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Collaborative Research: RESEARCH-PGR: Genetic and environmentally-induced functional variation in the rice RNA structurome

合作研究：RESEARCH-PGR：遗传和环境诱导的水稻 RNA 结构功能变异

基本信息

批准号：
2122357
负责人：
Philip Bevilacqua
金额：
$ 180万
依托单位：
Pennsylvania State Univ University Park
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2021
资助国家：
美国
起止时间：
2021-10-01 至 2025-09-30
项目状态：
未结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2122357&HistoricalAwards=false
关键词：
Collaborative Research RESEARCH PGR Genetic

项目摘要

Ribonucleic acids (RNA) are essential molecules in living organisms, including in plants. RNA can serve roles as both an informational molecule (genetic code) and a functional molecule (perform and regulate chemical reactions). RNA can fold into complex shapes that can control whether it stays intact or is degraded. This in turn can control how a plant responds to environmental stresses it faces such as heat and cold. The research involves the development of new experimental technologies to investigate RNA structures one molecule at a time and new computational technologies of artificial intelligence wherein a computer learns patterns that can predict RNA structure and its variation. Rice is an important world-wide crop, and the research applies these technologies to rice varieties that are grown in different parts of the world. There are thousands of different varieties of rice adapted to local environments and their RNAs often differ from each other by relatively few changes. Some of these changes will alter the shape of the RNA and thus the response of that rice variety to stress. A major goal of these study is to identify those changes that alter RNA shape and thereby affect temperature tolerance. Once identified, these shape-shifters could be engineered into specific rice varieties to breed crops more resistant to stress. Aspects of the research will involve high school students and their teachers, and research results and methods will be disseminated in public outreach activities. RNA structure is a primary determinant of gene expression. Individual copies of the same transcript can take on different structures as influenced by their microenvironment, but methods have been lacking to categorize this diversity. Single nucleotide polymorphisms (SNPs) also can affect RNA structure as “riboSNitches”; however, riboSNitches have not been studied in plants, and their conditionality on environmental conditions has not been assessed. Using rice (Oryza sativa) as the primary model system, the proposed research will develop new wet bench and computational approaches that will allow categorization of the mRNA “pan-structurome,” its consequent impacts on gene expression, and its functional association with respect to local climate conditions in rice landraces. Training will be provided to postdoctoral fellows, graduate students, undergraduates, and high school students and teachers. Broader Impacts will include development of the Oryza CLIMtools webtool to relate rice genotypes with climate variables and to identify beneficial structural haplotypes for use in development of elite rice cultivars. Impact will be broadened through technology including enhanced browser-based RNA structure-reactivity visualization and publicly available instructional screencasts. Collaborations with PUI Swarthmore College will engage undergraduate researchers in computational aspects of the project. Local high school students will perform whole plant physiological experiments, engaging a future generation of biologists and chemists. Finally, the 23rd Penn State Plant Biology Symposium, on RNA biology, will be organized, which will promote the global field of post-transcriptional gene regulation.This award was co-funded by the Plant Genome Research Program in the Division of Integrative Organismal Systems and the Genetic Mechanisms 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.

核糖核酸（RNA）是生物体（包括植物）的基本分子。RNA可以作为信息分子（遗传密码）和功能分子（执行和调节化学反应）。 RNA可以折叠成复杂的形状，可以控制它是保持完整还是被降解。这反过来又可以控制植物如何应对它所面临的环境压力，如热和冷。这项研究涉及新的实验技术的发展，以研究RNA结构一个分子的时间和新的人工智能计算技术，其中计算机学习模式，可以预测RNA结构及其变化。水稻是一种重要的世界性作物，这项研究将这些技术应用于世界不同地区种植的水稻品种。有成千上万种不同的水稻品种适应当地环境，它们的RNA通常彼此差异相对较小。其中一些变化会改变RNA的形状，从而改变水稻品种对压力的反应。这些研究的一个主要目标是确定那些改变RNA形状从而影响温度耐受性的变化。一旦确定，这些变形者可以被设计成特定的水稻品种，以培育更能抵抗压力的作物。研究的各个方面将涉及高中学生及其教师，研究结果和方法将在公共宣传活动中传播。RNA结构是基因表达的主要决定因素。相同转录本的单个拷贝可以因其微环境的影响而呈现不同的结构，但一直缺乏对这种多样性进行分类的方法。单核苷酸多态性（SNPs）也可以影响RNA结构作为“核糖核酸”;然而，核糖核酸还没有在植物中进行过研究，它们对环境条件的制约性也没有得到评估。使用水稻（水稻）作为主要模型系统，拟议的研究将开发新的湿台和计算方法，将允许分类的mRNA的“泛结构”，其对基因表达的影响，以及其功能与当地气候条件在水稻地方品种。培训将提供给博士后研究员，研究生，本科生，高中学生和教师。更广泛的影响将包括开发Oryza CLIMtools网络工具，将水稻基因型与气候变量联系起来，并确定用于开发优良水稻品种的有益结构单倍型。影响将通过技术扩大，包括增强的基于浏览器的RNA结构反应性可视化和公开的教学屏幕。与PUI Swarthmore College的合作将使本科研究人员参与该项目的计算方面。当地高中生将进行全植物生理实验，吸引未来一代的生物学家和化学家。最后，第23届宾夕法尼亚州立大学植物生物学研讨会，RNA生物学，将组织，这将促进全球转录后基因调控领域的发展。该奖项由整合有机体系统部的植物基因组研究计划和分子与细胞生物科学部的遗传机制群资助。该奖项反映了NSF的法定使命，并被认为值得支持通过使用基金会的知识价值和更广泛的影响审查标准进行评估。