Nature Methods, 27 April, 2026, DOI：https://doi.org/10.1038/s41592-026-03079-w

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

Xun Shan, Yimin Tang, Jinzhou Hu, Mingyuan Bian, Xuelong Yao, Lei Gao & Jiang Liu

Abstract

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.

Article link：https://www.nature.com/articles/s41592-026-03079-w