Developmental spatial transcriptome for the molecular annotation of germ layer formation and the acquisition of tissue lineage attributes of post-implantation mouse embryo

The blueprint of embryonic development is first visualized in the context of regionalization of cell fates of germ layer tissues in the post-implantation mouse embryo. Knowledge of the genetic and signaling activities that underpin gastrulation, lineage specification and tissue patterning has been gleaned from embryological experimentation and phenotypic analysis of loss- and gain-of-function genetic models. However, a comprehensive genome-wide molecular annotation of the mechanism of gastrulation has yet to be undertaken. Here, we reported the findings of a transcriptome study of cell populations at defined positions in the epiblast, ectoderm, mesoderm and endoderm of the pre-gastrulation and gastrulation stage embryos. This developmental and spatial transcriptome has defined the genealogy of sub-populations of cells in the germ layers. The transcriptome further identifies the molecular determinants such as the transcriptional factors and epigenetic entities, and the activity of signaling pathway and the transcriptional networks that drive the lineage commitment of the pluripotent epiblast cells and the germ layer precursors. By using spatial transcriptome of Geo-seq, we carried out transcriptome profiling on embryo sections at a high resolution of ~20 cells per sample. We then constructed a comprehensive spatial transcriptome map from the pre-gastrulation to late-gastrulation embryos that are visualized in a 3D embryonic model based on the sequencing data.胚胎发育的蓝图，最早可在植入后小鼠胚胎的胚层组织细胞命运区域化进程中得以可视化呈现。此前，关于支撑原肠作用（gastrulation）、谱系特化与组织模式建成的遗传及信号通路活动的相关认知，多来源于胚胎学实验以及功能丧失、功能获得型遗传模型的表型分析。然而，目前仍未开展针对原肠作用（gastrulation）机制的全基因组范围分子注释研究。本研究针对原肠胚前期与原肠作用（gastrulation）阶段小鼠胚胎中，定位于上胚层（epiblast）、外胚层（ectoderm）、中胚层（mesoderm）及内胚层（endoderm）特定位置的细胞群体开展转录组学分析，现将相关研究结果报道如下。该发育时空转录组明确了胚层内各细胞亚群的谱系起源关系。该转录组进一步鉴定出了包括转录因子与表观遗传调控因子在内的一系列分子决定因素，并揭示了驱动多能上胚层（epiblast）细胞及胚层前体细胞谱系定型的信号通路活性与转录调控网络。本研究依托Geo-seq空间转录组技术，以单样本约20个细胞的高分辨率对胚胎切片进行了转录组谱分析。随后，本研究基于测序数据构建了从原肠胚前期至晚期原肠作用（gastrulation）阶段小鼠胚胎的完整空间转录组图谱，并将其可视化呈现于三维胚胎模型中。