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

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.

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Publication Details

Journal
Nature Communications
Published
2024-09-28
DOI
https://doi.org/10.1038/s41467-024-52765-w
Citations
2
Primary Topic
RNA Research and Splicing
Type
article
Field-Weighted Citation Impact
0.47

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article

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

Hanmin Liu, Yu Liu, Zhihong Xue, Xiaowei Mao et al.
2 citations
Nature Communications
RNA Research and Splicing
0.47
article

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

Hanmin Liu, Yu Liu, Zhihong Xue, Xiaowei Mao, Yi Liu, Chong Chen, Yifei Li, Lu Chen, Chuan Wang, Hongyu Lu, Kaiyu Zhou, Jun Yan, Xiangfeng Wang, Yimin Hua, Hongyu Liao, Lin Yu, Yijia Ren
article en
2 citations

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.

Nature CommunicationsVol. 15(1)
University of Electronic Science and Technology of China (CN), Sichuan University (CN), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital (CN), Sichuan Research Center of New Materials (CN), China Agricultural University (CN), The University of Texas Southwestern Medical Center (US)
Foundation for the National Institutes of Health, Welch Foundation, European Molecular Biology Laboratory, National Natural Science Foundation of China, China Postdoctoral Science Foundation, Sichuan University, Yunnan University, National Institutes of Health, Beijing Nova Program, National Key Research and Development Program of China, National Key Research and Development Program of China Stem Cell and Translational Research
Openalex Percentile: Top 35%
RNA Research and Splicing
0.47
DOIOpen Access PDFOpenAlex
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