Identification and characterization of immune-related lncRNAs and lncRNA-miRNA-mRNA networks of Paralichthys olivaceus involved in Vibrio anguillarum infection

Abstract

Background Long non-coding RNAs (lncRNAs) structurally resemble mRNAs and exert crucial effects on host immune defense against pathogen infection. Japanese flounder (Paralichthys olivaceus) is an economically important marine fish susceptible to Vibrio anguillarum infection. To date, study on lncRNAs in flounder is scarce. Results Here, we reported the first systematic identification and characterization of flounder lncRNAs induced by V. anguillarum infection at different time points. A total of 2,368 lncRNAs were identified, 414 of which were differentially expressed lncRNAs (DElncRNAs) that responded significantly to V. anguillarum infection. For these DElncRNAs, 3,990 target genes (named DETGs) and 42 target miRNAs (named DETmiRs) were identified based on integrated analyses of lncRNA-mRNA and lncRNA-miRNA expressions, respectively. The DETGs were enriched in a cohort of functional pathways associated with immunity. In addition to modulating mRNAs, 36 DElncRNAs were also found to act as competitive endogenous RNAs (ceRNAs) that regulate 37 DETGs through 16 DETmiRs. The DETmiRs, DElncRNAs, and DETGs formed ceRNA regulatory networks consisting of 114 interacting DElncRNAs-DETmiRs-DETGs trinities spanning 10 immune pathways. Conclusions This study provides a comprehensive picture of lncRNAs involved in V. anguillarum infection. The identified lncRNAs and ceRNA networks add new insights into the anti-bacterial immunity of flounder.

Integrated Analysis of Transcriptome and Metabolome Reveals Distinct Responses of Pelteobagrus fulvidraco against Aeromonas veronii Infection at Invaded and Recovering Stage

“…Suppression on NDUFS1 and NDUFB8 in mammals accompanied by the decline of ATP provoked apoptosis [ 42 , 43 ]. In the present study, UQCRC2, NDUFS1 and NDUFB8 were significantly decreased, meanwhile, Prostaglandin F1α, the pro-apoptosis factor in mammals [ 44 , 45 ], was significantly up-regulated at the invaded stage in the present study, suggesting the engagement of apoptosis in the clearance of the invading pathogen as reported previously in human [ 46 ] and fish [ 47 , 48 ]. A study on Vibrio alginolyticus -infected zebra fish showed that the dying individuals exhibited excessive levels of inflammatory response compared to survivors [ 49 ].…”

Differential expression analysis of mRNAs, lncRNAs, and miRNAs expression profiles and construction of ceRNA networks in PEDV infection

“…(e) Venn diagram for the intersection of DE mRNAs between the two groups activating a large number of genes. Comparative analysis of the genomic characteristics of mRNAs and lncRNAs reveals that lncRNAs have shorter transcripts, fewer exons, and lower expression levels, which is consistent with the results of transcriptome analysis in different species [26][27][28]. In addition, the expression changes of randomly selected differentially expressed genes were confirmed by qRT-PCR analysis, indicating the accuracy of the sequencing results.…”

Integrated Analysis of lncRNA and circRNA Mediated ceRNA Regulatory Networks in Skin Reveals Innate Immunity Differences Between Wild-Type and Yellow Mutant Rainbow Trout (Oncorhynchus mykiss)

“…Under normal conditions fish maintain a healthy status by defending themselves against potential invaders using a repertoire of innate and specific defense mechanisms ( 27 ). However, prior researches mainly focused on identification and characterization of ceRNAs and ceRNA regulatory networks in fish spleen, liver, and intestine following artificial infection to explore the immune mechanisms of pathogen resistance ( 24 , 28 – 30 ), and no study on the involvement of ceRNA in fish skin without artificial infection has been documented. Owing to many biological and abiotic stresses presented in natural flowing water pond aquaculture environment, and intensified culture environment and high susceptibility to infectious disease make the industry vulnerable to disease outbreaks resulting in significant economic losses.…”