Contribution of cis-regulatory elements in a plant's response to environmental stress

环境压力，如高温，会对世界上许多作物的生长和产量产生负面影响。扎根于地下的植物有独特的策略来适应环境的变化，其中很大一部分涉及基因表达的重新编程。基因表达的控制部分是通过转录因子和顺式调控DNA元件之间的复杂相互作用实现的，这些DNA元件位于邻近的（启动子元件）或距离其靶基因很远的（远端调控元件）。虽然已经确定了许多关键基因赋予高温耐受性，但许多试图确定与耐受性性状相关的遗传变异的研究已经确定了位于顺式调控元件中的变异。尽管远端顺式调控元件（如增强子）在基因调控中的重要性已在许多真核生物基因组中得到证实，但它们对植物全基因组和胁迫特异性转录重编程的影响仍在很大程度上未知。我的研究计划的长期目标是确定远端顺式调控元件对植物应对环境胁迫的能力的贡献。作为第一步，我将重点关注一类特定的远端顺式调控元件，增强剂，在高温胁迫下的主食亚洲水稻（Oryza sativa）。与当前提案相关的具体目标包括：1：表征水稻高温胁迫下增强子的转录活性。2：研究高温胁迫下水稻基因组中不同类型的活性增强子。3：利用计算方法和功能验证鉴定候选增强子及其靶基因。我的研究计划将描述远端顺式调控DNA元件的作用及其与靶基因的相互作用，以了解植物基因组如何在环境胁迫下重编程基因表达。这些知识将是预测和优先考虑作物改良候选调控目标的关键。事实上，提供对环境压力的抵抗力一直是现代育种方法的主要目标，特别是在受高温影响很大的地区种植的水稻。这些研究中使用的方法将产生生物学洞察力和分析能力，可应用于其他作物植物和其他环境压力。

Environmental stresses, such as high temperature, can negatively impact the growth and yield of many crops in the world. Rooted in the ground, plants have unique strategies for being more resilient to changes in their environment, a major part of which involves the reprograming of gene expression. The control of gene expression is achieved in part by complex interactions between transcription factors and cis-regulatory DNA elements, which are located either adjacent to (promoter elements), or at large distances from (distal regulatory elements) their target genes. While a number of key genes have been identified to confer high temperature tolerance, many studies trying to identify genetic variants associated with tolerance traits have identified variants located within cis-regulatory elements. Whereas the importance of distal cis-regulatory elements, such as enhancers, in gene regulation has been shown in many eukaryotic genomes, their impact on genome-wide and stress-specific transcriptional reprograming remains largely unknown in plants. The long-term objective of my research program is to determine the contribution of distal cis-regulatory elements to a plant's ability to respond to environmental stressors. As a first step, I will focus on a specific class of distal cis-regulatory elements, enhancers, in the context of high temperature stress in the staple food Asian rice (Oryza sativa). The specific objectives associated with the current proposal include: 1: Characterize the transcriptional activity of enhancers in response to high temperature stress in rice. 2: Study the different types of active enhancers in the rice genome under high temperature stress. 3: Identify candidate enhancers and their target genes using computational methods and functional validation. My research program will characterize the roles of distal cis-regulatory DNA elements and their interaction with target genes to understand how plant genomes reprogram gene expression under environmental stress. This knowledge will be key to predict and prioritize candidate regulatory targets for crop improvement. Indeed, providing resistance to environmental stress, has been a major goal of modern breeding approaches, especially in rice which is grown in regions largely impacted by high temperatures. The approaches used in these studies will generate biological insight and analytical capabilities that can be applied to other crop plants and other environmental stresses.