Comparative analysis of the Illumina Mouse Methylation BeadChip and Reduced Representation Bisulphite Sequencing for routine DNA methylation analysis of murine samples

Summary

Researching the murine epigenome in disease models has been hampered by the lack of an appropriate and cost-effective DNA methylation array. Here, we performed a comprehensive, comparative analysis between the new Mouse Methylation BeadChip (MMB) and reduced representation bisulphite sequencing (RRBS) in two murine models of colorectal carcinogenesis, providing insight into the utility to each platforms in a real world environment.

In this resource article, we evaluate critically appraise the coverage, variability, ability to differential DNA methylation of both RRBS and MMB. We show that MMB is an effective tool for profiling the murine methylome that performs comparably to RRBS, identifying similar differentially methylated pathways. We provide insights into the relative strengths and weaknesses of each approach. Choice of technology is experiment dependent and will be predicated on the underlying biology being probed.

Motivation

Array-based platforms have been used extensively to evaluate human DNA methylation, however DNA methylation profiling of model systems has been limited to next generation sequencing based approaches. The commercial release of a murine DNA methylation array is of interest to the epigenetics community, however the performance of this platform versus existing sequencing based methodologies had not previously been evaluated. In this resource article, we attempt to provide insight into the performance of the MMB in a real-world setting.