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A Phosphoproteomic Landscape of Mammalian Preimplantation Development and Human Embryo Arrest

ABSTRACT: Protein phosphorylation coordinates signal flow and cell-state transitions, but its global dynamics during mammalian preimplantation development have remained largely unresolved. Here we establish a cross-species phosphoproteomic atlas of early embryos using ultrasensitive workflows, quantifying ~6,000 phosphorylation sites in mouse and ~1,500 in human. Fertilization initiates a rapid, phosphatase-dominated reset of the maternal phosphoproteome, followed by a stepwise reconstruction of phosphorylation programs that culminates around the morula-to-blastocyst transition. Although individual phosphosites show limited conservation between species, pathway-level regulation is preserved, with marked species-biased timing across developmental stages. In mouse embryos, broad dephosphorylation of maternal proteins accompanies pronuclear formation, whereas phosphorylation of translation machinery rises in parallel with translational activation at the blastocyst stage. Functional perturbations further demonstrate that coordinated kinase activity is essential for successful blastocyst formation. Extending these measurements to the clinical setting, single-embryo phosphoproteomics of 52 human 8-cell-arrested embryos reveals arrest-specific, largely unannotated phosphosites and a rewired kinase-signaling architecture, offering mechanistic insight into preimplantation failure. Together, these data provide a reference framework for phosphorylation dynamics in early development and highlight candidate signaling nodes for diagnosis and targeted intervention in human infertility.

ORGANISM(S): Homo Sapiens

SUBMITTER: Zilu Ye

PROVIDER: PXD072726 | iProX | Wed Jan 07 00:00:00 GMT 2026

REPOSITORIES: iProX

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Project description:Early embryogenesis is a unique developmental stage where genetic control of development is handed off from mother to zygote. Yet the contribution of this transition to the evolution of gene expression is poorly understood. Here we study two aspects of gene expression specific to early embryogenesis in Drosophila: sex-biased gene expression prior to the onset of canonical X chromosomal dosage compensation, and the contribution of maternally supplied mRNAs. We sequenced mRNAs from individual unfertilized eggs, precisely staged and sexed blastoderm embryos and compared levels between D. melanogaster, D. yakuba, D. pseudoobscura and D. virilis. First, we find that mRNA content is highly conserved for a given stage and that studies relying on pooled embryos may systematically overstate the degree of gene expression divergence. Unlike studies done on larvae and adults, where most species show a larger proportion of genes with male-biased expression, we find that transcripts in Drosophila embryos are largely female-biased in all species, likely due to incomplete dosage compensation prior to the activation of the canonical dosage compensation mechanism. The divergence of sex-biased gene expression across species is observed to be often due to a decrease of expression, the most drastic example of which is the overall reduction of male expression from the neo-X chromosome in D. pseudoobscura, leading to a pervasive female-bias on this chromosome. We see no evidence for a faster evolution of expression on the X chromosome in embryos (no “faster X” effect), unlike in adults and contrary to a previous study on pooled non-sexed embryos. Finally, we find that most genes are conserved in regard to their maternal or zygotic origin of transcription, and present evidence that differences in maternal contribution to the blastoderm transcript pool may be due to species-specific divergence of transcript degradation rates We sequenced mRNA from D. melanogaser, D. yakuba, D. pseudoobscura and D. virilis single unfertilized eggs (1 to 2 per species) and from both single female and male embryos (3 per sex per species).

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A Phosphoproteomic Landscape of Mammalian Preimplantation Development and Human Embryo Arrest

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