Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

Heritable epigenetic polymorphisms, such as differential cytosine methylation, can underlie phenotypic variation. Moreover, wild strains of the plant Arabidopsis thaliana differ in many epialleles3,4, and these can influence the expression of nearby genes. However, to understand their role in evolution, it is imperative to ascertain the emergence rate and stability of epialleles, including those that are not due to structural variation. We have compared genome-wide DNA methylation among 10 A. thaliana lines, derived 30 generations ago from a common ancestor. Epimutations at individual positions were easily detected, and close to 30,000 cytosines in each strain were differentially methylated. In contrast, larger regions of contiguous methylation were much more stable, and the frequency of changes was in the same low range as that of DNA mutations. Like individual positions, the same regions were often affected by differential methylation in independent lines, with evidence for recurrent cycles of forward and reverse mutations. Transposable elements (TEs) and short interfering RNAs (siRNAs) have been causally linked to DNA methylation. In agreement, differentially methylated sites were farther from TEs and showed less association with siRNA expression than invariant positions. The biased distribution and frequent reversion of epimutations have important implications for the potential contribution of sequence-independent epialleles to plant evolution.

可遗传的表观遗传多态性（epigenetic polymorphisms），例如差异性胞嘧啶甲基化（differential cytosine methylation），可作为表型变异的分子基础。此外，模式植物拟南芥（Arabidopsis thaliana）的野生株系在诸多表观等位基因（epiallele）上存在差异3,4，且此类表观等位基因可调控邻近基因的表达。然而，若要阐明表观等位基因在演化中的作用，必须确定其出现频率与稳定性——包括那些并非由结构变异引发的表观等位基因。本研究对10个拟南芥株系开展了全基因组DNA甲基化（genome-wide DNA methylation）比对分析，这些株系均由同一祖先株系历经30代繁育所得。单个位点的表观突变（epimutation）易于被检测到，且每个株系中近3万个胞嘧啶位点呈现差异性甲基化特征。与之相反，较大的连续甲基化区域稳定性更强，其甲基化状态改变的频率与DNA突变的频率处于同一低水平区间。与单个位点的情况类似，独立株系间的相同区域常出现差异性甲基化，且存在正向与反向突变循环发生的证据。转座因子（transposable elements, TEs）与小干扰RNA（short interfering RNAs, siRNAs）已被证实与DNA甲基化存在因果关联。与之相符，相较于恒定甲基化位点，差异性甲基化位点距离转座因子更远，且与小干扰RNA表达的关联程度更低。表观突变的偏态分布与高频回复现象，对于不依赖序列的表观等位基因在植物演化中的潜在贡献具有重要启示意义。