In anamniote vertebrate development, zygotic genome activation (ZGA) occurs after several cell divisions; this allows the investigation of events that precede transcription. Using zebrafish, Linderman et al. assayed the levels of histone H3 modifications in embryos before and after ZGA. They showed that both permissive and repressive histone modifications are localized to gene promoters of developmentally regulated and homeostatic genes before transcription begins, indicating pre-patterning of these genes. This implies that histone modifications can be instructive for developmental gene expression.