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: 10117841
• 负责人: Reza Kalhor
• 金额: $ 59.28万
• 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/10117841
• 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; 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.

项目概要/摘要 原肠胚形成是人体计划形成的关键过程，其破坏可能导致流产或分娩 尾部发育不全等缺陷在此过程中，多能细胞分化为初级胚层或胚层。 内胚层、中胚层和外胚层谱系随后产生了身体的所有细胞类型。 涉及对每个谱系特有的基因组进行广泛的三维 (3D) 重组。 这些重组的功能效应和潜在机制以及它们破坏的后果是 不太了解。 我们的目标是确定原肠胚形成期间谱系特异性基因组 3D 重组的动态以及如何 它们对表观遗传景观的破坏做出反应，我们的假设是每个谱系的基因组 3D 变化都有帮助。 通过使其承担这些细胞的转录程序来确定其在发育后期产生的细胞命运。 此外，如此重要的 3D 重组应该通过有丝分裂更忠实地继承，并且 染色质表观遗传标记，例如组蛋白修饰和 DNA 甲基化，对于它们的形成非常重要 该团队的成员开发了一些工具，为理解其作用创造了新的机会。 胚胎发育中的基因组 3D 组织包括可进行全局分析的邻近连接分析。 确定细胞群和单细胞中的基因组 3D 组织 我们还开发了尖端的和 小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胚小鼠胚胎中谱系特异性的高阶特征，评估 它们与发育后期基因表达的关联，评估它们在有丝分裂后重建的忠实程度 分裂，并检查它们如何受到疾病相关的表观遗传扰动的影响。 我们的长期目标是了解基因组结构动态在胚胎发生过程中命运决定中的作用 当细胞以高度编程的方式经历一系列谱系承诺时，我们提出的研究将。 通过表征胚胎发生过程中谱系特异性基因组 3D 组织及其 功能动力学以及与染色质表观遗传标记的联系。