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Biology of RNA G-quadruplexes

RNA G 四链体的生物学

基本信息

批准号：
10557098
负责人：
Pavel Ivanov
金额：
$ 37.59万
依托单位：
BRIGHAM AND WOMEN'S HOSPITAL
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-02-01 至 2025-01-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10557098
关键词：
3-Dimensional 7-deazaguanine Affect Base Pairing Binding Binding Proteins Biochemical Biological Biological Assay Biological Process Biological Testing Biology Biophysics Cancer Biology Cell physiology Cells Cellular Stress Collaborations DNA DNA Maintenance Data Development Disease Elements Etiology Eukaryotic Cell Event Functional disorder G-Quartets Gene Expression Genes Genetic Transcription Goals Growth Guanine Guanosine Homeostasis Human In Vitro Intervention Investigation Ions Laboratories Malignant Neoplasms Mediating Messenger RNA Metabolism Methods Molecular Molecular Target Mutation Nerve Degeneration Neurodegenerative Disorders Nucleic Acid Regulatory Sequences Nucleic Acids Pathologic Pathology Pathway interactions Physiological Process Proteins Proteomics Publishing RNA RNA Binding RNA Sequences RNA metabolism Regulation Regulatory Element Reporting Research Ribonucleic Acid Regulatory Sequences Role Stress Structure System Techniques Testing Therapeutic Transcript Translational Regulation Translations Work biological adaptation to stress biophysical techniques candidate selection genetic manipulation genome-wide analysis human disease in vivo interest mRNA Stability mRNA Translation novel novel strategies novel therapeutics permissiveness pharmacologic physiologic stressor posttranscriptional prevent telomere three dimensional structure transcriptome tumorigenic

项目摘要

Summary G-quadruplexes (G4s) are non-canonical secondary structures in nucleic acids that are formed by guanine-rich sequences. G4 structural and functional studies have largely focused on DNA G4s, and the number of biological functions assigned to these motifs has grown rapidly since the discovery of their involvement in telomere biology. RNA G4s (RG4s) are less studied, but interest is increasing due to their association with multiple processes. A comprehensive understanding of how RNA G4s contribute to cell physiology and pathophysiology is the long-term research goal of the applicant. Multiple reports clearly demonstrate that G4s are enriched in mRNA 5’- and 3’-untranslated regulatory regions. There is an increasing evidence that RG4s control gene expression at transcriptional and post- transcriptional levels, although such data is largely based on in vitro studies. Testing the biological significance of RG4s requires proving that RG4s exist in vivo. Intriguingly, RG4s appear predominantly unfolded in eukaryotic cells, whereas they are readily folded in vitro, suggesting that in cells RG4s are constitutively recognized and actively unfolded. We hypothesize that RG4 folding-unfolding regulates mRNA homeostasis. This hypothesis is based on our analysis of human transcriptome that identifies RG4s as stress-responsive RNA elements. We will test this hypothesis with three specific aims. In AIM1, we will determine and characterize the fraction of the human transcriptome that contains putative stress-responsive RG4s in living cells. In AIM2, we will identify bona fide RG4-binding proteins using a novel approach based on proteomic/biochemical analysis of interactions between the 7-deazaguanine RNA derivatives and proposed binding factors. In AIM 3, we will use functional assays to determine the biological significance of RG4s in mRNA stability, localization and translation. We will use biophysical and biochemical methods to validate selected RG4 candidates. This work will elucidate how RG4-mediated functions contribute to cellular mRNA homeostasis, and will identify physiologically significant RG4-binding partners, which in turn may reveal molecular targets and pathways with therapeutic potential. The understanding of cellular functions of RG4 motifs is particularly relevant to the biology of cancer and neurodegeneration. RNA regions containing RG4s significantly overlap with regions containing disease- associated mutations. The proposed studies may elucidate molecular events underlying normal and pathological aspects of cell physiology, and identify events contributing to the tumorigenic or neurodegenerative changes.

总结 G-四链体（G4）是核酸中的非规范二级结构，其通过以下方式形成：富含鸟嘌呤的序列G4结构和功能研究主要集中在DNA G4上，自发现这些基序以来，赋予这些基序的生物功能数量迅速增加参与端粒生物学。RNA G4（RG 4）的研究较少，但由于它们的特性，人们的兴趣正在增加。与多个进程关联。全面了解RNA G4如何有助于细胞生理学和病理生理学是申请人的长期研究目标。多个报告清楚地表明，G4富含mRNA的5 '和3'非翻译调控，地区越来越多的证据表明，RG 4在转录和转录后水平控制基因表达。转录水平，虽然这些数据主要是基于体外研究。测试生物学意义需要证明RG 4在体内存在。有趣的是，RG 4主要表现为未折叠，真核细胞，而它们在体外很容易折叠，这表明在细胞中RG 4是组成性的，被认可并积极展开。我们假设RG 4折叠-展开调节mRNA稳态。这一假设是基于我们对人类转录组的分析，该分析将RG 4鉴定为应激反应型。 RNA元件我们将以三个具体目标来检验这一假设。在AIM 1中，我们将确定和表征在生活中含有推定的应激反应RG 4的人转录组的部分细胞在AIM 2中，我们将使用基于以下的新方法来识别真正的RG 4结合蛋白 7-脱氮鸟嘌呤RNA衍生物和建议的7-脱氮鸟嘌呤RNA衍生物之间相互作用的蛋白质组学/生物化学分析结合因子在AIM 3中，我们将使用功能测定来确定RG 4在以下中的生物学意义： mRNA稳定性、定位和翻译。我们将使用生物物理和生物化学方法来验证 RG 4候选人这项工作将阐明RG 4介导的功能如何有助于细胞mRNA 体内平衡，并将鉴定生理学上显著的RG 4结合伴侣，这反过来可以揭示具有治疗潜力的分子靶点和途径。对RG 4基序的细胞功能的理解与癌症的生物学特别相关和神经退化含有RG 4的RNA区域与含有疾病的区域显著重叠- 相关突变拟议的研究可能阐明正常和细胞生理学的病理学方面，并鉴定有助于肿瘤发生或神经退行性改变

项目成果

期刊论文数量（12）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back.

DOI：
10.1093/nar/gkaa1126
发表时间：
2020-12-16
期刊：
Nucleic acids research
影响因子：
14.9
作者：
Kharel P;Becker G;Tsvetkov V;Ivanov P
通讯作者：
Ivanov P

Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome.

DOI：
10.1093/nar/gkaa674
发表时间：
2020-12-16
期刊：
Nucleic acids research
影响因子：
14.9
作者：
Tosar JP;Segovia M;Castellano M;Gámbaro F;Akiyama Y;Fagúndez P;Olivera Á;Costa B;Possi T;Hill M;Ivanov P;Cayota A
通讯作者：
Cayota A

Stress granule subtypes: an emerging link to neurodegeneration.

DOI：
10.1007/s00018-020-03565-0
发表时间：
2020-12
期刊：
Cellular and molecular life sciences : CMLS
影响因子：
0
作者：
Advani VM;Ivanov P
通讯作者：
Ivanov P

Nicked tRNAs are stable reservoirs of tRNA halves in cells and biofluids.

DOI：
10.1073/pnas.2216330120
发表时间：
2023-01-24
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
影响因子：
11.1
作者：
Costa, Bruno;Li Calzi, Marco;Castellano, Mauricio;Blanco, Valentina;Cuevasanta, Ernesto;Litvan, Irene;Ivanov, Pavel;Witwer, Kenneth;Cayota, Alfonso;Tosar, Juan Pablo
通讯作者：
Tosar, Juan Pablo

Identification of bona fide RNA G-quadruplex binding proteins.

真正的 RNA G 四链体结合蛋白的鉴定。