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Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing
Nucleic Acids Research ( IF 14.9 ) Pub Date : 2021-09-20 , DOI: 10.1093/nar/gkab885
Dalen Chan 1 , Chao Feng 1 , Whitney E England 1 , Dana Wyman 2 , Ryan A Flynn 3 , Xiuye Wang 4 , Yongsheng Shi 4 , Ali Mortazavi 2 , Robert C Spitale 1, 5
Affiliation  

RNA molecules can fold into complex structures and interact with trans-acting factors to control their biology. Recent methods have been focused on developing novel tools to measure RNA structure transcriptome-wide, but their utility to study and predict RNA-protein interactions or RNA processing has been limited thus far. Here, we extend these studies with the first transcriptome-wide mapping method for cataloging RNA solvent accessibility, icLASER. By combining solvent accessibility (icLASER) with RNA flexibility (icSHAPE) data, we efficiently predict RNA-protein interactions transcriptome-wide and catalog RNA polyadenylation sites by RNA structure alone. These studies showcase the power of designing novel chemical approaches to studying RNA biology. Further, our study exemplifies merging complementary methods to measure RNA structure inside cells and its utility for predicting transcriptome-wide interactions that are critical for control of and regulation by RNA structure. We envision such approaches can be applied to studying different cell types or cells under varying conditions, using RNA structure and footprinting to characterize cellular interactions and processing involving RNA.

中文翻译:

RNA中的不同功能元件通过正交RNA结构探测预测全转录组

RNA 分子可以折叠成复杂的结构并与反式作用因子相互作用以控制其生物学。最近的方法一直专注于开发新的工具来测量全转录组的 RNA 结构,但它们在研究和预测 RNA-蛋白质相互作用或 RNA 加工方面的效用迄今为止受到限制。在这里,我们使用第一个用于分类 RNA 溶剂可及性的全转录组映射方法 icLASER 扩展了这些研究。通过将溶剂可及性 (icLASER) 与 RNA 灵活性 (icSHAPE) 数据相结合,我们可以仅通过 RNA 结构有效地预测 RNA-蛋白质相互作用转录组范围和目录 RNA 多腺苷酸化位点。这些研究展示了设计新的化学方法来研究 RNA 生物学的能力。进一步,我们的研究举例说明了合并互补方法来测量细胞内的 RNA 结构及其在预测转录组范围内相互作用的效用,这些相互作用对于 RNA 结构的控制和调节至关重要。我们设想这些方法可以应用于研究不同细胞类型或不同条件下的细胞,使用 RNA 结构和足迹来表征涉及 RNA 的细胞相互作用和加工。
更新日期:2021-09-20
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