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：
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
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/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

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.

抽象的后生基因组通过将调节性DNA元素从靶标中解偶联而获得复杂的基因控制发起人并允许在距离处进行调节。那就可以在不同的细胞中以不同的方式表达类型和不同的环境信号或发展线索。不同的监管元素（增强子）靶向特定基因启动子，搜索过程是如何通过基因组拓扑塑造的在细胞核中以及如何通过中继的调节复合物制备增强子促销相互作用 RNA聚合酶II和控制转录活性的信号仍然是一个谜。我们的目标是了解能够在人类中增强子促销的分子和生物物理机制和其他哺乳动物细胞。实现这些目标，在本奖项期间，我们将完成以下：（i）仅与使用新型的单分子和超分辨率的调节复合物和基因活性的关联单个活细胞中基因组结构和功能的非侵入性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，增强子的机制发起人的通信和转录动力学；（iii）剖析个体的功能和相互依赖性构成了控制细胞身份基因的复杂调节景观中的增强子元素。我们的结果将建立定量框架，以理解转录调节的生物化学细胞核的拥挤环境以及使用软软来解释基因调节和基因组组织物质/聚合物物理和相关的生物物理概念。这些概念上的飞跃最终需要了解亚MB量表的物理染色质组织，该量表与调节基因组最相关互动。我们的集成结构功能方法将为功能验证和关键测试提供基因“调节”模型。拟议的研究不仅将提供大量的新知识关于启动子增强剂通信的机制，但也将为进一步研究奠定基因组拓扑/组织和基因表达调节的相互作用。