A variably imprinted epiallele impacts seed development

First author: Daniela Pignatta; Affiliations: Whitehead Institute for Biomedical Research (怀特黑德生物医学研究所): Cambridge, USA

Corresponding author: Mary Gehring 

The contribution of epigenetic variation to phenotypic variation is unclear. Imprinted genes, because of their strong association with epigenetic modifications, represent an opportunity for the discovery of such phenomena. In mammals and flowering plants, a subset of genes are expressed from only one parental allele in a process called gene imprinting. Imprinting is associated with differential DNA methylation and chromatin modifications between parental alleles. In flowering plants imprinting occurs in a seed tissue-endosperm. Proper endosperm development is essential for the production of viable (能养活的) seeds. We previously showed that in Arabidopsis thaliana intraspecific imprinting variation is correlated with naturally occurring DNA methylation polymorphisms. Here, we investigated the mechanisms and function of allele-specific imprinting of the class IV homeodomain-Leucine zipper (HD-ZIP) transcription factor HDG3. In imprinted strains, HDG3 is expressed primarily from the methylated paternally inherited allele. We manipulated the methylation state of endogenous HDG3 in a non-imprinted strain and demonstrated that methylation of a proximal transposable element is sufficient to promote HDG3 expression and imprinting. Gain of HDG3 imprinting was associated with earlier endosperm cellularization and changes in seed weight. These results indicate that epigenetic variation alone is sufficient to explain imprinting variation and demonstrate that epialleles (表观等位基因) can underlie variation in seed development phenotypes.

表观变异对于表型变异的贡献还不清楚。印记基因，由于其与表观修饰强烈相关，因而能够用以研究表观变异作用于表型变异。在哺乳动物和有花植物中，一类在某个生物学过程中只表达来自亲本一方等位基因的现象叫做基因印记。印记与亲本等位基因间不同程度的DNA甲基化和染色质修饰有关。在有花植物中，基因印记发生于种子的胚乳组织中。正确的胚乳发育对于种子的成活是非常重要的。作者先前的研究显示拟南芥种内基因印记变异与自然发生的DNA甲基化多态性相关。本文中，作者进一步研究了IV类HD-ZIP转录因子HDG3基因的等位基因特异性印记的机制和功能。在印记株系中，HDG3基因主要表达自甲基化的、遗传于父本的等位基因。作者手动修饰了一个非印记株系中的HDG3基因的甲基化状态，结果显示HDG3基因附近的一个转座元件的甲基化有助于促进HDG3基因的表达和印记。HDG3基因印记与胚乳更早细胞化及种子重量的改变相关。本文的研究结果揭示了表观变异足以解释印记变异，并显示表观等位基因可作用于种子发育表型的变异。

p.s. 表观等位基因（epialleles）：即表观遗传等位基因，是指DNA序列相同、但DNA甲基化模式却不同的等位基因。

通讯：Mary Gehring  (https://biology.mit.edu/profile/mary-gehring/)

个人简介：2005年，美国加利福尼亚大学伯克利分校，博士。

研究方向：植物表观遗传学。

doi: https://doi.org/10.1371/journal.pgen.1007469

Journal: PLOS Genetics

Published date: 05 November, 2018

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