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

摘要 后生动物基因组通过将调控元件与靶DNA解偶联来实现复杂的基因控制 推动者和允许有距离的监管。因此，一个基因可以在不同的细胞中差异表达。 在不同的环境信号或发育线索下。远端监管要素如何 (增强子)针对特定的基因启动子，搜索过程如何由基因组的拓扑结构塑造 以及调控复合体如何促进增强子-启动子之间的相互作用 RNA聚合酶II的信号和控制转录活性仍然是一个谜。我们的目标是 了解使人类增强启动子-启动子通信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)将增强子和目标启动子的动态交流与 利用新的单分子和超分辨技术研究调节复合体与基因活性的关系 单个活细胞基因组结构和功能的非侵入性4D成像方法； 确定不同类别的结构蛋白塑造基因组折叠、增强子- 启动子沟通和转录动力学；(Iii)剖析个体的功能和相互依赖关系 控制细胞特性基因的复杂调控环境中的组成增强子元件。我们的结果 将为理解转录调控的生物化学建立定量框架。 用于解释基因调控和基因组组织的软件。 物质/聚合物物理学及相关生物物理概念。这些概念的飞跃最终是需要的 了解亚Mb级别的物理染色质组织，该级别与调控基因组最相关 互动。我们的集成结构-功能方法将提供功能验证和关键测试 基因“远距离调控”模型。拟议的研究不仅将提供大量的新知识 对启动子-增强子交流机制的研究，也将为进一步研究 基因组拓扑/组织和基因表达调控的相互作用。

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.