**Background:** Skeletal muscle development is a complex process regulated by transcriptional and epigenetic mechanisms, including chromatin accessibility. While embryonic myogenesis in pigs has been studied, the postnatal dynamics of gene expression and chromatin openness remain poorly characterized. The domestic pig (Sus scrofa) is both a major protein source and a model for human muscle diseases. This study aimed to systematically map the transcriptome and accessible chromatin landscape of porcine Longissimus dorsi muscle at four postnatal time points to identify key genes, regulatory elements, and pathways controlling muscle growth and fiber type transformation.
**Methods:** Skeletal muscle biopsy samples were collected from the same Landrace pigs (full-sib barrows) at 0, 60, 120, and 180 days after birth, with three biological replicates per time point. Total RNA was extracted using the Trizol method, and RNA-seq libraries were sequenced on an Illumina HiSeqXTen as 150-bp paired-end reads, yielding an average of 44 million reads per library. Reads were aligned to the Sus scrofa 11.1 genome using Hisat2, with 96% overall mapping and 85–90% unique mapping. Differential expression analysis was performed using DESeq2 (|log2FC| ≥ 1, FDR < 0.05). ATAC-seq was performed on frozen muscle tissue using a modified protocol involving nuclear extraction, Tn5 transposition, and PCR amplification. Libraries were sequenced on the Illumina HiSeq X Ten platform. Reads were aligned with Bowtie2, and peaks were called using MACS2. Motif analysis was conducted with HOMER. Integrated analysis overlapped differentially accessible regions with differentially expressed genes. qRT-PCR validated 12 candidate genes, and functional assays (siRNA knockdown and overexpression in PK15 cells and porcine skeletal muscle satellite cells) assessed ACBD7's role in proliferation and myogenic marker expression.
**Key Results:** RNA-seq identified 8,554 effective differentially expressed genes across the four time points. ACBD7 and TMEM220 expression increased continuously with age, while ATP1A2 expression decreased. ATAC-seq identified 151,245 peaks at D0, 53,435 at D60, 30,494 at D120, and 40,911 at D180, with D0 showing the highest chromatin accessibility. Peaks were predominantly in intergenic and intronic regions, followed by promoters. Motif analysis revealed 59 co-differential motifs, with SP1 and EGR1 significantly enriched (FDR < 0.05) and predicted to regulate ACBD7. Integrated RNA-seq and ATAC-seq analysis identified overlapping genes in up-regulated (e.g., D60 vs D0_up: 32 genes; D120 vs D0_up: 106 genes) and down-regulated comparisons. Up-regulated overlapping genes were enriched in skeletal muscle cell differentiation, insulin response, and vascular endothelial cell migration pathways, involving DAPK1, PRKD1, TRIM24, NEDD4L, EGR1, and EGR2. Down-regulated overlapping genes were enriched in cell-cell adhesion and apoptosis, involving CYFIP2, DLG4, NTN1, CCN1, EGR1, FOS, HES1, and RHOB. KEGG enrichment of stage-shared ACRs (553) highlighted Wnt, FoxO, and mTOR signaling pathways. Differential ACRs between stages were enriched in TGF-beta, PI3K-Akt, cGMP-PKG, FoxO, AMPK, and insulin resistance pathways. qRT-PCR confirmed RNA-seq trends for ACBD7, TMEM220, THBS1, RHOB, PLK3, MYL9, LRTM1, IL18, BMP2, HES1, FOS, and CCN1. ACBD7 knockdown in PK15 cells significantly decreased MyOD1, PAX7, MYOG, and MyHC1 mRNA levels, while increasing MyHC2a, MyHC2b, and MyHC2X. ACBD7 overexpression in porcine skeletal muscle satellite cells significantly increased cell proliferation in Transwell assays.
**Clinical Implications:** This study provides the first systematic integration of transcriptomic and epigenomic data across postnatal skeletal muscle development in pigs. The identification of ACBD7 as a key regulator of myogenic marker expression and muscle fiber type transformation offers a potential target for improving meat quality traits in livestock. The chromatin accessibility maps and transcription factor binding predictions (SP1, EGR1) enhance understanding of the regulatory logic underlying muscle growth. These findings also have comparative value for studying human muscle development, regeneration, and metabolic diseases such as type 2 diabetes, given the physiological similarities between porcine and human skeletal muscle. The resource generated here may inform future breeding strategies and therapeutic approaches for muscle-related conditions.