1. Capture of RNA-binding proteins across mouse tissues using HARD-AP
- Author
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Yijia Ren, Hongyu Liao, Jun Yan, Hongyu Lu, Xiaowei Mao, Chuan Wang, Yi-fei Li, Yu Liu, Chong Chen, Lu Chen, Xiangfeng Wang, Kai-Yu Zhou, Han-Min Liu, Yi Liu, Yi-Min Hua, Lin Yu, and Zhihong Xue
- Subjects
Science - Abstract
Abstract RNA-binding proteins (RBPs) modulate all aspects of RNA metabolism, but a comprehensive picture of RBP expression across tissues is lacking. Here, we describe our development of the method we call HARD-AP that robustly retrieves RBPs and tightly associated RNA regulatory complexes from cultured cells and fresh tissues. We successfully use HARD-AP to establish a comprehensive atlas of RBPs across mouse primary organs. We then systematically map RNA-binding sites of these RBPs using machine learning-based modeling. Notably, the modeling reveals that the LIM domain as an RNA-binding domain in many RBPs. We validate the LIM-domain-only protein Csrp1 as a tissue-dependent RNA binding protein. Taken together, HARD-AP is a powerful approach that can be used to identify RBPomes from any type of sample, allowing comprehensive and physiologically relevant networks of RNA-protein interactions.
- Published
- 2024
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