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.