Screening and functional identification of lncRNAs under β-diketone antibiotic exposure to zebrafish (Danio rerio) using high-throughput sequencing

Long non-coding RNAs (lncRNAs) have attracted considerable research interest, but so far no data are available on the roles of lncRNAs and their target genes under chronic β-diketone antibiotic (DKAs) exposure to zebrafish (Danio rerio). Herein, we identified 1.66, 3.07 and 3.36×104 unique lncRNAs from the 0, 6.25 and 12.5mg/L DKA treatment groups, respectively. In comparison with the control group, the 6.25 and 12.5mg/L treatments led to up-regulation of 2064 and 2479 lncRNAs, and down-regulation of 778 and 954 lncRNAs, respectively. Of these, 44 and 39 lncRNAs in the respective 6.25 and 12.5mg/L treatments displayed significant differential expression. Volcano and Venn diagrams of the differentially expressed lncRNAs were constructed on the basis of the differentially expressed lncRNAs. After analyzing 10 lncRNAs and potential target genes, a complex interaction network was constructed between them. The consistency of 7 target genes (tenm3, smarcc1b, myo9ab, ubr4, hoxb3a, mycbp2 and CR388046.3), co-regulated by 3 lncRNAs (TCONS_00129029, TCONS_00027240 and TCONS_00017790), was observed between their qRT-PCR and transcriptomic sequencing. By in situ hybridization (ISH), abnormal expression of 3 lncRNAs was observed in hepatic and spleen tissues, suggesting that they might be target organs for DKAs. A similar abnormal expression of two immune-related target genes (plk3 and syt10), co-regulated by the 3 identified lncRNAs, was observed in liver and spleen by ISH. Histopathological observations demonstrated hepatic parenchyma vacuolar degeneration and clot formation in hepatic tissues, and uneven distribution of brown metachromatic granules and larger nucleus in spleen tissues resulting from DKA exposure. Overall, DKA exposure led to abnormal expression of some lncRNAs and their potential target genes, and these genes might play a role in immune functions of zebrafish.