School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia.
National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
Nat Plants. 2024 May;10(5):749-759. doi: 10.1038/s41477-024-01672-5. Epub 2024 Apr 19.
Epigenetic gene silencing induced by expanded repeats can cause diverse phenotypes ranging from severe growth defects in plants to genetic diseases such as Friedreich's ataxia in humans. The molecular mechanisms underlying repeat expansion-induced epigenetic silencing remain largely unknown. Using a plant model with a temperature-sensitive phenotype, we have previously shown that expanded repeats can induce small RNAs, which in turn can lead to epigenetic silencing through the RNA-dependent DNA methylation pathway. Here, using a genetic suppressor screen and yeast two-hybrid assays, we identified novel components required for epigenetic silencing caused by expanded repeats. We show that FOURTH ULP GENE CLASS 1 (FUG1)-an uncharacterized SUMO protease with no known role in gene silencing-is required for epigenetic silencing caused by expanded repeats. In addition, we demonstrate that FUG1 physically interacts with ALFIN-LIKE 3 (AL3)-a histone reader that is known to bind to active histone mark H3K4me. Loss of function of AL3 abolishes epigenetic silencing caused by expanded repeats. AL3 physically interacts with the chromodomain protein LIKE HETEROCHROMATIN 1 (LHP1)-known to be associated with the spread of the repressive histone mark H3K27me to cause repeat expansion-induced epigenetic silencing. Loss of any of these components suppresses repeat expansion-associated phenotypes coupled with an increase in IIL1 expression with the reversal of gene silencing and associated change in epigenetic marks. Our findings suggest that the FUG1-AL3-LHP1 module is essential to confer repeat expansion-associated epigenetic silencing and highlight the importance of post-translational modifiers and histone readers in epigenetic silencing.
扩展重复引起的表观基因沉默可导致多种表型，从植物的严重生长缺陷到人类的弗里德里希共济失调等遗传疾病。重复扩展诱导的表观遗传沉默的分子机制在很大程度上尚不清楚。使用具有温度敏感表型的植物模型，我们之前已经表明，扩展重复可以诱导小 RNA，小 RNA 可以通过 RNA 依赖性 DNA 甲基化途径导致表观遗传沉默。在这里，我们使用遗传抑制剂筛选和酵母双杂交测定，鉴定了由扩展重复引起的表观遗传沉默所必需的新组件。我们表明，未被表征的 SUMO 蛋白酶 FOURTH ULP GENE CLASS 1（FUG1）——在基因沉默中没有已知作用的蛋白酶——是由扩展重复引起的表观遗传沉默所必需的。此外，我们证明 FUG1 与 ALFIN-LIKE 3（AL3）相互作用，AL3 是一种已知与活性组蛋白标记 H3K4me 结合的组蛋白阅读器。AL3 的功能丧失会导致扩展重复引起的表观遗传沉默。AL3 与染色质域蛋白 LIKE HETEROCHROMATIN 1（LHP1）相互作用，已知 LHP1 与抑制性组蛋白标记 H3K27me 的扩散有关，导致重复扩展诱导的表观遗传沉默。这些组件中的任何一个的缺失都抑制了与重复扩展相关的表型，同时增加了 IIL1 的表达，导致基因沉默的逆转和表观遗传标记的相关变化。我们的研究结果表明，FUG1-AL3-LHP1 模块对于赋予重复扩展相关的表观遗传沉默是必不可少的，并强调了翻译后修饰因子和组蛋白阅读器在表观遗传沉默中的重要性。
