G4 Landscape Dynamics Underlies Neuroprotective Responses in Neonatal Hypoxic-Ischemic Brain Injury

Hypoxic Ischemic Encephalopathy (HIE) causes brain damage, ranging from mild to severe, in up to one million newborns worldwide every year. While HIE has been shown to modulate gene expression through epigenetic regulation, studies have primarily focused on limited loci, leaving a gap in genome-wide understanding. Using a neonatal mouse model that recapitulates human HIE pathology, we comprehensively profiled gene expression, DNA secondary structures, and histone modifications in the hippocampi of control, hypoxic, and hypoxic-ischemic mice. Our results demonstrate that both hypoxic and hypoxic-ischemic conditions reshape the hippocampal G-quadruplexes (G4s) landscape during the acute phase, following a strong transcriptional response in the hypoxic-ischemic hippocampi, whereas the hypoxic part displays a very moderate response. Substantial upregulation of stress-responsive genes in hypoxic-ischemic hippocampi correlated with G4 loss and the enrichment of active histone marks (H3K4me3 and H3K27ac) at promoters and CpG islands. Brain-specific enhancers also showed G4s depletion alongside asymmetric H3K27ac enrichment, suggesting a broader role for G4s in regulating mRNA expression and processing. Vulnerable hippocampal neurons (CA1/CA3) displayed pronounced G4 depletion following insult, while resilient neurons maintained low G4 occupancy. Together, these findings highlight the neuroprotective potential of G4s during acute neonatal hypoxia-ischemia, suggesting new directions for biomarker discovery and therapeutic development.