Dynamics of lineage-specific genome reorganization in gastrulation and their response to disease-associated epigenetic perturbations

原肠胚形成过程中谱系特异性基因组重组的动态及其对疾病相关表观遗传扰动的反应

• 批准号: 10595932
• 负责人: Reza Kalhor
• 金额: $ 8.93万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-20 至 2025-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10595932
• 关键词: 3-Dimensional; Address; Affect; Architecture; Bar Codes; Biological Assay; Cell Differentiation process; Cells; Chromatin; Congenital Abnormality; DNA; DNA Methylation; Data; Daughter; Development; Disease; Ectoderm; Embryo; Embryonic Development; Endoderm; Epigenetic Process; Event; Gene Activation; Gene Expression; Gene Expression Profile; Genetic Transcription; Genome; Genomics; Germ Layers; Goals; Heritability; Heterogeneity; Hi-C; Histones; Human; Human Development; Human body; Inherited; Inner Cell Mass; Knockout Mice; Lead; Ligation; Measures; Mesoderm; Mitosis; Mitotic; Molecular; Mus; Neurodevelopmental Disorder; Organogenesis; Population; Process; Research; Role; Specific qualifier value; Spontaneous abortion; Structure; System; Testing; Therapeutic; Variant; cell type; combinatorial; daughter cell; gastrulation; histone modification; human disease; in vivo; insight; member; mouse model; novel; programs; reconstruction; response; three dimensional structure; tool; zygote

PROJECT SUMMARY/ABSTRACT Gastrulation is a pivotal process for the formation of human body plan and its disruptions can lead to miscarriage or birth defects such as caudal dysgenesis. During this process, pluripotent cells differentiate into the primary germ layers or the endoderm, mesoderm, and ectoderm lineages that later create all of the body’s cell types. Such differentiation events involve extensive three-dimensional (3D) reorganizations of the genome that are specific to each lineage. However, the functional effects and the underlying mechanisms of these reorganization as well as consequences of their disruption are poorly understood. Our objective is to determine the dynamics of lineage-specific genome 3D reorganization during gastrulation and how they respond to disruptions in the epigenetic landscape. Our hypothesis is that genome 3D changes in each lineage help establish the cell fates it generates later in development by poising it to assume those cells’ transcriptional programs. We further hypothesize that such important 3D reorganizations should be more faithfully inherited through mitosis and and that chromatin epigenetic marks, such as histone modifications and DNA methylation, are important for their establishment. Members of this team have developed tools that create new opportunities for understanding the role of genome 3D organization in embryonic development. Among them are proximity ligation assays that allow for global determination of genome 3D organization in cell populations and single cells. We have also developed a cutting-edge and powerful in vivo combinatorial barcoding system in mice that enables us to decipher the lineal relationship between cells. Here we propose using these tools to identify lineage-specific higher-order features in gastrulating mouse embryos, assess their association with gene expression later in development, evaluate how faithfully they re-establish after mitotic divisions, and examine how they are affected by disease-related epigenetic perturbations. Our long-term goal is to understand the role of genome structure dynamics in fate determination during embryogenesis when cells undergo a succession of lineage commitments in highly programmed fashion. Our proposed research will broadly impact the field by characterizing lineage-specific genome 3D organization during embryogenesis, as well as its functional dynamics and connection with chromatin epigenetic marks.

项目摘要/摘要 原肠作用是人体计划形成的关键过程，原肠作用的中断会导致流产或分娩。 尾部发育不全等缺陷。在这个过程中，多能细胞分化为初级生殖层或 内胚层、中胚层和外胚层谱系，它们后来创造了人体所有的细胞类型。这样的差异化事件 涉及每个谱系特有的基因组的广泛三维(3D)重组。然而， 这些重组的功能影响和基本机制以及其中断的后果如下 人们对此知之甚少。 我们的目标是确定原肠胚过程中谱系特异的基因组3D重组的动态以及如何 它们对表观遗传格局的破坏做出反应。我们的假设是，每个谱系的基因组3D变化有助于 通过平衡细胞的转录程序来确定它在发育后期产生的细胞命运。我们 进一步假设，这种重要的3D重组应该更忠实地通过有丝分裂和 染色质表观遗传标记，如组蛋白修饰和DNA甲基化，对它们的 建制派。这个团队的成员开发了一些工具，为理解 胚胎发育中的基因组三维组织。其中包括邻近连接分析，它允许全球 细胞群体和单细胞中基因组三维组织的测定。我们还开发了一种尖端和 老鼠体内强大的组合条形码系统，使我们能够破译细胞之间的线性关系。 在这里，我们建议使用这些工具来识别原肠小鼠胚胎中特定于谱系的更高阶特征，评估 它们与发育后期基因表达的关系，评估它们在有丝分裂后重建的忠实程度 并研究它们如何受到与疾病相关的表观遗传学扰动的影响。 我们的长期目标是了解基因组结构动态在胚胎发育过程中决定命运的作用。 当细胞以高度程序化的方式经历一系列的世系承诺时。我们提议的研究将 通过表征胚胎发生过程中特定血统的基因组3D组织以及其 功能动力学及其与染色质表观遗传标记的联系。