Mechanisms of cotranscriptional RNA structure formation

项目摘要 RNA折叠成执行基本细胞功能的结构，包括基因调控、 基本的生化反应和基因组防御。在细胞中，新生RNA在出现时开始折叠， 从RNA聚合酶中分离出来因此，转录的方向和速率限制了 RNA可以折叠成的结构，新生RNA分子可以直接与转录RNA相互作用， 聚合酶来控制它们自身的合成。预测RNA一级序列的变化 因此，需要从机制上理解RNA折叠是如何影响其结构和功能的。 与转录协调。因为所有的RNA开始以共转录方式折叠， 将广泛影响我们对RNA生物学的认识， RNA生物技术的发展，以及我们识别和解决由RNA引起的人类疾病的能力。 RNA错误折叠。然而，探索共转录RNA结构形成的基本机制仍然存在 由于缺乏具有足够通量的定量方法来解决RNA的复杂性， 折叠过程拟议的研究将通过系统地剖析 使用新工具的共转录RNA折叠机制，可以评估组合序列 干扰影响RNA的结构和功能。这些研究的最初重点将是了解RNA如何 序列组成和转录动力学协调RNA三级结构的形成， 配体介导的核糖开关转录调控。这项工作将揭示基本的RNA折叠原理， 使准确和有效的共转录RNA结构的形成，这将提高我们的能力， 设计和表征RNA系统，用于生物医学和生物技术应用。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， 术语，将有助于预测理解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.