Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: small RNA-seq profiling in Arabidopsis thaliana Col, Ler, and Cvi parental and reciprocal F1 hybrid seeds. Arabidopsis thaliana

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. These data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds. Overall design: Sequencing of 12 small RNA samples from whole seeds 6 days after pollination.

植物种子发育过程中可发生印记基因（imprinted gene）表达，该过程与亲本等位基因（parental alleles）的差异化DNA甲基化（DNA methylation）显著相关，尤其在近端转座元件（transposable elements, TEs）区域。印记变异或可导致已观测到的亲本起源效应（parent-of-origin effects）对种子发育产生影响。本研究针对三种具有多样化种子表型的拟南芥（Arabidopsis）株系，探究了印记现象的种内变异（intraspecific variation），并结合DNA甲基化与小RNA（small RNAs）分析展开研究。绝大多数印记基因在所有供试株系中均表现出一致的亲本表达偏向性，但本研究鉴定出多例等位基因特异性印记现象，其与转座元件区域的种内表观遗传变异存在关联。我们基于甲基化变异特征，成功预测了其他株系中的印记现象。研究结论表明，即使在近期分化的基因型中，印记现象也存在固有变异，该变异源于种内表观等位基因（epiallele）变异。本研究数据证实，表观等位基因变异与基因组印记相互作用，进而在种子中产生全新的基因表达模式。实验设计概览：对授粉后6天的完整种子样本进行12份小RNA测序。