Ligand stabilization of DNA G-quadruplexes impairs zygotic genome activation and autophagy during mammalian maternal-to-zygotic transition

DNA G-quadruplexes (G4s) are non-canonical DNA structures prevalent in regulatory genomic regions and implicated in fundamental processes like transcription and replication. Their specific functions during mammalian early embryonic development remain poorly defined. This study examines their roles in mouse early development. By employing G4-stabilizing ligands alongside multi-omics techniques—including transcriptomics, CUT&Tag, and chromatin accessibility assays—we analyzed G4 dynamics and their influence on epigenetic regulation, gene expression, and autophagy. Findings indicate low G4 levels in oocytes and 4-cell embryos. Ligand-induced stabilization triggered abnormal G4 accumulation, resulting in severe developmental arrest primarily at the 2-cell stage. This excess disrupted transcriptional control, hindered DNA replication initiation, and altered histone modification programs and diminished chromatin accessibility, causing broad epigenetic dysregulation. Additionally, G4 accumulation specifically targeted autophagy-related genes, compromising embryonic autophagy through impaired lysosomal and mitochondrial function. In summary, aberrant G4 accumulation disrupts key epigenetic and cellular processes, leading to developmental arrest. This work clarifies the essential structural regulatory function of G4s in early embryogenesis and offers new perspectives on the origins of developmental disorders.