status of liver and stomach tissues was profiled using four different methods, whole-genome bisulphite sequencing (WG-BS), targeted bisulphite sequencing (Targeted-BS), methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA immunoprecipitation bisulphite sequencing (MeDIP-BS). We calculated DNA methylation levels using each method and compared the results. Results: MeDIP-BS yielded the most similar DNA methylation profile to WG-BS, with 20 times less data, suggesting remarkable cost savings and coverage efficiency compared with the other methods. Conclusion: MeDIP-BS is a practical cost-effective method for analyzing whole-genome DNA methylation that is highly accurate at base-pair resolution.

Keywords::

• DNA methylation analysis
• methylated DNA immunoprecipitation-bisulphite sequencing
• next-generation sequencing

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at:www.tandfonline.com/doi/full/10.2217/epi-2016-0038

Acknowledgements

The authors thank Seong Beom Cho for his support and discussion of the data.

Financial & competing interests disclosure

This research was supported by a fund (2014-E72002–00 [Yoon-La Choi]) by Research of Korea Centers for Disease Control and Prevention, and the Bio & Medical Technology Development Program of the National Research Foundation (NRF) (2012M3A9D1054622 [S Kim]), R&D Program for Society of the NRF (2013M3C8A1079312 [YK Shin]) funded by the Ministry of Science, ICT & Future Planning. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

Writing and editing assistance were provided by Editage (https://www.editage.com).

Ethical conduct of research

The authors state that they have obtained appropriate institutional review board approval or have followed the principles outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Additional information

Funding

This research was supported by a fund (2014-E72002–00 [Yoon-La Choi]) by Research of Korea Centers for Disease Control and Prevention, and the Bio & Medical Technology Development Program of the National Research Foundation (NRF) (2012M3A9D1054622 [S Kim]), R&D Program for Society of the NRF (2013M3C8A1079312 [YK Shin]) funded by the Ministry of Science, ICT & Future Planning. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. Writing and editing assistance were provided by Editage (https://www.editage.com).