ZNF331 modulates early embryonic transcription during zygotic genome activation in goat

Zygotic genome activation (ZGA) is a pivotal process during early embryogenesis, marking the maternal-to-zygotic transition. ZGA is regulated by a variety of epigenetic and transcriptional factors. However, the transcriptional regulatory mechanisms underlying ZGA in livestock species remain largely unclear. By integrating ATAC-seq and RNA-seq, we characterized chromatin accessibility and transcriptional dynamics in goat embryos. Transcriptional inhibition with α-amanitin markedly reduced promoter accessibility and disrupted RNA polymerase II (Pol II)-mediated transcription. Motif enrichment analysis identified ZNF331 as a potential regulator with specific upregulation at the 8-cell stage. Functional knockdown of ZNF331 resulted in impaired embryonic development, reduced blastocyst formation, and widespread transcriptome alterations. Mechanistically, ZNF331 depletion caused abnormal elevation of Pol II Ser5 phosphorylation, excessive transcriptional activity, maternal mRNA retention, and excessive activation of zygotic genes. Our study identifies ZNF331 as a critical regulator of goat ZGA, functioning through fine-tuning Pol II Ser5 phosphorylation to balance maternal transcript clearance and zygotic gene activation. These findings highlight the essential role of the ZNF331-Pol II axis in goat embryogenesis and suggest a potentially conserved mechanism across mammals.