Discovery and Function of Higher-Order RNA Structure

总结 RNA作为所有细胞中信息交换的中心管道，其作用被封装在两个 关键的观察。首先，很大一部分新发传染病是由RNA病毒引起的 包括埃博拉、基孔肯雅、寨卡和登革热。第二，更大比例的哺乳动物 基因组转录成各种非编码RNA（~70%），而不是翻译成蛋白质（1- 2%）。信使RNA、非编码RNA和病毒RNA的功能由线性序列控制， 碱基配对的二级结构，高级三级结构，以及涉及 蛋白质和小分子。总的来说，我们对RNA数量和复杂性的理解 RNA结构以及RNA结构如何驱动不同的生物功能是非常有限的。大多数方法 迄今为止开发的用于以高通量方式分析RNA结构的方法不能以高通量方式测量结构。 明确和准确的方式，使得很难界定之间的相互关系的广泛原则 RNA的结构与功能我们试图了解RNA结构在所有领域中的基本作用 生物学通过追求双管齐下的方法，涉及（1）发明，开发，并严格 验证高度精确的基于化学的技术，用于发现新的RNA结构， RNA和蛋白质之间相互作用的网络，然后（2）将这些技术应用于 具有广泛重要性的问题。在这里，我们建议询问结构和相互作用伙伴 致病性登革RNA病毒和Xist长非编码RNA。在这项工作中，我们将 专注于天然病毒和内源RNA的细胞内分析。这项工作预计将长期 影响有三大原因。第一，具有高级折叠和广泛蛋白质的RNA元件 网络很可能是功能的预兆。第二，可能存在结构褶皱， 不同于迄今为止已经分析的相对有限的结构类别。第三，RNA 具有高阶折叠的元件也包含裂缝和裂隙，这些裂缝和裂隙是小的- 分子配体-和新型药物-通过靶向RNA调节生物功能。

SUMMARY RNA functions as the central conduit of information exchange in all cells, a role encapsulated in two critical observations. First, a large fraction of emerging infectious diseases are caused by RNA viruses including Ebola, Chikungunya, Zika, and Dengue. Second, a much larger fraction of the mammalian genome is transcribed into diverse kinds of non-coding RNAs (~70%) than is translated into protein (1- 2%). The functions of messenger, non-coding, and viral RNAs are governed by the linear sequence, base-paired secondary structure, higher-order tertiary structure, and quaternary interactions involving proteins and small molecules. Overall, our understanding of the number and complexity of RNA structures and how RNA structure drives diverse biological functions is very limited. Most methods developed to date for analyzing RNA structure in high-throughput ways do not measure structure in a definitive and accurate way, making it difficult to define broad principles for interrelationships between RNA structure and function. We seek to understand the fundamental roles of RNA structure in all areas of biology by pursuing a two-pronged approach involving (1) inventing, developing, and rigorously validating highly accurate chemistry-based technologies for discovery of novel RNA structures and the networks of interactions between RNAs and proteins and then (2) applying these technologies to problems of broad importance. Here we propose to interrogate the structures and interaction partners of the pathogenic Dengue RNA virus and the Xist long non-coding RNA. Throughout this work, we will focus on in-cell analysis of native viral and endogenous RNAs. This work is expected to have long-term impact for three broad reasons. First, RNA elements with higher-order folds and extensive protein networks are likely to be harbingers of function. Second, there are likely to be structural folds that are different from the relatively limited classes of structures that have been analyzed to date. Third, RNA elements with higher-order folds also contain clefts and crevices that are ideal targets for small- molecule ligands – and novel drugs – that modulate biological function by targeting RNA.