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

DNA methylation is vital for development and diseases, yet no spatial DNA methylation profiling technology has been reported. Here we developed spatial 5mC-seq (SmC-seq), a microfluidic-based method providing unbiased genome-wide methylome at near single-cell resolution. Applying SmC-seq to mouse post-implantation development revealed a clear spatial heterogenous pattern of DNA methylation in inner cell mass-derived tissues. We identified a two-layer organization in the E8.5 ectoplacental cone with distinct methylation and proliferation states. Unexpectedly, a portion of maternal tissue with low DNA methylation level, enriched for nutrient-supplier progenitors, is observed in the middle region of decidua post-implantation. The hypomethylated regions in the nutrient-supplier progenitor cluster are associated with cell proliferation. Notably, the genes associated with hypomethylated regions in mature nutrient-supplier cluster are enriched in exocytosis and nutrient synthesis, linked to nutrient provision for embryogenesis before placental function. In summary, SmC-seq enables spatial DNA methylation mapping, advancing our understanding of biological events.