Subcellularly Resolved 3D Translatome in Mouse Oocytes and Early Embryos

Abstract

Spatial patterning of mRNA translation is a fundamental process in early embryogenesis. Existing RNA translation profiling methods lack subcellular spatial resolution at the single-molecule level, limiting our understanding of spatial RNA biology in embryogenesis. To address this, we profiled the spatial translatome of intact mouse embryos at near-genomic scale by adapting RIBOmap and incorporating multiplexed organelle staining. In oocytes, 2-cell and 4-cell embryos, we systematically analyzed RNA translation across three spatial scales: organelle, subcellular, and intercellular. We found that functionally related genes exhibit spatially and temporally controlled translation patterns near distinct organelles. Using Harmonics, a graph signal processing framework, we demonstrate that embryo asymmetry emerges at the first cell division and is amplified at later stages. This work paves the way for comprehensively investigating the fundamental spatial post-transcriptional regulation at the earliest moments of mammalian life.