Alternative splicing expands transcriptome diversity in eukaryotes. Impacting most human genes, alternative splicing can famously generate multiple protein isoforms from the same gene. However, it can also be used to control the final amounts of functional proteins, by generating non-productive transcripts that effectively downregulate gene expression.
Here, we investigated how alternative splicing was regulated during the first stages of embryonic development in mammals, when a major molecular event occurs: the awakening of the zygotic genome. Whereas the first steps are fully driven by the mRNAs and proteins deposited by the mother, the zygotic genome starts to be transcribed soon and takes full control of embryogenesis.
We found that the cells in the embryo undergoing zygotic genome activation (ZGA) exhibit the highest levels of exon skipping of all cell and tissue types (including the brain). However, this striking transcriptomic diversity is temporary, lasting only 1-2 cell cycles (Fig. 1a). Moreover, it mainly leads to the production of unproductive transcripts (Fig. 1b), effectively killing genes enriched for DNA damage responses (DDR) at ZGA, in line with the low reparative response of early embryos.
Remarkably, this is due to a developmentally programmed splicing failure (Fig. 1d): during oogenesis some core spliceosomal components (Snrpb/d2) are not deposited at sufficient levels and splicing for some genes fails when zygotic transcription starts. However, these core components are themselves strongly transcribed at ZGA, and thus their levels recover after 1-2 stages, giving rise to the peak-like splicing patterns.
This model makes a simple prediction: if we express Snrpb/d2 earlier, we should be able to “rescue” the failed splicing patterns (Fig. 1d). This is what we saw. Moreover, this also increased DDR in those “rescued” embryos.
In summary, we uncovered an evolutionarily conserved, developmentally programmed splicing failure during ZGA, which modules DDR. What we have not yet answered is: why would the embryo boycott itself at ZGA? Future research will tell…