URoL:Epigenetics 1: Collaborative Research: Novel epitransciptomics tools to understand and modulate interactions of modified RNAs with protein readers and erasers

在所有活着的有机体的细胞中，已经发现了超过150种类型的RNA分子的化学修饰。RNA修饰的存在可以改变RNA分子的功能或稳定性。RNA修饰可以被称为阅读器的特殊蛋白质识别，也可以被称为橡皮擦的其他蛋白质去除。一个悬而未决的问题是，阅读器和橡皮擦蛋白如何区分一种修饰和另一种修饰。这个项目试图通过使用生物物理、计算和蛋白质工程方法的组合来解决这个问题。这些结果有望为RNA修饰如何控制RNA功能提供新的见解，RNA修饰是分子生物学中一个未被探索的前沿。除了科学影响，这项研究还将为两名研究生提供教育经验，他们将在分子生物物理和生物化学的交叉学科以及实验和计算方法方面接受培训。该项目还将促进本科生和初中生，包括来自代表性不足群体的学生参与与STEM相关的活动。随着RNA修饰领域重新获得动力，现在人们理解，这些修饰对RNA的丰度和影响是由结合修饰的所谓读取器和识别RNA并催化去除修饰的擦除器之间的动态相互作用决定的。为了了解这些蛋白质如何识别和作用于它们的底物，将采取一种结合生物物理、计算和工程方法的跨学科方法。将提出两个基本问题：(1)特定的蛋白质阅读器和擦除器可以识别哪些RNA修饰，以及(2)与读取和擦除不同的RNA修饰相关的生物物理性质是什么？为了解决这些问题，将进行研究，以预测阅读器和擦除器识别一套RNA修饰的规则，并通过细胞分析中的直接测试来验证预测。这些结果将在RNA修饰的背景下扩展蛋白质识别的生物物理机制的基础知识，并为未来通过调节细胞中RNA修饰的水平来控制基因控制的合成方案的设计提供动力。该项目由理解生命规则：表观遗传学计划资助，作为NSF通过生物科学局新兴前沿部门管理的十大想法的一部分。共同资助由生物科学局分子和细胞生物科学部分子生物物理学项目提供。这一奖项反映了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。

In cells of all living organisms, over 150 types of chemical modifications have been found on RNA molecules. The presence of RNA modifications can alter the function or stability of the RNA molecules. RNA modifications can be recognized by specialized proteins called readers, and they can be removed by other proteins called erasers. An unsolved question is how reader and eraser proteins distinguish one modification from another. This project seeks to address that question by using a combination of biophysical, computational, and protein engineering approaches. The results are expected to provide new insights into how RNA function is controlled by RNA modification, an underexplored frontier in molecular biology. In addition to the scientific impact, the research will provide educational experiences for two graduate students, who will be trained at the interdisciplinary intersection of molecular biophysics and biochemistry, as well as experimental and computational methods. The project will also promote engagement in STEM-related activities by undergraduates and by students in middle and high school, including those from underrepresented groups. As the field of RNA modifications has re-gained momentum, it is now understood that the abundance and effects of these modifications on RNA are determined by the dynamic interplay between so-called readers that bind the modifications and erasers that recognize RNA and catalyze removal of the modification. To understand how these proteins recognize and act on their substrates, an interdisciplinary approach, combining biophysical, computational, and engineering methods, will be taken. Two fundamental questions will be asked: (1) what RNA modifications can be recognized by specific protein readers and erasers, and (2) what biophysical properties are associated with reading versus erasing different RNA modifications? To address these questions, studies will be conducted to predict the rules whereby readers and erasers recognize a suite of RNA modifications and to validate the predictions by direct tests in cellular assays. The results will expand fundamental knowledge of the biophysical mechanisms of protein recognition, in the context of RNA modifications, and provide impetus for future design of synthetic schemes to control gene control by tuning levels of RNA modification in cells.This project is funded by the Understanding the Rules of Life: Epigenetics Program, administered as part of NSF's Ten Big Ideas through the Division of Emerging Frontiers in the Directorate for Biological Sciences. Co-funding is provided by the Molecular Biophysics Program, Division of Molecular and Cellular Biosciences, Directorate for Biological Sciences.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.