Mechanisms of enhancer-promoter communication, genome organization and transcription control

增强子-启动子通讯、基因组组织和转录控制的机制

• 批准号: 10343329
• 负责人: Alexandros Pertsinidis
• 金额: $ 48.43万
• 依托单位: SLOAN-KETTERING INST CAN RESEARCH
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-08-01 至 2026-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10343329
• 关键词: 3-Dimensional; 4D Imaging; Acute; Adopted; Adult; Architecture; Award; Base Pairing; Binding; Biochemical; Biochemistry; Biology; Biophysical Process; Biophysics; CRISPR interference; Cell Communication; Cell Nucleus; Cell physiology; Cells; Chromatin; Chromatin Loop; Communication; Complex; Crowding; Cues; DNA; DNA Polymerase II; Data; Development; Disease; Distal; Distant; Elements; Embryo; Enhancers; Ensure; Environment; Frequencies; Gene Expression; Gene Expression Regulation; Genes; Genetic Enhancer Element; Genetic Transcription; Genome; Genomics; Goals; Health; Human; Image; Imaging Techniques; Imaging technology; Individual; Kinetics; Knowledge; Mammalian Cell; Mediating; Messenger RNA; Methodology; Methods; Modeling; Molecular; Monitor; Nuclear Structure; Physics; Polymers; Positioning Attribute; Process; Production; Proteins; RNA Polymerase II; Regenerative Medicine; Regulation; Regulatory Element; Resolution; Role; Shapes; Signal Transduction; Specific qualifier value; Structure; System; Testing; Therapeutic; Therapeutic Intervention; Time; Transcriptional Activation; Transcriptional Regulation; Validation; Work; YY1 Transcription Factor; biophysical techniques; cell type; cellular engineering; cohesin; differential expression; genomic locus; human disease; imaging capabilities; imaging modality; live cell imaging; novel; novel strategies; optical imaging; preventive intervention; programs; promoter; single molecule; spatiotemporal; transcription factor

ABSTRACT Metazoan genomes achieve complex gene control by uncoupling regulatory DNA elements from target promoters and allowing regulation at a distance. Thus, a gene can be differentially expressed in different cell types and under different environmental signals or developmental cues. How distal regulatory elements (enhancers) target specific gene promoters, how the search process is shaped by the topology of the genome in the nucleus and how enhancer-promoter interactions are facilitated by regulatory complexes that relay signals to the RNA Polymerase II and control transcription activity remains a mystery. Our goal is to understand molecular and biophysical mechanisms that enable enhancer-promoter communication in human and other mammalian cells. Towards these goals and during the period of this award we will accomplish the following: (i) visualize the dynamic communication of enhancers and target promoters simultaneously with the association of regulatory complexes and gene activity, using novel single-molecule and super-resolution approaches for non-invasive 4D imaging of structure and function of the genome in single live cells; (ii) determine mechanisms by which different classes of architectural proteins shape genome folding, enhancer- promoter communication and transcription kinetics; (iii) dissect the function and interdependencies of individual constituent enhancer elements within complex regulatory landscapes controlling cell identity genes. Our results will establish quantitative frameworks for understanding the biochemistry of transcription regulation in the crowded environment of the nucleus and for interpreting gene regulation and genome organization using soft- matter/polymer physics and related biophysical concepts. These conceptual leaps are needed to ultimately understand physical chromatin organization at sub-Mb scales, the scale most relevant for regulatory genome interactions. Our integrated structure-function approach will provide functional validation and critical tests for gene “regulation-at-a-distance” models. The proposed studies will not only provide substantial new knowledge on the mechanisms of promoter-enhancer communication but will also set the stage for further studies of the interplay of genome topology/organization and gene expression regulation.

抽象的 后生动物基因组通过将调控DNA元件与靶标解偶联来实现复杂的基因控制 促进者并允许远程监管。因此，一个基因可以在不同的细胞中差异表达。 类型和不同的环境信号或发育线索。远端调控元件如何 （增强子）针对特定基因启动子，搜索过程如何由基因组拓扑决定 细胞核中的增强子-启动子相互作用如何通过传递的调控复合物促进 向 RNA 聚合酶 II 发出信号并控制转录活性仍然是一个谜。我们的目标是 了解促进人类增强子-启动子沟通的分子和生物物理机制 和其他哺乳动物细胞。为了实现这些目标，在获奖期间，我们将实现 以下：（i）可视化增强子和目标启动子的动态通信，同时 使用新型单分子和超分辨率将调控复合物与基因活性关联起来 对单个活细胞中基因组结构和功能进行非侵入性 4D 成像的方法； (二) 确定不同类别的结构蛋白塑造基因组折叠、增强子的机制 启动子通讯和转录动力学； (iii) 剖析个人的功能和相互依赖性 控制细胞身份基因的复杂调控环境中的组成增强子元件。我们的成果 将建立定量框架来理解转录调控的生物化学 细胞核的拥挤环境，并使用软件解释基因调控和基因组组织 物质/聚合物物理学和相关的生物物理学概念。最终需要这些概念上的飞跃 了解亚 Mb 尺度的物理染色质组织，该尺度与调控基因组最相关 互动。我们的集成结构功能方法将为 基因“远距离调控”模型。拟议的研究不仅会提供大量新知识 启动子-增强子通讯机制的研究，但也将为进一步研究奠定基础 基因组拓扑/组织与基因表达调控的相互作用。