Capture of RNA-binding proteins across mouse tissues using HARD-AP

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 ()
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Yijia Ren: Sichuan University
Hongyu Liao: Sichuan University
Jun Yan: China Agricultural University
Hongyu Lu: Sichuan University
Xiaowei Mao: University of Electronic Science and Technology of China
Chuan Wang: Sichuan University
Yi-fei Li: Sichuan University
Yu Liu: Sichuan University
Chong Chen: Sichuan University
Lu Chen: Sichuan University
Xiangfeng Wang: China Agricultural University
Kai-Yu Zhou: Sichuan University
Han-Min Liu: Sichuan University
Yi Liu: University of Texas Southwestern Medical Center
Yi-Min Hua: Sichuan University
Lin Yu: Sichuan University
Zhihong Xue: Sichuan University

Nature Communications, 2024, vol. 15, issue 1, 1-20

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.

Date: 2024
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DOI: 10.1038/s41467-024-52765-w

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