哥伦比亚大学Marko Jovanovic团队的一项最新研究发现了SPIDR可以实现RNA-蛋白相互作用的多路映射，并揭示了细胞应激下选择性翻译抑制的机制。2025年7月22日出版的《细胞》杂志发表了这项成果。
为了克服这一限制，该研究组开发了SPIDR （RBP靶点的分裂池鉴定），这是一种高度复用的分裂池方法，可以同时分析数十个RBP的结合位点。SPIDR为不同种类的RBP识别精确的单核苷酸结合位点。利用SPIDR，该研究组发现了LARP1与18S rRNA之间的相互作用，并将这种相互作用解析为40S核糖体主题冷冻电镜（cro-em）的mRNA进入通道，为LARP1在翻译抑制中的作用提供了潜在的机制解释。该团队探索了RBP在mTOR抑制下结合的变化，并发现在mTOR抑制下，4EBP1优先与翻译抑制的mRNA结合。SPIDR有潜力通过在前所未有的规模上快速、从头发现RNA-蛋白质相互作用，显著提高他们对RNA生物学的理解。
据悉，RNA结合蛋白（RBP）调节mRNA生命周期的所有阶段，但目前的方法通常是一次绘制一个RBP蛋白的RNA靶标。
附：英文原文
Title: SPIDR enables multiplexed mapping of RNA-protein interactions and uncovers a mechanism for selective translational suppression upon cell stress
Author: Erica Wolin, Jimmy K. Guo, Mario R. Blanco, Isabel N. Goronzy, Darvesh Gorhe, Wenzhao Dong, Andrew A. Perez, Abdurrahman Keskin, Elizabeth Valenzuela, Ahmed A. Abdou, Carl R. Urbinati, Ross Kaufhold, H. Tomas Rube, Jailson Brito Querido, Mitchell Guttman, Marko Jovanovic
Issue&Volume: 2025-07-22
Abstract: RNA-binding proteins (RBPs) regulate all stages of the mRNA life cycle, yet current methods generally map RNA targets of RBPs one protein at a time. To overcome this limitation, we developed SPIDR (split-and-pool identification of RBP targets), a highly multiplexed split-pool method that profiles the binding sites of dozens of RBPs simultaneously. SPIDR identifies precise, single-nucleotide binding sites for diverse classes of RBPs. Using SPIDR, we uncovered an interaction between LARP1 and the 18S rRNA and resolved this interaction to the mRNA entry channel of the 40S ribosome using cryoelectron microscopy (cryo-EM), providing a potential mechanistic explanation for LARP1’s role in translational suppression. We explored changes in RBP binding upon mTOR inhibition and identified that 4EBP1 preferentially associates with translationally repressed mRNAs upon mTOR inhibition. SPIDR has the potential to significantly advance our understanding of RNA biology by enabling rapid, de novo discovery of RNA-protein interactions at an unprecedented scale.
DOI: 10.1016/j.cell.2025.06.042
Source: https://www.cell.com/cell/abstract/S0092-8674(25)00743-3