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genomebiology.com

Background The oocyte-to-embryo transition (OET) converts terminally differentiated gametes into a totipotent embryo and is critically controlled by maternal mRNAs and proteins, while the genome is silent until zygotic genome activation. How the transcriptome, translatome, and proteome are coordinated during this critical developmental window remains poorly understood. Results Utilizing a highly sensitive and quantitative mass spectrometry approach, we obtain high-quality proteome data spanning seven mouse stages, from full-grown oocyte (FGO) to blastocyst, using 100 oocytes/embryos at each stage. Integrative analyses reveal distinct proteome reprogramming compared to that of the transcriptome or translatome. FGO to 8-cell proteomes are dominated by FGO-stockpiled proteins, while the transcriptome and translatome are more dynamic. FGO-originated proteins frequently persist to blastocyst while corresponding transcripts are already downregulated or decayed. Improved concordance between protein and translation or transcription is observed for genes starting translation upon meiotic resumption, as well as those transcribed and translated only in embryos. Concordance between protein and transcription/translation is also observed for proteins with short half-lives. We built a kinetic model that predicts protein dynamics by incorporating both initial protein abundance in FGOs and translation kinetics across developmental stages. Conclusions Through integrative analyses of datasets generated by ultrasensitive methods, our study reveals that the proteome shows distinct dynamics compared to the translatome and transcriptome during mouse OET. We propose that the remarkably stable oocyte-originated proteome may help save resources to accommodate the demanding needs of growing embryos. This study will advance our understanding of mammalian OET and the fundamental principles governing gene expression.

aem.asm.org

american society for microbiology (asm) journals deliver up-to-date and authoritative coverage of both basic and clinical microbiology. join our authors.

genome.cshlp.org

an international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

geneious.com

Geneious Prime is the world’s leading bioinformatics software for molecular biology and sequence analysis. Geneious Biologics streamlines antibody discovery and screening with intuitive cloud-based software

rna-seqblog.com

This is a class recording of VTPP 638 "Analysis of Genomic Signals" at Texas A&M University. No RNA-Seq background is needed, and it comes with a lot of free resources that help you learn how to do RNA-seq analysis. You will learn: (1) The basic concept of RNA-sequencing (2) How to design your experiment: library