PlantSynBio: Deciphering the grammar of crop regulatory DNA for precise engineering of gene expression
PlantSynBio:破译作物调控 DNA 的语法以实现基因表达的精确工程
基本信息
- 批准号:2240888
- 负责人:
- 金额:$ 200万
- 依托单位:
- 依托单位国家:美国
- 项目类别:Standard Grant
- 财政年份:2023
- 资助国家:美国
- 起止时间:2023-03-01 至 2026-02-28
- 项目状态:未结题
- 来源:
- 关键词:
项目摘要
Plant researchers and breeders agree that technological advances are needed to meet the future demands for agricultural products, especially in light of the accelerating climate crisis. Although traditional plant breeding and fertilizer application have produced large increases in agricultural yields in the past, yields have plateaued in recent years. This project uses novel genome-scale technology and advanced analysis methods to identity and characterize the tens of thousands of genetic elements that drive growth and environmental resilience in maize and tomato, crops that represent two major classes of plants. The large size of the resulting data sets enables systematic computational analyses of these elements and allows for design of synthetic elements with desirable features. The applicability and safety of these designs for future crop engineering will be examined in maize and tomato plants in the laboratory. Today’s plant researchers and breeders need to be fluent in conducting genome-scale experiments and applying advanced computational methods. This project will provide funds for the training and the career development of several undergraduate students and postdoctoral fellows.The limited understanding of plant gene regulation and lack of diverse, plant-derived regulatory elements to drive transgenes have hampered plant synthetic biology. To facilitate plant synthetic biology, this project will apply massively parallel reporter assays and machine learning to decipher the grammar of gene-regulatory elements in maize and tomato, including enhancers, promoters, insulators and terminators, and their local interactions in response to four common environmental conditions. The salient features of these regulatory elements and element combinations will be identified by convolutional neural network models, which will be used to evolve and design synthetic elements with desired features. Designed promoter and enhancer elements, along with plant-derived insulators and terminators, will serve as building blocks for synthetic biology applications. Model inferences will be tested in transgenic crops with engineered native regulatory elements and through the integration of multi-gene reporter cassettes whose tunable and programmable activity is driven by synthetic regulatory elements. This project’s results will propel plant gene regulation and crop synthetic biology beyond current knowledge and tools, and jumpstart crop engineering efforts.This award was co-funded by the Plant Genome Research Program in the Division of Integrative Organismal Systems and the Systems and Synthetic Biology cluster 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.
植物研究人员和育种者一致认为,需要技术进步来满足未来对农产品的需求,特别是在气候危机日益加剧的情况下。虽然传统的植物育种和化肥使用在过去大大增加了农业产量,但近年来产量已趋于平稳。该项目使用新的基因组规模技术和先进的分析方法来识别和表征推动玉米和番茄生长和环境适应能力的数万种遗传元素,这两种作物代表着两大类植物。所产生的数据集的大小使得能够对这些元素进行系统的计算分析,并允许设计具有所需特征的合成元素。这些设计在未来作物工程中的适用性和安全性将在实验室里用玉米和番茄植株进行检验。今天的植物研究人员和育种者需要熟练地进行基因组规模的实验并应用先进的计算方法。该项目将为几名本科生和博士后的培训和职业发展提供资金。对植物基因调控的有限了解,以及缺乏多样化的植物衍生调控元件来驱动转基因,阻碍了植物合成生物学的发展。为了促进植物合成生物学,该项目将应用大规模并行报告分析和机器学习来破译玉米和番茄中基因调控元件的语法,包括增强子、启动子、绝缘子和终止子,以及它们在四种常见环境条件下的局部相互作用。这些调节元件和元件组合的显著特征将由卷积神经网络模型识别,该模型将用于进化和设计具有所需特性的合成元件。设计的启动子和增强子元件,以及植物来源的绝缘体和终止子,将作为合成生物学应用的基石。模型推论将在转基因作物中进行测试,这些转基因作物带有工程的本地调控元件,并通过整合多基因报告盒进行测试,这些报告盒的可调和可编程活动由合成的调控元件驱动。该项目的成果将推动植物基因调控和作物合成生物学超越目前的知识和工具,并启动作物工程努力。该奖项由整合组织系统部门的植物基因组研究计划以及分子和细胞生物科学部门的系统和合成生物学集群共同资助。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。
项目成果
期刊论文数量(5)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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Christine Queitsch其他文献
Christine Queitsch的其他文献
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{{ truncateString('Christine Queitsch', 18)}}的其他基金
REU Site: Big Data Science and Science Communication
REU 网站:大数据科学与科学传播
- 批准号:
1950024 - 财政年份:2020
- 资助金额:
$ 200万 - 项目类别:
Standard Grant
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 - 财政年份:2018
- 资助金额:
$ 200万 - 项目类别:
Continuing Grant
REU Site: Discoveries in Genomics and Proteomics
REU 网站:基因组学和蛋白质组学的发现
- 批准号:
1659680 - 财政年份:2017
- 资助金额:
$ 200万 - 项目类别:
Continuing Grant
2015 Molecular Mechanisms in Evolution Gordon Research Conference held 28 Jun - 3 Jul 2015 at Stonehill College, Easton MA.
2015年进化分子机制戈登研究会议于2015年6月28日至7月3日在马萨诸塞州伊斯顿斯通希尔学院举行。
- 批准号:
1540359 - 财政年份:2015
- 资助金额:
$ 200万 - 项目类别:
Standard Grant
Using the Plant Heat Stress Response to Probe Genome-wide Regulatory Landscapes for Functional Relevance
利用植物热应激反应来探测全基因组调控景观的功能相关性
- 批准号:
1516701 - 财政年份:2015
- 资助金额:
$ 200万 - 项目类别:
Standard Grant
EAGER: RNA Polymerase V as a Novel Capacitor of Phenotypic Variation in Arabidopsis thalian
EAGER:RNA 聚合酶 V 作为拟南芥表型变异的新型电容器
- 批准号:
1242744 - 财政年份:2012
- 资助金额:
$ 200万 - 项目类别:
Standard Grant
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