TRTech-PGR: MAPPING AND FUNCTIONAL CHARACTERIZATION OF CIS-REGULATORY MODULE VARIATION IN PLANTS

转录因子是与靶基因调节区的短DNA序列基序结合的蛋白质，从而控制与植物发育程序和环境反应有关的基因表达变化。在作物物种中，转录因子及其结合的调控区域的变异一直是驯化和现代育种过程中生产力提高的常见驱动因素，并继续为进一步的性状工程提供巨大的潜力。然而，在植物基因组中，绝大多数转录因子-DNA结合事件及其引发的基因表达变化在很大程度上仍未确定，限制了满足现代农业挑战的新品种的开发。在这个项目中，将生成详细的调控信息图和新的方法，以确定转录因子结合和基因表达变异性之间的关系，为合理设计具有改良性状的作物提供新的工具。这些方法有可能从根本上改变作物改良战略，以充分满足不断增长的全球人口的需求。为了扩大该项目的影响范围，在该奖项下工作的科学家将为不同背景的学生提供基因组学和生物信息学方面的专门培训。很大一部分植物遗传变异是受调控的，位于非编码区，这些区域通常在玉米等基因组中广泛存在。从这些空间中挖掘功能元件是一个重大挑战，部分原因是虽然潜在的转录因子(TF)结合位点在基因组中自然丰富，但实际上只有一小部分结合并能够影响表达。因此，对植物转铁蛋白结合事件及其对转录输出的贡献进行经验编目是理解转录网络和性状变异的优先事项。该项目将开发TF-DNA相互作用方法，使多种遗传背景能够进行比较分析，从而产生保守调控区和可与转录程序链接的加入特定变体的高分辨率图谱。这一方法将应用于两个具有不同基因组特性的物种：玉米，一种主要的单子叶作物，基因组很大；拟南芥，一种基因组紧凑的模式优子植物。由于许多转录因子不是孤立地发挥作用，而是与其他可以改变其DNA结合活性的蛋白质相互作用，因此该项目还将开发技术来更好地了解转录因子对转录调控的贡献。为了直接将TF结合事件与表型结果联系起来，将通过精确的基因组编辑来确定控制植物结构和生殖发育的关键基因中的特定调控元件的功能。这些实验将展示如何利用调控区域的调制来产生基因表达水平或空间表达模式的细微变化，从而可能导致有利的表型。该奖项由整合组织系统部门的植物基因组研究计划和分子和细胞生物科学部门的遗传机制计划联合支持。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Transcription factors are proteins that bind to short DNA sequence motifs in regulatory regions of their target genes and thus control the gene expression changes responsible for plant developmental programs and environmental responses. In crop species, variation in transcription factors and the regulatory regions they bind have been frequent drivers of productivity gains during domestication and modern breeding, and continue to offer great potential for further trait engineering. Yet, in plant genomes, the vast majority of transcription factor-DNA binding events and the gene expression changes they elicit remain largely uncharacterized, restricting the development of new varieties that meet the challenges of modern agriculture. In this project, detailed regulatory information maps and new methodologies will be generated to identify relationships between transcription factor binding and variability in gene expression, providing new tools for the rational design of crops with improved traits. These methods have the potential to fundamentally transform crop improvement strategies to adequately feed the expanding global population. To extend the reach of the project, scientists working under this award will provide specialized training in genomics and bioinformatics to students with diverse backgrounds. A large portion of plant genetic variation is regulatory and resides in non-coding regions, spaces that are often vast in genomes such as maize. Mining functional elements from these spaces represents a major challenge, in part because while potential transcription factor (TF) binding sites are naturally abundant within a genome, only a small fraction is actually bound and able to affect expression. Empirically cataloging plant TF binding events and their contribution to transcriptional outputs is therefore a priority for understanding transcriptional networks and trait variation. This project will develop TF-DNA interaction methods that enable comparative analysis of multiple genetic backgrounds, resulting in the generation of high-resolution maps of conserved regulatory regions and accession-specific variants that can be linked to transcriptional programs. This approach will be applied in two species with different genomic properties: maize, a major monocot crop with a large genome; and Arabidopsis, a model eudicot with a compact genome. Because many TFs do not function in isolation but instead interact with other proteins that can alter their DNA binding activity, this project will also develop techniques to better understand the contribution of TF pairs to transcriptional regulation. To directly link TF binding events to phenotypic outcomes, specific regulatory elements in key genes controlling plant architecture and reproductive development will be functionally characterized through precise genome editing. Such experiments will demonstrate how modulation of regulatory regions can be used to create subtle changes in gene expression levels or spatial expression patterns that may result in advantageous phenotypes.This award is supported jointly by the Plant Genome Research Program in the Division of Integrative Organismal Systems and the Genetic Mechanisms Program in the Division of Molecular and Cellular Biosciences.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.