Deep sequencing, profiling and detailed annotation of microRNAs in Takifugu rubripes

MicroRNAs are involved in ovarian physiology of greater amberjack (Seriola dumerili) under captivity

Gonad maturation is critical for the reproductive success of any organism, and in fish, captivity can significantly affect their reproductive performance, leading to maturation incompetence and spawning failure. The greater amberjack (Seriola dumerili), a fish species recently introduced to aquaculture fails to undergo oocyte maturation, ovulation, and spawning when reared in aquaculture facilities. Since confinement has been shown to influence gonad maturation and completion of the reproductive cycle, investigations into epigenetic mechanisms may shed light on the reasoning behind the reproductive dysfunctions of fish under captivity. Among the known important epigenetic regulators are small non-coding RNAs (sncRNAs), and in particular microRNAs (miRNAs). In this study, immature, maturing (late vitellogenesis), and spent ovaries of captive greater amberjack were collected, and the differential expression of miRNAs in the three different ovarian development stages was examined. Expression patterns of conserved and novel miRNAs were identified, and potential targets of highly differentially expressed miRNAs were detected. Additionally, read length distribution showed two prominent peaks in the three different ovarian maturation stages, corresponding to miRNAs and putative piwi-interacting RNAs (piRNAs), another type of ncRNAs with a germ-cell specific role. Furthermore, miRNA expression patterns and their putative target mRNAs are discussed, in relevance with the different ovarian maturation stages of captive greater amberjack. Overall, this study provides insights into the role of miRNAs in the reproductive dysfunctions observed in fish under captivity and highlights the importance of epigenetic mechanisms in understanding and managing the reproductive performance of economically important fish species.

Feeding Strategy to Use Beef Tallow and Modify Farmed Tiger Puffer Fatty Acid Composition

A 12-week feeding experiment was conducted to evaluate the effects of replacing fish oil (FO) with beef tallow (BT) on the fatty acid composition of farmed tiger puffer (Takifugu rubripes). Two replacement strategies were used: a standard Graded Dietary Replacement of FO with BT (GDR strategy) and Alternate Feeding between FO- and BT-based Diets (AFD strategy). The positive and negative control diets were formulated with 6% FO (FO-C group) or BT (BT-C group) as the sole added lipid source. In the GDR strategy, three experimental diets were formulated, with 25, 50 and 75% of the added FO in the FO-C diet replaced with BT, named 25BT, 50BT and 75BT, respectively. In the AFD strategy, alternated feeding patterns between the FO-C and BT-C diet-namely, 1, 2 and 3 weeks with BT-C followed by 1 week feeding with FO-C (1BT-1FO, 2BT-1FO and 3BT-1FO, respectively)-were applied. Each diet or feeding strategy was assigned to triplicate tanks. The results showed that dietary BT inclusion reduced the contents of long-chain polyunsaturated fatty acids (LC-PUFA) in both the muscle and liver (edible tissues for this species) of the experimental fish, and the liver displayed a more drastic decrease than the muscle. The LC-PUFA content linearly decreased with the decreasing dietary FO levels in the GDR strategy. However, in the AFD strategy, a linear relationship was not observed between the LC-PUFA content and the FO feeding duration. The 3BT-1FO treatment resulted in higher LC-PUFA content than 2BT-1FO. When comparing the two strategies with the same final FO administration level-namely, 50BT vs. 1BT-1FO, and in particular, 75BT vs. 3BT-1FO-the AFD strategy resulted in higher LC-PUFA contents in both the muscle and liver than the GDR strategy. In conclusion, when FO was replaced with BT in the diets, alternate feeding between FO- and BT-based diets resulted in a higher LC-PUFA content than the standard direct replacement. Three weeks of feeding with BT-C followed by one week of feeding with FO-C appeared to be a good alternate feeding pattern. This study provided a promising strategy of FO-sparing in fish farming when the LC-PUFA contents were maintained as high as possible.

Transcriptome analysis revealed gene expression feminization of testis after exogenous tetrodotoxin administration in pufferfish Takifugu flavidus

Tetrodotoxin (TTX) is a deadly neurotoxin and usually accumulates in large amounts in the ovaries but is non-toxic or low toxic in the testis of pufferfish. The molecular mechanism underlying sexual dimorphism accumulation of TTX in ovary and testis, and the relationship between TTX accumulation with sex related genes expression remain largely unknown. The present study investigated the effects of exogenous TTX treatment on Takifugu flavidus. The results demonstrated that exogenous TTX administration significantly incresed level of TTX concentration in kidney, cholecyst, skin, liver, heart, muscle, ovary and testis of the treatment group (TG) than that of the control group (CG). Transcriptome sequencing and analysis were performed to study differential expression profiles of mRNA and piRNA after TTX administration of the ovary and testis. The results showed that compared with female control group (FCG) and male control group (MCG), TTX administration resulted in 80 and 23 piRNAs, 126 and 223 genes up and down regulated expression in female TTX-treated group (FTG), meanwhile, 286 and 223 piRNAs, 2 and 443 genes up and down regulated expression in male TTX-treated group (MTG). The female dominant genes cyp19a1, gdf9 and foxl2 were found to be up-regulated in MTG. The cyp19a1, whose corresponding target piRNA uniq_554482 was identified as down-regulated in the MTG, indicating the gene expression feminization in testis after exogenous TTX administration. The KEGG enrichment analysis revealed that differentially expressed genes (DEGs) and piRNAs (DEpiRNAs) in MTG vs MCG group were more enriched in metabolism pathways, indicating that the testis produced more metabolic pathways in response to exogenous TTX, which might be a reason for the sexual dimorphism of TTX distribution in gonads. In addition, TdT-mediated dUTP-biotin nick end labeling staining showed that significant apoptosis was detected in the MTG testis, and the role of the cell apoptotic pathways was further confirmed. Overall, our research revealed that the response of the ovary and testis to TTX administration was largely different, the ovary is more tolerant whereas the testis is more sensitive to TTX. These data will deepen our understanding on the accumulation of TTX sexual dimorphism in Takifugu.

The emerging role of microRNAs in fish ovary: A mini review

MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression primarily at the post-transcriptional levels. It is now well established that miRNAs are crucial regulators of many developmental and physiological processes, including reproduction. In teleosts, expression profiling studies have shown that miRNAs are expressed in the fish ovary and their levels are regulated during follicle development and by hormones. Using CRISPR/Cas9 mediated gene knockout strategies, several recent studies have provided strong evidence that miR-202 and miR-200s on chromosome 23 play critical roles in regulating ovarian development, oogenesis, and ovulation. In this mini review, we provide a brief overview of canonical miRNA biogenesis and functions; summarize miRNAs that are expressed in fish ovary; and discuss the emerging role of miRNAs in regulating fish ovarian functions.

Identification of sex differentiation-related microRNA and long non-coding RNA in Takifugu rubripes gonads

Although sex determination and differentiation are key developmental processes in animals, the involvement of non-coding RNA in the regulation of this process is still not clarified. The tiger pufferfish (Takifugu rubripes) is one of the most economically important marine cultured species in Asia, but analyses of miRNA and long non-coding RNA (lncRNA) at early sex differentiation stages have not been conducted yet. In our study, high-throughput sequencing technology was used to sequence transcriptome libraries from undifferentiated gonads of T. rubripes. In total, 231 (107 conserved, and 124 novel) miRNAs were obtained, while 2774 (523 conserved, and 2251 novel) lncRNAs were identified. Of these, several miRNAs and lncRNAs were predicted to be the regulators of the expression of sex-related genes (including fru-miR-15b/foxl2, novel-167, novel-318, and novel-538/dmrt1, novel-548/amh, lnc_000338, lnc_000690, lnc_000370, XLOC_021951, and XR_965485.1/gsdf). Analysis of differentially expressed miRNAs and lncRNAs showed that three mature miRNAs up-regulated and five mature miRNAs were down-regulated in male gonads compared to female gonads, while 79 lncRNAs were up-regulated and 51 were down-regulated. These findings could highlight a group of interesting miRNAs and lncRNAs for future studies and may reveal new insights into the function of miRNAs and lncRNAs in sex determination and differentiation.

mirnaQC: a webserver for comparative quality control of miRNA-seq data

Although miRNA-seq is extensively used in many different fields, its quality control is frequently restricted to a PhredScore-based filter. Other important quality related aspects like microRNA yield, the fraction of putative degradation products (such as rRNA fragments) or the percentage of adapter-dimers are hard to assess using absolute thresholds. Here we present mirnaQC, a webserver that relies on 34 quality parameters to assist in miRNA-seq quality control. To improve their interpretability, quality attributes are ranked using a reference distribution obtained from over 36 000 publicly available miRNA-seq datasets. Accepted input formats include FASTQ and SRA accessions. The results page contains several sections that deal with putative technical artefacts related to library preparation, sequencing, contamination or yield. Different visualisations, including PCA and heatmaps, are available to help users identify underlying issues. Finally, we show the usefulness of this approach by analysing two publicly available datasets and discussing the different quality issues that can be detected using mirnaQC.

Identification and analysis of miRNAs in the normal and fatty liver from the Holstein dairy cow

MicroRNAs (miRNAs) are a class of non-coding short RNAs with ∼22 nts in length, which play important roles in the regulation of numerous biological processes in animals. In this study, two small RNA libraries from fatty (S01) and normal livers (S02) from Holstein Dairy Cow (HDC) were sequenced through deep sequencing. A total of 12,964,411 and 15,426,289 clean reads were obtained, representing 370 known and 182 novel miRNAs, respectively. The characterization, expression pattern, potential functions and target genes of these miRNAs were investigated. Analysis identified 66 upregulated and seven downregulated differentially expressed miRNAs (DIE-miRNAs). To verify the sequencing results, 10 DIE-miRNAs were selected for qRT-PCR, and the results were confirmed to be consistent with the miRNA sequencing. In addition, a total of 5,578 targets of the 73 DIE-miRNAs were predicted. GO analysis revealed that DIE-miRNAs targets are associated with cellular process, cell part and molecular transducer activity. KEGG pathway analysis showed that Arrhythmogenic right ventricular cardiomyopathy, Axon guidance, Ether lipid metabolism and Cocaine addiction were closely associated with liver metabolism. These findings will provide valuable information for further functional verification of miRNAs between normal and fatty liver, as might exploit new attractive miRNAs biomarkers for diseases detection in HDC.

Dietary taurine stimulates the hepatic biosynthesis of both bile acids and cholesterol in the marine teleost, tiger puffer (Takifugu rubripes)

Taurine (TAU) plays important roles in the metabolism of bile acids, cholesterol and lipids. However, little relevant information has been available in fish where TAU has been identified as a conditionally essential nutrient. The present study aimed to investigate the effects of dietary TAU on the metabolism of bile acids, cholesterol and lipids in tiger puffer, which is both an important aquaculture species and a good research model, having a unique lipid storage pattern. An 8-week feeding trial was conducted in a flow-through seawater system. Three experimental diets differed only in TAU level, that is, 1·7, 8·2 and 14·0 mg/kg. TAU supplementation increased the total bile acid content in liver but decreased the content in serum. TAU supplementation also increased the contents of total cholesterol and HDL-cholesterol in both liver and serum. The hepatic bile acid profile mainly includes taurocholic acid (94·48 %), taurochenodeoxycholic acid (4·17 %) and taurodeoxycholic acid (1·35 %), and the contents of all these conjugated bile acids were increased by dietary TAU. The hepatic lipidomics analysis showed that TAU tended to decrease the abundance of individual phospholipids and increase those of some individual TAG and ceramides. The hepatic mRNA expression study showed that TAU stimulated the biosynthesis of both bile acids and cholesterol, possibly via regulation of farnesoid X receptor and HDL metabolism. TAU also stimulated the hepatic expression of lipogenic genes. In conclusion, dietary TAU stimulated the hepatic biosynthesis of both bile acids and cholesterol and tended to regulate lipid metabolism in multiple ways.

Molecular basis of spermatogenesis and sperm quality

Spermatozoan quality can be evaluated in different ways, here we focus on the analysis of DNA, RNA and epigenetic status of germ cells. These characterizations also can be the bases for explaining sperm quality at other levels, so we will see how some of these molecules could affect other sperm quality markers. Moreover, we consider the possibility of using some of these molecules as predictors of sperm quality in terms of the ability to produce healthy offspring. The relevant effect of different types of RNA molecules in germ line specification and spermatogenesis and the importance of germ cell DNA integrity and a proper epigenetic pattern will be also discussed. Although most studies at this level have been performed in mammals, some information is available for fish; these recent discoveries in fish models are included. We provide a general overview on how these molecules could have a deep influence in the final sperm quality.

Deep Illumina sequencing reveals conserved and novel microRNAs in grass carp in response to grass carp reovirus infection

Background

The grass carp hemorrhagic disease caused by the grass carp reovirus (GCRV) is a major disease that hampers the development of grass carp aquaculture. The mechanism underlying GCRV pathogenesis and hemorrhagic symptoms is still unknown. MicroRNAs (miRNAs) are key regulators involved in various biological processes. The aim of this study was to identify conserved and novel miRNAs in grass carp in response to GCRV infection, as well as attempt to reveal the mechanism underlying GCRV pathogenesis and hemorrhagic symptoms.

Results

Grass carp were infected with GCRV, and spleen samples were collected at 0 (control), 1, 3, 5, 7, and 9 days post-infection (dpi). These samples were used to construct and sequence small RNA libraries. A total of 1208 miRNAs were identified, of which 278 were known miRNAs and 930 were novel miRNAs. Thirty-six miRNAs were identified to exhibit differential expression when compared with the control, and 536 target genes were predicted for the 36 miRNAs. GO and KEGG enrichment analyses of these target genes showed that many of the significantly enriched terms were associated with immune response, blood coagulation, hemostasis, and complement and coagulation cascades, especially the GO term “blood coagulation” and pathway “complement and coagulation cascades.” Ten representative target genes involved in “complement and coagulation cascades” were selected for qPCR analysis, and the results showed that the expression patterns of these target genes were significantly upregulated at 7 dpi, suggesting that the pathway “complement and coagulation cascades” was strongly activated.

Conclusion

Conserved and novel miRNAs in response to GCRV infection were identified in grass carp, of which 278 were known miRNAs and 930 were novel miRNAs. Many of the target genes involved in immune response, blood coagulation, hemostasis, and complement and coagulation cascades. Strong activation of the pathway “complement and coagulation cascades” may have led to endothelial-cell and blood-cell damage and hemorrhagic symptoms. The present study provides a new insight into understanding the mechanism underlying GCRV pathogenesis and hemorrhagic symptoms.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3562-4) contains supplementary material, which is available to authorized users.

Shrimp miRNAs regulate innate immune response against white spot syndrome virus infection

MicroRNAs are short noncoding RNAs of RNA interference pathways that regulate gene expression through partial complementary base-pairing to target mRNAs. In this study, miRNAs that are expressed in white spot syndrome virus (WSSV)-infected Penaeus monodon, were identified using next generation sequencing. Forty-six miRNA homologs were identified from WSSV-infected shrimp hemocyte. Stem-loop real-time RT-PCR analysis showed that 11 out of 16 selected miRNAs were differentially expressed upon WSSV infection. Of those, pmo-miR-315 and pmo-miR-750 were highly responsive miRNAs. miRNA target prediction revealed that the miRNAs were targeted at 5'UTR, ORF, and 3'UTR of several immune-related genes such as genes encoding antimicrobial peptides, signaling transduction proteins, heat shock proteins, oxidative stress proteins, proteinases or proteinase inhibitors, proteins in blood clotting system, apoptosis-related proteins, proteins in prophenoloxidase system, pattern recognition proteins and other immune molecules. The highly conserved miRNA homolog, pmo-bantam, was characterized for its function in shrimp. The pmo-bantam was predicted to target the 3'UTR of Kunitz-type serine protease inhibitor (KuSPI). Binding of pmo-bantam to the target sequence of KuSPI gene was analyzed by luciferase reporter assay. Correlation of pmo-bantam and KuSPI expression was observed in lymphoid organ of WSSV-infected shrimp. These results implied that miRNAs might play roles as immune gene regulators in shrimp antiviral response.

Discovery and functional characterization of novel miRNAs in the marine medaka Oryzias melastigma

The marine medaka Oryzias melastigma has often been used as a marine fish model to investigate the biological responses to environmental stresses and pollutants in marine environments. miRNAs are post-transcriptional regulators of many biological processes in a variety of organisms, and have been shown to be affected by environmental stresses, but the novel miRNA profile of marine medaka has not been reported. Using both genome and small RNA sequencings coupled with different bioinformatics analyses, we have discovered 58, 82, 234, and 201 unannotated miRNAs in the brain, liver, ovary and testis tissues of marine medaka, respectively. Furthermore, these novel miRNAs were found to target genes with tissue-specific roles such as neuron development and synaptic transmission in the brain, glucose and fat metabolism in the liver and steroidogenesis in the gonads. We here report, for the first time, novel miRNA profile of marine medaka, which will provide a foundation for future biomarkers and transgenerational studies for the assessment of environmental stresses and pollutions in the marine environments. In a boarder context, our data will provide novel insight into our knowledge of miRNome and miR research.

Integrated analysis of miRNA and mRNA expression profiles in tilapia gonads at an early stage of sex differentiation

Background

MicroRNAs (miRNAs) represent a second regulatory network that has important effects on gene expression and protein translation during biological process. However, the possible role of miRNAs in the early stages of fish sex differentiation is not well understood. In this study, we carried an integrated analysis of miRNA and mRNA expression profiles to explore their possibly regulatory patterns at the critical stage of sex differentiation in tilapia.

Results

We identified 279 pre-miRNA genes in tilapia genome, which were highly conserved in other fish species. Based on small RNA library sequencing, we identified 635 mature miRNAs in tilapia gonads, in which 62 and 49 miRNAs showed higher expression in XX and XY gonads, respectively. The predicted targets of these sex-biased miRNAs (e.g., miR-9, miR-21, miR-30a, miR-96, miR-200b, miR-212 and miR-7977) included genes encoding key enzymes in steroidogenic pathways (Cyp11a1, Hsd3b, Cyp19a1a, Hsd11b) and key molecules involved in vertebrate sex differentiation (Foxl2, Amh, Star1, Sf1, Dmrt1, and Gsdf). These genes also showed sex-biased expression in tilapia gonads at 5 dah. Some miRNAs (e.g., miR-96 and miR-737) targeted multiple genes involved in steroid synthesis, suggesting a complex miRNA regulatory network during early sex differentiation in this fish.

Conclusions

The sequence and expression patterns of most miRNAs in tilapia are conserved in fishes, indicating the basic functions of vertebrate miRNAs might share a common evolutionary origin. This comprehensive analysis of miRNA and mRNA at the early stage of molecular sex differentiation in tilapia XX and XY gonads lead to the discovery of differentially expressed miRNAs and their putative targets, which will facilitate studies of the regulatory network of molecular sex determination and differentiation in fishes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2636-z) contains supplementary material, which is available to authorized users.

Comparison of miRNA expression profiles in pituitary-adrenal axis between Beagle and Chinese Field dogs after chronic stress exposure

MicoRNAs (miRNAs), usually as gene regulators, participate in various biological processes, including stress responses. The hypothalamus–pituitary–adrenal axis (HPA axis) is an important pathway in regulating stress response. Although the mechanism that HPA axis regulates stress response has been basically revealed, the knowledge that miRNAs regulate stress response within HPA axis, still remains poor. The object of this study was to investigate the miRNAs in the pituitary and adrenal cortex that regulate chronic stress response with high-throughput sequencing. The pituitary and adrenal cortex of beagles and Chinese Field dogs (CFD) from a stress exposure group (including beagle pituitary 1 (BP1), CFD pituitary 1 (CFDP1), beagle adrenal cortex 1 (BAC1), CFD adrenal cortex 1 (CFDAC1)) and a control group (including beagle pituitary 2 (BP2), CFD pituitary 2 (CFDP2), beagle adrenal cortex 2 (BAC2), CFD adrenal cortex 2 (CFDAC2)), were selected for miRNA-seq comparisons. Comparisons, that were made in pituitary (including BP1 vs. BP2, CFDP1 vs. CFDP2, BP1 vs. CFDP1 and BP2 vs. CFDP2) and adrenal cortex (including BAC1 vs. BAC2, CFDAC1 vs. CFDAC2, BAC1 vs. CFDAC1 and BAC2 vs. CFDAC2), showed that a total of 39 and 18 common differentially expressed miRNAs (DE-miRNAs) (Total read counts > 1,000, Fold change > 2 & p-value < 0.001), that shared in at least two pituitary comparisons and at least two adrenal cortex comparisons, were detected separately. These identified DE-miRNAs were predicted for target genes, thus resulting in 3,959 and 4,010 target genes in pituitary and adrenal cortex, respectively. Further, 105 and 10 differentially expressed genes (DEGs) (Fold change > 2 & p-value < 0.05) from those target genes in pituitary and adrenal cortex were obtained separately, in combination with our previous corresponding transcriptome study. Meanwhile, in line with that miRNAs usually negatively regulated their target genes and the dual luciferase reporter assay, we finally identified cfa-miR-205 might play an important role by upregulating MMD in pituitary and hippocampus, thus enhancing the immune response, under chronic stress exposure. Our results shed light on the miRNA expression profiles in the pituitary and adrenal cortex with and without chronic stress exposure, and provide a new insight into miR-205 with its feasible role in regulating chronic stress in the pituitary and hippocampus through targeting MMD.

Coordinated microRNA and messenger RNA expression profiles for understanding sexual dimorphism of gonads and the potential roles of microRNA in the steroidogenesis pathway in Nile tilapia (Oreochromis niloticus)

Sexual dimorphism is a widespread phenomenon in animals. However, the potential role of microRNAs (miRNAs) in regulating this dimorphism is not fully understood. In our study, we used an integrated approach to identify functional targets of miRNA by combining the paired expression profiles of miRNAs and messenger RNAs (mRNAs) in ovaries and testes of young Nile tilapia, Oreochromis niloticus. The results revealed that 67 upregulated and nine downregulated miRNAs and 2299 upregulated and 3260 downregulated genes were identified in the ovary compared with those in the testis (P < 0.01). The target genes of differentially expressed miRNAs were predicted and overlapped with the differentially expressed mRNAs. Furthermore, Kyoto Encyclopedia of Genes and Genomes pathway analyses were conducted in these coincident genes. By correlating miRNA-mRNA and predicting computational target, two types of negatively regulatory miRNA-mRNA correlations (upregulated or downregulated miRNA and downregulated or upregulated mRNA) were obtained. Seven functional miRNA-target gene pairs, miR-17-5p/DMRT1, miR-20a/DMRT1, miR-138/CYP17A2, miR-338/CYP17A2, miR-200a/CYP17A2, miR-456/AMH, and miR-138/AMH, were predicted at the sequence level and further detected by real-time polymerase chain reaction on the basis of the significantly negative relationships. Our results suggest that the integrated analysis of miRNA and mRNA expression profiling can provide novel insights into the molecular mechanism of sexual dimorphism.

Micromanaging metabolism-a role for miRNAs in teleost energy metabolism

MicroRNAs (miRNAs) are small, non-protein coding RNA sequences, which are found in most eukaryotes. Since their initial discovery, miRNAs have emerged as important regulators of many biological processes. One of the most important processes profoundly regulated by miRNAs is energy metabolism. Traditionally, metabolic functions of miRNAs have been studied in genome-sequenced mammalian organisms, especially the mouse model. However, partially driven by commercial interest in aquaculture, increasingly feasible large-scale molecular techniques have resulted in the characterization of miRNA repertoires, and importantly, several genome sequences of several (commercially important) teleost species, which also hold important roles as research models in the comparative physiology of energy metabolism. This review aims to introduce the recent advances in miRNA research in teleost fish and to describe the current knowledge of miRNA function in teleost energy metabolism. The most pressing research needs and questions to determine metabolic roles of miRNAs in teleost models are presented, as well as applicable technical approaches and current bottlenecks. Rainbow trout, which possess the advantages of newly available molecular tools and a long history as comparative research model in teleost energy metabolism, are discussed as a promising research model to address these questions.