Genome-wide identification of long non-coding RNAs in pigs and their roles in muscle development.

Abstract

Objective Long non-coding RNAs (lncRNAs) are important regulators of complex traits in pigs and the systematic annotation and functional roles of these genes remain poorly understood. This study aimed to construct a comprehensive porcine lncRNA atlas and explore the regulatory role of lncRNAs in muscle development. Methods We integrated 8,871 strand-specific RNA-seq datasets to identify porcine lncRNAs. Their transcriptional features, tissue specificity, evolutionary conservation, and eQTL-supported regulatory relationships were characterized. Single-cell RNA-seq, Hi-C, H3K27ac ChIP-seq, and population differentiation analyses were further incorporated to investigate candidate lncRNAs involved in muscle development. Results We identified 50,203 porcine lncRNA genes with stronger tissue specificity and lower expression abundance than protein-coding genes. A subset of lncRNAs showed sequence conservation across mammals. Integration with pigGTEx data identified extensive eQTL-supported lncRNA-mRNA candidate regulatory pairs enriched in active promoter and enhancer chromatin states. Single-cell and multi-omics analyses highlighted PRANCR as a candidate regulator of postnatal muscle growth in Laiwu pigs. A highly differentiated enhancer variant (chr5:g.34155013T>C; Sscrofa11.1) may alter SOX8 binding and regulate PRANCR expression in satellite stem cells. Conclusion This study provides the most comprehensive porcine lncRNA resource currently available and proposes a potential enhancer-lncRNA regulatory mechanism that contributes to muscle development in pigs.