Pou5f3 and Sox19b select gene expression repertoire at Zygotic Genome Activation

PouV and SoxB1 family transcription factors (TFs) have emerged as master regulators of cell fate transitions. To investigate the genetic interactions between Pou5f3 and Sox19b in zebrafish embryos passing through Zygotic Genome Activation (ZGA), we combined time-resolved mutant transcription analysis using the novel tool RNA-sense, chromatin state and phenotypic assays. We distinguish four types of embryonic enhancers, differentially regulated by the two TFs. Pou5f3 is critical for activation of enhancer types 1 and 2, which are responsible for transcription of genes involved in gastrulation and ventral genes. Pou5f3 or Sox19b prevent premature activation of type 3 and 4 enhancers, which are responsible for transcription of organogenesis regulators, differentiation factors and dorsal genes. We also show that the balance between Sox19b and Pou5f3 is important for bulk ZGA timing. Our results uncover how independent activities of maternal Pou5f3 and Sox19b add up or antagonize to determine the early gene expression repertoire.