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

核糖核酸(RNA)是包括植物在内的生物体中必不可少的分子。RNA既可以作为信息分子(遗传密码)，也可以作为功能分子(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好还是降解。这反过来可以控制植物对其面临的环境压力(如热和冷)的反应。这项研究包括开发新的实验技术，一次研究一个分子的RNA结构，以及人工智能的新计算技术，其中计算机学习可以预测RNA结构及其变异的模式。水稻是一种重要的世界性农作物，这项研究将这些技术应用于种植在世界不同地区的水稻品种。适应当地环境的水稻有数以千计的不同品种，它们的RNAs通常只有相对较少的变化。其中一些变化将改变RNA的形状，从而改变该水稻品种对胁迫的反应。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。一旦发现，这些变形器可以被改造成特定的水稻品种，以培育出更耐逆境的作物。研究的各个方面将涉及高中生和他们的老师，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。由于微环境的影响，同一转录本的各个副本可以呈现不同的结构，但一直缺乏对这种多样性进行分类的方法。单核苷酸多态(SNPs)也可以像“riboSNitches”一样影响RNA结构；然而，riboSNitches在植物中还没有被研究过，也没有对它们对环境条件的条件性进行评估。利用水稻(Oryza Sativa)作为主要的模式系统，这项拟议的研究将开发新的湿实验台和计算方法，从而能够对水稻地方品种中的mRNA“泛结构”、其对基因表达的影响以及它与当地气候条件的功能联系进行分类。将为博士后研究员、研究生、本科生和高中生和教师提供培训。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提供的教学截屏。与Pui Swarthmore学院的合作将使本科生研究人员参与该项目的计算方面。当地的高中生将进行全植物生理实验，聘请下一代生物学家和化学家。最后，将组织关于RNA生物学的第23届宾夕法尼亚州立大学植物生物学研讨会，这将促进全球转录后基因调控领域的发展。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遗传机制集群共同资助。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。

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.