Profiling DNA methylation differences between inbred mouse strains on the Illumina Human Infinium MethylationEPIC microarray

The Illumina Infinium MethylationEPIC provides an efficient platform for profiling DNA methylation in humans at over 850,000 CpGs. Model organisms such as mice do not currently benefit from an equivalent array. Here we used this array to measure DNA methylation in mice. We defined probes targeting conserved regions and performed differential methylation analysis and compared between the array-based assay and affinity-based DNA sequencing of methyl-CpGs (MBD-seq) and reduced representation bisulfite sequencing. Mouse samples consisted of 11 liver DNA from two strains, C57BL/6J (B6) and DBA/2J (D2), that varied widely in age. Linear regression was applied to detect differential methylation. In total, 13,665 probes (1.6% of total probes) aligned to conserved CpGs. Beta-values (β-value) for these probes showed a distribution similar to that in humans. Overall, there was high concordance in methylation signal between the EPIC array and MBD-seq (Pearson correlation r = 0.70, p-value 0.7). In terms of differential methylation, no EPIC probe detected a significant difference between age groups at a Benjamini-Hochberg threshold of 10%, and the MBD-seq performed better at detecting age-dependent change in methylation. However, the top most significant probe for age (cg13269407; uncorrected p-value = 1.8 x 10−5) is part of the clock CpGs used to estimate the human epigenetic age. For strain, 219 EPIC probes detected significant differential methylation (FDR cutoff 10%) with ~80% CpGs associated with higher methylation in D2. This higher methylation profile in D2 compared to B6 was also replicated by the MBD-seq data. To summarize, we found only a small subset of EPIC probes that target conserved sites. However, for this small subset the array provides a reliable assay of DNA methylation and can be effectively used to measure differential methylation in mice.

Illumina Infinium甲基化EPIC阵列（Illumina Infinium MethylationEPIC）是一款高效的人类DNA甲基化图谱分析平台，可在超过85万个CpG位点上检测人类的DNA甲基化水平。目前，模式生物（如小鼠）尚无等效的同类阵列可供使用。本研究利用该阵列开展小鼠DNA甲基化水平检测：我们首先筛选靶向保守区域的探针，开展差异甲基化分析，并将该阵列检测方法与基于亲和富集的甲基化CpG DNA测序（MBD-seq）、简化代表性亚硫酸氢盐测序进行了比对。小鼠样本包含11份肝脏组织DNA，取自C57BL/6J（B6）和DBA/2J（D2）两个品系，样本年龄跨度较大。本研究采用线性回归模型检测差异甲基化位点。最终共有13665个探针（占总探针数的1.6%）可比对至保守CpG位点。这些探针的β值（β-value）分布特征与人类样本中的分布高度相似。整体而言，EPIC阵列与MBD-seq的甲基化信号具有高度一致性（Pearson相关系数r=0.70，p值=0.7）。在差异甲基化分析方面，以Benjamini-Hochberg校正阈值10%为标准，未检测到EPIC阵列探针在年龄组间存在显著差异的甲基化位点；而MBD-seq在检测甲基化水平随年龄变化的位点方面表现更优。不过，与年龄相关性最显著的探针（cg13269407；未校正p值=1.8×10^-5）属于用于估算人类表观遗传年龄的时钟CpG位点集合。在品系差异分析方面，有219个EPIC阵列探针在品系间检测到显著的差异甲基化（错误发现率（False Discovery Rate，FDR）阈值10%），其中约80%的CpG位点在D2品系中呈现更高的甲基化水平。D2品系相较于B6品系的高甲基化特征，也得到了MBD-seq数据的验证。综上，本研究发现仅存在少量可靶向保守位点的EPIC阵列探针；但针对这部分探针而言，该阵列可实现可靠的DNA甲基化检测，并可有效用于小鼠的差异甲基化分析。