果蝇腺嘌呤到次黄嘌呤RNA编辑的适应性进化和功能研究

Adenosine-to-inosine (A-to-I) editing is an evolutionarily conserved mechanism that participates in many biological processes in a wide range of species. In Drosophila, A-to-I editing mainly occurs in the nervous systems, and a considerable number of the editing sites are located in the protein-coding regions. We recently identified 2,114 A-to-I editing sites in the brain editomes of D. melanogaster, and 678 (32.1%) of those sites are nonsynonymous and would change the protein sequences after editing. The nonsynonymous editing sites are significantly enriched in neural genes. We detected strong signals of adaption after we contrasted the observed ratio of nonsynonymous/synonymous (N/S) editing sites to the expected N/S ratio under randomness. By deep sequencing the editomes in brains of D. simulans and D. pseudoobscura, we observed a large number of editing sites are evolutionarily conserved, and we observed even pronounced pattern of adaptation for the editing sites that are commonly observed across species. Here we propose to combine mRNA-Seq and Ribo-Seq to in-depth pursue the evolutionary principles and functional consequences of RNA editing in multiple neural tissues of D. melanogaster and seven sibling species. We are particularly interested in the following questions: 1) Can we observe different editing patterns between different neural tissues? What are the general evolutionary principles of editing across multiple Drosophila species? 2) Do RNA editing participate in stress response by increasing proteomic diversity? Is this process associated the gene expression plasticity? 3) Do the editing events in microRNAs and the 3’ UTRs of mRNAs play important roles in regulating gene expression? Resolutions of these questions will help us understand the functional sequences of RNA editing at the molecular level, and our results will also provide insights on the relationship between RNA editing and local adaptation as well as the molecular mechanism of human diseases.

A-to-I RNA编辑是动物中广泛存在的转录后修饰，具有重要生物学意义。果蝇的RNA编辑主要发生在神经系统，我们新近在黑腹果蝇大脑转录组中鉴定了2114个A-to-I编辑位点，其中678（32.1%）个潜在改变蛋白质序列。通过对近缘种拟果蝇和拟暗果蝇大脑中RNA编辑的深度测序及进化基因组学分析，我们发现非同义RNA编辑呈现非常强的正向选择信号，而且主要富集在神经功能相关的基因。在此申请中，我们将以黑腹果蝇不同群体及七个亲缘种为材料，结合转录组测序和核糖体图谱技术，对A-to-I编辑的功能和演化进行更加深入的研究：1）果蝇不同神经组织的RNA编辑组及在果蝇不同物种间的演化规律；2）RNA编辑是否通过增加蛋白质多态性参与胁迫应答；3）RNA编辑对mRNA稳定性及翻译调控的影响及作用机制。研究结果将有利于理解RNA编辑和生物体对环境适应的关系，且为RNA编辑可能导致人类疾病的分子机理提供参考。

由ADAR蛋白介导的腺嘌呤到次黄嘌呤（A-to-I）的RNA编辑是后生动物中广泛存在的转录后修饰。由于I会被识别为G，因此A-to-I RNA编辑在不改变基因组序列的情况下，时空特异性地增加了转录组和蛋白组的多样性。我们之前的工作已经报道了在果蝇中存在大量改变氨基酸的非同义RNA编辑位点（Nonsyn），这些编辑位点呈现出适应性信号，受到正向自然选择。在此项目中，我们运用多物种数据并结合转录组测序和核糖体图谱技术，进一步对果蝇A-to-I编辑的功能和演化进行更加深入的研究，并完成了立项时提出的目标。我们发现：1) RNA编辑位点在演化过程中不断扩张，一旦建立起来的编辑位点通常会被自然选择所维持下来。2) RNA编辑在相距较远的进化枝上呈现趋同适应性演化。3) 在后生动物中，具有适应性的RNA编辑位点倾向于在mRNA上紧密连锁，表明这些位点可能具有上位效应，被自然选择所偏好。4) 非同义RNA编辑位点可能通过维持蛋白质多样性参与果蝇的胁迫应答。5) 果蝇Adar自身编辑位点通过调控翻译速率对ADAR蛋白总体活性进行负反馈调节，维持细胞内总体RNA编辑水平的稳态。本项目的研究结果有利于理解RNA编辑的生物学意义以及在生物体对环境适应中的作用。