1. Capture of RNA-binding proteins across mouse tissues using HARD-AP.
- Author
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Ren, Yijia, Liao, Hongyu, Yan, Jun, Lu, Hongyu, Mao, Xiaowei, Wang, Chuan, Li, Yi-fei, Liu, Yu, Chen, Chong, Chen, Lu, Wang, Xiangfeng, Zhou, Kai-Yu, Liu, Han-Min, Liu, Yi, Hua, Yi-Min, Yu, Lin, and Xue, Zhihong
- 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. RNA-binding proteins (RBPs) modulate all aspects of RNA metabolism. Here the authors introduce a method named HARD-AP that effectively isolates RBPs and their closely associated RNA regulatory complexes from both cultured cells and fresh tissues. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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