Pluripotency factors determine gene expression repertoire at zygotic genome activation

Awakening of zygotic transcription in animal embryos relies on maternal pioneer transcription factors. The interplay of global and specific functions of these proteins remains poorly understood. Here, we analyzed nucleosome positioning, H3K27 acetylation and time-resolved transcription in zebrafish embryos lacking pluripotency factors Pou5f3 and Sox19b. We show that Pou5f3 and Sox19b modify chromatin in a largely independent manner. The bulk transcriptional onset does not require Sox19b and Pou5f3, but is sensitive to their balance. Pou5f3 docks H3K27ac on the enhancers of genes involved in gastrulation and ventral fate specification. Sox19b facilitates Pou5f3 access to a half of these enhancers. The genes regulating mesendodermal and dorsal fates are primed for activation independently of Pou5f3 and Sox19b. Strikingly, simultaneous loss of both factors leads to premature expression of differentiation genes. Our results uncover how independent activities of maternal Pou5f3 and Sox19b synergize or antagonize to determine the early gene expression repertoire.