Integrated ceRNA network analysis reveals the lncRNA-miRNA-mRNA axis in hypoxic stress response of yellow catfish...

Hypoxia poses a serious threat to aquatic organisms, yet the regulatory roles of non-coding RNAs, particularly the competing endogenous RNA (ceRNA) network, in fish under hypoxic stress remain poorly understood. In this study, we conducted whole-transcriptome sequencing of yellow catfish (Pelteobagrus fulvidraco) liver tissue under hypoxic conditions to systematically identify hypoxia-responsive lncRNAs and miRNAs and construct a comprehensive ceRNA network. A total of 14 differentially expressed lncRNAs (DElncs) and 112 miRNAs (DEmiRs) were identified. Functional enrichment analysis revealed that the target genes of DElncs were significantly involved in mitochondrial membrane permeability, energy metabolism, and the HIF-1 and mTOR signaling pathways, while those of DEmiRs were enriched in MAPK, calcium, and ErbB signaling pathways. Furthermore, we identified 22 DEmiRs commonly regulated under both hypoxic and hypoxic-bacterial dual stresses, representing core regulators of environmental adaptation. By integrating expression correlation and target prediction, we constructed the first lncRNA-miRNA-mRNA ceRNA network in hypoxic yellow catfish, comprising 5 DElncs, 11 DEmiRs, and 17 ceDETGs. Within this network, lnc162 (significantly down-regulated) and lnc1375 (markedly up-regulated) may act to regulate key apoptotic and metabolic genes such as fosb, sgk1, pkm, and hopx by sponging specific miRNAs, as predicted by our ceRNA analysis. These results reveal that lncRNAs mediate hypoxic adaptation by coordinating apoptosis and metabolic reprogramming via ceRNA mechanisms. Our study provides novel insights into the molecular basis of hypoxia tolerance in teleosts and offers potential genetic targets for breeding hypoxia-resistant fish strains.