Integrated analysis of RNA expression profiles and regulatory networks in porcine liver in response to cold stress

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BACKGROUND: Cold stress affects animal husbandry severely. It has adverse effects on both production performance and animal health, thus directly reducing economic efficiency of animal production. Pigs are more susceptible to cold stress owing to absence of brown adipose tissue, an important organ for non-shivering thermogenesis. However, the knowledge on response to cold stress remains limited. To investigate the molecular mechanisms behind cold tolerance, we analyzed RNA expression profiles and regulatory networks in livers of pigs raised in a short-term low-temperature environment at transcriptome level. RESULTS: A total of 1,205 protein-coding genes, 122 lncRNAs and 52 miRNAs were involved in response to cold stress by RNA sequencing. Through integrated analysis of lncRNA and small RNA sequencing data, 533 mRNAs and two Kyoto Encyclopedia of Genes and Genomes pathways, PI3K-Akt and MAPK, were identified as critical for response to cold stress. Among the 533 mRNAs 47 were involved in PI3K-Akt or MAPK pathway and nine were shared by the both. Five out of the nine mRNAs such as EGFR, HGF, IGF1, PDGFD and EGFR2 belong to growth factors or the receptors. Based on the nine mRNAs and the differentially expressed lncRNAs and miRNAs ceRNA network was identified in which AKT was identified as the top hub gene, followed by PRKCA. Additionally, the ceRNA network was validated and PRKCA/ssc-miR-6782-3p/MSTRG.14353.2 was first constructed with molecular biology experiments. CONCLUSIONS: The study elucidates the critical genes, signaling pathways and the regulatory networks in regulating response to cold stress in porcine livers. The findings will contribute to fully revealing the mechanisms behind cold response and improving cold tolerance in pigs, which will benefit pig production.

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