Epigenetics and Transcriptomics Core

表观遗传学和转录组学核心

• 批准号: 10494613
• 负责人: Konstantinos Chronis
• 金额: $ 34.41万
• 依托单位: UNIVERSITY OF ILLINOIS AT CHICAGO
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-20 至 2027-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10494613
• 关键词: ATAC-seq; Anti-Inflammatory Agents; Biogenesis; Bioinformatics; Biological Assay; Biological Response Modifiers; Biometry; Blood Cells; Blood Vessels; Cell Count; Cell physiology; Cell surface; Cells; ChIP-seq; Chromatin; Coupled; DNA Sequencing Facility; Data; Data Files; Data Set; Data Storage and Retrieval; Development; Endoplasmic Reticulum; Endothelial Cells; Endothelium; Environment; Epigenetic Process; Event; Foundations; Gene Expression; Generations; Genes; Genetic; Genetic Transcription; Genome; Genomics; Goals; Grant; Homeostasis; Immune; Immune signaling; Individual; Infection; Inflammation; Inflammatory Response; Injury; Innate Immune System; Instruction; Investigation; Libraries; Lung; Maps; Methodology; Methods; Mining; Mitochondria; Modeling; Molecular; Natural Immunity; Neutrophil Activation; Organ; Pathway interactions; Phagocytes; Preparation; Process; Production; Pulmonary Circulation; Reproducibility; Resolution; Role; Sampling; Scanning; Signal Pathway; Signal Transduction; Sphingosine-1-Phosphate Receptor; Standardization; System; Technology; Testing; Validation; analytical tool; base; comparative; data integration; data sharing; epigenomics; gene network; gene regulatory network; genome-wide; injury and repair; lung injury; next generation sequencing; programs; pulmonary function; repair model; response; stem cells; transcriptome sequencing; transcriptomics; ubiquitin-protein ligase; vascular injury

ABSTRACT The function of the Epigenetics and Transcriptomics Core (Core B) is to identify the key gene networks and cis-regulatory mechanisms that define the pulmonary endothelium as an innate immune ‘organ’ during lung injury and repair. Core B will provide high-throughput production and optimal mining of genome-wide gene expression and chromatin datasets, for all three projects in this Program. The Core B leader has pioneered such approaches in stem cells and is now applying these analysis platforms to lung endothelial cells in a comprehensive and integrative manner. We have optimized the methods for several next generation sequencing approaches, including low cell number RNA-seq, ChIP-seq and ATAC-seq, and can effectively collect, manage, analyze, integrate, and interpret the generated data specifically in freshly isolated endothelial cells. By combining all four technologies we will develop a multi-dimensional view of the epigenetic programming of endothelial cells (EC) and reveal their modulatory interactions with circulating immune cells. On this basis, Core B will provide a foundation for the more specific and sophisticated needs of each individual project. Indeed, each project focuses on gene regulatory networks that are among the most robustly regulated across lung injury and repair models. Through the development and use of epigenetic and transcriptomic assays coupled with next generation sequencing, Core B will assist each Project in uncovering the molecular mechanisms and develop testable hypothesis about genes associated with EC innate immunity and their role in inflammatory response. These include the exploration of the epigenetic and transcriptomic changes that occur in response to endoplasmic reticulum localized Y143phosphorylated sphingosine 1 phosphate receptor 1 (S1PR1), as EC convert from an anti-inflammatory to an immune-active lineage in Project 1; delineate the cis-regulatory mechanisms and chromatin-based pathways that control the expression of ubiquitin E3 ligase CHFR in Project 2; and examine the role of epigenetic programs in the initiation of lung endothelial cell mitophagy and mitochondrial biogenesis as well as the downstream effectors of mitophagy-induced signals in Project 3. Ultimately, Core B represents a central conduit for genomic and bioinformatic flow of data for this PPG, providing data-generation, data-storage and data-sharing functions and therefore contributing significantly to further understanding the immune regulatory function of lung endothelium.

抽象的 表观遗传学和转录组学核心（Core B）的功能是识别关键基因网络和 将肺内皮定义为肺损伤期间的先天免疫“器官”的顺式调节机制 和修复。 Core B将提供高通量生产和全基因组基因表达的优化挖掘 和染色质数据集，适用于本计划中的所有三个项目。 Core B 领导者开创了这样的先河 干细胞方法，现在正在将这些分析平台应用于肺内皮细胞 全面、综合的方式。我们优化了几种下一代测序的方法 方法，包括低细胞数RNA-seq、ChIP-seq和ATAC-seq，并且可以有效地收集、管理、 特别是在新鲜分离的内皮细胞中分析、整合和解释生成的数据。通过结合 通过所有四种技术，我们将开发内皮细胞表观遗传编程的多维视图 （EC）并揭示它们与循环免疫细胞的调节相互作用。在此基础上，Core B将提供 为每个项目的更具体和复杂的需求奠定了基础。事实上，每个项目都侧重于 基因调控网络是肺损伤和修复模型中受到最严格调控的网络之一。 通过开发和使用表观遗传和转录组分析以及下一代 测序，Core B将协助每个项目揭示分子机制并开发可测试的 关于与 EC 先天免疫相关的基因及其在炎症反应中的作用的假设。这些 包括探索内质反应中发生的表观遗传和转录组变化 网状局部 Y143 磷酸化鞘氨醇 1 磷酸受体 1 (S1PR1)，作为 EC 从 项目 1 中对免疫活性谱系的抗炎作用；描述顺式监管机制和 项目 2 中控制泛素 E3 连接酶 CHFR 表达的基于染色质的途径；并检查 表观遗传程序在肺内皮细胞线粒体自噬和线粒体生物发生启动中的作用 以及项目 3 中线粒体自噬诱导信号的下游效应器。最终，核心 B 代表了 该 PPG 的基因组和生物信息数据流的中央管道，提供数据生成、数据存储 和数据共享功能，因此有助于进一步了解免疫 肺内皮的调节功能。