Integrative Analysis of ATAC-Seq and RNA-Seq Identifies Key Genes Affecting Muscle Development in Ningxiang Pigs

Meat production traits in pigs are critical economic characteristics, primarily influenced by the formation and development of skeletal muscle. Skeletal muscle development is regulated by a complex transcriptional network, which partly relies on chromatin accessibility for initiation. Ningxiang pigs, a renowned Chinese indigenous breed, are highly valued for their tender meat. However, studies focusing on skeletal muscle development in Ningxiang pigs, particularly from the perspective of chromatin accessibility, have not yet been reported. Based on this, the present study selected several key time points in the skeletal muscle development of Ningxiang pigs to perform Transposase-Accessible Chromatin Sequencing (ATAC-seq) and RNA sequencing (RNA-seq). This was carried out to identify key open chromatin regions and genes during different growth stages, which could influence skeletal muscle development in Ningxiang pigs. We collected longissimus dorsi muscle samples at postnatal days 14 (D14), 28 (D28), 85 (D85), 165 (D165), and 250 (D250). For each age, three individuals were collected for ATAC-seq and RNA-seq. After initial differential analysis among different ages, we identified 6412 differentially accessible chromatin peaks and 1464 differentially expressed genes. To clarify the key candidate transcription factors affecting the development of skeletal muscle in Ningxiang pigs, motif analysis of differential peaks revealed potential cis-regulatory elements with binding sites for transcription factors, including Fosl2 and JunB. Correlation analysis identified 56 overlapping genes and a significant positive correlation (r = 0.73, p = 1 × 10^-14) between gene expression and chromatin accessibility. Key candidate genes such as HOXA10, closely related to skeletal muscle development, were specifically examined. These results enhance our understanding of the genetic and epigenetic regulatory mechanisms of porcine skeletal muscle development, providing a robust foundation for future molecular studies.