Uncovering sources of variability in maternal mRNA decay and zygotic mRNA accumulation during zebrafish maternal-to-zygotic transition

Degradation of maternally deposited mRNAs is critical for early development. Early metazoan embryos are transcriptionally silent, and exclusively rely on maternally provided mRNAs and proteins. As embryogenesis proceeds, the maternal-to-zygotic transition (MZT) establishes distinct developmental programs via a massive degradation of maternal mRNAs and production of new zygotic transcripts to replace them. Multiple works have globally characterized the zebrafish MZT. But measured decay of maternal and accumulation zygotic copies frequently vary, and the sources of this variability remain unclear. To study this variability in depth, we analyzed 10 temporal RNA-Seq datasets of zebrafish early embryos that were published by multiple labs. We used a linear model to describe temporal changes in mRNA levels of each gene in each dataset, and classified genes according to expression levels of mature and precursor mRNA before and after MZT. Comparing mRNA dynamics of genes between datasets, we demonstrate that some genes (e.g., naa30, mark3a) are highly consistent between datasets, but other genes (e.g., ppan) show significant differences. Functionally, non-variable genes were associated with developmental regulation, while variable genes were more associated with basal cellular functions. We aim to further explore what variation is explained by genetic polymorphism and/or intrinsic properties of the biological system, and connect it to putative regulatory signals. For example, we identified single nucleotide polymorphic sites (SNPs) showing different percentages between datasets and are testing their connection to degradation differences. These results will provide insights into the regulation of maternal mRNA degradation in embryos, with important implications in development and fertility.