通过 SHAPE 对病毒 RNA 基因组进行物理和功能分析。
Physical and Functional Analysis of Viral RNA Genomes by SHAPE.
机构信息
Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA; email:
出版信息
Annu Rev Virol. 2019 Sep 29;6(1):93-117. doi: 10.1146/annurev-virology-092917-043315. Epub 2019 Jul 23.
Abstract
RNA viruses encode the information required to usurp cellular metabolism and gene regulation and to enable their own replication in two ways: in the linear sequence of their RNA genomes and in higher-order structures that form when the genomic RNA strand folds back on itself. Application of high-resolution SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) structure probing to viral RNA genomes has identified numerous new regulatory elements, defined new principles by which viral RNAs interact with the cellular host and evade host immune responses, and revealed relationships between virus evolution and RNA structure. This review summarizes our current understanding of genome structure-function interrelationships for RNA viruses, as informed by SHAPE structure probing, and outlines opportunities for future studies.
摘要
RNA 病毒通过两种方式编码所需的信息来篡夺细胞代谢和基因调控，并实现自身复制：一种是通过其 RNA 基因组的线性序列，另一种是通过基因组 RNA 链自身回折形成的高级结构。高分辨率 SHAPE（通过引物延伸进行选择性 2'-羟乙酰基分析）结构探测技术在病毒 RNA 基因组中的应用，已经鉴定出许多新的调控元件，定义了病毒 RNA 与宿主细胞相互作用和逃避宿主免疫反应的新原则，并揭示了病毒进化与 RNA 结构之间的关系。本文综述了 SHAPE 结构探测技术揭示的 RNA 病毒基因组结构与功能关系的最新认识，并概述了未来研究的机会。
相似文献
1
Physical and Functional Analysis of Viral RNA Genomes by SHAPE.通过 SHAPE 对病毒 RNA 基因组进行物理和功能分析。
Annu Rev Virol. 2019 Sep 29;6(1):93-117. doi: 10.1146/annurev-virology-092917-043315. Epub 2019 Jul 23.
2
RNA Structures and Their Role in Selective Genome Packaging.RNA 结构及其在选择性基因组包装中的作用。
Viruses. 2021 Sep 8;13(9):1788. doi: 10.3390/v13091788.
3
Global organization of a positive-strand RNA virus genome.正链 RNA 病毒基因组的全球组织。
PLoS Pathog. 2013;9(5):e1003363. doi: 10.1371/journal.ppat.1003363. Epub 2013 May 23.
4
Exploring the architecture of viral RNA genomes.探索病毒 RNA 基因组的结构。
Curr Opin Virol. 2015 Jun;12:66-74. doi: 10.1016/j.coviro.2015.03.018. Epub 2015 Apr 14.
5
RNA viruses: genome structure and evolution.RNA病毒：基因组结构与进化
Curr Opin Genet Dev. 1991 Dec;1(4):485-93. doi: 10.1016/s0959-437x(05)80196-0.
6
Cis-acting RNA elements in positive-strand RNA plant virus genomes.正链RNA植物病毒基因组中的顺式作用RNA元件。
Virology. 2015 May;479-480:434-43. doi: 10.1016/j.virol.2015.02.032. Epub 2015 Mar 7.
7
Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: Implications for virus evolution and host persistence.正链RNA病毒基因组中基因组规模有序RNA结构（GORS）的检测：对病毒进化和宿主持续性的影响。
RNA. 2004 Sep;10(9):1337-51. doi: 10.1261/rna.7640104. Epub 2004 Jul 23.
8
Structure-first identification of RNA elements that regulate dengue virus genome architecture and replication.结构优先鉴定调控登革热病毒基因组结构和复制的 RNA 元件。
Proc Natl Acad Sci U S A. 2023 Apr 11;120(15):e2217053120. doi: 10.1073/pnas.2217053120. Epub 2023 Apr 3.
9
High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states.高通量SHAPE分析揭示了HIV-1基因组RNA中在不同生物学状态下高度保守的结构。
PLoS Biol. 2008 Apr 29;6(4):e96. doi: 10.1371/journal.pbio.0060096.
10
Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA.功能分析揭示 G/U 对对于传染性非编码类病毒 RNA 的复制和运输至关重要。
Nucleic Acids Res. 2020 Apr 6;48(6):3134-3155. doi: 10.1093/nar/gkaa100.
引用本文的文献
1
Improving RNA Secondary Structure Prediction Through Expanded Training Data.通过扩展训练数据改进RNA二级结构预测
bioRxiv. 2025 May 3:2025.05.03.652028. doi: 10.1101/2025.05.03.652028.
2
Exploiting functional regions in the viral RNA genome as druggable entities.将病毒RNA基因组中的功能区域开发为可成药实体。
Elife. 2025 Jul 2;13:RP103923. doi: 10.7554/eLife.103923.
3
Codon-deoptimized single-round infectious virus for therapeutic and vaccine applications.用于治疗和疫苗应用的密码子去优化单轮感染性病毒。
Sci Rep. 2025 Jul 1;15(1):22033. doi: 10.1038/s41598-025-05643-4.
4
Analysis of natural structures and chemical mapping data reveals local stability compensation in RNA.对天然结构和化学图谱数据的分析揭示了RNA中的局部稳定性补偿。
Nucleic Acids Res. 2025 Jun 20;53(12). doi: 10.1093/nar/gkaf565.
5
Analysis of natural structures and chemical mapping data reveals local stability compensation in RNA.对天然结构和化学图谱数据的分析揭示了RNA中的局部稳定性补偿。
bioRxiv. 2024 Dec 12:2024.12.11.627843. doi: 10.1101/2024.12.11.627843.
6
Viral RNA Interactome: The Ultimate Researcher's Guide to RNA-Protein Interactions.病毒 RNA 相互作用组：RNA-蛋白质相互作用的终极研究人员指南。
Viruses. 2024 Oct 30;16(11):1702. doi: 10.3390/v16111702.
7
Analysis of the abundance and diversity of RNA secondary structure elements in RNA viruses using the RNAsselem Python package.使用 RNAsselem Python 包分析 RNA 病毒中 RNA 二级结构元件的丰度和多样性。
Sci Rep. 2024 Nov 19;14(1):28587. doi: 10.1038/s41598-024-80240-5.
8
Mapping the structural landscape of the yeast Ty3 retrotransposon RNA genome.绘制酵母 Ty3 反转录转座子 RNA 基因组的结构景观。
Nucleic Acids Res. 2024 Sep 9;52(16):9821-9837. doi: 10.1093/nar/gkae494.
9
The myriad roles of RNA structure in the flavivirus life cycle.RNA 结构在黄病毒生命周期中的多种作用。
RNA Biol. 2024 Jan;21(1):14-30. doi: 10.1080/15476286.2024.2357857. Epub 2024 May 26.
10
Recruitment of multi-segment genomic RNAs by Bluetongue virus requires a preformed RNA network.蓝舌病毒通过多片段基因组 RNA 的募集需要一个预先形成的 RNA 网络。
Nucleic Acids Res. 2024 Aug 12;52(14):8500-8514. doi: 10.1093/nar/gkae404.
本文引用的文献
1
Structure mapping of dengue and Zika viruses reveals functional long-range interactions.登革热和 Zika 病毒的结构映射揭示了功能上的长程相互作用。
Nat Commun. 2019 Mar 29;10(1):1408. doi: 10.1038/s41467-019-09391-8.
2
Integrative Analysis of Zika Virus Genome RNA Structure Reveals Critical Determinants of Viral Infectivity. Zika 病毒基因组 RNA 结构的综合分析揭示了病毒感染力的关键决定因素。
Cell Host Microbe. 2018 Dec 12;24(6):875-886.e5. doi: 10.1016/j.chom.2018.10.011. Epub 2018 Nov 21.
3
Pervasive tertiary structure in the dengue virus RNA genome.登革热病毒 RNA 基因组中的普遍三级结构。
Proc Natl Acad Sci U S A. 2018 Nov 6;115(45):11513-11518. doi: 10.1073/pnas.1716689115. Epub 2018 Oct 19.
4
COMRADES determines in vivo RNA structures and interactions.COMRADES 可用于体内 RNA 结构和相互作用的测定。
Nat Methods. 2018 Oct;15(10):785-788. doi: 10.1038/s41592-018-0121-0. Epub 2018 Sep 10.
5
High-throughput determination of RNA structures.高通量 RNA 结构测定。
Nat Rev Genet. 2018 Oct;19(10):615-634. doi: 10.1038/s41576-018-0034-x.
6
Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing.高分辨率 SHAPE 探测揭示的 mRNA 结构的普遍调控功能。
Cell. 2018 Mar 22;173(1):181-195.e18. doi: 10.1016/j.cell.2018.02.034. Epub 2018 Mar 15.
7
Probing the Structures of Viral RNA Regulatory Elements with SHAPE and Related Methodologies.利用SHAPE及相关方法探究病毒RNA调控元件的结构
Front Microbiol. 2018 Jan 9;8:2634. doi: 10.3389/fmicb.2017.02634. eCollection 2017.
8
Structural divergence creates new functional features in alphavirus genomes.结构分化在甲病毒基因组中创造了新的功能特征。
Nucleic Acids Res. 2018 Apr 20;46(7):3657-3670. doi: 10.1093/nar/gky012.
9
Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements.对正链 RNA 病毒中 RNA 结构的探测揭示了结构元件的选择压力。
Nucleic Acids Res. 2018 Mar 16;46(5):2573-2584. doi: 10.1093/nar/gkx1273.
10
The roles of five conserved lentiviral RNA structures in HIV-1 replication.五种保守的慢病毒 RNA 结构在 HIV-1 复制中的作用。
Virology. 2018 Jan 15;514:1-8. doi: 10.1016/j.virol.2017.10.020. Epub 2017 Nov 9.
Zotero 插件