CeRNA network mediated by lncRNA-miRNA-mRNA of Pelteobagrus fulvidraco plays a dual function of immunity and lipid metabolism in response to Aeromonas veronii infection

Abstract

Competitive endogenous RNAs (ceRNAs) have emerged as essential immune regulators bridging the non-coding RNAs (ncRNAs) and mRNAs in mammals, generating interactive networks across the transcriptome as a whole. In fish immunity, ceRNA trinities, consisted of long ncRNAs (lncRNAs), microRNAs (miRNAs) and mRNAs, are reported sporadically. To date, the involvement of ceRNAs in yellow catfish (Pelteobagrus fulvidraco) is unknown. Here, we reported the first lncRNA-mediated ceRNA network in yellow catfish infected with Aeromonas veronii (A. veronii) for different time points. The linear ncRNAs, including miRNAs and lncRNAs, were systematically identified and characterized, especially those were differentially expressed induced by A. veronii stimulation (named DEmiRs and DElncs). These DEmiRs and DElncs extensively influenced the expression of immune genes as well as lipid metabolic genes by direct interaction. In particular, DElncs in yellow catfish were found to act as ceRNAs that modulate target genes (ceDETGs) through sponging corresponding DEmiRs. Accordingly, a key ceRNA network was constructed based on the results of functional enrichment and the connectivity of ceDETGs. This ceRNA network consisted of 44 DElncs, 6 DEmiRs and 15 ceDETGs, regulating a dual function of immunity and lipid remodeling in response to A. veronii infection. The results of this study provide a comprehensive picture of the ceRNA regulatory network engaged in yellow catfish defense response. The obtained ncRNAs and dual-function ceRNA network add new insights into the anti-bacterial immunity of teleost fish.