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

Journal: Nature communications
PMID: 39341811

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.

Authors

  • Yijia Ren
    Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China.
  • Hongyu Liao
    Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China.
  • Jun Yan
    Department of Statistics, University of Connecticut, Storrs, CT 06269, USA.
  • Hongyu Lu
    School of Pharmacy, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China. mpbolhy@126.com.
  • Xiaowei Mao
    Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China.
  • Chuan Wang
    Department of Endocrinology and Metabolism, Qilu Hospital, Shandong University, Jinan, China.
  • Yi-Fei Li
    Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China.
  • Yu Liu
    Research Center of Information Technology, Beijing Academy of Agriculture and Forestry Science, Beijing, China.
  • Chong Chen
    Department of Orthorpaedic Surgery, Peking Union Medical College Hospital, No.1 Shuaifuyuan, Dongcheng district, Beijing, 100730, People's Republic of China.
  • Lu Chen
    Ultrasonic Department, Zhongda Hospital Affiliated to Southeast University, Nanjing, 210009, China.
  • Xiangfeng Wang
    Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China.
  • Kai-Yu Zhou
    Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China.
  • Han-Min Liu
    Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China.
  • Yi Liu
    Department of Interventional Therapy, Ningbo No. 2 Hospital, Ningbo, China.
  • Yi-Min Hua
    Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China. drhuayimin@scu.edu.cn.
  • Lin Yu
    Department of Computer Science, The University of Texas at Dallas, Richardson, Texas 75080, United States.
  • Zhihong Xue
    Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China. xuez@scu.edu.cn.

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