Evolutionary patterns of DNA methylation in insects

DNA methylation is an epigenetic modification that is evolutionary conserved across eukaryotes. Recent comparative studies in different eukaryotic groups have shown that the patterns of DNA methylation can substantially vary across taxa. However, the mechanisms that underlie this variability are poorly understood. To address this we analyzed a dataset comprised of 46 single-base resolution methylomes from species located at key positions on the insect phylogenetic tree. We conjectured that insects, due to preexisting knowledge on their phylogenetic relationships and their inferred diversity in DNA methylation patterns, would constitute a great model group for studying the mechanisms responsible for the evolutionary transitions between DNA methylation patterns. For example, studies have shown that holometabolous insects are characterized by sparse methylation of genes, while in many species DNA methylation is even extremely reduced or lost. Computational inferences combined with limited experimental evidence suggest that hemimetabolous insects possess substantially higher levels of DNA methylation that is targeted to the entirety of gene bodies. Thus, we aim to: 1) Characterize DNA methylation patterns across insects. 2) Reconstruct the evolutionary history of DNA methylation patterns in insects. 3) Identify mechanisms that underlie the transitions between DNA methylation patterns.

DNA甲基化（DNA methylation）是一类在真核生物（eukaryotes）中具有进化保守性的表观遗传修饰（epigenetic modification）。近期针对不同真核类群的比较研究表明，DNA甲基化模式在不同分类单元（taxa）间存在显著差异。然而，这种甲基化模式变异背后的分子机制仍未得到充分阐释。
为解决这一科学问题，本研究分析了一套包含46个单碱基分辨率甲基化组（single-base resolution methylomes）的数据集，这些数据来自昆虫系统发育树（phylogenetic tree）关键分支位置的物种。鉴于已有研究对昆虫系统发育关系的清晰认知，以及其DNA甲基化模式已被揭示的丰富多样性，我们认为昆虫是研究DNA甲基化模式进化转变机制的理想模式类群。
例如，已有研究显示全变态昆虫（holometabolous insects）的特征为基因甲基化水平较低且分布稀疏，而在许多物种中，DNA甲基化甚至会大幅降低甚至完全丢失。结合有限的实验证据进行的计算推断显示，半变态昆虫（hemimetabolous insects）的DNA甲基化水平显著更高，且甲基化位点遍布整个基因本体（gene bodies）。
据此，本研究的研究目标如下：1）系统刻画昆虫类群的DNA甲基化模式；2）重建昆虫DNA甲基化模式的进化历史；3）解析驱动DNA甲基化模式转变的分子机制。