RESEARCH-PGR: Enhancer discovery and design in agriculturally important crop plants

研究-PGR：重要农业作物的增强剂发现和设计

• 批准号: 1748843
• 负责人: Christine Queitsch
• 金额: $ 329.43万
• 依托单位: University of Washington
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-07-01 至 2022-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1748843&HistoricalAwards=false
• 关键词: RESEARCH; PGR; Enhancer; discovery; design

With climate change threatening global food security, this team will use its expertise in technology development, plant gene regulation and genomics to provide essential tools to make crops better able to withstand environmental stresses. Patterns of gene expression that dictate plant responses to the environment and changes during development are directed by DNA sequences called transcriptional enhancers. In plants, fewer than 20 plant enhancers have ever been characterized yet understanding them is crucial for crop engineering and breeding. Using novel, genome-scale technology, this team will discover large numbers of transcriptional enhancers in the cereal crops maize, sorghum, rice and wheat, particularly those driving gene expression in response to heat and cold stress. The team will then compare heat- or cold-specific enhancers among these species and among different varieties of each species, determine what differences among them are associated with differences in plant performance under heat and cold stress, and identify the protein factors that bind to these enhancers to influence gene expression. After validating the function of these enhancer sequences in heat and cold tolerance, beneficial natural variants of them will be identified for crop improvement efforts. In addition, the team will introduce mutations into these candidates to try and improve them and carry out massively parallel functional assays of enhancer fragments to develop a toolkit of synthetic enhancers with defined strengths and specificities for future crop engineering. This project broadly impacts plant research, crop engineering and breeding; it also impacts the education of future plant genome scholars through targeted outreach efforts, including summer research internships for undergraduate students.This project will apply a novel combination of ATAC- and STARR-seq to discover large numbers of regulatory elements that actively drive transcription in maize and sorghum. Limited studies in rice and wheat will allow for species-level comparisons. The team will focus on transcriptional enhancers, in particular enhancers that drive gene regulation in response to heat and cold stress. With enhancer sequences in hand, the team will characterize condition-specific enhancers that are conserved or diverged between maize and sorghum, determine phenotype-associated enhancer variation, and identify the transcription factors binding these enhancers through motif searches. In-depth comparisons of sorghum and maize enhancers will yield insights into genome evolution after genome duplication in addition to insights into sorghum's greater stress tolerance. The team will also carry out mutagenesis and massively parallel functional assays of enhancer fragments in order to computationally derive synthetic enhancers of defined strength and specificity for crop engineering. Securing food supplies through crop engineering holds immense public interest and the pursuit of this goal enables this team to effectively reach out to diverse groups and students. The outreach program, a distributed network of undergraduate plant genomics scholars, builds on the success of existing programs at partner sites by providing additional funding for four students. Participants will be able to join the program for a second year at another site to acquire new skills and to experience a different research environment.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.

随着气候变化威胁全球粮食安全，该团队将在技术开发，植物基因调节和基因组学方面使用其专业知识，以提供必不可少的工具，使农作物更好地能够承受环境压力。基因表达的模式决定植物对环境的反应和发育过程中的变化，由称为转录增强子的DNA序列指示。在植物中，植物增强剂的特征少于20种，但了解它们对于作物工程和繁殖至关重要。使用新颖的基因组规模技术，该团队将发现谷物农作物玉米，高粱，大米和小麦的大量转录增强剂，尤其是那些响应热量和冷应激而驱动基因表达的人。然后，团队将比较这些物种之间以及每个物种的不同品种之间的热或冷特异性增强子，确定它们之间的差异与热量和冷应激下的植物性能差异有关，并确定与这些增强子结合的蛋白质因子影响基因表达。在验证了这些增强子序列在热和冷耐受性中的功能之后，将确定它们的有益自然变体用于作物改善工作。此外，该团队将向这些候选人引入突变，以尝试改进它们，并对增强子片段进行大规模平行的功能测定，以开发具有具有确定优势和特异性的合成增强剂工具包，以实现未来的作物工程。该项目广泛影响植物研究，作物工程和育种；它还通过有针对性的外展工作，包括针对本科生的夏季研究实习，影响未来植物基因组学者的教育。该项目将采用ATAC-和Starr-Seq的新型组合，以发现大量的监管元素，这些监管元素积极推动玉米和高粱的转录。在大米和小麦方面的有限研究将允许物种水平的比较。该团队将专注于转录增强剂，特别是增强子，这些增强剂响应热量和冷压力而驱动基因调节。在手头增强子序列的情况下，该团队将表征特定条件特异性的增强子，这些增强子在玉米和高粱之间保持较高或差异，确定与表型相关的增强子变化，并通过基序搜索确定与这些增强子结合的转录因子。高粱和玉米增强剂的深入比较还将在基因组复制后对基因组进化的见解，除了洞悉高粱较大的胁迫耐受性。该团队还将对增强子片段进行诱变和大规模平行的功能测定，以便在计算上得出造物工程的定义强度和特异性的合成增强子。通过作物工程确保食品供应具有巨大的公众利益，并且追求这一目标使该团队能够有效地接触不同的群体和学生。 Outreach计划是一个本科植物基因组学者的分布式网络，基于合作伙伴网站现有计划的成功，通过为四名学生提供额外资金。参与者将能够在另一个网站加入该计划，以获得新的技能并体验不同的研究环境。该奖项反映了NSF的法定任务，并被认为是值得通过基金会的知识分子优点和更广泛影响的评估标准来通过评估来获得支持的。

项目成果

Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters.

• DOI: 10.1038/s41477-021-00932-y
• 发表时间: 2021-06
• 期刊: NATURE PLANTS
• 影响因子: 18
• 作者: Jores, Tobias;Tonnies, Jackson;Wrightsman, Travis;Buckler, Edward S.;Cuperus, Josh T.;Fields, Stanley;Queitsch, Christine
• 通讯作者: Queitsch, Christine

Editorial overview: Technology development as a driver of biological discovery

• DOI: 10.1016/j.pbi.2020.06.001
• 发表时间: 2020-04-01
• 期刊: CURRENT OPINION IN PLANT BIOLOGY
• 影响因子: 9.5
• 作者: Cuperus, Josh T.;Queitsch, Christine
• 通讯作者: Queitsch, Christine