Spatial Control of Pattern Formation in Early Vertebrate Development

项目摘要/摘要 胚胎发育是由基因表达的空间模式的出现来定义的，这 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在 空间和时间。虽然新兴技术使基因表达的精确量化成为可能 在单细胞中，整合转录信息和空间细胞异质性的策略 一直都很缺乏。在这里，我们建议结合空间转录和表观基因组图谱来 重建早期羊水胚胎的调控结构。通过在低温下进行RNA-seq- 对于禽类胚胎的切片，我们将沿着体轴建立一组转录坐标。 这些参数将允许我们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。为了测试这一点 方法我们组装了一个虚拟胚胎的原型，它由包含以下元素的像素组成 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，揭示了雏鸡原肠胚高度调控的复杂性。 由于这很可能反映在原肠形成细胞的基因组组织中，因此这一研究的第二个目标 提议使用笛卡尔方法来探索太空中染色质的调节。我们将确定如何 染色质可及性和组蛋白修饰沿胚胎的三个轴变化，并且 组装活性基因组元素的三维图谱。我们将使用这些高分辨率的模型 羊膜原肠胚用来定义控制不同领域出现的基因调控程序 祖细胞的数量。最终，我们的目标是定义基因调控网络如何在太空中运作 在发育中的胚胎中驱动图案的形成。

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.