Agorio Astrid, Durand Stéphanie, Fiume Elisa, Brousse Cécile, Gy Isabelle, Simon Matthieu, Anava Sarit, Rechavi Oded, Loudet Olivier, Camilleri Christine, Bouché Nicolas
Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
PLoS Genet. 2017 Jan 6;13(1):e1006551. doi: 10.1371/journal.pgen.1006551. eCollection 2017 Jan.
The extent of epigenetic variation is currently well documented, but the number of natural epialleles described so far remains very limited. Determining the relevance of epigenetic changes for natural variation is an important question of research that we investigate by isolating natural epialleles segregating in Arabidopsis recombinant populations. We previously described a genetic incompatibility among Arabidopsis strains based on the silencing of a gene involved in fitness. Here, we isolated a new epiallele resulting from the silencing of a transfer-RNA editing gene in an Arabidopsis accession from the Netherlands (Nok-1). Crosses with the reference accession Col-0 show a complete incompatibility between this epiallele and another locus localized on a different chromosome. We demonstrate that conversion of an unmethylated version of this allele occurs in hybrids, associated with modifications of small RNA populations. These epialleles can also spontaneously revert within the population. Furthermore, we bring evidence that neither METHYLTRANSFERASE 1, maintaining methylation at CGs, nor components of RNA-directed DNA methylation, are key factors for the transmission of the epiallele over generations. This depends only on the self-reinforcing loop between CHROMOMETHYLASE 3 and KRYPTONITE, involving DNA methylated in the CHG context and histone H3 lysine 9 methylation. Our findings reveal a predominant role of this loop in maintaining a natural epiallele.
目前，表观遗传变异的程度已有充分记录，但迄今为止所描述的天然表观等位基因数量仍然非常有限。确定表观遗传变化与自然变异的相关性是一个重要的研究问题，我们通过分离拟南芥重组群体中分离的天然表观等位基因来进行研究。我们之前描述了基于一个与适应性相关基因的沉默而导致的拟南芥品系间的遗传不相容性。在这里，我们从荷兰的一个拟南芥种质（Nok-1）中分离出一个由转运RNA编辑基因沉默产生的新表观等位基因。与参考种质Col-0杂交显示，该表观等位基因与位于不同染色体上的另一个位点之间完全不相容。我们证明，该等位基因的未甲基化版本在杂种中发生转换，这与小RNA群体的修饰有关。这些表观等位基因在群体中也能自发回复。此外，我们证明，维持CG位点甲基化的甲基转移酶1和RNA指导的DNA甲基化的组分都不是该表观等位基因世代传递的关键因素。这仅取决于染色质甲基转移酶3和氪石之间的自我强化环，该环涉及CHG背景下的DNA甲基化和组蛋白H3赖氨酸9甲基化。我们的研究结果揭示了这个环在维持天然表观等位基因方面的主要作用。
