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）：几十年来，人们已经认识到通过RNA聚合酶沿着DNA双螺旋转录可以增强局部DNA超螺旋。这个过程已经通过“双超螺旋结构域”模型得到了优雅的解释，其中在易位RNA聚合酶之前产生正DNA超螺旋，在其后面产生负超螺旋。然而，分子水平的详细机制仍然未知。例如，DNA 拓扑屏障如何影响转录耦合 DNA 超螺旋 (TCDS) 尚未完全了解。该研究的长期目标是了解TCDS和DNA拓扑屏障的分子机制和生物学功能。本应用的目的是确定哪些特性使某些 DNA 环和包裹蛋白发挥拓扑屏障的作用并阻止超螺旋扩散，研究 DNA 拓扑屏障如何调节大肠杆菌细胞中的 TCDS，并检查局部、瞬时 TCDS 如何发挥作用激活体内基因表达。我们的中心假设是，RNA 聚合酶产生的 TCDS 是大肠杆菌细胞中染色体重塑的主要力量，其中细胞使用基于核蛋白的拓扑屏障将 TCDS 限制在局部区域，从而极大地影响附近的耦合 DNA 事务。我们的假设是在我们实验室产生的强有力的初步数据的基础上制定的，并将通过追求以下三个具体目标进行测试：1）确定DNA拓扑屏障的分子机制并检查DNA拓扑屏障如何将超螺旋限制在局部区域并影响TCDS的效率； 2) 检查DNA拓扑屏障在大肠杆菌细胞TCDS中的作用； 3) 研究瞬时、动态TCDS如何激活大肠杆菌细胞中的转录以及DNA拓扑屏障如何影响TCDS的转录激活效率。来自拟议实验的信息最终将使我们更好地了解 TCDS 的机制，特别是 DNA 拓扑屏障在 TCDS 中的作用以及耦合的基因转录和表达。

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