Maternal undernutrition during gestation induces enduring genome-wide DNA methylation alterations in the skeletal muscle of postnatal beef cattle

Maternal nutrition exerts long-term effects on offspring development, potentially mediated by epigenetic mechanisms. This study aimed to characterize the genome-wide DNA methylation profile of skeletal muscle in postnatal cattle and to determine the long-term impacts of maternal undernutrition on DNA methylation in offspring muscle. Wagyu cows were assigned to either nutritional-adequate control (CNT; n = 4, 120% of requirements) or nutritional-restricted (NR; n = 4, 60% of requirements) group from day 35 of gestation until parturition. After birth, all offspring received identical diets, and longissimus thoracis muscle (LM) biopsies were collected at 300 days of age for DNA methylation analysis using whole-genome bisulfite sequencing. Irrespective of maternal diet, DNA methylation levels in offspring muscle gradually decreased across the CpG from the upstream region toward the transcription start site, reached their lowest level at the transcription start site, and increased throughout the gene body. Compared with the CNT group, NR offspring LM exhibited 7076 hypomethylated and 6104 hypermethylated regions (|methylation difference| > 20%, Q < 0.05). Among genomic features, promoter and 5' untranslated regions exhibited the greatest susceptibility to methylation changes, with 0.96% and 1.09% of these regions being hypomethylated in NR offspring LM relative to CNT. Genes containing differentially methylated regions in distal upstream (1-5-kb upstream from transcription start site) regions or promoters were associated with fundamental biological processes such as gene expression regulation, protein function, cell and tissue development, cytoskeletal and contractile organization, and neurodevelopment (P < 0.05). An overlap-based integrative analysis of DNA methylation and gene expression data identified seven candidate epigenetically regulated genes, including neuronal precursor cell-expressed developmentally downregulated 4 (Entrez Gene ID: 507781) and solute carrier family 30 (zinc transporter) member 1 (Entrez Gene ID: 522265). Although only seven candidate genes were identified through integrative analysis, more than 13,000 differentially methylated regions were maintained in offspring muscle. These findings suggest that maternal undernutrition induces changes in DNA methylation patterns during the fetal stage that persist postnatally, and may contribute to long-term effects on muscle metabolism, growth efficiency, and meat quality.