Integrated analysis of DNA methylation and transcriptome profiles in broiler heart and lung tissues reveals epigenetic regulatory mechanisms underlying ascites syndromeAll supporting data is included in the manuscript and supplementary files. Raw sequencing data are available in the GSA database under accession numbers CRA028061 (RNA-seq) and CRA027783 (WGBS), publicly accessible at .

Ascites syndrome (AS), a prevalent nutritional and metabolic disorder in broilers, causes substantial economic losses to the poultry industry. However, its comprehensive molecular mechanisms, particularly the interplay between epigenetic regulation and transcriptional dynamics, remain incompletely elucidated. This study compared AS broilers and normal broilers by routine hematological examinations and blood gas indicators. These analyses revealed significant abnormalities in AS broilers. Histological examination of myocardial tissue using HE staining revealed cardiac tissue damage in AS broilers. To investigate the underlying mechanisms, an integrated multi-omics analysis was performed using whole genome bisulfite sequencing and transcriptome data. This approach identified 891 genes in heart tissue and 1,424 genes in lung tissue with expression levels negatively correlated with promoter methylation. Among these, 191 genes were shared between the two tissues and were functionally associated with metabolic disturbances (glycolysis/gluconeogenesis, ether lipid metabolism), dysregulated signaling pathways (TGF-β, Notch, and calcium signaling), increased vascular permeability, and persistent inflammation in AS broilers. Validation via qPCR and bisulfite sequencing confirmed a significant negative correlation between the expression levels of HEMK1 and PMEPA1 and the methylation levels of their promoter CpG islands, supporting their roles as candidate genes in AS pathogenesis. Collectively, this study identifies key pathways and genes associated with AS development, providing valuable insights into its underlying mechanisms and potential preventive strategies.