Wightman Federico Fuchs, Yang Grant, Martin des Taillades Yves J, L'Esperance-Kerckhoff Casper, Grote Scott, Allan Matthew F, Herschlag Daniel, Rouskin Silvi, Hagler Lauren D
Department of Microbiology, Harvard School of Medicine, Boston, Massachusetts, 02115, United States.
Department of Biochemistry, Stanford University, Stanford, California, 94305, United States.
bioRxiv. 2024 Sep 26:2024.09.26.615187. doi: 10.1101/2024.09.26.615187.
In recent years, RNA has been increasingly recognized for its essential roles in biology, functioning not only as a carrier of genetic information but also as a dynamic regulator of gene expression through its interactions with other RNAs, proteins, and itself. Advances in chemical probing techniques have significantly enhanced our ability to identify RNA secondary structures and understand their regulatory roles. These developments, alongside improvements in experimental design and data processing, have greatly increased the resolution and throughput of structural analyses. Here, we introduce SEISMICgraph, a web-based tool designed to support RNA structure research by offering data visualization and analysis capabilities for a variety of chemical probing modalities. SEISMICgraph enables simultaneous comparison of data across different sequences and experimental conditions through a user-friendly interface that requires no programming expertise. We demonstrate its utility by investigating known and putative riboswitches and exploring how RNA modifications influence their structure and binding. SEISMICgraph's ability to rapidly visualize adenine-dependent structural changes and assess the impact of pseudouridylation on these transitions provides novel insights and establishes a roadmap for numerous future applications.
近年来，RNA在生物学中的重要作用越来越受到认可，它不仅作为遗传信息的载体，还通过与其他RNA、蛋白质以及自身的相互作用，作为基因表达的动态调节因子发挥作用。化学探测技术的进步显著提高了我们识别RNA二级结构并理解其调节作用的能力。这些进展，连同实验设计和数据处理方面的改进，极大地提高了结构分析的分辨率和通量。在这里，我们介绍SEISMICgraph，这是一个基于网络的工具，旨在通过为各种化学探测方式提供数据可视化和分析功能来支持RNA结构研究。SEISMICgraph通过一个无需编程专业知识的用户友好界面，能够同时比较不同序列和实验条件下的数据。我们通过研究已知和假定的核糖开关，并探索RNA修饰如何影响它们的结构和结合，来证明其效用。SEISMICgraph快速可视化腺嘌呤依赖性结构变化以及评估假尿苷化对这些转变影响的能力提供了新的见解，并为众多未来应用建立了路线图。
