2. Academic Validation
  3. In situ proximity labeling of proteins associated with circRNA and RNA G-quadruplexes

In situ proximity labeling of proteins associated with circRNA and RNA G-quadruplexes

  • Nat Chem Biol. 2025 Aug 7. doi: 10.1038/s41589-025-01993-2.
Jing Mo # 1 2 3,  Zonggui Chen # 4,  Manman Cui # 5,  Xin Fang 1,  Ruihan Li 1,  Shanshan Qin 1,  Zhenlin Zhou 1,  Mei Sun 1,  Jinjun Wu 2 3 6,  Chuan He 2 3,  Fang Wang 7,  Haojian Zhang 8,  Xiang Zhou 9,  Xiaocheng Weng 10
Affiliations

Affiliations

  • 1 State Key Laboratory of Metabolism and Regulation in Complex Organisms, College of Chemistry and Molecule Sciences, Taikang Center for Life and Medical Sciences, Department of Otorhinolaryngology-Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China.
  • 2 Department of Chemistry, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
  • 3 Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
  • 4 Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
  • 5 Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China.
  • 6 School of Bioengineering and Health, Wuhan Textile University, Wuhan, China.
  • 7 Wuhan University School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.
  • 8 Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China. haojian_zhang@whu.edu.cn.
  • 9 State Key Laboratory of Metabolism and Regulation in Complex Organisms, College of Chemistry and Molecule Sciences, Taikang Center for Life and Medical Sciences, Department of Otorhinolaryngology-Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China. xzhou@whu.edu.cn.
  • 10 State Key Laboratory of Metabolism and Regulation in Complex Organisms, College of Chemistry and Molecule Sciences, Taikang Center for Life and Medical Sciences, Department of Otorhinolaryngology-Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China. xcweng@whu.edu.cn.
  • # Contributed equally.
PMID: 40775047 DOI: 10.1038/s41589-025-01993-2
Abstract

Profiling the protein interactome of specific RNA loci aids in understanding the molecular mechanisms of regulatory RNA. However, current RNA-centric methods have sufficient space for improvement in terms of efficiency and biocompatibility. Here we developed TurboID-assisted proximity labeling of targeted RNA-interacting proteins (TAPRIP), in which the proximity labeling enzyme miniTurbo is attached to an RNA-targeting element, CIRTS3, to label the targeted RNA-interacting proteins, which are then analyzed by mass spectrometry. We profiled the interactome of mCherry circular RNA (circRNA) and found that HNRNPK modulates the expression of mCherry circRNA and Other endogenous circRNAs by binding their flanking introns. Targeting the BCL2 RNA G-quadruplex structure, we found that RBM12 promotes BCL2 translation by binding RNA G-quadruplexes and recruiting ribosomes. RBM12 knockdown markedly reduced proliferation and clonogenicity in MOLM-13, MV4-11 and THP-1 acute myeloid leukemia cells. These findings established the foundation for a versatile technique for analyzing the protein interactome of specific RNA sequences in live cells.

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