Evolution of epigenetic regulation in beetles (Coleoptera)

昆虫在实现表观遗传调控的方式上表现出显着的进化灵活性。即使在甲虫类(鞘翅目)中，一些物种也依赖于CpG甲基化，而其他物种似乎没有表现出任何功能相关的CpG甲基化水平。相应地，编码DNA甲基转移酶的基因(Dnmt1和Dnmt3)在一些甲虫物种中已经部分或完全丢失(如卡氏赤眼蜂)或完全丢失(如黄皮松毛虫)。令人惊讶的是，即使在缺乏CpG甲基化的物种中，这些Dnmt基因的敲除也可以产生强烈的甚至致命的影响，这表明Dnmt具有额外的功能。另一方面，目前还不清楚，在这类物种中，哪些其他表观遗传过程可能取代了CpG甲基化。在脊椎动物中，组蛋白修饰在基因调控中起着重要作用。组蛋白修饰系统的许多核心成分甚至从动物到植物都是保守的。组蛋白修饰和DNA甲基化都是机制上相似的全球调节因子，它们都会产生沿基因组设置的标记，但在物质基础上是不同的。因此，我们的项目有以下三个主要目标：(1)了解表观遗传调控系统的进化；(2)阐明DNA甲基转移酶的替代功能；(3)评估DNA甲基化和组蛋白修饰之间的相互依赖关系。在与核心项目和该计划的其他几个拟议项目的密切合作下，我们将利用生物信息学、测序技术的组合力量来分析十种甲虫的表观遗传过程(甲基序列、切割和标签、RNAseq)和功能验证(RNAi)。因此，我们的项目解决了像表观遗传调控这样关键的东西令人惊讶的进化灵活性，将提供迫切需要的关于表观遗传调控系统进化的基本知识，甚至更普遍地，超越昆虫。

Insects show a remarkable evolutionary flexibility concerning the means by which epigenetic regulation is achieved. Even within the group of beetles (Coleoptera), some species rely on CpG methylation, while other species do not seem to show any functionally relevant levels of CpG methylation. Accordingly, genes encoding DNA methyltransferases (Dnmt1 and 3 genes) have been partially (e.g., Tribolium castaneum) or completely (e.g., Dendroctonus ponderosae) lost in some beetle species. Surprisingly, knock-down of these Dnmt genes can have strong and even lethal effects, even in species lacking CpG methylation, suggesting additional functions of DNMTs. On the other hand, it is still unclear, which other epigenetic processes could have replaced CpG methylation in such species. In vertebrates, histone modification plays a major role in gene regulation. Many core components of the histone modification system are even conserved from animals to plants. Both, histone modification and DNA methylation are global regulators that are mechanistically similar in the sense that they give rise to marks being set along the genome but distinct with respect to their material basis. However, the combined mode of control may range from the mere coexistence to indispensable and rich crosstalk.Our project thus has the following three main aims: (1) Understanding the evolution of epigenetic regulation systems; (2) Elucidating alternative functions of DNA methyltransferases; (3) Assessing the mutual dependences between DNA methylation and histone modification. In close collaboration with both Core projects and several other proposed projects of this SPP, we will make use of the combined power of bioinformatics, sequencing technology to analyse epigenetic processes (Methyl-Seq, Cut&Tag, RNAseq) and functional validation (RNAi) in ten beetle species. Our project addressing the surprising evolutionary flexibility in something as crucial as epigenetic regulation will thus provide urgently needed basic knowledge of the evolution of epigenetic regulation systems even more generally, beyond insects.