Deciphering lineage specification during early embryogenesis in mouse gastruloids using multilayered proteomics

Gastrulation is a critical stage in embryonic development during which the germ layers are established. Advances in sequencing technologies led to the identification of gene regulatory programs that control the emergence of the germ layers and their derivatives. However, proteome-based studies of early mammalian development are scarce. To overcome this, we utilized gastruloids and a multilayered mass spectrometry-based proteomics approach to investigate the global dynamics of (phospho) protein expression during gastruloid differentiation. Our findings revealed many proteins with temporal expression and unique expression profiles for each germ layer, which we also validated using single-cell proteomics technology. Additionally, we profiled enhancer interaction landscapes using P300 proximity labeling, which revealed numerous gastruloid-specific transcription factors and chromatin remodelers. Subsequent degron-based perturbations combined with single-cell RNA sequencing (scRNA-seq) identified a critical role for ZEB2 in mouse and human somitogenesis. Overall, this study provides a rich resource for developmental and synthetic biology communities endeavoring to understand mammalian embryogenesis. [Display omitted] •Mouse gastruloid formation is associated with global rewiring of the (phospho) proteome•The three germ layers exhibit distinct protein expression profiles•P300 proximity labeling reveals global enhancer interactomes•ZEB2 plays a key role in mouse and human somitogenesis Stelloo et al. applied mass spectrometry-based proteomics technologies on gastruloids and mouse embryos to characterize global protein expression dynamics during early mouse embryonic development. Using P300 proximity labeling, they identified gastruloid-specific enhancer-binding proteins. Subsequent investigation revealed a role for ZEB2, a gastruloid-specific transcription factor, during mouse and human somitogenesis.