Chromatin architecture as a determinant of dendritic cell function

染色质结构作为树突状细胞功能的决定因素

• 批准号: 10041680
• 负责人: Connie Krawczyk
• 金额: $ 28.5万
• 依托单位: VAN ANDEL RESEARCH INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-06-01 至 2022-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10041680
• 关键词: ATAC-seq; Address; Architecture; Bioinformatics; Biological Assay; Cell physiology; Cells; Cellular biology; Chromatin; Complex; Coupled; Data; Dendritic Cells; Diet; Disease; Enhancers; Ensure; Environment; Environmental Risk Factor; Epigenetic Process; Foundations; Future; Gene Activation; Gene Expression; Genes; Genetic; Genetic Variation; Goals; Health; Heterogeneity; Histones; Human; Immune; Immune System Diseases; Immune response; Immunity; Immunization; Individual; Inflammation; Innate Immune System; Knowledge; Maps; Measures; Mediating; Mouse Strains; Nature; Obesity; Oncogenic Viruses; Outcome; Phenotype; Post-Translational Protein Processing; Research; Sampling; Sentinel; Stimulus; Surveys; T-Lymphocyte; Techniques; Technology; Transposase; Variant; epigenetic variation; epigenome; epigenomics; experience; genome-wide analysis; immunoregulation; in vivo; insight; non-genetic; novel; nuclease; nutrition; peripheral tolerance; programs; promoter; response; transcriptome sequencing; tumor

PROJECT SUMMARY/ABSTRACT Immune heterogeneity, mediated by epigenetic and genetic mechanisms, complicates our understanding of immune regulation and disease. As sentinels, immune cells constantly survey their environment, and this information is presumably encoded epigenetically to direct cellular responses. Despite this understanding, little is known about epigenetic variation in immune cells and how it relates to immune phenotype heterogeneity. It is essential to investigate the relationship between epigenetic variation and immune response heterogeneity in order to better understand individual immunity. We will study dendritic cells (DCs), cells of the innate immune system, that engage in distinct cellular programs in response to environmental stimuli and are essential for protective immune responses. OVERALL OBJECTIVES: Our objective is to determine whether chromatin states in DCs underlie immune phenotype variation. We will characterize the degree of diversity in the epigenome of five mouse strains with known immune phenotype variation. We will map chromatin accessibility (ATAC-Seq) and select histone PTMs using a novel low-input chromatin mapping technique Cleavage Under Targets and Release Using Nuclease (CUT&RUN) and compare to gene expression in the steady state and following immune stimulation. We will determine the extent of gene or enhancer priming in DCs that occurs to enable rapid gene expression following stimulation and identify regulatory networks that drive DC function. Our studies will reveal the dynamic and static aspects of the epigenome in response to stimulation and determine the extent to which epigenetic programming underlies differential activation. We will begin to dissect the interplay between genetic and epigenetic variation in immune cells and how it relates to immune phenotype heterogeneity. These concepts have been poorly studied in in vivo-derived DCs due to technical limitations that have been overcome by recent advances in low-input technologies for genome-wide studies. We have assembled a team that will ensure the completion of this project. Our collaborators bring extensive expertise in bioinformatics and epigenetic techniques, and coupled with our extensive experience in DC biology, creates a unique team to address the proposed questions. IMPACT: Upon completion of this research, we will have provided a major conceptual advance defining the relationship between chromatin states and function in DCs. We will have described the static versus dynamic aspects of the epigenome in response to immune stimulation. These studies will also give us new insights into the importance of the chromatin architecture for immune phenotype variation. These studies will lay the foundation for future study of how environmental perturbation of the epigenome—by conditions such as inflammation, nutrition, obesity, and overall health—interacts with genetics to impact immune cell programming and immune response heterogeneity.

项目概要/摘要 由表观遗传和遗传机制介导的免疫异质性使我们对免疫的理解变得复杂 作为哨兵，免疫细胞不断地调查它们的环境，这些信息是 尽管有这样的认识，但人们对它可能通过表观遗传编码来指导细胞反应知之甚少。 免疫细胞的表观遗传变异及其与免疫表型异质性的关系至关重要。 表观遗传变异与免疫反应异质性之间的关系，以便更好地理解 我们将研究树突状细胞（DC），这是先天免疫系统的细胞，它们参与不同的免疫系统。 响应环境刺激的细胞程序对于保护性免疫反应至关重要。 总体目标：我们的目标是确定 DC 中的染色质状态是否是免疫表型的基础 我们将表征具有已知免疫的五种小鼠品系的表观基因组的多样性程度。 我们将绘制染色质可及性 (ATAC-Seq) 并使用新型低输入选择组蛋白 PTM。 染色质作图技术使用核酸酶进行目标切割和释放 (CUT&RUN) 并与基因进行比较 在稳定状态下和免疫刺激后的表达我们将确定基因或增强子的程度。 DC 中的启动是为了在刺激后实现快速基因表达，并识别调节网络 我们的研究将揭示表观基因组响应刺激的动态和静态方面。 并确定表观遗传编程在差异激活的基础上我们将开始剖析 免疫细胞遗传和表观遗传变异之间的相互作用及其与免疫表型的关系 异质性。 由于技术限制已被克服，这些概念在体内衍生的 DC 中的研究很少 通过全基因组研究低投入技术的最新进展，我们组建了一个团队，以确保 我们的合作者带来了生物信息学和表观遗传学技术方面的丰富专业知识，以及 加上我们在 DC 生物学方面的丰富经验，创建了一个独特的团队来解决所提出的问题。 影响：完成这项研究后，我们将提供定义这种关系的重大概念进展 我们将描述 DC 中染色质状态和功能之间的静态与动态方面。 这些研究也将使我们对免疫刺激的重要性有新的认识。 这些研究将为未来研究免疫表型变异的染色质结构奠定基础。 表观基因组的环境扰动——炎症、营养、肥胖和整体状况等因素 健康——与遗传学相互作用，影响免疫细胞编程和免疫反应异质性。