Evolutionary interactions between plant genomes and transposable elements

食物供应依赖于植物作物。 大多数农作物的产量可以通过基因改良，但这种改良需要对植物基因的功能有基本的了解。在植物中最常见的基因被称为转座因子，但令人惊讶的是，这些基因通常不满足生产目的。 相反，它们是古代入侵植物DNA的残留物，可能是病毒。 在入侵之后，病毒利用植物的机制来复制自己，然后它们的DNA永久地留在植物基因中，同时保留了复制更多自己的能力。 为了对抗这些元素的入侵和繁殖，植物试图使它们失去能力，使它们无法复制自己。 但植物如何识别转座因子使其失效还不清楚。 了解这一步骤对于理解植物基因的历史和功能至关重要，它也可能为转基因作物的过程提供信息。 该奖项的重点是了解植物如何识别转座因子，使其失去功能。该奖项还将在用于研究植物基因的方法和计算工具方面对博士后和研究生进行培训，从而产生更广泛的社会影响。植物与其转座因子之间的相互作用代表了一种持续的冲突。元素试图繁殖，而植物试图通过表观遗传沉默来控制它们的繁殖。表观遗传反应的一个重要组成部分是小RNA，它通过序列相似性将植物的沉默机制引导到它们的基因组靶标。由于这种相似性，小RNA的定位提供了关于其假定靶点以及它们可能起源的基因座的见解。 然而，最初的小RNA是如何产生的尚不清楚。 先前的研究表明，玉米（Zea mays）中的小RNA优先映射到形成二级结构的元件区域。在我们的研究系统中特别容易折叠的区域（Sirevirus元件）也是其功能所必需的。据推测，转座因子的折叠区域被直接加工成小RNA，从而启动宿主沉默反应。这些折叠区域被预测是重要的主机响应的启动，也是植物和它们的主机之间的进化军备竞赛的焦点。 第一个预测将通过将来自玉米Sirevirus元件的折叠区域转基因插入拟南芥中来测试，以查看这些区域是否足以引发植物反应。 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）中的小RNA和Sirevirus元件来检验。 如果折叠区域是宿主-元件相互作用的位点，那么小RNA应该优先映射到这些区域。

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.