斯坦福大学Paul A. Khavari研究小组取得一项新突破。他们报道了irCLIP-RNP和Re-CLIP揭示了RNA上动态蛋白质组装的模式。相关论文于2025年3月26日发表在《自然》杂志上。

RNA结合蛋白（rbp）控制多种过程，包括RNA剪接、稳定性、运输和翻译。功能失调的RNA-RBP相互作用有助于人类疾病的发病机制；然而，表征RNA上多蛋白组装的性质和动力学一直具有挑战性。为了解决这个问题，该课题组人员将基于非同位素连接的紫外光诱导交联和免疫沉淀与质谱（irCLIP-RNP）相结合，以鉴定与任何感兴趣的RBP共结合RNA的RNA依赖性相关蛋白（RDAPs）。irCLIP-RNP定义了RNA上多聚体蛋白组装的景观，揭示了RBP-RNA关联模式，包括RDAPs和初级RBPs之间的细胞类型选择性组合关系。irCLIP-RNP还定义了响应表皮生长因子（EGF）的动态RDAPs重塑，揭示了EGF诱导的UPF1在HNRNPC附近的募集促进了细胞增殖mRNAs的剪接监视。为了鉴定同时被多个所研究的RBPs共结合的RNA，还开发了顺序免疫沉淀irCLIP （Re-CLIP）方法。Re-CLIP证实了在irCLIP-RNP中观察到的结合关系，并发现HNRNPC和UPF1 RBP在RND3和DDX3X mRNAs上共同结合。irCLIP-RNP和Re-CLIP提供了一个识别和表征活细胞中动态RNA-蛋白组装的框架。

附：英文原文

Title: irCLIP-RNP and Re-CLIP reveal patterns of dynamic protein assemblies on RNA

Author: Ducoli, Luca, Zarnegar, Brian J., Porter, Douglas F., Meyers, Robin M., Miao, Weili, Riley, Nicholas M., Srinivasan, Suhas, Jackrazi, Leandra V., Yang, Yen-Yu, Li, Zhouxian, Wang, Yinsheng, Bertozzi, Carolyn R., Flynn, Ryan A., Khavari, Paul A.

Issue&Volume: 2025-03-26

Abstract: RNA-binding proteins (RBPs) control varied processes, including RNA splicing, stability, transport and translation1,2,3. Dysfunctional RNA–RBP interactions contribute to the pathogenesis of human disease1,4,5; however, characterizing the nature and dynamics of multiprotein assemblies on RNA has been challenging. Here, to address this, non-isotopic ligation-based ultraviolet-light-induced cross-linking and immunoprecipitation6 was combined with mass spectrometry (irCLIP-RNP) to identify RNA-dependent associated proteins (RDAPs) co-bound to RNA with any RBP of interest. irCLIP-RNP defined landscapes of multimeric protein assemblies on RNA, revealing patterns of RBP–RNA associations, including cell-type-selective combinatorial relationships between RDAPs and primary RBPs. irCLIP-RNP also defined dynamic RDAP remodelling in response to epidermal growth factor (EGF), revealing that EGF-induced recruitment of UPF1 adjacent to HNRNPC promotes splicing surveillance of cell proliferation mRNAs. To identify the RNAs simultaneously co-bound by multiple studied RBPs, a sequential immunoprecipitation irCLIP (Re-CLIP) method was also developed. Re-CLIP confirmed binding relationships observed in irCLIP-RNP and identified HNRNPC and UPF1 RBP co-binding on RND3 and DDX3X mRNAs. irCLIP-RNP and Re-CLIP provide a framework to identify and characterize dynamic RNA–protein assemblies in living cells.

DOI: 10.1038/s41586-025-08787-5

Source: https://www.nature.com/articles/s41586-025-08787-5