Quantitative and mechanistic dissection of messenger RNA stability

RNA分子的稳定性可能存在很大差异，这直接影响了它们的功能，例如，通过调节mrna产生的蛋白质量。长链RNA的稳定性是如何通过序列、化学修饰、结构和RNA结合蛋白（rbp）的相互作用来确定的，以及这是如何根据RNA的来源而变化的，目前还知之甚少。理解决定RNA稳定性的编码是理解基因表达调控在多种生理和病理背景下（包括发育、传染病和肿瘤）如何重定向的关键。这对于有效设计新的RNA疗法以及了解mrna和lncrna中的哪些突变会产生有害后果也很重要。在转录过程中安装的m6A RNA修饰最近成为RNA稳定性的主要决定因素，其他决定因素由RNA结合蛋白（rbp）决定，其他决定因素尚不清楚，特别是对于非在细胞核中产生的RNA。在这个跨学科的联合提案中，我们旨在定量、功能、生化和结构上剖析序列元件、化学修饰、结构和rbp如何影响mRNA的稳定性。它将最先进的高通量RNA分析和计算生物学（由Ulitsky和Schwartz实验室提供的专业知识）与尖端的生化和结构方法（由Meister和Fischer实验室提供）相结合，揭示序列，加工，mRNA修饰和rbp如何协同决定mRNA的稳定性。总之，这些研究将提供一个详细的机制理解顺式和反式决定决定mRNA的生命周期。我们的研究也将对开发与生物医学和其他领域相关的新型RNA技术具有很高的价值。

RNA molecules can differ substantially in their stability, which directly impacts their function, e.g., through regulating the amount of protein produced by mRNAs. How the stability of long RNAs is determined via an interplay of sequence, chemical modifications, structure, and RNA binding proteins (RBPs), and how this varies depending on the origin of the RNA remains poorly understood. Understanding the codes determining RNA stability is key for understanding how regulation of gene expression is redirected in diverse physiological and pathological contexts, including development, infectious disease, and tumors. It is also important for effective design of new RNA therapies and for understanding which mutations in mRNAs and lncRNAs can have detrimental consequences. The m6A RNA modification, which is installed during transcription has recently emerged as a major determinant of RNA stability, with additional determinants set by RNA binding proteins (RBPs), andothers remaining unclear, in particular for RNAs that are are not produced in the nucleus. In this interdisciplinary joint proposal, we aim to quantitatively, functionally, biochemically, and structurally dissect how sequence elements, chemical modifications, structure and RBPs impact mRNA stability. It synergizes state-of-the art high-throughput RNA assays and computational biology (expertise provided by the Ulitsky and Schwartz labs), with cutting-edge biochemical and structural approaches (provided by the Meister and Fischer labs), to unravel how sequence, processing, mRNA modifications and RBPs synergize to dictate mRNA stability. Together, these studies will provide a detailed mechanistic understanding of the cis and trans determinants dictating the mRNA life cycle. Our investigations will also be highly valuable for developing novel RNA technologies relevant for biomedicine and beyond.