植物体内RNA二级结构探测方法的研究进展

doi:10.13560/j.cnki.biotech.bull.1985.2022-0518

摘要/Abstract

摘要：

生物体内的RNA因氢键等作用配对折叠形成复杂的二级结构及三级结构，并根据环境产生动态变化，由此行使功能。植物中的基因表达调控及配体感应都与RNA的结构相关，RNA结构也被认为是转录后调控的一项影响因素，RNA的结构对与之互作的蛋白的结构和功能产生影响，因此研究RNA功能过程中解析RNA结构尤为关键。目前，RNA二级结构的探测实验方法从X-射线经过酶切及化学探针标记，发展至结合高通量测序即可建构模型。此外，机器学习等方法也为RNA结构的探测提供了新的思路。本文综述了影响体内RNA结构的因素及近年来用于植物体内RNA结构预测的方法，讨论了现有方法的应用限制下对RNA二级结构预测新方法开发的意义及存在的问题，展望计算机预测方法与实验方法未来的发展趋势，旨为后续RNA结构相关研究提供方法参考。

关键词: RNA结构, 二级结构, 探测方法, 植物生理

Abstract:

RNAs fold into complex secondary and tertiary structures via hydrogen bond pairing to enable their diverse functions in cells after dynamic changes according to environment. RNA structure is considered to be related to the regulation of gene expression and ligand sensing in plants, and is also considered to be an important factor in post-transcriptional regulation. Structured RNA can also affect the dimensional structure of RNA binding proteins and their functions. Thus, the analysis of RNA structure is particularly critical in the study of RNA function. At present, various detection methods for RNA secondary structure（RSS）has been developed from X-ray to enzyme digestion and chemical probe labeling, which can be combined with high-throughput sequencing to construct models. In addition, machine learning and other methods also provide new ideas for the detection of RNA structure. In this review, we summarize the factors affecting the RNA structure in vivo and recent reported methods for probing RNA structure in vivo, discuss the significances of developing novel prediction methods for RSS under the limitations of current methods as well as the issues, and prospect the future development trend of computer prediction methods and experimental methods, aiming to provide a methodological reference for subsequent research on RNA structure.

Key words: RNA structure, secondary structure, detection methods, plant physiology

周晞雯, 成柯, 朱鸿亮. 植物体内RNA二级结构探测方法的研究进展[J]. 生物技术通报, 2023, 39(2): 51-62.

ZHOU Xi-wen, CHENG Ke, ZHU Hong-liang. Research Progress in the Approaches to in vivo RNA Secondary Structure Profiling in Plants[J]. Biotechnology Bulletin, 2023, 39(2): 51-62.

图/表 2

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试剂 Reagents	体内或体外 In vivo or in vitro	标记位点 Targeted sites	方法 Methods	材料种类 Species
DMS	体内&体外 In vivo & in vitro	C N³，A N¹，U N⁷	DMS-seq，Structure-seq，DMS-MaPseq，Dance-MAP	拟南芥 Arabidopsis thaliana^[30] 大肠杆菌 Escherichia coli^[37] 酵母细胞 Saccharomyces^[38] 创伤弧菌 Vibrio vulnificus^[39]
NAI, 1M7, NMIA, BzCN, _NAI-N3	体内&体外 In vivo & in vitro	2'-OH	SHAPE-seq, icSHAPE, SHAPE-MaPseq	斑马鱼 Danio rerio 小鼠 Mus musculus 拟南芥 Arabidopsis thaliana 水稻 Oryza sativa^[26]
甲基乙二醛 Methylglyoxal	体内&体外 In vivo & in vitro	C N³，4-NH₂，A N¹,6-NH₂，G N¹,2-NH₂	RIC-seq	小鼠 Mus musculus^[40] 枯草芽孢杆菌Bacillus subtilis 大肠杆菌 Escherichia coli^[41]
EDC	体内&体外 In vivo & in vitro	G N¹，U N³	Structure-seq	小鼠 Mus musculus^[42]
PDS, NAI	体外 In vitro		rG4-seq	HeLa细胞 HeLa cells 大肠杆菌 Escherichia coli 拟南芥 Arabidopsis thaliana^[43-44]
CMCT	体外 In vitro	U N³，G N1	CIRC-seq	小鼠 Mus musculus^[45-46]
CMCT, DMS	体外 In vitro	C N³，A N¹，U N⁷, G N¹	CIRS-seq	小鼠 Mus musculus^[47]
RNase V1, RNase S	体外 In vitro		PARS	酵母 Saccharomyces^[36] 人体淋巴细胞Human lymphoblastoid cell^s[9]
RNase P1	体外 In vitro		Fragseq	小鼠 Mus musculus^[48]
RNase V1 and RNase One	体外 In vitro		ssRNA-seq, dsRNA-seq，PIP-seq	果蝇Drosophila melanogaster 秀丽隐杆线虫Caenorhabditis elegans^[49] 拟南芥 Arabidopsis thali^ana[50]

试剂 Reagents	体内或体外 In vivo or in vitro	标记位点 Targeted sites	方法 Methods	材料种类 Species
DMS	体内&体外 In vivo & in vitro	C N³，A N¹，U N⁷	DMS-seq，Structure-seq，DMS-MaPseq，Dance-MAP	拟南芥 Arabidopsis thaliana^[30] 大肠杆菌 Escherichia coli^[37] 酵母细胞 Saccharomyces^[38] 创伤弧菌 Vibrio vulnificus^[39]
NAI, 1M7, NMIA, BzCN, _NAI-N3	体内&体外 In vivo & in vitro	2'-OH	SHAPE-seq, icSHAPE, SHAPE-MaPseq	斑马鱼 Danio rerio 小鼠 Mus musculus 拟南芥 Arabidopsis thaliana 水稻 Oryza sativa^[26]
甲基乙二醛 Methylglyoxal	体内&体外 In vivo & in vitro	C N³，4-NH₂，A N¹,6-NH₂，G N¹,2-NH₂	RIC-seq	小鼠 Mus musculus^[40] 枯草芽孢杆菌Bacillus subtilis 大肠杆菌 Escherichia coli^[41]
EDC	体内&体外 In vivo & in vitro	G N¹，U N³	Structure-seq	小鼠 Mus musculus^[42]
PDS, NAI	体外 In vitro		rG4-seq	HeLa细胞 HeLa cells 大肠杆菌 Escherichia coli 拟南芥 Arabidopsis thaliana^[43-44]
CMCT	体外 In vitro	U N³，G N1	CIRC-seq	小鼠 Mus musculus^[45-46]
CMCT, DMS	体外 In vitro	C N³，A N¹，U N⁷, G N¹	CIRS-seq	小鼠 Mus musculus^[47]
RNase V1, RNase S	体外 In vitro		PARS	酵母 Saccharomyces^[36] 人体淋巴细胞Human lymphoblastoid cell^s[9]
RNase P1	体外 In vitro		Fragseq	小鼠 Mus musculus^[48]
RNase V1 and RNase One	体外 In vitro		ssRNA-seq, dsRNA-seq，PIP-seq	果蝇Drosophila melanogaster 秀丽隐杆线虫Caenorhabditis elegans^[49] 拟南芥 Arabidopsis thali^ana[50]