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Selection of reference genes for microRNA quantitative expression analysis in Chinese perch, Siniperca chuatsi.

ABSTRACT: Real-time quantitative reverse transcription PCR (RT-qPCR) is one of the most effective and sensitive techniques in gene expression assay, for which selection of reference genes is a prerequisite. In teleost species, such as Chinese perch, the expression profiling of miRNAs as reference genes for RT-qPCR has not been intensively studied. In the present study, the expression profiles of six miRNAs (miR-101a, miR-146a, miR-22a, miR-23a, miR-26a and let-7a) and one small nuclear RNA (U6) were assayed with RT-qPCR in different adult tissues, developmental stages and growth conditions of Chinese perch, Siniperca chuatsi. The analyses revealed that embryonic developmental stage is an important variability factor in the expression stability of miRNAs. All six miRNAs exhibited better expression consistency than U6 in most of the conditions examined, and therefore, they may be more suitable as a reference gene for miRNA quantification. When different tissues and developmental stages were considered, miR-22a demonstrated the most consistent expression pattern, and the best combination of reference genes was miR-22a and miR-23a. Our study offers useful data for selecting miRNAs as reference genes for RT-qPCR analysis of miRNAs in teleost fishes under different conditions.

SUBMITTER: Zhu X

PROVIDER: S-EPMC4425082 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature

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Selection of reference genes for microRNA quantitative expression analysis in Chinese perch, Siniperca chuatsi.

Zhu Xin X Li Yu-Long YL Chen Dun-Xue DX Wu Ping P Yi Tan T Chen Tao T Zhang Jian-She JS Chu Wu-Ying WY

International journal of molecular sciences 20150414 4

Real-time quantitative reverse transcription PCR (RT-qPCR) is one of the most effective and sensitive techniques in gene expression assay, for which selection of reference genes is a prerequisite. In teleost species, such as Chinese perch, the expression profiling of miRNAs as reference genes for RT-qPCR has not been intensively studied. In the present study, the expression profiles of six miRNAs (miR-101a, miR-146a, miR-22a, miR-23a, miR-26a and let-7a) and one small nuclear RNA (U6) were assay ...[more]

PMID: 25874758

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Project description:p53, as an important tumor suppressor protein, has recently been implicated in host antiviral defense. The present study found that the expression of mandarin fish (Siniperca chuatsi) p53 (Sc-p53) was negatively associated with infectious spleen and kidney necrosis virus (ISKNV) and Siniperca chuatsi rhabdovirus (SCRV) proliferation as well as the expression of glutaminase 1 (GLS1) and glutaminolysis pathway-related enzymes glutamate dehydrogenase (GDH) and isocitrate dehydrogenase 2 (IDH2). This indicated that Sc-p53 inhibited the replication and proliferation of ISKNV and SCRV by negatively regulating the glutaminolysis pathway. Moreover, it was confirmed that miR145-5p could inhibit c-Myc expression by targeting the 3' untranslated region (UTR). Sc-p53 could bind to the miR145-5p promoter region to promote its expression and to further inhibit the expression of c-Myc. The expression of c-Myc was proved to be positively correlated with the expression of GLS1 as well. All these suggested a negative relationship between the Sc-p53/miR145-5p/c-Myc pathway and GLS1 expression and glutaminolysis. However, it was found that after ISKNV and SCRV infection, the expressions of Sc-p53, miR145-5p, c-Myc, and GLS1 were all significantly upregulated, which did not match the pattern in normal cells. Based on the results, it was suggested that ISKNV and SCRV infection altered the Sc-p53/miR145-5p/c-Myc pathway. All of above results will provide potential targets for the development of new therapeutic strategies against ISKNV and SCRV. IMPORTANCE Infectious spleen and kidney necrosis virus (ISKNV) and Siniperca chuatsi rhabdovirus (SCRV) as major causative agents have caused a serious threat to the mandarin fish farming industry (J.-J. Tao, J.-F. Gui, and Q.-Y. Zhang, Aquaculture 262:1-9, 2007, https://doi.org/10.1016/j.aquaculture.2006.09.030). Viruses have evolved the strategy to shape host-cell metabolism for their replication (S. K. Thaker, J. Ch'ng, and H. R. Christofk, BMC Biol 17:59, 2019, https://doi.org/10.1186/s12915-019-0678-9). Our previous studies showed that ISKNV replication induced glutamine metabolism reprogramming and that glutaminolysis was required for efficient replication of ISKNV and SCRV. In the present study, the mechanistic link between the p53/miR145-5p/c-Myc pathway and glutaminolysis in the Chinese perch brain (CPB) cells was provided, which will provide novel insights into ISKNV and SCRV pathogenesis and antiviral treatment strategies.

Project description:The purpose of this study was to evaluate the potential of a host-associated Bacillus subtilis 1-C-7 as a probiotic for Chinese perch (Siniperca chuatsi). Four test diets were formulated to contain graded levels of B. subtilis 1-C-7 at 0 (CY), 0.85 × 108 (Y1), 0.95 × 109 (Y2) and 0.91 × 1010 (Y3) CFU/kg diet. The test fish with initial weight 30.0 ± 1.2 g were fed the 4 test diets with 3 replicates in an indoor water-flow aquaculture system with 12 net cages (40 fish/cage) for 10 wk. At the conclusion of the feeding trial, the probiotic effects of B. subtilis on Chinese perch were analyzed based on growth performance, serum biochemical indices, histologic morphology of liver and gut, gut microbiota and the resistance to Aeromonas hydrophila. The results showed that the percentage of weight gain had no significant change in the Y1 and Y2 groups (P > 0.05) but decreased in the Y3 group compared to that in the CY group (P < 0.05). The fish in the Y3 group displayed the highest activity of serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) among these 4 groups (P < 0.05). The fish in the CY group had the highest value of malondialdehyde in the liver (P < 0.05) and showed severe nuclear migration and vacuolization of hepatocytes. The morphology indicated that all test fish had poor intestinal health. However, the fish in the Y1 group had a relatively normal intestinal histologic structure. The mid gut microbial diversity analysis showed that dietary B. subtilis supplementation increased the abundance of probiotics such as Tenericutes and Bacteroides, whereas it reduced the abundance of pernicious bacteria such as Proteobacteria, Actinobacteria, Thermophilia and Spirochaetes. The challenge test showed that dietary B. subtilis supplementation increased the resistance to A. hydrophila in Chinese perch. In conclusion, dietary supplementation of 0.85 × 108 CFU/kg B. subtilis 1-C-7 could improve the intestinal microbiota, intestinal health and disease resistance in Chinese perch, but more or excessive supplementation could reduce growth performance and have negative effects on health.

Dataset Information

Selection of reference genes for microRNA quantitative expression analysis in Chinese perch, Siniperca chuatsi.

Publications

Selection of reference genes for microRNA quantitative expression analysis in Chinese perch, Siniperca chuatsi.

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