Integrative ATAC-Seq and RNA-Seq analysis identifies key genes for intramuscular fat content in Laiwu pigs

Intramuscular fat (IMF) is a key indicator of pork quality. Laiwu pigs represent a valuable model for studying IMF deposition due to their extremely high IMF content, yet the regulatory mechanisms of chromatin accessibility in skeletal muscle remain unclear. To dissect the epigenetic and transcriptional mechanisms underlying IMF deposition, we performed integrative ATAC-seq and RNA-seq analysis on longissimus thoracis (LT) muscle of six pigs with extreme IMF phenotypes, selected from a population of 79 Laiwu pigs.

We characterized group-shared accessible chromatin peaks, defined as peaks consistently detected across biological replicates within each group. A total of 22,059 and 14,149 peaks were identified in the high-IMF (IMF-H) and low-IMF (IMF-L) groups, respectively. Motif enrichment analysis of these peaks revealed that IMF-H peaks were enriched for lipid metabolism-related transcription factors (JunB, Fra1, Atf3, Fra2), whereas IMF-L peaks harbored muscle development-related factors (CTCF, Mef2c, Mef2d, BORIS). Comparative analysis between the two groups identified 5,573 upregulated and 3,806 downregulated differential peaks, including 525 group-shared differential peaks. Integrative analysis of ATAC-seq and RNA-seq data uncovered 294 group-shared differential accessible chromatin region (ACR)-linked genes expressed in LT muscle, which were significantly enriched in fat deposition pathways like glycosphingolipid biosynthesis and cholesterol metabolism. Of these genes, 108 were significantly correlated with IMF content in the 79-pig population. Among them, we prioritized promoter ACR-linked CTSL (top 10 highest IMF correlation) and GTF3C3 (with the most significant ACR at its transcription start site), both carrying IMF-associated SNPs in ACRs, as candidate regulators for their potential role in transcriptional control.

This study reveals distinct chromatin accessibility patterns linked to IMF deposition in Laiwu pigs and refines the regulatory network of porcine IMF. The identified candidate genes and regulatory elements provide valuable molecular targets for breeding strategies to improve IMF content and meat quality in pigs.