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，小鼠甲基化组（methylome）的研究仍局限于基于测序的技术手段。本研究针对无毛小鼠表皮的全基因组DNA甲基化水平，分别采用Illumina公司新近推出的Infinium小鼠甲基化芯片（Infinium Mouse Methylation BeadChip）与全基因组亚硫酸氢盐测序（whole genome bisulphite sequencing, WGBS）两种方法开展对比分析。同时，本研究通过设置新鲜表皮与新鲜冷冻表皮两组对照，探究了样本储存条件对检测结果的影响。本研究对比了两种方法均覆盖的123,851个CpG位点的DNA甲基化水平。结果显示，WGBS与该芯片所得的DNA甲基化水平呈现极强相关性（皮尔逊相关系数r=0.984）。本研究在WGBS甲基化分析中设置了15条reads的比对阈值；即便将阈值下调至10条reads，两种方法所得的DNA甲基化水平仍无显著差异。无论是通过Infinium小鼠甲基化芯片（r=0.999）还是WGBS（r=0.994）分析，新鲜样本与新鲜冷冻样本的DNA甲基化水平均呈现极强相关性。本研究结论表明，两种分析方法在小鼠表皮DNA甲基化研究中整体表现相当；同时证实，新鲜表皮与新鲜冷冻表皮在该类研究中同样适用。具体方法的选择则需根据研究的特定目标以及实验室可用资源而定。