H3K4me3-dependent transcript elongation drives hypoxia-enhanced zygotic genome activation

Hypoxia provides benefits for assisted reproductive technologies (ART) in clinical practice, yet its mechanisms are poorly understood. Here, we show that hypoxic culture enhances mouse blastocyst formation and reduces developmental arrest during zygotic genome activation (ZGA), with zygotic gene expression closely mimicking physiological in vivo patterns during major ZGA. Mechanistically, hypoxia specifically increases H3K4me3 enrichment at zygotic gene promoters and decreases it at transposable elements and oocyte-specific domains in late 2-cell embryos. Chromatin-accessible regions, RNA polymerase II (Pol II)-enriched regions, and Pol II Ser2 phosphorylation (Ser2P)-enriched regions exhibit higher H3K4me3 enrichment in hypoxia-cultured late 2-cell embryos. Global Pol II and Ser2P are increased under hypoxia and they were recruited to hypoxia-induced H3K4me3 regions to initiate transcription and elongation. Importantly, Pol2 and Ser2P signals increased after CPI-455 treatment, which inhibited KDMs and increased H3K4me3. Hypoxia increases promoter H3K4me3, promoting chromatin accessibility and transcription initiation/elongation to orchestrate acute zygotic gene transcription. Our data bridge the gap between the benefits of hypoxic ART and the epigenetic mechanisms of ZGA regulation, providing a theoretical foundation to optimize ART protocols and improve clinical success.