• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法,用中文像聊天一样搜索,搜遍4000万医学文献。AI智能推荐,让科研检索更轻松。

立即免费搜索

文件翻译

保留排版,准确专业,支持PDF/Word/PPT等文件格式,支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述,25分钟生成高质量综述,智能提取关键信息,辅助科研写作。

立即免费体验

探究动态 RNA 结构组及其功能。

Probing the dynamic RNA structurome and its functions.

机构信息

Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA.

Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands.

出版信息

Nat Rev Genet. 2023 Mar;24(3):178-196. doi: 10.1038/s41576-022-00546-w. Epub 2022 Nov 8.

DOI:10.1038/s41576-022-00546-w
PMID:36348050
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9644009/
Abstract

RNA is a key regulator of almost every cellular process, and the structures adopted by RNA molecules are thought to be central to their functions. The recent fast-paced evolution of high-throughput sequencing-based RNA structure mapping methods has enabled the rapid in vivo structural interrogation of entire cellular transcriptomes. Collectively, these studies are shedding new light on the long underestimated complexity of the structural organization of the transcriptome - the RNA structurome. Moreover, recent analyses are challenging the view that the RNA structurome is a static entity by revealing how RNA molecules establish intricate networks of alternative intramolecular and intermolecular interactions and that these ensembles of RNA structures are dynamically regulated to finely tune RNA functions in living cells. This new understanding of how RNA can shape cell phenotypes has important implications for the development of RNA-targeted therapeutic strategies.

摘要

RNA 是几乎每个细胞过程的关键调节剂,并且 RNA 分子采用的结构被认为是其功能的核心。基于高通量测序的 RNA 结构图谱方法的快速发展,使得对整个细胞转录组的快速体内结构研究成为可能。总的来说,这些研究揭示了转录组(RNA 结构组)结构组织的长期被低估的复杂性,为其提供了新的视角。此外,最近的分析通过揭示 RNA 分子如何建立复杂的分子内和分子间替代相互作用网络,以及这些 RNA 结构的组合如何动态调节以精细调整活细胞中 RNA 功能,对 RNA 结构组是静态实体的观点提出了挑战。这种对 RNA 如何塑造细胞表型的新理解,对于开发针对 RNA 的治疗策略具有重要意义。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0bec/9644009/4ad192cb8fc1/41576_2022_546_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0bec/9644009/fdc493f4d058/41576_2022_546_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0bec/9644009/f20726b3ef9a/41576_2022_546_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0bec/9644009/fba88df920d4/41576_2022_546_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0bec/9644009/24346a4a518c/41576_2022_546_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0bec/9644009/8942502a027b/41576_2022_546_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0bec/9644009/9da9fba8041e/41576_2022_546_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0bec/9644009/4ad192cb8fc1/41576_2022_546_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0bec/9644009/fdc493f4d058/41576_2022_546_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0bec/9644009/f20726b3ef9a/41576_2022_546_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0bec/9644009/fba88df920d4/41576_2022_546_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0bec/9644009/24346a4a518c/41576_2022_546_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0bec/9644009/8942502a027b/41576_2022_546_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0bec/9644009/9da9fba8041e/41576_2022_546_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0bec/9644009/4ad192cb8fc1/41576_2022_546_Fig7_HTML.jpg

相似文献

1
Probing the dynamic RNA structurome and its functions.探究动态 RNA 结构组及其功能。
Nat Rev Genet. 2023 Mar;24(3):178-196. doi: 10.1038/s41576-022-00546-w. Epub 2022 Nov 8.
2
Dawn of the in vivo RNA structurome and interactome.体内RNA结构组和相互作用组的黎明。
Biochem Soc Trans. 2016 Oct 15;44(5):1395-1410. doi: 10.1042/BST20160075.
3
The RNA structurome: transcriptome-wide structure probing with next-generation sequencing.RNA 结构组学:利用新一代测序技术进行转录组范围的结构探测。
Trends Biochem Sci. 2015 Apr;40(4):221-32. doi: 10.1016/j.tibs.2015.02.005. Epub 2015 Mar 18.
4
Profiling of RNA Structure at Single-Nucleotide Resolution Using nextPARS.利用 nextPARS 进行单核苷酸分辨率的 RNA 结构分析。
Methods Mol Biol. 2021;2284:51-62. doi: 10.1007/978-1-0716-1307-8_4.
5
RNAdt: An online tutorial and data portal for the RNA structurome era.RNAdt:RNA结构组学时代的在线教程与数据门户。
Biosystems. 2020 Mar;189:104065. doi: 10.1016/j.biosystems.2019.104065. Epub 2019 Oct 24.
6
RNA Framework for Assaying the Structure of RNAs by High-Throughput Sequencing.通过高通量测序分析 RNA 结构的 RNA 框架。
Methods Mol Biol. 2021;2284:63-76. doi: 10.1007/978-1-0716-1307-8_5.
7
Decoding the RNA structurome.解析RNA结构组
Curr Opin Struct Biol. 2016 Feb;36:142-8. doi: 10.1016/j.sbi.2016.01.007. Epub 2016 Feb 26.
8
Genome-Wide Probing of RNA Structures In Vitro Using Nucleases and Deep Sequencing.利用核酸酶和深度测序对体外RNA结构进行全基因组探测
Methods Mol Biol. 2016;1361:141-60. doi: 10.1007/978-1-4939-3079-1_9.
9
nextPARS: parallel probing of RNA structures in Illumina.nextPARS:Illumina 中 RNA 结构的并行探测。
RNA. 2018 Apr;24(4):609-619. doi: 10.1261/rna.063073.117. Epub 2018 Jan 22.
10
Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.核苷酸分辨率下 RNA 结构探测实验的差异分析:揭示 RNA 结构的调控功能。
Nat Commun. 2022 Jul 22;13(1):4227. doi: 10.1038/s41467-022-31875-3.

引用本文的文献

1
Integrating experimental feedback improves generative models for biological sequences.整合实验反馈可改进生物序列生成模型。
Nucleic Acids Res. 2025 Aug 27;53(16). doi: 10.1093/nar/gkaf832.
2
Controlling intermolecular base pairing in Drosophila germ granules by mRNA folding and its implications in fly development.通过mRNA折叠控制果蝇生殖颗粒中的分子间碱基配对及其对果蝇发育的影响。
Nat Commun. 2025 Aug 30;16(1):8135. doi: 10.1038/s41467-025-62973-7.
3
SHAPE-based chemical probes for studying preQ-RNA interactions in living bacteria.

本文引用的文献

1
Pervasive transcriptome interactions of protein-targeted drugs.蛋白质靶向药物的全基因组转录组相互作用。
Nat Chem. 2023 Oct;15(10):1374-1383. doi: 10.1038/s41557-023-01309-8. Epub 2023 Aug 31.
2
In vivo single-molecule analysis reveals COOLAIR RNA structural diversity.体内单分子分析揭示了 COOLAIR RNA 的结构多样性。
Nature. 2022 Sep;609(7926):394-399. doi: 10.1038/s41586-022-05135-9. Epub 2022 Aug 17.
3
Acylation probing of "generic" RNA libraries reveals critical influence of loop constraints on reactivity.酰化探针“通用” RNA 文库揭示了环约束对反应性的关键影响。
用于研究活细菌中preQ-RNA相互作用的基于SHAPE的化学探针。
bioRxiv. 2025 Jul 21:2025.07.21.665968. doi: 10.1101/2025.07.21.665968.
4
AlignmentFold and AlignmentPartition: Improving the align-then-fold approach for RNA secondary structure prediction.比对折叠与比对划分:改进用于RNA二级结构预测的先比对后折叠方法
bioRxiv. 2025 Jul 28:2025.07.23.666478. doi: 10.1101/2025.07.23.666478.
5
SEISMICgraph: a web-based tool for RNA structure data visualization.SEISMICgraph:一种用于RNA结构数据可视化的基于网络的工具。
Nucleic Acids Res. 2025 Jul 19;53(14). doi: 10.1093/nar/gkaf701.
6
Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis.利用RNA二级结构集合图谱和共变分析在活细胞中鉴定保守的RNA调控开关。
Nat Biotechnol. 2025 Jul 25. doi: 10.1038/s41587-025-02739-0.
7
Searching for druggable targets.寻找可成药靶点。
Elife. 2025 Jul 2;14:e107757. doi: 10.7554/eLife.107757.
8
Comprehensive datasets for RNA design, machine learning, and beyond.用于RNA设计、机器学习及其他领域的综合数据集。
Sci Rep. 2025 Jul 1;15(1):21417. doi: 10.1038/s41598-025-07041-2.
9
Structural heterogeneity and dynamics in the apical stem loop of s2m from SARS-CoV-2 Delta by an integrative NMR spectroscopy and MD simulation approach.通过综合核磁共振光谱和分子动力学模拟方法研究新冠病毒Delta变异株s2m顶端茎环的结构异质性和动力学
Nucleic Acids Res. 2025 Jun 20;53(12). doi: 10.1093/nar/gkaf552.
10
TAS-seq enables subcellular single-stranded adenosine profiling by signal peptide-assisted adenosine deamination.TAS-seq通过信号肽辅助的腺苷脱氨作用实现亚细胞单链腺苷分析。
Cell Rep Methods. 2025 Jul 21;5(7):101087. doi: 10.1016/j.crmeth.2025.101087. Epub 2025 Jun 25.
Cell Chem Biol. 2022 Aug 18;29(8):1341-1352.e8. doi: 10.1016/j.chembiol.2022.05.005. Epub 2022 Jun 2.
4
How does RNA fold dynamically?RNA 如何动态折叠?
J Mol Biol. 2022 Sep 30;434(18):167665. doi: 10.1016/j.jmb.2022.167665. Epub 2022 Jun 1.
5
Computational Approaches for RNA Structure Ensemble Deconvolution from Structure Probing Data.从结构探测数据中对 RNA 结构集合进行去卷积的计算方法。
J Mol Biol. 2022 Sep 30;434(18):167635. doi: 10.1016/j.jmb.2022.167635. Epub 2022 May 17.
6
SHAPE-enabled fragment-based ligand discovery for RNA.基于形状的片段先导化合物发现技术在 RNA 中的应用
Proc Natl Acad Sci U S A. 2022 May 17;119(20):e2122660119. doi: 10.1073/pnas.2122660119. Epub 2022 May 13.
7
Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch.转录共转录 RNA 链交换是嘌呤感应转录核糖开关基因调控机制的基础。
Nucleic Acids Res. 2022 Nov 28;50(21):12001-12018. doi: 10.1093/nar/gkac102.
8
Global mapping of RNA homodimers in living cells.在活细胞中对 RNA 同源二聚体进行全局映射。
Genome Res. 2022 May;32(5):956-967. doi: 10.1101/gr.275900.121. Epub 2022 Mar 24.
9
Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP.使用 DANCE-MaP 发现 7SK RNA 中的大规模、细胞状态响应变构开关。
Mol Cell. 2022 May 5;82(9):1708-1723.e10. doi: 10.1016/j.molcel.2022.02.009. Epub 2022 Mar 22.
10
Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells.感染细胞中 SARS-CoV-2 基因组的二级结构组合。
Nat Commun. 2022 Mar 2;13(1):1128. doi: 10.1038/s41467-022-28603-2.