Unified Transcriptome and Mechanics Map of the Intact Mammalian Preimplantation Embryo In Situ

Abstract The development and maintenance of multicellular tissues requires that cell states be closely coupled to their local environment, including geometric and mechanical cues. However, studying this coupling in intact tissues has been challenging, because existing measurement technologies cannot simultaneously assess mechanical properties and molecularly defined cell states. To address this gap, we introduce the Unified Transcriptome and Mechanics Map (UTMM), a method for concurrent measurement of the transcriptome and cytoplasmic stiffness (high-frequency elastic modulus) within intact 3D multicellular structures. UTMM relies on two innovations: (1) a targeted in situ RNA sequencing approach for intact 3D embryos (3DISS), and (2) a strategy that leverages high-frequency intracellular organelle fluctuations to infer cell-level stiffness in vivo . We applied UTMM to mouse embryos from the zygote through the morula stage to characterize how RNA expression and cytoplasmic stiffness become coupled during early lineage specification. Our data reveal that, in the early morula, transcriptional and morphological distinctions emerge between trophectoderm and inner cell mass (ICM) lineages, coinciding with a gradual decrease in cytoplasmic stiffness (softening) across all cells from the 2-cell through morula stages. Furthermore, we observe that early lineage biases align with differential mechanical properties, reflecting distinct emerging developmental programs. When we delayed this softening process via mechanical perturbation, embryonic progression was impeded, highlighting the functional importance of coordinated mechanical and transcriptional changes. Together, these results demonstrate UTMM’s ability to bridge molecular and mechanical dynamics in multicellular systems, providing a powerful framework for investigating how biomechanical cues shape cell fate decisions in intact tissues. One Sentence Summary Joint 3D in situ quantification of spatial transcriptome and cytoplasm mechanics in preimplantation mammalian embryos