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中国生物工程杂志

CHINA BIOTECHNOLOGY
中国生物工程杂志
中国生物工程杂志  2023, Vol. 43 Issue (7): 77-87    DOI: 10.13523/j.cb.2211057
综述     
RNA结合蛋白质谱鉴定技术研究进展*
孙若航,陈瑞冰**()
天津大学药物科学与技术学院 天津 300072
Advances in Ide.pngication of RNA-binding Proteins Based on Mass Spectrometry
Ruo-hang SUN,Rui-bing CHEN**()
School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
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摘要：

RNA结合蛋白在细胞中通过与RNA结合参与调控RNA的整个生命周期,在基因表达和生命进程中发挥着重要作用。RNA和蛋白质的结合异常与多种疾病的发生与发展密切相关,因此,探索RNA-蛋白质相互作用对研究潜在的生物功能和临床病理机制至关重要。近年来,随着鉴定技术的不断进步与革新,许多新的非经典RNA结合蛋白不断被发现。这些RNA结合蛋白大多数缺乏已知的RNA结合结构域,RNA与蛋白质之间复杂、多样的相互作用关系仍需进一步探究。从高通量鉴定和靶向鉴定两个方面,对基于质谱分析的RNA结合蛋白鉴定技术的最新进展进行综述,并着重讨论其技术原理、应用领域和优缺点,以期为更好地探索RNA-蛋白质相互作用的生物学功能及其在临床疾病中的作用机制提供参考。
关键词： RNA结合蛋白;  RNA-蛋白质相互作用;  蛋白质组学;  质谱    
Abstract:

RNA-binding proteins (RBPs) can bind RNAs through RNA-binding domains and regulate the fate or functions of their bound RNAs. RBPs are responsible for all the steps of RNA metabolism throughout their life cycle and are involved in many other cellular processes related to cell’s survival, replication, and adaption to environmental changes. RNA-protein interactions are essential to cell homeostasis, and their defects are associated with various diseases. Therefore, the characterization of RBPs is crucial to depict their functions and underlying molecular mechanisms. Recently, several methods have been developed and extensively applied to ide.pngy RBPs, uncovering many previously unannotated RBPs. However, the majority of the newly discovered RBPs lack classical RNA-binding domains, thus highlighting the complexity and diversity of RNA-protein interactions. Here, the progress in the ide.pngication of RBPs based on mass spectrometry was reviewed, from two aspects: high-throughput ide.pngication and targeted ide.pngication. Moreover, their technical principles, application areas, and strengths and limitations were discussed, providing new perspectives to better understand the biological significance and clinical implications of RNA-protein interactions.
Key words: RNA-binding protein    RNA-protein interaction    Proteomics    Mass spectrometry
收稿日期: 2021-11-29 出版日期: 2023-08-03
ZTFLH:  Q71  
基金资助: 国家自然科学基金(21974094)
通讯作者: **电子信箱:rbchen@tju.edu.cn   
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引用本文:

孙若航, 陈瑞冰. RNA结合蛋白质谱鉴定技术研究进展*[J]. 中国生物工程杂志, 2023, 43(7): 77-87.

Ruo-hang SUN, Rui-bing CHEN. Advances in Ide.pngication of RNA-binding Proteins Based on Mass Spectrometry. China Biotechnology, 2023, 43(7): 77-87.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.2211057    或    https://manu60.magtech.com.cn/biotech/CN/Y2023/V43/I7/77

图1  RIC策略示意图
图2  基于RNA标记的高通量RBPs鉴定技术示意图
图3  基于RNA理化性质的高通量鉴定技术示意图
图4  体外靶向RBPs鉴定技术示意图
图5  体内靶向RBPs鉴定技术示意图
方法 应用 优势 局限性 参考文献
RIC Poly(A)-RBPome 体内,无需核苷酸标记 交联,只适用于poly(A)RNA [12,14???? -19]
RBR-ID RBPome 体内,无需核苷酸标记,适用于
各种RNA		 交联,假阳性和假阴性 [21]
RICK、CARIC RBPome 体内,适用于各种RNA 交联,核苷酸标记 [22-23]
PP探针RNA标记 RBPome 体内,体外RNA标记,适用于
各种RNA		 交联,非特异性富集 [24]
基于AGPC的方法 RBPome 体内,无需核苷酸标记,适用于
各种RNA,覆盖率高		 交联,非特异性富集 [25???-29]
TRAPP RBPome 体内,无需核苷酸标记,适用于
各种RNA		 交联,非特异性富集 [30]
R-DeeP、DIF-FRAC RBPome 体内,无需核苷酸标记,无需交联 分析复杂,假阳性和假阴性 [31-32]
RNA沉降技术 MALAT1、SLERT RNA-蛋白质结合力强 体外,高丰度蛋白干扰 [4,34]
蛋白微阵列 小核仁RNA、
SNORD50A等		 无需裂解细胞,灵敏度高 体外,重组蛋白质性质影响鉴定结果 [35,36]
CHART、ChIRP、RAP NEAT1、MALAT1、Xist 体内,内源性,特异性强 交联,探针设计复杂,样本需求量大 [37??-40]
MS2-BioTRAP 淋巴增强因子-1(lymphoid enhancer factor-1)mRNA 体内 RNA、蛋白质外源表达 [41]
RAPID Zika病毒RNA 体内,直接标记蛋白质 RNA、蛋白质外源表达 [42]
TOBAP-MS HULC 体内,直接标记蛋白质,无需蛋白质
外源表达		 RNA外源表达 [43]
CBRIP U1小核RNA 体内 交联,gRNA设计,间接标记蛋白质 [44]
CRUIS NORAD 体内,直接标记蛋白质 gRNA设计 [45]
CARPID Xist、DANCR、MALAT1 体内,直接标记蛋白质 gRNA设计 [46]
表1  RBPs的高通量和靶向鉴定方法
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