Discovery and Function of Higher-Order RNA Structure

摘要 RNA在所有细胞中充当信息交换的中心通道，这一角色被封装在两个 批判性观察。首先，很大一部分新出现的传染病是由rna病毒引起的。 包括埃博拉、基孔肯雅、寨卡和登革热。其次，哺乳动物的比例要大得多 基因组转录成各种各样的非编码RNA(~70%)，而不是翻译成蛋白质(1- 2%)。信使、非编码和病毒RNA的功能由线性序列控制， 碱基配对的二级结构、高阶三级结构和四元相互作用 蛋白质和小分子。总的来说，我们对RNA的数量和复杂性的理解 结构和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 到目前为止，为以高通量方式分析RNA结构而开发的方法不能在 明确而准确的方式，使得很难为相互关系定义广泛的原则 RNA的结构和功能。我们试图了解RNA结构在所有领域中的基本作用 通过追求双管齐下的方法，包括(1)发明、开发和严格地 验证基于化学的高精度技术发现新的RNA结构和 RNA和蛋白质之间的相互作用网络，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交互伙伴 致病性登革热RNA病毒和Xist Long非编码RNA。在这项工作中，我们将 专注于原生病毒和内源性RNA的细胞内分析。这项工作有望具有长期性。 造成影响的原因有三个。第一，具有高阶折叠和广泛蛋白质的RNA元件 网络很可能是功能的先驱。其次，可能存在结构性褶皱，这些褶皱 与迄今已分析的相对有限的结构类别不同。第三，核糖核酸 具有更高级别褶皱的元素也包含裂隙和缝隙，这些裂隙和缝隙是小型- 通过靶向RNA来调节生物功能的分子配体和新型药物。

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.