Spatial Control of Pattern Formation in Early Vertebrate Development

早期脊椎动物发育中模式形成的空间控制

• 批准号: 10673415
• 负责人: Marcos Simoes-Costa
• 金额: $ 87.01万
• 依托单位: BOSTON CHILDREN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-08-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10673415
• 关键词: Spatial; Control; Pattern; Formation; Early

PROJECT SUMMARY / ABSTRACT Embryonic development is defined by the emergence of spatial patterns of gene expression, which organize progenitor cells into the blueprint of tissues and organs. To understand how genetic information gives rise to tridimensional arrangements of cells, we need to assess how genomes are regulated in space and time. While emerging technologies have allowed for precise quantification of gene expression in single cells, strategies to integrate transcriptomic information and spatial cellular heterogeneity have been lacking. Here, we propose to combine spatial transcriptomics and epigenomic profiling to reconstruct the regulatory architecture of the early amniote embryo. By conducting RNA-seq in cryo- sections of the avian embryo, we will establish a set of transcriptomic coordinates along the body axes. These parameters will allow us to position single-cell RNA-seq datasets in a tridimensional grid that will be used to reconstruct spatial patterns of gene expression on a genome-wide scale. To test this approach we assembled a prototype of this virtual embryo, which is composed of pixels containing regulatory information from all genes expressed in the genome. This model allowed us to recreate spatial expression patterns, uncovering a high degree of regulatory complexity in the chick gastrula. Since this is likely to be reflected in the genomic organization of gastrulating cells, a second aim of this proposal is to use a Cartesian approach to explore chromatin regulation in space. We will establish how chromatin accessibility and histone modifications change along the three axes of the embryo, and assemble tridimensional maps of active genomic elements. We will use these high- resolution models of the amniote gastrula to define the gene regulatory program that controls the emergence of distinct fields of progenitor cells. Ultimately, our goal is to define how the gene regulatory networks operate in space to drive pattern formation in the developing embryo.

项目总结/摘要 胚胎发育是由基因表达的空间模式的出现来定义的， 将祖细胞组织成组织和器官的蓝图。为了了解基因信息是如何 产生了细胞的三维排列，我们需要评估基因组是如何被调节的， 空间和时间。虽然新兴技术已经允许精确量化基因表达， 在单细胞中，整合转录组信息和空间细胞异质性的策略已经 一直缺乏。在这里，我们建议将联合收割机空间转录组学和表观基因组学分析相结合， 重建早期胚胎的调控结构。通过在低温下进行RNA测序， 鸟类胚胎的切片，我们将建立一套转录组学坐标沿着身体轴。 这些参数将使我们能够在三维网格中定位单细胞RNA-seq数据集， 用于在全基因组范围内重建基因表达的空间模式。为了验证这一 我们组装了这个虚拟胚胎的原型，它由包含以下内容的像素组成 来自基因组中表达的所有基因的调控信息。这个模型让我们能够重现 空间表达模式，揭示了鸡原肠胚高度的监管复杂性。 由于这可能反映在原肠胚细胞的基因组组织中，因此本发明的第二个目的是： 一个建议是使用笛卡尔方法来探索空间中的染色质调控。我们将确定 染色质可及性和组蛋白修饰沿着胚胎的三个轴发生变化， 组装活性基因组元件的三维图谱。我们将使用这些高分辨率的 的胚胎原肠胚，以确定基因调控程序，控制不同领域的出现， 祖细胞。最终，我们的目标是确定基因调控网络如何在太空中运作。 来驱动发育中的胚胎形成图案。