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

基本信息

批准号：
10672880
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
项目类别：
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/10672880
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 Oncogene Deregulation 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 Visualization Work YY1 Transcription Factor biophysical techniques cell fixing cell type cellular engineering cohesin differential expression genomic locus human disease imaging capabilities imaging modality live cell imaging nonbinary novel novel strategies optical imaging preventive intervention programs promoter single molecule spatiotemporal superresolution imaging transcription factor ultra high resolution

项目摘要

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启动子并允许远距离调节，因此，基因可以在不同细胞中差异表达。类型以及不同环境信号或发育线索下的远端调控元件的情况。（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，我们将实现以下目标：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的结构和功能进行非侵入性 4D 成像的方法 (ii) 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）剖析个体的功能和相互依赖性我们的结果是控制细胞身份基因的复杂调控环境中的组成增强子元件。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我们的集成结构功能方法将为功能验证和关键测试提供支持。基因“远距离调控”模型不仅将提供大量新知识。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。