Molecular Mechanisms of Promoter-Terminator Gene Looping

启动子-终止子基因循环的分子机制

• 批准号: 8865248
• 负责人: Xin Liu
• 金额: $ 30.53万
• 依托单位: UT SOUTHWESTERN MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-03-02 至 2020-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8865248
• 关键词: Address; Binding; Biochemical; Biochemistry; Biological Assay; Biological Phenomena; Biology; C-terminal; Cell physiology; Chemicals; Chromatin; Chromatin Loop; Chromatin Structure; Complex; Coupled; Crystallography; DNA; DNA Polymerase I; DNA Polymerase III; DNA-Directed RNA Polymerase; Development; Elements; Enhancers; Environment; Essential Genes; Eukaryota; Eukaryotic Cell; Event; Gene Expression Regulation; Genes; Genetic; Genetic Transcription; Genome; Genomics; Goals; HIV; In Vitro; Intercistronic Region; Interphase; Link; Macromolecular Complexes; Maintenance; Maps; Mediating; Memory; Messenger RNA; Mitochondrial RNA; Molecular; Molecular Conformation; Nuclear; Nuclear Pore Complex; Pathway interactions; Phosphoric Monoester Hydrolases; Physiological; Plant Genes; Play; Polyadenylation; Polymerase; Process; Promoter Regions; Proviruses; RNA; RNA Binding; RNA Polymerase II; Recycling; Regulation; Research; Role; Series; Signal Transduction; Site; Structure; Surface; Synthetic Genes; System; Terminator Regions; Testing; Titrations; Transcript; Transcription Factor TFIIB; Transcription Initiation; Transcriptional Regulation; Untranslated RNA; Yeasts; base; biochemical tools; cancer cell; cohesin; condensin; crosslink; gene function; gene terminator; global run on sequencing; human GTF2B protein; human disease; in vivo; insight; mutant; new therapeutic target; promoter; public health relevance; research study; structural biology; tool; transcription factor; transcription factor TFIIIC; tumorigenesis

 DESCRIPTION (provided by applicant): Accumulating evidence has indicated that high-order genome structures influence transcription and mediate critical co-transcriptional crosstalk among distinct DNA elements. The functional significance of a variety of types of chromatin loops (e.g. promoter-terminator, enhancer-promoter, and interchromosomal) in gene regulation during development and in cancer cells has been demonstrated recently. Essential factors from the transcription initiation and mRNA 3'-end cleavage and polyadenylation (poly(A)) machineries have been shown to form complexes to confer promoter-terminator gene looping. The general transcription factor TFIIB mediates a critical interaction network involving Ssu72 (a pol II C-terminal domain phosphatase) and Rna15 (the poly(A) RNA-binding subunit of the cleavage factor IA complex). Gene looping is a widespread phenomenon in yeast and has also been identified for mammalian genes, plant genes, and human immunodeficiency virus provirus. In addition, gene looping has been connected to a number of fundamental cellular processes, which include transcription reinitiation, maintenance of transcriptional memory, and control of transcriptional directionality. In the proposed research, we will address the following key questions: (1) how do TFIIB and TFIIB- centered gene looping complexes regulate transcription (Aim 1), (2) what is the structural and biochemical basis for the pol II transcription-coupled gene loop establishment and maintenance (Aim 2), and (3) what are the mechanisms and physiological consequences of gene looping-dependent pol II reinitiation (Aim 3)? Our broad hypothesis is that unique macromolecular complexes formed by nuclear factors and non-coding RNAs mediate gene looping and create unique local chromatin environments to control pol II transcription. Specifically, we will test this hypothesis by (1) biochemically and structurally mapping binding interfaces of the TFIIB-centered gene looping complexes and connect them to the gene looping process directly in vivo, (2) revealing the pathways of TFIIB-dependent gene loop formation during the course of transcription and identifying additional nuclear factors (e.g. cohesin, condensin, nuclear pore complexes, and TFIIIC) required for gene looping, and (3) determining pol II and transcription factor dynamics on chromatin governed by gene loops with tools including the competition ChIP, the nuclear anchor-away system, and the chemically induced artificial gene looping system. Collectively, built upon our preliminary results these studies will provide the molecular mechanisms of gene looping and its mediated co-transcriptional crosstalk. In addition, we will link gene looping to other cellular pathways by identifying additional nuclear factors critical for this process. Finally, our studies may offer insights into the common principles of all types of transcription-dependent chromatin loops implicated in development and human disease and hence suggest novel targets for therapeutics.

 描述（由适用提供）：累积证据表明，高阶基因组结构会影响转录并介导不同的DNA元素之间的关键共同转录串扰。最近已经证明了多种类型的染色质环（例如启动子终端，增强子促进剂和染色体互感体）在发育过程中和癌细胞中的基因调节中的功能意义。转录启动和mRNA 3'-末端裂解和聚腺苷酸化（poly（a））机器的基本因素已被证明可以形成复合物以赋予启动子末端基因循环。一般转录因子TFIIB介导了涉及SSU72（pol II C末端结构域磷酸酶）和RNA15（裂解因子IA复合物的Pol（A）RNA结合亚基）的关键相互作用网络。基因循环是酵母中一种广泛的现象，也已被确定为哺乳动物基因，植物基因和人类免疫缺陷病毒病毒病毒病毒病毒病毒。此外，基因循环已连接到许多基本的细胞过程，其中包括重新定位，转录记忆的维持以及转录方向性的控制。在拟议的研究中，我们将解决以下关键问题：（1）TFIIB和以TFIIB为中心的基因循环复合物如何调节转录（AIM 1），（2）POL II转录耦合基因的结构和生化基础是什么 循环建立和维护（AIM 2），以及（3）基因循环依赖性pol II重新引起的机制和物理后果是什么（AIM 3）？我们广泛的假设是，由核因素和非编码RNA形成的独特的大分子复合物介导基因环，并创建独特的局部染色质环境来控制POL II转录。具体而言，我们将通过（1）以（1）为中心的基因基因循环复合物的生化和结构映射结合界面进行生化和结构映射的结合界面，并将它们直接连接到体内的基因上环过程，（2）揭示TFIIB依赖性基因在转录和核孔中固定的核因子和核因子（E. e。基因循环所需的TFIIIC），以及（3）通过基因环的染色质和转录因子动力学，由基因环的转录因子动力学，其中包括竞争芯片，核锚定系统以及化学诱导的人工基因环路系统。总的来说，基于我们的初步结果，这些研究将提供基因循环的分子机制及其介导的共转录串扰。此外，我们将通过确定对此过程至关重要的其他核因子来将基因环路与其他细胞途径联系起来。最后，我们的研究可能会深入了解在发育和人类疾病中实施的所有类型的转录依赖性染色质环的共同原理，因此提出了新的治疗靶标。