Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands.
Department of Medical Microbiology, Molecular Virology Laboratory, Leiden University Medical Center, Leiden, The Netherlands.
Nat Commun. 2022 Mar 31;13(1):1722. doi: 10.1038/s41467-022-29398-y.
The rapidly growing popularity of RNA structure probing methods is leading to increasingly large amounts of available RNA structure information. This demands the development of efficient tools for the identification of RNAs sharing regions of structural similarity by direct comparison of their reactivity profiles, hence enabling the discovery of conserved structural features. We here introduce SHAPEwarp, a largely sequence-agnostic SHAPE-guided algorithm for the identification of structurally-similar regions in RNA molecules. Analysis of Dengue, Zika and coronavirus genomes recapitulates known regulatory RNA structures and identifies novel highly-conserved structural elements. This work represents a preliminary step towards the model-free search and identification of shared and conserved RNA structural features within transcriptomes.
RNA 结构探测方法的迅速普及导致可用的 RNA 结构信息越来越多。这就需要开发有效的工具，通过直接比较它们的反应性谱来识别具有结构相似性的 RNA，从而发现保守的结构特征。在这里，我们介绍了 SHAPEwarp，这是一种主要基于序列不可知的 SHAPE 引导算法，用于识别 RNA 分子中具有结构相似性的区域。对登革热、寨卡和冠状病毒基因组的分析再现了已知的调控 RNA 结构，并鉴定了新的高度保守的结构元件。这项工作代表了在无模型的情况下，在转录组中搜索和识别共享和保守的 RNA 结构特征的初步步骤。
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