Transcription-Coupled DNA Supercoiling

转录偶联 DNA 超螺旋

• 批准号: 8762585
• 负责人: Fenfei Leng
• 金额: $ 31.72万
• 依托单位: FLORIDA INTERNATIONAL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-01 至 2018-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8762585
• 关键词: Affect; Anti-Bacterial Agents; Antineoplastic Agents; Autistic Disorder; Binding; Biological Process; Camptothecin; Cells; Chromatin Loop; Chromosomes; Ciprofloxacin; Complex; Coupled; DNA; DNA Ligation; DNA Topoisomerases; DNA biosynthesis; DNA-Directed RNA Polymerase; Data; Diffusion; Doxorubicin; Escherichia coli; Fragile X Syndrome; Gene Expression; Genes; Genetic Recombination; Genetic Transcription; Genome Stability; Goals; Hereditary Disease; Human; Huntington Disease; Knowledge; Laboratories; Lac Repressors; Malignant Neoplasms; Mediating; Modeling; Molecular; Nature; Nucleoproteins; Plasmids; Play; Predisposition; Process; Processed Genes; Property; Proteins; Research; Role; Salmonella; Salmonella typhimurium; Sequence-Specific DNA Binding Protein; Site; Superhelical DNA; System; Testing; Transcriptional Activation; Twin Multiple Birth; Work; base; driving force; in vivo; promoter; protein function; public health relevance; research study; stem

DESCRIPTION (provided by applicant): For decades, it has been recognized that transcribing along the DNA double helix by a RNA polymerase can enhance localized DNA supercoiling. This process has been elegantly explained by a "twin-supercoiled- domain" model in which positive DNA supercoils are generated ahead of a translocating RNA polymerase and negative supercoils behind it. However, detailed mechanisms at the molecular level are still unavailable. For instance, how DNA topological barriers affect transcription-coupled DNA supercoiling (TCDS) has not been fully understood. The long-term goal of the proposed research is to understand the molecular mechanisms and biological functions of TCDS and DNA topological barriers. The objectives of this application are to determine what properties make certain DNA-looping and -wrapping proteins function as topological barriers and block supercoil diffusion, to study how DNA topological barriers regulate TCDS in E. coli cells, and to examine how localized, transient TCDS activates gene expression in vivo. Our central hypothesis is that TCDS by RNA polymerases is a major chromosome remodeling force in E. coli cells where the cells use nucleoprotein-based, topological barriers to confine TCDS to localized regions and, as a result, greatly influence the nearby, coupled DNA transactions. Our hypothesis has been formulated on the basis of strong preliminary data produced in our laboratory and will be tested by pursuing the following three specific aims: 1) to determine molecular mechanisms of DNA topological barriers and examine how the DNA topological barriers confine supercoils to localized regions and affect the efficiency of TCDS; 2) to examine the role of DNA topological barriers in TCDS in E. coli cells; 3) to investigate how transient, dynamic TCDS activates transcription in E. coli cells and how DNA topological barriers affect the efficiency of transcription activation by TCDS. Information from the proposed experiments will ultimately provide us with a better understanding of the mechanisms of TCDS, especially the roles of DNA topological barriers in TCDS and the coupled gene transcription and expression.

描述（由申请人提供）：数十年来，人们已经认识到，RNA聚合酶沿DNA双螺旋转录可以增强局部DNA超螺旋。这个过程用“双蛋白酶结构域”模型优雅地解释了，在该模型中，在其背后的RNA聚合酶和负超级锅中生成了阳性DNA超旋翼。但是，分子水平的详细机制仍然无法使用。例如，DNA拓扑障碍如何影响转录耦合的DNA超螺旋架（TCD）尚未完全了解。拟议的研究的长期目标是了解TCD和DNA拓扑障碍的分子机制和生物学功能。该应用的目标是确定哪些特性使某些DNA循环和 - 包装蛋白充当拓扑障碍并阻止超副膜扩散，以研究DNA拓扑障碍如何调节大肠杆菌细胞中的TCD，并检查局部化的瞬态，短暂性TCD在体内激活基因表达。我们的中心假设是，RNA聚合酶的TCD是大肠杆菌细胞中主要的染色体重塑力，在该染色体中，细胞使用基于核蛋白的基于核蛋白的拓扑障碍，将TCD局限于局部区域，因此极大地影响了附近的DNA交易。我们的假设是基于实验室中产生的强有初步数据提出的，将通过追求以下三个特定目的来测试：1）确定DNA拓扑障碍的分子机制，并研究DNA拓扑障碍如何将超级循环限制在局部区域和局部区域并影响TCD的效率； 2）检查DNA拓扑障碍在大肠杆菌细胞中TCD中的作用； 3）研究瞬态，动态TCD如何激活大肠杆菌细胞中的转录以及DNA拓扑障碍如何影响TCD的转录激活效率。提出的实验的信息最终将使我们更好地了解TCD的机制，尤其是DNA拓扑障碍在TCD和耦合基因转录和表达中的作用。

项目成果

RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals.

RNA 拓扑异构酶普遍存在于生命的各个领域，并与动物的多核糖体相关

• DOI: 10.1093/nar/gkw508
• 发表时间: 2016-07-27
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Ahmad M;Xue Y;Lee SK;Martindale JL;Shen W;Li W;Zou S;Ciaramella M;Debat H;Nadal M;Leng F;Zhang H;Wang Q;Siaw GE;Niu H;Pommier Y;Gorospe M;Hsieh TS;Tse-Dinh YC;Xu D;Wang W
• 通讯作者: Wang W