Silverman Ian M, Berkowitz Nathan D, Gosai Sager J, Gregory Brian D
Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, USA.
Adv Exp Med Biol. 2016;907:29-59. doi: 10.1007/978-3-319-29073-7_2.
RNA molecules of all types fold into complex secondary and tertiary structures that are important for their function and regulation. Structural and catalytic RNAs such as ribosomal RNA (rRNA) and transfer RNA (tRNA) are central players in protein synthesis, and only function through their proper folding into intricate three-dimensional structures. Studies of messenger RNA (mRNA) regulation have also revealed that structural elements embedded within these RNA species are important for the proper regulation of their total level in the transcriptome. More recently, the discovery of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) has shed light on the importance of RNA structure to genome, transcriptome, and proteome regulation. Due to the relatively small number, high conservation, and importance of structural and catalytic RNAs to all life, much early work in RNA structure analysis mapped out a detailed view of these molecules. Computational and physical methods were used in concert with enzymatic and chemical structure probing to create high-resolution models of these fundamental biological molecules. However, the recent expansion in our knowledge of the importance of RNA structure to coding and regulatory RNAs has left the field in need of faster and scalable methods for high-throughput structural analysis. To address this, nuclease and chemical RNA structure probing methodologies have been adapted for genome-wide analysis. These methods have been deployed to globally characterize thousands of RNA structures in a single experiment. Here, we review these experimental methodologies for high-throughput RNA structure determination and discuss the insights gained from each approach.
所有类型的RNA分子都会折叠成复杂的二级和三级结构，这些结构对其功能和调控至关重要。诸如核糖体RNA（rRNA）和转运RNA（tRNA）等结构RNA和催化RNA是蛋白质合成的核心参与者，并且只有通过正确折叠成复杂的三维结构才能发挥功能。对信使RNA（mRNA）调控的研究还表明，这些RNA分子中嵌入的结构元件对于转录组中其总量的正确调控很重要。最近，微小RNA（miRNA）和长链非编码RNA（lncRNA）的发现揭示了RNA结构对基因组、转录组和蛋白质组调控的重要性。由于结构RNA和催化RNA数量相对较少、高度保守且对所有生命都很重要，早期许多RNA结构分析工作绘制出了这些分子的详细视图。计算方法和物理方法与酶促和化学结构探测协同使用，以创建这些基本生物分子的高分辨率模型。然而，最近我们对RNA结构对编码RNA和调控RNA重要性的认识不断扩展，这使得该领域需要更快且可扩展的高通量结构分析方法。为了解决这个问题，核酸酶和化学RNA结构探测方法已被应用于全基因组分析。这些方法已被用于在单个实验中对数千个RNA结构进行全局表征。在这里，我们回顾这些用于高通量RNA结构测定的实验方法，并讨论从每种方法中获得的见解。
