Evolutionary interactions between plant genomes and transposable elements

植物基因组和转座元件之间的进化相互作用

• 批准号: 1655808
• 负责人: Brandon Gaut
• 金额: $ 91.6万
• 依托单位: University of California-Irvine
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-15 至 2022-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1655808&HistoricalAwards=false
• 关键词: Evolutionary; interactions; between; plant; genomes; Evolutionary; interactions; between; plant; genomes

The food supply relies on plant crops. The production of most crops can be improved genetically, but this improvement requires a basic understanding of the functions of plant genes. The genes found most often in plants are called transposable elements, but surprisingly these genes usually do not fill a productive purpose. Instead, they are are the remnants of ancient invasions of the plant's DNA, probably by viruses. After invading, the viruses used the machinery of the plant to make copies of themselves and then their DNA remained permanently among the plant genes while retaining the ability make more copies of themselves. To counter the invasion and propagation of these elements, the plant tries to disable them, making them incapable of copying themselves. But it is not known how plants recognize transposable elements to disable them. Understanding this step is crucial for understanding the history and function of plant genes, and it may also inform processes used for genetically engineering crops. This award focuses on understanding how a plant recognizes transposable elements to disable them. The award will also train postdoctoral and graduate students in the methods and computational tools used to study plant genes creating a broader societal impact. Interactions between a plant and its transposable elements represent an ongoing conflict. Elements seek to propagate while plants try to control their propagation through epigenetic silencing. An important component of the epigenetic response is small RNAs, which guide the plant's silencing machinery to their genomic targets by sequence similarity. Because of this similarity, the mapping locations of small RNAs provide insights about their putative targets and also about the loci from which they may have originated. It is not known, however, how the initial small RNAs are generated. Previous work has shown that small RNAs in maize (Zea mays) map preferentially to regions of the element that form secondary structures. The regions that are particularly prone to folding in our study system (Sirevirus elements) are also necessary for their function. It is hypothesized that folding regions of transposable elements are processed directly into small RNAs, thereby initiating the host silencing response. These folding regions are predicted to be important for the initiation of the host response and also to be the focus of an evolutionary arms race between plants and their hosts. The first prediction will be tested by inserting folding regions from maize Sirevirus elements into Arabidopsis thaliana transgenically, to see if these regions are sufficient to initiate a plant response. The latter prediction will be examined by studying small RNAs and Sirevirus elements in several different plants, including maize and other grain crops. If the folding regions are the locus of host-element interactions, then small RNAs should preferentially map to these regions.

食物供应依赖于植物作物。 大多数农作物的产量可以从遗传上改善，但是这种改进需要对植物基因功能的基本了解。在植物中最常发现的基因称为可转座元素，但令人惊讶的是，这些基因通常不会填补生产目的。 取而代之的是，它们是植物DNA古代入侵的残余物，可能是病毒。 入侵后，这些病毒使用植物的机械制作自身的副本，然后将其DNA永久保留在植物基因中，同时保留能力，使自己更多地副本。 为了应对这些元素的入侵和传播，该植物试图禁用它们，使它们无法复制自己。 但是，尚不知道植物如何识别可转移的元素来禁用它们。 了解这一步骤对于理解植物基因的历史和功能至关重要，并且也可能为用于基因工程作物的过程提供信息。 该奖项的重点是了解植物如何识别可替代的元素来禁用它们。该奖项还将在研究植物基因的方法和计算工具中培训博士后和研究生，从而产生更广泛的社会影响。植物及其可转移元素之间的相互作用代表了持续的冲突。元素试图传播植物，试图通过表观遗传沉默来控制其传播。表观遗传反应的一个重要组成部分是小型RNA，它通过序列相似性将植物的沉默机制引导到其基因组靶标。由于这种相似性，小型RNA的映射位置提供了有关其假定目标以及它们可能产生的基因座的见解。 但是，尚不清楚如何生成最初的小RNA。 先前的工作表明，玉米（Zea Mays）中的小RNA优先映射到形成二级结构的元素区域。在我们的研究系统中特别容易折叠的区域（Sirevirus Elements）对于它们的功能也是必需的。假设可转座​​元件的折叠区域直接处理成小的RNA，从而启动宿主沉默响应。预计这些折叠区对于启动宿主反应至关重要，也是植物及其宿主之间进化的军备竞赛的重点。 第一个预测将通过将玉米西里病毒元素的折叠区域插入拟南芥中，以查看这些区域是否足以引发植物反应，从而测试第一个预测。 后一种预测将通过研究几种不同植物（包括玉米和其他谷物作物）中的小RNA和Sirevirus元素来研究。 如果折叠区是宿主元素相互作用的轨迹，则小RNA应优先映射到这些区域。