Super Pol II Domains enhance minor ZGA through 3D-interaction to ensure the integrity of major transcriptional waves in ZGA delayed mammals (H3K4me3)

Zygotic genome activation (ZGA) represents the inaugural post-fertilization transcription event. In mouse, RNA polymerase II (Pol II) initiates embryonic transcription through a step-wise transition, but the ZGA initiation process remains unclear in non-rodents. Here, Pol II profiling in bovine and porcine embryos, combined with multi-omics data across four mammalian species, revealed strong intergenic Pol II clusters, termed super Pol II domains (SPDs), that boost minor ZGA gene expression via chromatin interactions in bovine. Intriguingly, a similar strategy was found in human embryos, which also exhibit delayed ZGA followed by rapid up-regulation of minor ZGA genes. By contrast, these genes are precociously activated in porcine and mouse gametes before fertilization. Moreover, disruption of SPD structure, which decreases two minor ZGA genesKLF17orDUXAexpression, and knockdown them in bovine, leads to aberrant gene activation and impeded embryogenesis. Our findings highlight SPD enhancement as a species-specific evolutionary adaptation for initiating transcription in bovine and human embryos, thus illustrating previously underappreciated diversity in mammalian reproductive developmental strategies. The multiomics data (methylation, ChIP-seq,RNA-seq and Hi-C) on gametes and early embryos in bovine and porcine.

合子基因组激活（Zygotic genome activation, ZGA）是受精后首个转录事件。在小鼠中，RNA聚合酶II（RNA polymerase II, Pol II）通过逐步过渡启动胚胎转录，但非啮齿类动物的ZGA起始过程仍未明确。本研究针对牛和猪胚胎开展Pol II谱型分析，结合四种哺乳动物的多组学数据，发现了显著的基因间Pol II簇，将其命名为超级Pol II结构域（super Pol II domains, SPDs），该结构域可通过染色质相互作用增强牛的次要ZGA基因表达。值得注意的是，人类胚胎中也存在类似策略：其ZGA同样表现出延迟特征，随后次要ZGA基因会快速上调。与之相反，猪和小鼠配子中的此类基因会在受精前被提前激活。此外，破坏SPD结构会降低两个次要ZGA基因KLF17和DUXA的表达，在牛胚胎中敲低这两个基因会导致基因激活异常及胚胎发育受阻。本研究结果显示，SPD增强作用是牛和人类胚胎启动转录的物种特异性进化适应机制，从而揭示了哺乳动物生殖发育策略中此前未被充分认知的多样性。本研究附带的多组学数据涵盖甲基化、染色质免疫共沉淀测序（ChIP-seq）、RNA测序（RNA-seq）及Hi-C测序，来源于牛和猪的配子及早期胚胎。