RNA表观遗传调控的进化

In the last years, our knowledge of RNA modification, such as Adenosine-to-inosine (A-to-I) RNA editing, RNA methylation and RNA pseudouridylation, has noticeably expanded. However, little is known about the evolutionary pattern of such RNA epigenetic regulation. In this project, we propose to study the adaptive roles of such molecular processes, using A-to-I RNA editing as an example. A-to-I RNA editing, catalysed by adenosine deaminases acting on RNA (ADAR), diversifies the transcriptome and promotes functional diversity. It is especially important in brain functions in that animal models depleted with ADAR often exhibit neuronal and behavioral phenotypes and editing events are enriched in neuronal genes. Previously, we established a pioneering framework to catalog RNA editing sites using RNA sequencing data alone. By applying this framework in different organisms, we revealed a large number of editing sites. Based on this observation, we propose to study the evolutionary pattern of A-to-I RNA editing by combining comparative genomics, functional genomics and Cas9/CRISPR genome engineering approaches, using the Drosophila genus as a model. We will examine the evolutionary pattern of RNA editing between Drosophila species. We will investigate the cis-element evolution of RNA editing events. We will identify editing sites which are subject to adaptive selection and then test their functional consequence using Cas9/CRISPR genome engineering approach. These observations together will help to reveal how evolution shapes the RNA editing landscape. The approaches established here can be adapted to other RNA modification types and may help to reveal the impact of RNA epigenetic regulation in genome evolution.

RNA修饰，包括A-to-I RNA编辑、RNA甲基化和RNA假尿嘧啶化等是生物学研究的前沿课题。但对这些RNA表观遗传调控的进化我们还知之甚少。本项目拟以A-to-I RNA编辑为例探讨这些表观遗传调控现象的进化模式。A-to-I RNA编辑是共转录水平的表观遗传调控机制，它使得一个基因序列可能产生多种不同的RNA，从而促进遗传信息在RNA水平的多样化。我们前期基于转录组定位RNA编辑位点方法的建立揭示了其在动物中的广泛性。在此基础上，我们将以黑腹果蝇不同品系以及其他相关果蝇物种为模型，利用比较基因组学、功能基因组学和基因组编辑等手段，揭示A-to-I RNA编辑的进化模式，从全基因组水平鉴定受正选择的RNA编辑位点，通过功能实验验证受正选择的RNA编辑位点的适应性功能。通过这些研究，最终促进我们对RNA编辑这一基因调控机制的进化机制的认识，揭示基因调控在适应性表型分化中的重要性。

申请者在本项目中致力于RNA表观遗传修饰的进化研究。项目开展以来取得的主要学术进展有3项：（1）以13个果蝇物种为模式生物，我们系统的揭示了基因组的顺式调控元件进化如何介导mRNA A-to-I编辑位点的起源、丢失和维持。（2）我们发现miRNA编辑在人类的多种组织中普遍存在，而在小鼠和果蝇中高水平的RNA编辑只发生在神经组织中。人类神经和非神经组织中被编辑的miRNA分别获得了两组不同的新靶基因，这些靶基因分别与认知和多种器官发育功能密切相关，暗示着miRNA的RNA编辑可能进化出人类特异的调控非神经类组织器官发育的新功能。(3)我们发现m5C位点在人和老鼠之间并不保守，说明m5C在物种间的进化主要受顺式调控的影响。申请者以共同通讯或通讯作者在PLOS Genetics，Genome Research，Nature Structural & Molecular Biology发表论文3篇。研究成果被Science，Nature Structural & Molecular Biology撰文推荐。在执行的三年间，已完成当初制定的各项目标，在本项目支持下，本研究团队共发表学术论文3篇，培养3名博士、3名硕士研究生和1名专职科研人员。我们的研究成果为接下来系统研究RNA表观遗传修饰进化的具体分子调控机制打下了坚实的基础。