Mechanisms of cotranscriptional RNA structure formation

项目总结 RNA折叠成结构，执行基本的细胞功能，包括基因调节，催化 基本的生化反应和基因组防御。在细胞中，新生的RNA在出现时开始折叠 在转录过程中从RNA聚合酶中分离出来。因此，转录的方向和速度受到限制 RNA可以折叠成的结构，新生的RNA分子可以直接与转录的RNA相互作用 控制自身合成的聚合酶。预测RNA一级序列的变化将如何 因此，影响其结构和功能需要从机械上理解RNA折叠是如何 与转录相协调。因为所有的RNA都开始以共转录方式折叠，了解RNA是如何折叠的 功能二级和三级结构将广泛影响我们对RNA生物学的知识， RNA生物技术的发展，以及我们识别和解决由以下原因引起的人类疾病的能力 RNA错误折叠。然而，对共转录RNA结构形成的基本机制的探索仍然存在 由于缺乏具有足够吞吐量的定量方法来解决RNA的复杂性而具有挑战性 折叠过程。拟议的研究将通过系统地解剖来解决这一挑战 共转录RNA折叠机制使用新工具，可以评估组合序列如何 扰动会影响RNA的结构和功能。这些研究的最初焦点将是了解RNA是如何 序列组成和转录动力学协调了RNA三级结构的形成，从而使 核糖开关对配体介导的转录调控。这项工作将揭示基本的RNA折叠原理 能够准确和高效地形成共转录的RNA结构，这将提高我们的能力 设计和表征用于生物医学和生物技术应用的RNA系统。更广泛地说，这些 研究将建立一个研究共转录RNA结构和功能的框架，从长远来看， 术语，将有助于预见性地理解RNA如何折叠以及序列突变如何导致 RNA折叠成功能失调的状态。

PROJECT SUMMARY RNA folds into structures that perform fundamental cellular functions including gene regulation, the catalysis of essential biochemical reactions, and genome defense. In cells, nascent RNA begins to fold when it emerges from an RNA polymerase during transcription. Consequently, the direction and rate of transcription constrains the structures that RNA can fold into, and nascent RNA molecules can interact directly with transcribing RNA polymerases to control their own synthesis. Predicting how changes in the primary sequence of an RNA will affect its structure and function therefore requires a mechanistic understanding of how RNA folding is coordinated with transcription. Because all RNAs begin to fold cotranscriptionally, understanding how RNA folds into functional secondary and tertiary structures will broadly impact our knowledge of RNA biology, the development of RNA biotechnology, and our ability to identify and address human diseases that are caused by RNA misfolding. However, probing the basic mechanisms of cotranscriptional RNA structure formation remains challenging due to the lack of quantitative methods with sufficient throughput to address the complexity of RNA folding processes. The proposed research will address this challenge by systematically dissecting cotranscriptional RNA folding mechanisms using new tools that can assess how combinatorial sequence perturbations affect RNA structure and function. The initial focus of these studies will be to understand how RNA sequence composition and transcription kinetics coordinate the formation of RNA tertiary structures that enable ligand-mediated transcription regulation by riboswitches. This work will uncover basic RNA folding principles that enable accurate and efficient cotranscriptional RNA structure formation, which will advance our ability to both engineer and characterize RNA systems for biomedical and biotechnological applications. More broadly, these studies will establish a framework for investigating cotranscriptional RNA structure and function that, in the long term, will contribute to a predictive understanding of how RNA folds and how sequence mutations can cause RNA to fold into dysfunctional states.