Protein expression landscape of mouse embryos during pre-implantation development

Pre-implantation embryo development is an intricate and precisely regulated process orchestrated by maternally inherited proteins and newly synthesized proteins following zygotic genome activation. Although genomic and transcriptomic studies have enriched our understanding of genetic programs underlying this process, the protein expression landscape remains unexplored. Using quantitative mass spectrometry, we identified nearly 5000 proteins from 8000 mouse embryos of each stage (zygote, 2-cell, 4-cell, 8-cell, morula, blastocyst). We found that protein expression of zygote, morula and blastocyst show apparent difference from 2- to 8-cell embryos. Analysis of protein phosphorylation led to extraction of critical kinases and signal transduction pathways. We identified novel factors and proved that they play important roles in early embryo development. Combined analysis of transcriptomic and proteomic data reveals coordinated control of RNA degradation, transcription and translation, and identifies novel exon junction-derived peptides. Our study provides an invaluable resource for further mechanistic studies and suggests novel players governing pre-implantation embryo development. Overall design: We performed RNA-sequencing of Rrp9 knock-down embryos in morula stage