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

项目总结/摘要 胃肠道发育是人体计划形成的关键过程，其中断可能导致流产或分娩 缺陷，如尾部发育不全。在此过程中，多能细胞分化成初级胚层或 内胚层、中胚层和外胚层谱系，这些谱系后来创造了身体的所有细胞类型。这种分化事件 涉及广泛的三维（3D）重组的基因组是特定于每一个血统。但 这些重组的功能效应和基本机制以及其中断的后果是 不太了解。 我们的目标是确定在原肠胚形成期间谱系特异性基因组3D重组的动力学，以及 它们会对表观遗传的破坏做出反应。我们的假设是，每个谱系中的基因组3D变化有助于 通过使其承担这些细胞的转录程序，建立其在发育后期产生的细胞命运。我们 我进一步假设，这种重要的3D重组应该通过有丝分裂更忠实地遗传， 染色质表观遗传标记，如组蛋白修饰和DNA甲基化，对于它们的生物学行为很重要。 建立。该团队的成员开发了一些工具，为理解 胚胎发育中的基因组3D组织。其中包括邻近连接测定法，其允许全局连接。 确定细胞群和单细胞中的基因组3D组织。我们还开发了一种先进的， 在小鼠中使用强大的体内组合条形码系统，使我们能够破译细胞之间的直系关系。 在这里，我们建议使用这些工具来识别原肠形成小鼠胚胎中的谱系特异性高阶特征，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。 部门，并检查它们是如何受到疾病相关的表观遗传扰动。 我们的长期目标是了解胚胎发生过程中基因组结构动态在命运决定中的作用 当细胞以高度程序化的方式经历一系列谱系承诺时。我们的研究计划将 通过表征胚胎发生过程中谱系特异性基因组3D组织及其 功能动力学和与染色质表观遗传标记的联系。

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.