An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo

Abstract

Early mouse embryos have an atypical translational machinery comprised of cytoplasmic lattices, poorly competent for translation. Thus, the impact of transcriptomic changes on the operational levels of proteins has likely been overestimated in the past. To find out, we used liquid chromatography-tandem mass spectrometry to detect and quantify 6,550 proteins in the oocyte and in six developmental stages (from zygote to blastocyst) collected in triplicates, and we also performed mRNA sequencing.In contrast to the known split between the 2-cell and 4-cell stages at the transcript level, on the protein level the oocyte-to-embryo transition appeared to last until the morula stage. In general, protein abundance profiles were weakly correlated with those of their cognate mRNAs and we found little or no concordance between changes in protein and transcript expression relative to the oocyte at early stages. However, concordance increased towards morula and blastocyst, hinting at a more direct coupling of proteins with transcripts at these stages, in agreement with the increase in free ribosome abundance. Independent validation by immunofluorescence and qPCR confirmed the existence of genes featuring strongly positively and negatively correlated protein and transcript. Moreover, consistent coverage of most known protein complexes indicates that our dataset represents a large fraction of the expressed proteome. Finally, we identified 20 markers, including members of the endoplasmic reticulum pathway, for discriminating between early and late stages.This resource contributes towards closing the gap between the 'predicted' phenotype, based on mRNA, and the 'actual' phenotype, based on protein, of the mouse embryo.

The regulation of mammalian maternal-to-embryonic transition by Eukaryotic translation initiation factor 4E

“…This is accompanied by the degradation of almost all the maternally inherited transcripts (4). Some understanding of the details of reprogramming of the proteome in the early embryo in mammals is also now emerging (5)(6)(7). Many proteins present within the oocyte are also detected in the zygote, however, a proportion are rapidly lost after fertilization (5).…”

“…This is accompanied by the increased protein expression of many components of the ubiquitin/proteosome protein degradation. A range of other proteins are present at higher levels in the zygote than the oocyte and include proteins associated the citrate cycle pathway, glucan metabolism, lipid binding proteins, and fatty acid metabolism (5)(6)(7). This early round of new translation also includes components of the transcriptional machinery (8) and translational activity is required for the successful activation of the embryonic genome (9).…”

“…This early round of new translation also includes components of the transcriptional machinery (8) and translational activity is required for the successful activation of the embryonic genome (9). After EGA the new transcriptome is subject to a further round of translation, however, this does not result in a strong correlation between the RNA species generated at EGA and the cellular proteome until the morula and blastocyst stages (5,6).…”