Responses of functional miRNA-mRNA regulatory modules to a high-fat diet in the liver of hybrid yellow catfish (Pelteobagrus fulvidraco × P. vachelli).

Fatty liver disease is common in cultured yellow catfish as a result of high fat contents in feeds. However, little is known about the mechanism by which the excessive deposition of liver fat causes fatty liver disease. Hybrid yellow catfish (Pelteobagrus fulvidraco♀ × P. vachelli♂) were fed a high-fat diet (HFD) or a normal-fat diet (NFD) for 60 days. Compared with the NFD group, the HFD group showed lower growth performance, higher hepatosomatic and viscerosomatic indexes, increased hepatic triglyceride and cholesterol contents, and more and larger lipid droplets in liver tissue. Whole transcriptome mRNA libraries and microRNA libraries from fish in the NFD and HFD groups were constructed by high-throughput sequencing. Twelve miRNAs were differentially expressed (DE) between the HFD and NFD groups. Seven negatively correlated DE miRNA-DE mRNA pairs were selected, and the expression patterns of both were confirmed using qRT-PCR. Hybrid yellow catfish showed mediated oxidative degradation of liver glucose and fatty acid peroxidation, regulation of antioxidant enzyme activity, and various immune and inflammatory responses to fat deposition and stress. These findings have important biological significance for protecting the liver against stress, as well as economic significance for establishing healthy aquaculture conditions.

Effects of exposure to Streptococcus iniae on microRNA expression in the head kidney of genetically improved farmed tilapia (Oreochromis niloticus).

BACKGROUND: Genetically improved farmed tilapia (GIFT, Oreochromis niloticus) are susceptible to infection by Streptococcus iniae when maintained in modern intensive culture systems. GIFT are commercially important fishes that are cultured widely in southern China. The role of microRNAs (miRNAs) in the regulatory response of GIFT to S. iniae infection has been underestimated and has not yet been well studied. Head kidney has an important immune function in teleost fishes. The main aim of this study was to determine the possible function of miRNAs in head kidney of S. iniae-infected GIFT. MiRNAs are small, non-coding RNAs that regulate gene expression by binding to the 3'-untranslated regions of their target mRNAs. MiRNAs are known to regulate immune-regulated signaling and inflammatory response pathways. RESULTS: High-throughput deep sequencing of two libraries (control group [CO] and infected group [IN]) of RNA extracted from GIFT head kidney tissues generated 12,089,630 (CO) and 12,624,975 (IN) clean reads. Bioinformatics analysis identified 1736 and 1729 conserved miRNAs and 164 and 165 novel miRNAs in the CO and IN libraries, respectively. Three miRNAs (miR-310-3p, miR-92, and miR-127) were found to be up-regulated and four miRNAs (miR-92d-3p, miR-375-5p, miR-146-3p, and miR-694) were found to be down-regulated in the S. iniae-infected GIFT. The expressions of these miRNAs were verified by quantitative real-time PCR. RNAhybrid and TargetScan were used to identify complementary miRNA and mRNA target sites, and the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases were used to annotate and predict potential downstream regulation of biological pathways. Seven target genes, which encode immune-related proteins (complement C3, cytidine deaminase, regulator of G-protein Rgs22, mitogen-activated protein kinase Mapk1, metabotropic glutamate receptorm GluR8, calcium-sensing receptor CaSR, and microtubule-associated protein Map1S) were predicted to play crucial roles in the GIFT response to S. iniae infection. CONCLUSIONS: S. iniae outbreaks have hindered the development of the tilapia industry in China. Understanding the miRNA transcriptome of S. iniae-infected GIFT is important for exploring the immune responses regulated by miRNAs as well as for studying novel regulated networks to prevent and treat S. iniae infections in the future.

miR-489-3p Regulates the Oxidative Stress Response in the Liver and Gill Tissues of Hybrid Yellow Catfish (Pelteobagrus fulvidraco♀ × P. vachelli♂) Under Cu2+ Exposure by Targeting Cu/Zn-SOD.

Copper/zinc superoxide dismutase (Cu/Zn-SOD) plays critical roles in protecting cells and tissues against oxidative damage. Excessive copper ions (Cu2+) in water can damage the cells of aquatic organisms, leading to impaired growth and development and reduced antioxidant defenses. Many regulatory factors control the response to excess Cu2+. Among them, microRNAs (miRNAs) are important small RNAs that regulate the expression of their target genes and participate in the oxidative stress response. In the present study, we used bioinformatics and dual luciferase reporter gene analyses to demonstrate that the miR-489-3p of hybrid yellow catfish (Pelteobagrus fulvidraco♀ × P. vachelli♂) binds to the 3'-untranslated region (UTR) of its target gene, which encodes a Cu/Zn-SOD. The regulatory relationship between this miRNA and its target gene Cu/Zn-SOD was analyzed using qRT-PCR and luciferase activity assays. We also investigated the effect of the loss of miR-489-3p expression on the oxidative stress response of hybrid yellow catfish exposed to Cu2+. The Cu/Zn-SOD 3'UTR region was found to be fully complementary to positions 2-9 of the 5'-end seed region of miR-489-3p. The miR-489-3p expression levels were negatively related to Cu/Zn-SOD expression. Silencing of miR-489-3p up-regulated Cu/Zn-SOD expression in the liver and gill tissues, increased activities of SOD and catalase, and reduced the malondialdehyde content. This study is the first to demonstrate that miR-489-3p targets Cu/Zn-SOD to mediate the oxidative response to metal stress. These findings provide a theoretical basis for further studies on the response to oxidative stress caused by metals in cultured fish, and provide an experimental basis for the management of the culture environment.