Structural and functional determinants of biomolecular condensates in transcription organization

转录组织中生物分子凝聚体的结构和功能决定因素

• 批准号: 10714536
• 负责人: Jan-Hendrik Spille
• 金额: $ 33.92万
• 依托单位: UNIVERSITY OF ILLINOIS AT CHICAGO
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-22 至 2028-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10714536
• 关键词: Binding Sites; Biological Process; Cell Nucleus; Cell physiology; Cells; Chromatin; Chromatin Structure; Data; Development; Disease; Elements; Enhancers; Epigenetic Process; Genetic Transcription; Genomics; Health; Informal Social Control; Knowledge; Link; Membrane; Microscopy; Modeling; Modification; Molecular; Mus; Nature; Nuclear; Organelles; Phase; Physical condensation; Proteins; Regulatory Element; Research; Resolution; Structure; Surface; Testing; Time; Transcriptional Regulation; Vision; biophysical model; embryonic stem cell; genome-wide analysis; programs; scaffold; self organization; superresolution microscopy; transcription factor

Many cellular processes use phase separation to sequesters biomolecules into membraneless organelles or condensates. This concept is of particular importance in the cell nucleus. Most nuclear condensates are associated with specific chromatin loci. Thus, chromatin organization and biomolecular condensate formation are closely related. Topology, epigenetic modification, or enzymatic activity are possible links between the chromatin scaffold and protein condensation. We have previously described condensates that concentrate transcription machinery at super-enhancers but understanding of cell-to-cell variability and locus specific features that nucleate condensates is missing. Preliminary data indicates that active chromatin decorates the surface of transcription condensates below the resolution limit of conventional microscopy. Making use of recent developments in multiplexed super-resolution microscopy of both chromatin elements and protein factors, we will characterize the nature of the chromatin enrichment layer and determine if it reflects the condensate surface as an active interface that regulates transcription. We will for the first time directly observe the interplay of local chromatin topology, epigenetic signatures, and condensate formation in a specific model locus in mouse embryonic stem cells. By scrutinizing with genomic resolution how each of the regulatory elements in the locus interacts with the condensate we will determine if chromatin structures such as enhancer hubs nucleate condensates, or if condensates induce specific chromatin topologies by connecting active elements. Finally, we will investigate at the molecular level how condensate constituents interact with the microenvironment and associated chromatin elements, and test the hypothesis that retention of transcription factors boosts binding site occupancy and stabilizes condensates at regulatory chromatin. Targeted perturbation and locus-specific observation will allow us to answer this question and begin to identify genome-wide rules that predict where precisely chromatin-supported condensates form. The overall vision for this research program is to develop an integrated view of chromatin organization and condensate formation. Experimental data will inspire new conceptual frameworks and help us integrate the full complexity of condensates into paradigms of biological function such as transcription regulation. We expect that new biophysical models of self-organization and self-regulation will emerge from our studies of intracellular condensates.

许多细胞过程使用相分离将生物分子隔离到无膜细胞器中 或凝结物。这个概念在细胞核中特别重要。大多数核凝聚体 与特定染色质位点相关。因此，染色质组织和生物分子凝聚体 的形成密切相关。拓扑、表观遗传修饰或酶活性是可能的联系 染色质支架和蛋白质凝结之间。我们之前已经描述过冷凝物 将转录机制集中在超级增强子上，但了解细胞间的变异性 以及成核凝聚物缺失的位点特异性特征。初步数据表明，活跃 染色质装饰转录凝聚物的表面，低于常规分辨率极限 显微镜。利用多重超分辨率显微镜的最新进展 染色质元素和蛋白质因子，我们将表征染色质富集的性质 层并确定它是否将凝结水表面反映为调节的活性界面 转录。我们将首次直接观察局部染色质拓扑的相互作用， 小鼠胚胎干特定模型位点的表观遗传特征和凝聚体形成 细胞。通过基因组分辨率检查基因座中的每个调控元件如何相互作用 通过冷凝物，我们将确定染色质结构（例如增强子中心）是否成核 凝聚物，或者凝聚物是否通过连接活性元件诱导特定的染色质拓扑。 最后，我们将在分子水平上研究冷凝成分如何与 微环境和相关染色质元素，并检验保留的假设 转录因子可增强结合位点的占据并稳定调节染色质处的凝聚物。 有针对性的扰动和特定位点的观察将使我们能够回答这个问题并开始 确定全基因组规则，准确预测染色质支持的凝聚物的形成位置。 该研究计划的总体愿景是开发染色质组织的综合视图 和凝结水的形成。实验数据将激发新的概念框架并帮助我们 将冷凝物的全部复杂性整合到转录等生物功能范例中 规定。我们期望新的自组织和自我调节的生物物理模型将会出现 来自我们对细胞内凝聚物的研究。