Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during early mammalian organogenesis [10X_Dnmt]

Perturbation of DNA methyltransferases and of the active demethylation pathway via TET enzymes results in severe developmental defects and embryonic lethality. Dynamic control of DNA methylation is therefore vital for embryogenesis, yet the underlying mechanisms remain poorly understood. Here we report a single-cell transcriptomic atlas from a variety of DNA methylation mutant mouse embryos during mouse early organogenesis. We show that both the maintenance and de novo methyltransferase enzymes are dispensable for the formation of all major cell types at E8.5. However, DNA methyltransferases are required for silencing of prior or alternative cell fates such as pluripotency and extraembryonic programmes. Deletion of all three TET enzymes produces substantial lineage biases, in particular, a failure to generate primitive erythrocytes. Single-cell multi-omics profiling moreover reveals that this is linked to a failure to demethylate distal regulatory elements in Tet triple-knockout embryos. This study therefore provides a detailed analysis of the effects of perturbing DNA methylation on mouse organogenesis at whole organism scale, and affords new insights into the regulatory mechanisms of cell fate decisions. 18 mouse embryos collected at E8.5 from Dnmt1, Dnmt3a, Dnmt3b homozygous mutants and matching wildtype controls processed using 10x genomics scRNA-seqDNA甲基转移酶（DNA methyltransferases）与经由TET酶（TET enzymes）介导的主动去甲基化通路发生扰动时，会引发严重的发育缺陷与胚胎致死。因此，DNA甲基化的动态调控对胚胎发生至关重要，但其背后的核心调控机制仍有待深入解析。 本研究报道了小鼠早期器官发生阶段，多种DNA甲基化突变小鼠胚胎的单细胞转录组图谱（single-cell transcriptomic atlas）。研究显示，在胚胎发育第8.5天（E8.5），维持型与从头型DNA甲基转移酶均非所有主要细胞类型形成的必需因子。然而，DNA甲基转移酶对于沉默前体细胞或备选细胞命运程序（如多能性程序与胚外发育程序）是不可或缺的。 三种TET酶全部敲除会导致显著的谱系偏向性，尤其无法生成原始红细胞（primitive erythrocytes）。进一步的单细胞多组学（single-cell multi-omics）分析揭示，该表型与TET三敲除（Tet triple-knockout）胚胎的远端调控元件去甲基化失败密切相关。 本研究在全生物体层面详细解析了DNA甲基化扰动对小鼠器官发生的影响，为细胞命运决定的调控机制提供了全新的研究视角。本研究针对E8.5阶段采集的18枚Dnmt1、Dnmt3a、Dnmt3b纯合突变小鼠胚胎及其匹配的野生型对照胚胎，采用10x Genomics单细胞RNA测序（scRNA-seq）技术进行了处理与分析。