Dissecting Small Noncoding RNA Landscapes in Mouse Preimplantation Embryos and Human Blastoids for Modeling Early Human Embryogenesis

Small non-coding RNAs (sncRNA) exert regulatory functions in mammalian cells; however, their expression dynamics and contribution during preimplantation development are not entirely understood. In this study, we apply Small-Seq to generate a comprehensive single-cell atlas of sncRNA expression in mouse oocytes, sperm, and embryos (2-cell to 64-cell stages), and compare these dynamics with human embryos at equivalent stages. In both species, all sncRNA subtypes are expressed, but only microRNAs (miRNAs) and small nucleolar RNAs (snoRNAs) display cell type-specific patterns. In mice and humans, miRNAs and snoRNAs from the Dlk1-Dio3 locus were upregulated in the inner cell mass (ICM). Human trophectoderm (TE) is enriched with primate-specific C19MC miRNAs, which show relatively low expression in the ICM. In contrast, the mouse lacks a TE-specific hotspot, as C2MC miRNAs are higher in the ICM. Nonetheless, differentiation-associated miRNAs (e.g., miR-24-3p, miR-200c-3p) are high in the TE of both species. Further, we profile the sncRNAs of human blastoids (stem-cell-based embryo model) and determine that they largely recapitulate the human blastocyst. We envision broad utility of this dataset as a resource for future studies seeking to dissect the functions of individual sncRNAs in early development, and for advancing applications in stem cell-based embryo models and assisted reproductive technologies.