RESEARCH-PGR: Elucidating the role of epitranscriptome on adaptation to abiotic stresses in cereals

植物的固定特性使它们容易受到高温和干旱等环境压力的影响。因此，植物已经进化出许多机制来识别和响应这种胁迫，通过打开和关闭特定的基因集来响应特定的条件。这种控制的一部分包括调节RNA水平，这是通过读取基因DNA而产生的中间分子。传统上，科学家认为RNA的活性只受DNA序列的控制，但最近的发现表明，RNA分子的稳定性也受到高度控制。最近，人们发现，这种对RNA稳定性的控制可以通过在组成RNA分子的单个碱基上添加或移除小分子，如甲基来实现。这种新的调控形式被称为表位转录组学，在很大程度上还没有在植物中被探索，它对于改良水稻等作物以更好地耐受高温和干旱胁迫具有潜在的价值。该项目旨在表征所有这些对RNA的修饰，并确定哪些修饰可以提高植物对环境胁迫的耐受性。为了实现这一目标，该项目将利用和开创RNA分离和测序方面的进展，以及分析大量测序数据的新计算工具。这些方法和工具将可供其他科学小组使用，以便他们能够迅速将相同的技术应用于他们的研究问题。植物已经开发了许多调节机制来识别并随后指导精确的转录组调节，以适当地对非生物应激源做出反应。然而，在应激反应过程中指导真核细胞转录组重编程的机制仍然很不清楚。最近的大量研究表明，转录后过程对植物基因表达的调控与转录调控一样重要。共价RNA核苷酸化学修饰(如甲基化)已被发现具有广泛的和生理上相关的显着转录后调节效应。然而，对RNA共价修饰(表位翻译组？)的作用的理解在植物转录组的转录后调控中发挥作用还处于初级阶段，特别是在考虑谷类作物时。这些修饰可能会对产量、品质和对各种胁迫的耐受性产生直接影响。该项目利用基因组、进化和生物信息学方法以及新的分析软件包和基于网络的工具相结合来解决这一重大差距。其结果将是重要的、新的机制见解、研究RNA共价修饰功能的资源，以及潜在的开发更具抗逆性的作物的新方法。最后，该团队将在EPIC-COGE框架内开发表位转录数据及其分析的数据生命周期管理、分析和可视化系统。除了我们的新发现将对RNA表位转录和谷物作物改良领域产生更广泛的影响外，还将开发一个新的培训计划，为作为数据驱动科学的生物学的未来培养下一代表位转录研究人员。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。

The stationary nature of plants leaves them vulnerable to environmental stresses such as heat and drought. Thus, plants have evolved many mechanisms to recognize and respond to such stresses by turning on and off specific sets of genes in response to certain conditions. Part of this control includes regulating RNA levels, which are intermediary molecules made from reading the DNA of genes. Traditionally, scientists believed that the activity of RNA was controlled only by the sequence of the DNA, but recent discoveries have shown that the stability of the RNA molecules is also highly controlled. Recently, it was discovered that this control of RNA stability can be achieved through the addition or removal of small molecules, such as methyl groups, to the individual bases that make up RNA molecules. This new form of regulation, called epitranscriptomics, is largely unexplored in plants and is potentially valuable for improving crops, such as rice, to better tolerate heat and drought stress. This project aims to characterize all these modifications to RNA and identify those that may improve plant tolerance to environmental stresses. To accomplish this goal, the project will leverage and pioneer advances in RNA isolation and sequencing as well as new computational tools to analyze large amounts of sequencing data. These methods and tools will be made available for other science groups so that they can rapidly apply the same techniques to their research questions.Plants have developed numerous regulatory mechanisms to recognize and subsequently direct precise transcriptome regulation to properly respond to abiotic stressors. However, the mechanisms responsible for directing eukaryotic transcriptome reprogramming during stress response are still quite unclear. Significant recent attention has revealed that post-transcriptional processes are just as important to plant gene expression regulation as transcriptional regulation. Covalent RNA nucleotide chemical modifications (e.g. methylation) have been found to have significant post-transcriptional regulatory effects that are both widespread and physiologically relevant. However, understanding of the roles RNA covalent modifications (the ?epitranscriptome?) play in post-transcriptional regulation of the plant transcriptome is in its infancy, especially when considering cereal crops. These modifications are likely to have a direct impact on yield, quality, and tolerance to various stresses. The project addresses this significant gap using a combination of genomic, evolutionary, and bioinformatics approaches together with new analytical software packages and web-based tools. The result will be important, new mechanistic insights, resources for studying the functions of RNA covalent modifications and potentially new ways to develop more stress resistant crop plants. Finally, this team will develop a data life-cycle management, analysis, and visualization system for epitranscriptomics data and their analysis within the EPIC-CoGe framework. In addition to the broader impacts that our new findings will have on the fields of RNA epitranscriptomics and cereal crop improvement, a novel training program will be developed that will prepare the next generation of epitranscriptomics researchers for the future of biology as a data-driven science.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.