Spatial 5mC-seq profiling of embryos and decidua after implantation in mammal

DNA methylation plays key roles in development and diseases. However, no spatial DNA methylation profiling technology has been reported until now. Here, we developed a spatial 5mC-seq method (SmC-seq) based on a microfluidic system. The SmC-seq can provide a non-biased genome-wide methylome at about single-cell scale (10 μm in width per channel). We further applied this SmC-seq to explore the spatiotemporal dynamics of DNA methylation during post-implantation development in mouse. A clear spatial heterogeneous pattern of DNA methylation among inner cell mass-derived tissues can be observed. Additionally, we identified a two-layer organization in the ectoplacental cone at the E8.5 stage, characterized by distinct DNA methylation patterning and proliferation states. Unexpectedly, a portion of maternal tissue with low DNA methylation level, enriched for nutrient-supplier progenitor cell, is observed in the middle region of maternal decidua after implantation. The hypomethylated regions in the nutrient-supplier progenitor cell cluster are associated with cell proliferation. Interestingly, the genes associated with hypomethylated regions in the mature nutrient-supplier cell cluster are enriched in exocytosis and nutrient synthesis, which is associated with nutrient provision before functional placenta is formed to support mammalian embryogenesis. In summary, SmC-seq enables spatial mapping of DNA methylation and facilitates our understanding of various biological events.