Integrative Multi-Omics Analysis Identifies Candidate MicroRNA Regulatory Networks Associated With High-Altitude...

MicroRNAs (miRNAs) are key posttranscriptional regulators of gene expression and play important roles in physiological responses to hypoxia, particularly in the cardiovascular system. However, the regulatory roles of miRNAs in cardiopulmonary tissues during high-altitude adaptation remain poorly understood. Tibetan pigs are a high-altitude-adapted breed with strong hypoxia tolerance, making them an ideal model for investigating the molecular mechanisms underlying high-altitude adaptation. In this study, we compared miRNA expression profiles between Tibetan pigs and low-altitude Meishan pigs and integrated multi-omics data to investigate miRNA-mediated regulatory networks, with a particular focus on target genes and 3'UTR genetic variation. Small RNA and mRNA sequencing of heart and lung tissues identified 70 differentially expressed miRNAs and 453 candidate target genes associated with hypoxia adaptation, which were significantly enriched in pathways such as vascular smooth muscle contraction. Integrative analysis of whole-genome resequencing data from 20 Tibetan pigs and 17 Meishan pigs further revealed that genetic variants within 3'UTR regions may contribute to the modulation of miRNA-mRNA interactions. Notably, we identified a highly differentiated SNP within the predicted miR-221-5p binding site in the 3'UTR of RAB17, suggesting a potential role of this variant in posttranscriptional regulation. Dual-luciferase reporter assays and functional validation further supported a regulatory interaction between miR-221-5p and the RAB17 3'UTR. Collectively, these findings provide an integrative multi-omics framework for elucidating candidate miRNA regulatory networks associated with high-altitude adaptation and highlight the potential contribution of miRNA-mediated posttranscriptional regulation and 3'UTR genetic variation to high-altitude adaptation in Tibetan pigs.