Epigenetic Impact of Sleep Timing in Children: Novel DNA Methylation Signatures via SWAG Analysis

Pediatric obesity is rising globally, and emerging evidence suggests that sleep timing may influence metabolic health through epigenetic mechanisms. This study investigated epigenome-wide DNA methylation patterns associated with bedtime in children and explored their biological relevance. Children aged 6-10 years were classified as early (≤8:30 PM) or late (>8:30 PM) bedtime groups. Saliva-derived DNA was analyzed using the Illumina Infinium MethylationEPIC BeadChip Array, and the Sparse Wrapper Algorithm (SWAG) was applied to identify differentially methylated loci. A total of 1006 CpG sites, representing 571 unique genes, were significantly associated with bedtime (<i>p</i> < 0.001). Significant methylation differences were observed between early and late bedtime groups, with <i>ABCG2</i>, <i>ABHD4</i>, <i>MOBKL1A</i>, <i>AK3</i>, <i>SDE2</i>, <i>PRAMEF4</i>, <i>CREM</i>, <i>CDH4</i>, <i>BRAT1</i>, and <i>SDK1</i> showing the most consistent variation. Functional enrichment analyses (Gene Ontology, KEGG, and DisGeNET) conducted on the SWAG-identified gene set revealed enrichment in biological processes including peptidyl-lysin demethylation, regulation of sodium ion transport, DNA repair, and lipo-protein particle assembly. Key KEGG pathways included circadian entrainment, neurotransmission (GABAergic, dopaminergic, and glutamatergic), growth hormone synthesis, and insulin secretion. DisGeNET analysis identified associations with neurodevelopmental disorders and cognitive impairment. Cross-comparison with established sleep and obesity gene sets identified ten overlapping genes(<i>CDH4</i>, <i>NR3C2</i>, <i>ACTG1</i>, <i>COG5</i>, <i>CAT</i>, <i>HDAC4</i>, <i>FTO</i>, <i>DOK7</i>, <i>OCLN</i>, and <i>ATXN1</i>). These findings suggest that variations in bedtime during childhood may epigenetically modify genes regulating circadian rhythm, metabolism, neuronal connectivity, and stress response, potentially predisposing to later-life developmental, and metabolic challenges.