Failure to maintain DNA methylation patterns during plant development can occasionally give rise to so-called “spontaneous epimutations”. These stochastic methylation changes are sometimes heritable across generations and thus accumulate in plant genomes over time. Recent evidence indicates that spontaneous epimutations have a major role in shaping patterns of methylation diversity in plant populations. Using single CG dinucleotides as units of analysis, previous work has shown that the epimutation rate is several orders of magnitude higher than the genetic mutation rate. While these large rate differences have obvious implications for understanding genome-methylome co-evolution, the functional relevance of single CG methylation changes remains questionable. In contrast to single CG, solid experimental evidence has linked methylation gains and losses in larger genomic regions with transcriptional variation and heritable phenotypic effects. Here we show that such region-level changes arise stochastically at about the same rate as those at individual CG sites, are only marginal dependent on region size and cytosine density, but strongly dependent on chromosomal location. We also find consistent evidence that region-level epimutations are not restricted to CG contexts but also frequently occur in non-CG regions at the genome-wide scale. Taken together, our results support the view that many differentially methylated regions (DMRs) in natural populations originate from epimutation events and may not be effectively tagged by proximal SNPs. This possibility reinforces the need for epigenome-wide association studies (EWAS) in plants as a way to identify the epigenetic basis of complex traits.

在植物发育过程中未能保持 DNA 甲基化模式有时会导致所谓的“自发表观突变”。这些随机甲基化变化有时可以跨代遗传，因此随着时间的推移在植物基因组中积累。最近的证据表明，自发表观突变在塑造植物种群甲基化多样性模式方面具有重要作用。使用单个 CG 二核苷酸作为分析单位，先前的工作表明表观突变率比基因突变率高几个数量级。虽然这些巨大的速率差异对于理解基因组-甲基化组共同进化具有明显的意义，但单个 CG 甲基化变化的功能相关性仍然值得怀疑。与单一的CG相比，可靠的实验证据已将较大基因组区域的甲基化得失与转录变异和可遗传的表型效应联系起来。在这里，我们表明这种区域水平的变化以与单个 CG 位点的变化率大致相同的速率随机出现，仅略微依赖于区域大小和胞嘧啶密度，但强烈依赖于染色体位置。我们还发现一致的证据表明，区域级表观突变不仅限于 CG 环境，而且还经常发生在全基因组规模的非 CG 区域。总之，我们的结果支持这样一种观点，即自然种群中的许多差异甲基化区域 (DMR) 源自表观突变事件，并且可能无法被近端 SNP 有效标记。