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.

摘要 表观遗传学和转录组学核心（核心B）的功能是识别关键基因网络， 顺式调节机制，将肺内皮定义为肺损伤期间的先天免疫“器官” 和修复。核心B将提供高通量生产和全基因组基因表达的最佳挖掘 和染色质数据集，在这个计划的所有三个项目。核心B领导者开创了这样的 目前正在将这些分析平台应用于肺内皮细胞， 全面和综合的方式。我们已经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，可以有效地收集，管理， 分析、整合和解释所产生的数据，特别是在新鲜分离的内皮细胞中。通过组合 所有这四种技术，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，核心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最受调控的。 通过开发和使用表观遗传学和转录组学检测， 核心B将协助每个项目揭示分子机制，并开发可测试的 关于EC先天免疫相关基因及其在炎症反应中作用的假说。这些 包括探索内质网反应中发生的表观遗传和转录组学变化， 内质网定位的Y143磷酸化鞘氨醇1磷酸受体1（S1 PR 1），作为EC从 在项目1中抗炎至免疫活性谱系;描述顺式调节机制， 在项目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子。最终，核心B表示 该PPG的基因组和生物信息学数据流的中心管道，提供数据生成、数据存储 和数据共享功能，因此对进一步了解免疫做出了重大贡献 肺内皮的调节功能。