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

OBJECTIVELong non-coding RNAs (lncRNAs) regulates 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.

METHODSWe used 8,871 strand-specific RNA-seq datasets to identify porcine lncRNAs. Their transcriptional characteristics, tissue specificity, evolutionary conservation, and expression quantitative trait locus (eQTL)-supported regulatory relationships were esamined. Single-cell RNA-seq, Hi-C, H3K27ac ChIP-seq, and population differentiation analyses were further incorporated to investigate candidate lncRNAs involved in muscle development.

RESULTSWe identified 50,203 porcine lncRNA genes with greater tissue specificity and lower expression levels than protein-coding genes. A subset of lncRNAs showed sequence conservation across mammals. Integration with pigGTEx data identified extensive eQTLsupported 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 distinct enhancer variation (chr5:g.34155013T>C; Sscrofa11.1) could affect SOX8 binding and regulate PRANCR expression in satellite stem cells.

CONCLUSIONThe current 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.