*Gastrulation* Single-cell RNA sequencing of mouse embryos with Tal1 (Scl) knockout - Bertie Gottgens (Gastrulation_RNA_Seq-sc-3711)

Tracing early mammalian lineage decisions by single cell genomics. Lewis Wolpert famously called gastrulation the most important time in your life. During this fascinating process, a pluripotent stem cell population in the early embryo gives rise to the three germ layers from which all organ systems develop. Cell signalling and transcriptional networks are known to regulate aspects of gastrulation, but the precise mechanisms have not been investigated at the single cell level. Thus, new principles remain to be discovered that govern the exit from naive pluripotency, epigenetic priming, stochasticity in transcriptional programmes, symmetry breaking, and acquisition of heritable transcriptome patterns. We have brought together a consortium of experts in single cell genomics, mammalian postimplantation development, and computational biology to comprehensively tackle this challenge. We will apply recently established single cell genomics techniques for DNA, RNA, and DNA methylation to profile the majority of the cells in mouse postimplantation embryos. This will result in epigenetic and gene expression maps of most cells together with experimentally determined lineage relationships, hence populating a Waddingtonian landscape. Based on such maps, combinations of transcription factors and epigenetic modifiers will be used to experimentally direct differentiation in human iPS cells.基于单细胞基因组学（single cell genomics）解析哺乳动物早期谱系决定事件。刘易斯·沃尔珀特曾留下知名论断，称原肠胚形成（gastrulation）是生命中最为关键的阶段。在这一引人入胜的发育过程中，早期胚胎内的多能干细胞（pluripotent stem cell）群体会分化为三胚层（three germ layers），所有器官系统均由这三胚层发育而来。目前已知细胞信号转导与转录调控网络可调控原肠胚形成的部分环节，但其精确机制尚未在单细胞层面得到系统解析。因此，调控原始态多能性退出、表观遗传预编程、转录程序随机性、对称性破缺以及可遗传转录组模式获得的全新生物学原则，仍有待发掘。本研究联合了单细胞基因组学、哺乳动物着床后发育以及计算生物学领域的专家组成研究联盟，以期全面攻克这一科学难题。我们将运用新近建立的单细胞基因组学技术，针对DNA、RNA及DNA甲基化进行检测，以刻画小鼠着床后胚胎中的绝大多数细胞。由此将获得绝大多数细胞的表观遗传图谱与基因表达图谱，并结合实验确定的谱系关联，从而完整填充沃丁顿表观遗传景观（Waddingtonian landscape）的细节。基于上述图谱，研究团队将结合转录因子与表观遗传修饰因子的组合，在人类诱导多能干细胞（iPS cells）中实验性诱导其定向分化。