Comparison of global DNA methylation analysis by whole genome bisulfite sequencing and the Infinium Mouse Methylation BeadChip using fresh and fresh-frozen mouse epidermis

Until recently, studying the murine methylome was restricted to sequencing-based methods. In this study we compared the global DNA methylation levels of hairless mouse epidermis using the recently released Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulphite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of 123,851 CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.999) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study’s aims and the available resources in the laboratory.

直至近期，对小鼠甲基组的探究主要限于基于测序的方法。在本研究中，我们采用Illumina近期发布的Infinium小鼠甲基化 beads芯片以及全基因组亚硫酸氢盐测序（WGBS）技术，对比了无毛小鼠表皮的全局DNA甲基化水平。此外，我们还通过使用新鲜和新鲜冷冻的表皮样本，研究了样本储存条件对DNA甲基化的影响。我们对比了由bead芯片和WGBS覆盖的123,851个CpG位点的DNA甲基化水平。WGBS和bead芯片获得的DNA甲基化水平高度相关（Pearson相关系数r = 0.984）。在WGBS甲基化分析中，我们应用了15个读数的阈值。即使在10个读数的阈值下，与bead芯片获得的结果相比，DNA甲基化水平亦未观察到显著差异。当使用bead芯片（r = 0.999）和WGBS（r = 0.994）分析新鲜和新鲜冷冻样本的DNA甲基化水平时，相关性亦极为显著。据此，我们得出结论：两种分析方法在研究小鼠表皮DNA甲基化方面通常效果相当，且发现新鲜和新鲜冷冻的表皮可以同等程度地应用于此类研究。具体方法的选择将取决于研究的具体目标和实验室可利用的资源。