Institute of Molecular Biology, Ackermannweg 4, 55128, Mainz, Germany.
Nat Commun. 2020 Jun 3;11(1):2789. doi: 10.1038/s41467-020-16555-4.
RNA-binding proteins play key roles in regulation of gene expression via recognition of structural features in RNA molecules. Here we apply a quantitative RNA pull-down approach to 186 evolutionary conserved RNA structures and report 162 interacting proteins. Unlike global RNA interactome capture, we associate individual RNA structures within messenger RNA with their interacting proteins. Of our binders 69% are known RNA-binding proteins, whereas some are previously unrelated to RNA binding and do not harbor canonical RNA-binding domains. While current knowledge about RNA-binding proteins relates to their functions at 5' or 3'-UTRs, we report a significant number of them binding to RNA folds in the coding regions of mRNAs. Using an in vivo reporter screen and pulsed SILAC, we characterize a subset of mRNA-RBP pairs and thus connect structural RNA features to functionality. Ultimately, we here present a generic, scalable approach to interrogate the increasing number of RNA structural motifs.
RNA 结合蛋白通过识别 RNA 分子中的结构特征，在基因表达调控中发挥关键作用。在这里，我们应用一种定量的 RNA 下拉方法研究了 186 个进化上保守的 RNA 结构，并报告了 162 个相互作用的蛋白质。与全局 RNA 互作组捕获不同，我们将信使 RNA 中的单个 RNA 结构与其相互作用的蛋白质联系起来。在我们的结合蛋白中，69%是已知的 RNA 结合蛋白，而有些则以前与 RNA 结合无关，也不具有典型的 RNA 结合结构域。虽然目前关于 RNA 结合蛋白的知识与它们在 5'或 3'-UTR 上的功能有关，但我们报告了相当数量的蛋白结合到 mRNA 编码区的 RNA 折叠上。通过体内报告基因筛选和脉冲 SILAC，我们对一部分 mRNA-RBP 对进行了特征分析，从而将结构 RNA 特征与功能联系起来。最终，我们在这里提出了一种通用的、可扩展的方法来研究越来越多的 RNA 结构基序。
