Data_Sheet_3_Diversity of Fungal DNA Methyltransferases and Their Association With DNA Methylation Patterns.docx

DNA methyltransferases (DNMTs) are a group of proteins that catalyze DNA methylation by transferring a methyl group to DNA. The genetic variation in DNMTs results in differential DNA methylation patterns associated with various biological processes. In fungal species, DNMTs and their DNA methylation profiles were found to be very diverse and have gained many research interests. We reviewed fungal DNMTs in terms of their biological functions, protein domain structures, and their associated epigenetic regulations compared to those known in plant and animal systems. In addition, we summarized recent reports on potential RNA-directed DNA methylation (RdDM) related to DNMT5 in fungi. We surveyed up to 40 fungal species with published genome-wide DNA methylation profiles (methylomes) and presented the associations between the specific patterns of fungal DNA methylation and their DNMTs based on a phylogenetic tree of protein domain structures. For example, the main DNMTs in Basidiomycota, DNMT1 with RFD domain + DNMT5, contributing to CG methylation preference, were distinct from RID + Dim-2 in Ascomycota, resulting in a non-CG methylation preference. Lastly, we revealed that the dynamic methylation involved in fungal life stage changes was particularly low in mycelium and DNA methylation was preferentially located in transposable elements (TEs). This review comprehensively discussed fungal DNMTs and methylomes and their connection with fungal development and taxonomy to present the diverse usages of DNA methylation in fungal genomes.

DNA甲基转移酶（DNA methyltransferases，DNMTs）是一类能够通过向DNA转移甲基基团来催化DNA甲基化的蛋白质。DNMTs的遗传变异会导致差异化的DNA甲基化模式，这类模式与多种生物学过程相关联。在真菌物种中，DNMTs及其DNA甲基化谱呈现出高度多样性，因此受到了大量研究关注。本综述对比植物与动物系统中已探明的DNMTs相关研究，从生物学功能、蛋白质结构域特征以及相关表观遗传调控机制等方面对真菌DNMTs进行了梳理总结。此外，我们还汇总了近期关于真菌中与DNMT5相关的潜在RNA介导的DNA甲基化（RNA-directed DNA methylation，RdDM）的研究报道。我们检索了多达40个已发布全基因组DNA甲基化谱（甲基化组，methylomes）的真菌物种，并基于蛋白质结构域的系统发育树，阐述了真菌特异性DNA甲基化模式与其DNMTs之间的关联。例如，担子菌门（Basidiomycota）中的核心DNMTs为携带RFD结构域的DNMT1与DNMT5，二者共同介导CG甲基化偏好性；而子囊菌门（Ascomycota）中的核心DNMTs则为RID与Dim-2，其介导的甲基化偏好性为非CG甲基化，二者特征截然不同。最后，我们揭示了参与真菌生命周期阶段变化的动态甲基化在菌丝体（mycelium）中水平普遍较低，且DNA甲基化主要富集于转座元件（transposable elements，TEs）中。本综述全面探讨了真菌DNMTs与甲基化组，及其与真菌发育与分类学的关联，以此阐明DNA甲基化在真菌基因组中的多样调控功能。