Reciprocal zebrafish-medaka hybrids reveal maternal control of zygotic genome activation timing

The sperm and egg contribute unequally to the newly formed zygote. While the sperm provides mainly paternal DNA, the egg provides both maternal DNA and the bulk of the future embryonic cytoplasm. Most embryonic processes like the onset of zygotic transcription are thought to depend on maternal cytoplasmic components, but this has not been tested rigorously. Here we report the establishment of a reciprocal zebrafish-medaka hybrid system which enables unequivocal distinction between maternal and paternal gene products. By combining expression of zebrafish Bouncer on the medaka egg with artificial egg activation, we demonstrate the in vitro generation of paternal zebrafish/maternal medaka (reripes) hybrid embryos. These hybrids complement the previously reported paternal medaka/maternal zebrafish (latio) hybrid embryos1, providing a versatile tool to dissect parental control mechanisms during early development. With this system, we investigated maternal vs. paternal control of zygotic genome activation (ZGA) timing. RNA-seq and ATAC-seq analyses of the purebred fish species and hybrids revealed that the onset of ZGA is primarily governed by the egg. Combining these datasets with proteome-wide analysis of early medaka and zebrafish embryogenesis highlights new potential regulators of ZGA, including Znf281b. Overall, our study establishes the reciprocal zebrafish-medaka hybrid system as a versatile tool to study parent-of-origin effects in vertebrate embryos.