Regulatory Mechanisms Linking Spatial Gene Control and Genome Organization

连接空间基因控制和基因组组织的调控机制

• 批准号: 10712390
• 负责人: Sreejith Janardhanan Nair
• 金额: $ 38.38万
• 依托单位: GEORGETOWN UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-08-01 至 2028-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10712390
• 关键词: 3-Dimensional; Acute; Address; Architecture; Binding; Biological; Biological Assay; Biophysics; CRISPR screen; Cells; Chromatin; Chromatin Structure; Communication; Complex; Cues; Data; Disease; Enhancers; Enzymes; Event; Exposure to; Gene Expression; Gene Expression Regulation; Genes; Genetic Transcription; Genome; Genomics; Homeostasis; Imaging Device; Knowledge; Ligands; Link; Mammalian Cell; Membrane; Mentors; Molecular; Nuclear; Nuclear Hormone Receptors; Organelles; Pathway interactions; Physical condensation; Prevalence; Property; Proteins; Proteome; RNA; Regulation; Regulatory Element; Reporting; Repression; Research; Research Personnel; Role; Science; Shapes; Signal Induction; Signal Transduction; Structure; Technology; Training; Untranslated RNA; Work; genetic approach; genome-wide; genomic tools; innovation; insight; multidisciplinary; mutation screening; next generation; next generation sequencing; novel; programs; prototype; solid state; spatiotemporal; superresolution imaging; tool; transcription factor

PROJECT SUMMARY Cellular homeostasis is maintained by signaling events that turn on downstream transcription factors to rapidly activate or repress hundreds of genes. The application of next-generation sequencing technologies and super- resolution imaging in the past decade has revealed the central role of non-coding regulatory elements called enhancers in the spatio-temporal control of mammalian gene expression. Recent evidence indicates that acute signaling events assemble the enhancer-bound transcriptional complex as membraneless compartments known as condensates. An important question is how these organelles interact with larger nuclear bodies to shape three-dimensional genome organization and spatial gene control. We have identified three critical challenges that limit our understanding of spatial gene control. Our research program is focused on solving these challenges to fill the critical knowledge gaps in signal-induced gene regulation. Challenge 1) Understand how enhancer communication works. In addition to controlling primary target genes, several pathway-specific enhancers engage in long-distance interactions. Our data indicate that enhancer hubs facilitate genome-wide coordination of signaling programs. The prevalence and regulatory features of this mechanism in signal-activated gene programs are just beginning to be explored. We will use prototypic type I and type II nuclear hormone receptors to study the role of enhancer hubs in transcription coordination. Challenge 2) Elucidate the interaction of non- coding genome and disordered proteome in gene control. We have reported that the ligand-induced enhancer condensates are composed of proteins with intrinsically disordered regions (IDR) and RNAs. Although a common feature of many transcriptional complexes, the molecular and enzymatic regulation of the assembly, dissolution, and material properties of transcriptional condensates are largely unknown. We will use single-cell CRISPR screening strategies, mutational scans, biophysical and genomics assays to identify enzymes controlling signaling-activated enhancers by modifying the IDR structure. Challenge 3) Unravel the cell biological basis of the spatial genome organization. The eukaryotic genome is compartmentalized based on the transcriptional states of the chromatin. Our data indicate that several nuclear architectural structures and transcriptional condensates act as solid-state anchors to facilitate long-distance enhancer interaction and organize chromatin architecture. To gain mechanistic insights into the role of common nuclear bodies in genome organization, we will employ genetic strategies to transiently degrade these organelles and assess the impact on three-dimensional chromatin structure and enhancer function using imaging and genomics tools. By addressing these questions at the intersection of non-coding genome, nuclear condensates, and gene regulation, we will unravel a cell biological basis of spatial gene control. This research will also contribute to developing innovative research tools to fill the knowledge gaps in the regulatory roles of the non-coding genome while facilitating the training and mentoring of the next generation of researchers in multidisciplinary science.

项目摘要 细胞内稳态是通过信号事件维持的，这些信号事件开启下游转录因子， 激活或抑制数百个基因。下一代测序技术和超级测序技术的应用 在过去的十年中，分辨率成像揭示了非编码调节元件的核心作用，称为 增强子在哺乳动物基因表达的时空控制。最近的证据表明， 信号事件将增强子结合的转录复合物组装成已知的无膜区室， 作为冷凝物。一个重要的问题是，这些细胞器如何与较大的核体相互作用， 三维基因组组织和空间基因控制。我们确定了三个关键挑战 限制了我们对空间基因控制的理解我们的研究计划专注于解决这些挑战 填补信号诱导基因调控的关键知识空白。挑战1）了解增强剂如何 沟通工作。除了控制主要靶基因外，几种途径特异性增强子 进行远距离互动。我们的数据表明，增强子中心促进了全基因组的协调 信号程序。该机制在信号激活基因中的普遍性及其调控特点 项目才刚刚开始探索。我们将使用原型I型和II型核激素受体 研究增强子枢纽在转录协调中的作用。挑战2）阐明非 基因控制中的编码基因组和无序蛋白质组。我们已经报道了配体诱导的 增强子凝聚物由具有固有无序区（IDR）的蛋白质和RNA组成。虽然 许多转录复合物的共同特征，组装的分子和酶调节， 溶解和转录缩合物的材料性质在很大程度上是未知的。我们将使用单细胞 CRISPR筛选策略、突变扫描、生物物理学和基因组学分析以识别酶 通过修饰IDR结构控制信号激活增强子。挑战3）解开细胞 空间基因组组织的生物学基础。真核生物的基因组是基于 染色质的转录状态。我们的数据表明，一些核建筑结构和 转录缩合物作为固态锚促进长距离增强子相互作用， 组织染色质结构。为了获得对基因组中常见核体作用的机理性见解， 组织，我们将采用遗传策略来瞬时降解这些细胞器并评估其影响 使用成像和基因组学工具研究三维染色质结构和增强子功能。通过 在非编码基因组、核浓缩物和基因的交叉点上解决这些问题， 调节，我们将解开空间基因控制的细胞生物学基础。这项研究也将有助于 开发创新的研究工具，以填补非编码基因组调控作用的知识空白 同时促进多学科科学下一代研究人员的培训和指导。