Gene expression dynamics before and after zygotic genome activation in Drosophila early embryogenesis
Post-transcriptional gene regulatory mechanisms are fundamental for the determination of gene expression dynamics and especially crucial for the earliest stages of animal development in which transcription is nearly silent. Here we performed high-resolution gene expression level change analysis in Drosophila maternal-to-zygotic transition (MZT). Intriguingly, we found that both stable transcript expression and an increase in translation efficiency can be crucial for protein upregulation prior to zygotic gene activation (ZGA), whereas such features diminished following ZGA. The results suggested that there are distinct regulatory mechanisms for protein upregulation pre- and post-ZGA in Drosophila embryos. Further, this study is the first to report the proteome-wide quantitative changes in protein ubiquitination in Drosophila MZT. Our results indicate that timely ubiquitination of the distinct target proteins during MZT are essential for the downregulation of protein expression levels. Profiling of the RNA-associated proteome changes in Drosophila MZT suggested that RNA-binding activities can be regulated without the respective change in net protein expression levels for over 200 proteins, including Pcid2, Sym, and Cpsf73. Taken together, we report a diverse array of features that mediate post-transcriptionally regulated gene expression dynamics in Drosophila MZT. Overall design: RNA-seq on drosophila embryos and unfertilized eggs were conducted in high-temporal resolution.