Research Progress in the Approaches to in vivo RNA Secondary Structure Profiling in Plants

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

Abstract

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

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.

Figures/Tables 2

References 75

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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]