Look at that Precious Fry… She has Her Mother’s Protein
Summary by Matt Monaghan: da Silva Pescador G;Baia Amaral D;Varberg JM;Zhang Y;Hao Y;Florens L;Bazzini AA; (2024, October 22). Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. Cell reports. https://pubmed.ncbi.nlm.nih.gov/39302832/
Image credit: Wikimedia Commons (Porsche997SBS)
A sperm cell and an egg cell fuse together to form a zygote in a process known as fertilization. Before fertilization, the egg has its own transcriptional and translational processes. These processes change after fertilization. The maternal-to-zygotic transition (MZT) is a crucial stage of development to switch biochemical processes from gamete control to embryo control (1). Genes can be pure zygotic (only from the zygote genome), pure maternal (gene products like RNA or protein from the egg cell and present since fertilization), or maternal-zygotic (both). Activation of zygotic genes typically happens in zebrafish between 2- and 4-hours post fertilization (hpf). The MZT is marked by degradation of older mRNAs that were provided by the oocyte. With the use of quantitative protein profiling and RNA-seq data across embryogenesis, da Silva Pescador et. al were able to trace temporal dynamics of RNA and protein to gain insight into what happens and when during this transition.
The authors found that proteins have less dramatic fluctuations than mRNA in early development. Increasing protein levels were positively correlated with overall transcript levels. Decreasing protein level did not necessarily correlate with less efficient translation, suggesting active protein degradation. Strikingly, some “zygotic proteins” were present at fertilization - before zygotic genome activation (ZGA). To understand protein origins (egg or sperm), the authors analyzed RNA-seq data from oocytes and sperm as well as proteomics data sets from oocytes. This indicated possible pre MZT protein inheritance from both egg and sperm.
To identify novel candidate factors involved in MZT, the authors searched for proteins that are rapidly translated immediately preceding MZT. They explored one such candidate, a putative transcription factor called znf281b, employing CRISPR-Cas13d to target the znf281b RNA transcripts. As the RNA for znf281b is maternally deposited and ZGA has not yet happened in their stage of interest, the authors could not use traditional CRISPR-Cas9, which cuts DNA. Alternatively, CRISPR-Cas13d uses a guide RNA to specifically detect a single-stranded RNA for the Cas protein to cut. As a result, the authors used CRISPR-Cas13d to target znf281b RNA and knock it down. This targeted knockdown showed developmental delays at 6 hpf, resembling genome activation failure phenotypes disrupting gastrulation. This shows that znf281b is essential for early stages of development. These experiments demonstrate a proof-of-concept that targeted knockdown aimed by proteomic data can reveal new maternal factor functions.
Altogether, this work lends a view into the complicated world of RNA and protein dynamics during MZT. This work brings to our attention the importance of understanding that mRNA level may not, on its own, reflect protein level due to post translational regulation, translation control, and protein stability. There is still more work to be done surrounding how RNA and protein levels relate during MZT.
Bibliography:
Vastenhouw NL, Cao WX, Lipshitz HD. The maternal-to-zygotic transition revisited. Development. 2019 Jun 12;146(11):dev161471. doi: 10.1242/dev.161471. PMID: 31189646.