Single-cell RNA-seq of mouse embryos E4.5 to E7.5. First batch.

Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan. Recent studies employing single cell RNA-sequencing have identified major transcriptional changes associated with germ layer specification. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell fate choice remains unresolved, and the coordination between different epigenetic layers is unclear. Here we describe the first single cell triple-omics map of chromatin accessibility, DNA methylation and RNA expression during the exit from pluripotency and the onset of gastrulation in mouse embryos. We find dynamic dependencies between the different molecular layers, with evidence for distinct modes of epigenetic regulation. The initial exit from pluripotency coincides with the establishment of a global repressive epigenetic landscape, followed by the emergence of local lineage-specific epigenetic patterns during gastrulation. Notably, cells committed to mesoderm and endoderm undergo widespread coordinated epigenetic rearrangements, driven by loss of methylation in enhancer marks and a concomitant increase of chromatin accessibility. In striking contrast, the epigenetic landscape of ectodermal cells is already established in the early epiblast. Hence, regulatory elements associated with each germ layer are either epigenetically primed or epigenetically remodelled prior to overt cell fate decisions during gastrulation, providing the molecular logic for a hierarchical emergence of the primary germ layers. Useful links: Parsed data: (ftp://ftp.ebi.ac.uk/pub/databases/scnmt_gastrulation) Github repository: (https://github.com/rargelaguet/scnmt_gastrulation) 758 single cells isolated from mouse embryos at E4.5, E5.5, E6.5 and E7.5 and processed using scNMT-seq (Clark et al 2018) NOTE: The GSE133725 Series supplementary file, embryo_cell_counts_matrix_030719.tsv, contains total 2971 processed data columns for both GSE121650 (758 cells) and GSE133725 (2213 cells) samples.原肠胚形成过程中三个初级胚层的构建是脊椎动物躯体模式建立的关键环节。近期依托单细胞RNA测序（single cell RNA-sequencing）的研究已明确与胚层特化相关的核心转录调控变化。这些变化伴随全局表观遗传重编程，但表观基因组在早期细胞命运抉择中的调控作用仍未阐明，不同表观遗传层面之间的协同机制亦尚不明确。本研究首次报道了小鼠胚胎脱离多能性状态并进入原肠胚形成起始阶段期间，染色质可及性、DNA甲基化与RNA表达的单细胞三重组学（triple-omics）图谱。本研究揭示了不同分子层面间的动态调控关联，并发现存在多种独特的表观遗传调控模式。细胞初始脱离多能性的过程，与全局抑制性表观遗传景观的建立相契合；随后在原肠胚形成阶段，会出现谱系特异性的局部表观遗传特征。值得注意的是，定向分化为中胚层与内胚层的细胞会发生广泛的协同表观遗传重排，该过程由增强子标记区域的甲基化缺失以及染色质可及性的同步升高共同驱动。与之形成鲜明对比的是，外胚层细胞的表观遗传景观在早期上胚层阶段便已奠定。因此，在原肠胚形成过程中出现明确细胞命运抉择之前，各胚层相关的调控元件要么已完成表观遗传预编程，要么已发生表观遗传重塑，这为初级胚层的层级化发生提供了分子层面的逻辑依据。 相关资源链接： 解析后数据集：(ftp://ftp.ebi.ac.uk/pub/databases/scnmt_gastrulation) GitHub仓库：(https://github.com/rargelaguet/scnmt_gastrulation) 本数据集包含从小鼠胚胎E4.5、E5.5、E6.5及E7.5时期分离的758个单细胞，采用scNMT-seq技术进行处理（Clark等人，2018年）。 备注：GSE133725系列补充文件embryo_cell_counts_matrix_030719.tsv中包含GSE121650（758个细胞）与GSE133725（2213个细胞）两个样本集共计2971个处理后的数据列。