Data from: Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could contribute to observed parent-of-origin effects on seed development. We investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three Arabidopsis strains with diverse seed phenotypes. The majority of imprinted genes were parentally biased in the same manner among all strains. However, we identified several examples of allele-specific imprinting correlated with intraspecific epigenetic variation at a TE. We successfully predicted imprinting in additional strains based on methylation variability. We conclude that there is standing variation in imprinting even in recently diverged genotypes due to intraspecific epiallelic variation. Our data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds.植物种子发育过程中会发生印记基因（imprinted gene）的表达现象，该过程与亲本等位基因的差异DNA甲基化紧密相关，尤其在近端转座因子（transposable elements，TEs）区域更为显著。印记变异可能对已观测到的亲本起源效应介导的种子发育过程产生影响。我们针对3株具有多样化种子表型的拟南芥菌株，开展了印记的种内变异研究，并同步进行DNA甲基化与小RNA分析。多数印记基因在所有受试菌株中均呈现出一致的亲本偏好性表达模式，但我们仍鉴定出多例等位基因特异性印记现象，其与转座因子区域的种内表观遗传变异存在相关性。我们基于甲基化变异特征，成功预测了其余菌株中的印记现象。我们得出结论：即便在近期分化的基因型类群中，也存在因种内表观等位基因变异导致的印记现存变异。本研究数据证实，表观等位基因变异与基因组印记（genomic imprinting）相互作用，可在种子中催生全新的基因表达模式。