Mechanisms Regulating Zygotic Genome Activation

A universal feature of early development is the transition from maternal to zygotic control. Following fertilization, the embryo is transcriptionally inactive for a defined period in which development is governed by maternal factors. For the embryo to develop further, zygotic nuclei must awaken in the process of zygotic genome activation (ZGA) which culminates in spatiotemporally restricted gene expression patterns that drive cell fate determination. The precise timing of ZGA onset is stereotyped and critical for early developmental transitions. The goal of this research is to elucidate the molecular mechanisms governing ZGA, including how a ‘licensing’ system controls the precise timing of onset. Reduced female reproductive success is a rising global issue; understanding the maternal to zygotic handoff and essential mechanisms that safeguard these early developmental transitions are critical to deciphering its etiology. Pioneer transcription factors, such as those in Pouf and Sox families are required for ZGA. They bind closed chromatin and recruit factors to open it for transcription, and their nuclear accumulation is temporally regulated, rising sharply prior to ZGA. Whether they are sufficient to control ZGA licensing and how their nuclear partitioning drives transcriptional onset are not known. To fill these gaps, we will use Xenopus embryos that undergo a stereotyped spatial sequence of ZGA onset: first in animal pole (AP) cells and later in vegetal pole (VP) cells. These cells are the same developmental age but have different timing of ZGA, providing a powerful system to identify the key factors that govern genome activation. We will test the hypothesis that pluripotency factor nuclear accumulation underlies the spatiotemporally ordered pattern of ZGA. We will measure and manipulate Pou5f3 and Sox3 levels in Xenopus AP and VP cells, and quantify chromatin accessibility and zygotic transcription. These experiments will reveal the extent to which pluripotency factors pattern the major wave of ZGA onset. Multiple distinct repressive mechanisms have been proposed to suppress premature ZGA in early embryogenesis, including histones and immature nuclear pore complexes. We hypothesize a nuclear import competition mechanism suppresses early partitioning of factors that activate ZGA, that histones function as the repressor and that de-repression is mediated by increasing nucleocytoplasm (NC) ratio which repartitions histones to the genome. To test this model, we will use slbp2 mutant zebrafish embryos that contain reduced levels of core histones and vary NLS motif strengths of pluripotency factors. We will measure nuclear enrichment of pluripotency factors and timing for chromatin remodeling and ZGA onset. The major wave of zygotic transcription comprises multiple ZGA control systems, including genes with NC-dependent and timed onset. We will test the hypothesis that Pou5f3 and Sox3 binding predicts NC-dependent but not time- dependent gene expression. This will reveal how zygotic gene expression integrates distinct ZGA regulatory mechanisms for spatiotemporally patterned lineage commitment. Revealing the molecular mechanisms that license ZGA will provide critical new insights on systems that safeguard the fidelity of embryo development. Project Number: 1R35GM161628-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of General Medical Sciences (NIGMS) | Principal Investigator: Matthew Good | Institution: UNIVERSITY OF PENNSYLVANIA, PHILADELPHIA, PA | Award Amount: $460,771 | Activity Code: R35 | Study Section: Special Emphasis Panel[ZRG1 CDB-E (55)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11260323