RNA-Binding Proteome Analysis and Functional Explorations★

doi:10.6023/A23070316

Acta Chimica Sinica ›› 2024, Vol. 82 ›› Issue (1): 53-61.DOI: 10.6023/A23070316 Previous Articles Next Articles

Special Issue: 庆祝《化学学报》创刊90周年合辑

Review

RNA结合蛋白的组学解析与功能探索^★

曾如馨, 陈鹏^*()

北京大学化学与分子工程学院化学生物学系北京大学合成与功能生物分子中心北京 100871

投稿日期:2023-07-02 发布日期:2023-08-14

作者简介:

曾如馨, 2023年博士毕业于北京大学化学与分子工程学院, 就读期间曾获北京大学博士研究生校长奖学金. 2018年加入陈鹏教授课题组, 主要研究方向为时空分辨的蛋白质和蛋白质翻译后修饰、蛋白质互作组学.

陈鹏, 北京大学化学与分子工程学院教授、化学生物系主任, 新基石研究员. 长期致力于化学与生命科学前沿交叉研究, 系统地发展了适用于活细胞的化学反应, 为生命问题的探索提供了创新的工具和研究方式. 尤其是提出并发展了“生物正交剪切反应”, 突破了在活细胞内研究蛋白质功能的技术瓶颈, 并应用于蛋白质药物开发和蛋白质组学研究, 开拓了生物正交化学新方向, 受到国内外同行的高度重视和应用. 现任中国化学会化学生物学专业委员会主任、美国化学会ACS Chemical Biology执行主编等.

^★庆祝《化学学报》创刊90周年.

基金资助:
项目受科技部国家重点研发计划(2021YFA1302603)

RNA-Binding Proteome Analysis and Functional Explorations^★

Ruxin Zeng, Peng R. Chen()

Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871

Received:2023-07-02 Published:2023-08-14
Contact: * E-mail: pengchen@pku.edu.cn
About author:
^★Dedicated to the 90th anniversary of Acta Chimica Sinica.
Supported by:
National Key Research and Development Programmes of the Ministry of Science and Technology of China(2021YFA1302603)

Post-transcriptional regulations play a critical role in diverse biological processes, and a series of RNA-protein interactions are involved in their underlying mechanism. RNA-binding proteins (RBPs) are key participants and executors in entire life cycle of RNA, affecting the operation of biological processes and the maintenance of cellular homeostasis. The RNA-binding proteome profiling therefore provides crucial information for discovering biological markers and targets of diseases. An array of RBPs capturing methods have been developed in recent years, ranging from profiling binding proteins of specific RNA to unbiased global RBPs identification, and even to exploring the functional aspects of RBPs such as spatial distribution and/or post-translational modifications. This review will focus on tool development for RBP proteomics and functional proteome characterization, and finally discusses bottlenecks and future prospects of this exciting direction of RBP proteomics.

Key words: RNA-binding proteins, RNA binding proteome, phase separation, spatial distribution, post-translational modifications

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Ruxin Zeng, Peng R. Chen. RNA-Binding Proteome Analysis and Functional Explorations^★[J]. Acta Chimica Sinica, 2024, 82(1): 53-61.

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Fig. & Tab. 4

Figure 1. Function of RNA-binding proteins. RNA-binding proteins are involved in the entire life of RNA, including selective splicing, transport, stabilization, processing, translation and degradation, as well as the formation of membrane-less organelles[3?????-9]. The Figure includes the gene names of some RBPs involved in the relevant process

Figure 2. Profiling RNA binding proteome of specific RNAs. (a) RNA-protein complexes captured by oligonucleotides[38-39,42]. (b) Proteins interacted with specific RNA labeled by proximity labeling enzyme[43-44]

Figure 3. Unbiased methods for profiling RNA binding proteome. (a) RBR-ID developed by 4-SU[46]. (b) RICK/CARIC method developed by 5-EU combined with click reaction[47-48]. (c) RBPs extraction by phase separation[50??-53]

Figure 4. Tool and prospect of functional RNA binding proteomics. Profiling subcellular RNA-binding proteomes with proximity labeling techniques and profiling post-translational modification proteome of RBP with corresponding enrichment methods

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RNA结合蛋白的组学解析与功能探索^★

RNA-Binding Proteome Analysis and Functional Explorations^★

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RNA结合蛋白的组学解析与功能探索★

RNA-Binding Proteome Analysis and Functional Explorations★

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Abstract

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Fig. & Tab. 4

References 80

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RNA结合蛋白的组学解析与功能探索^★

RNA-Binding Proteome Analysis and Functional Explorations^★