美国加州大学旧金山分校Hani Goodarzi研究团队实现人类转录组中的RNA结构开关的系统搜索。2024年7月16日，《自然—方法学》杂志在线发表了这项成果。

研究人员提出了一种全面的计算和实验方法——SwitchSeeker，用于系统地识别功能性RNA结构开关。研究人员将SwitchSeeker应用于人类转录组，识别出245个潜在的RNA开关。为了验证该方法，研究人员对RORC（RAR相关孤儿受体C）转录本3'非翻译区的一个先前未知的RNA开关进行了表征。结合冷冻电镜技术，通过体内硫酸二甲酯（DMS）诱变谱分析与测序（DMS-MaPseq），确认了该开关的两种可替代结构构象。

此外，研究人员使用基因组规模的CRISPR筛选鉴定出通过该RNA结构开关调节基因表达的反式因子。结果表明，无义介导的mRNA降解以构象特异性的方式作用于这个元件。SwitchSeeker提供了一种无偏、实验驱动的方法，可用于发现塑造真核基因表达景观的RNA结构开关。

研究人员表示，RNA结构开关是细菌基因表达的重要调控因子，但其在后生动物中的表征仍然有限。

附：英文原文

Title: A systematic search for RNA structural switches across the human transcriptome

Author: Khoroshkin, Matvei, Asarnow, Daniel, Zhou, Shaopu, Navickas, Albertas, Winters, Aidan, Goudreau, Jackson, Zhou, Simon K., Yu, Johnny, Palka, Christina, Fish, Lisa, Borah, Ashir, Yousefi, Kian, Carpenter, Christopher, Ansel, K. Mark, Cheng, Yifan, Gilbert, Luke A., Goodarzi, Hani

Issue&Volume: 2024-07-16

Abstract: RNA structural switches are key regulators of gene expression in bacteria, but their characterization in Metazoa remains limited. Here, we present SwitchSeeker, a comprehensive computational and experimental approach for systematic identification of functional RNA structural switches. We applied SwitchSeeker to the human transcriptome and identified 245 putative RNA switches. To validate our approach, we characterized a previously unknown RNA switch in the 3 untranslated region of the RORC (RAR-related orphan receptor C) transcript. In vivo dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq), coupled with cryogenic electron microscopy, confirmed its existence as two alternative structural conformations. Furthermore, we used genome-scale CRISPR screens to identify trans factors that regulate gene expression through this RNA structural switch. We found that nonsense-mediated messenger RNA decay acts on this element in a conformation-specific manner. SwitchSeeker provides an unbiased, experimentally driven method for discovering RNA structural switches that shape the eukaryotic gene expression landscape.

DOI: 10.1038/s41592-024-02335-1

Source: https://www.nature.com/articles/s41592-024-02335-1