Cgi-miR-92d indirectly regulates TNF expression by targeting CDS region of lipopolysaccharide-induced TNF-α factor 3 (CgLITAF3) in oyster Crassostrea gigas

Ficus hirta Vahl. alleviate LPS induced apoptosis via down-regulating of miR-411 in orange-spotted grouper (Epinephelus coioides) spleen cell

Ficus hirta Vahl. (FhV) has been shown to have antimicrobial and antiviral efficacy. To further ascertain the pharmacological properties of FhV., and to search for alternatives to antibiotics. An in vitro experiment was carried out to evaluate what influence FhV. would have on LPS-induced apoptosis. In this study, Fas, an apoptosis receptor, was cloned, which included a 5'-UTR of 39 bp, an ORF of 951 bp, a protein of 316 amino acids, and a 3'-UTR of 845 bp. EcFas was most strongly expressed in the spleen tissue of orange-spotted groupers. In addition, the apoptosis of fish spleen cells induced by LPS was concentration-dependent. Interestingly, appropriate concentrations of FhV. alleviated LPS-induced apoptosis. Inhibition of miR-411 further decreased the inhibitory effect of Fas on apoptosis, which reduced Bcl-2 expression and mitochondrial membrane potential, enhanced the protein expression of Bax and Fas. More importantly, the FhV. could activate miR-411 to improve this effect. In addition, luciferase reporter assays showed that miR-411 binds to Fas 3'-UTR to inhibit Fas expression. These findings provide evidence that FhV. alleviates LPS-induced apoptosis by activating miR-411 to inhibit Fas expression and, therefore, provided possible strategies for bacterial infections in fish.

Increased abundances of potential pathogenic bacteria and expressions of inflammatory cytokines in the intestine of oyster Crassostrea gigas after high temperature stress

High temperature stress is a significant threat to the health of oysters, but the effects on their intestinal performances are not well understood. In this study, the effects of high temperature stress on the intestinal histology, immune response and associated microbiota were investigated in Crassostrea gigas after rearing at 20, 25 and 28 °C for 21 days. With the increase of temperature, shortened and shed microvilli as well as increased goblet cells were observed in the intestines of oysters. The transcripts of cytokines CgIL17-5, CgTNF-2 and CgTGF-β and apoptosis-related gene CgCaspase-3 in intestine increased with the increasing temperature. Further, the diversity and composition of the oyster intestinal microbiota changed after high temperature stress. The 16S rRNA gene copy number per ng of DNA in the T25 (5.16 × 10⁵) and T28 (1.63 × 10⁵) groups were higher than that in the control group (8.62 × 10⁴). The Chao 1 index in the T25 (238.00) and T28 (240.17) groups was lower than that in the control group (279.00). The Shannon index decreased progressively with the increasing temperature, with the value in the T28 group (4.44) significantly lower than that in the control group (5.40) (p < 0.05). The abundances of potential pathogenic bacteria such as Acinetobacter, Pseudomonas, Vibrio and Endozoicomonas increased while that of probiotic bacteria Bacillus decreased after high temperature exposure. Functional prediction indicated that the pathways associated with bacterial proliferation were enriched at 25 °C, while those involved in protein synthesis were blocked at 28 °C. Collectively, these results suggested that high temperature stress led to an increased abundances of potential pathogenic bacteria and expressions of inflammatory cytokines in the intestine, which may consequently affect the functional integrity of the intestinal barrier in oysters.

A novel miRNA, Cse-miR-33, functions as an immune regulator by targeting CsTRAF6 in Chinese tongue sole (Cynoglossus semilaevis)

The tumor necrosis factor receptor-associated factor 6 (TRAF6) can act as a fundamental adaptor protein in a chain reaction of signal transduction and cascade events to finish off immune defenses. However, immunomodulatory research on TRAF6 gene is still limited in fish. In this study, a novel miRNA, Cse-miR-33 was identified from the whole genome of Chinese tongue sole (Cynoglossus semilaevis). After separate infections with three different Vibrio strains (V. harveyi, V. anguillarum, V. parahemolyticus) and one virus (nervous necrosis virus, NNV), the expressions of CsTRAF6 and Cse-miR-33 displayed significant time-dependent changes in immune related tissues and the trends were opposite in general. Through target gene prediction and dual luciferase reporter assay, Cse-miR-33 was proven to regulate CsTRAF6 by combining with 3'-UTR sequence of the gene. The results of qRT-PCR and western blotting (WB) analyses showed that Cse-miR-33 blocked the translation of CsTRAF6 protein at post-transcriptional level, rather than degrading the target mRNA. Further experiment indicated that Cse-miR-33 inhibitor largely reduced the death rate of Chinese tongue sole caused by V. harveyi and NNV. The expressions of CsTRAF6-associated immune genes (such as CsIL-1R, CsMYD88, CsIRAK1, CsTNFα, CsIL6 and CsIL8) were also significantly changed in response to Cse-miR-33 agomir and inhibitor. The study suggested that Cse-miR-33 affected the immune response via targeting CsTRAF6 in C. semilaevis, which would provide us deep insights into miRNA-mediated regulatory network and help improve the immunity in fish.

MicroRNA ssa-mir-196a-4 deceases lgr8 expression in testis development of Chinese tongue sole (Cynoglossus semilaevis)

MicroRNAs (miRNAs) contribute to gonadal development in animals. However, there is little information about miRNA regulation function involved in gonadal development in fish. Our group previously identified sex-related miRNAs of Chinese tongue sole (Cynoglossus semilaevis) during sex determination and differentiation by small RNA sequencing. In the present study, we characterized ssa-mir-196a-4 and its expression in testis and verified its interaction with lgr8. miRNA ssa-mir-196a-4 precursor was predicted to have a typical hairpin structure and highly conserved among various fish species. Fluorescence in situ hybridization (FISH) of ssa-mir-196a-4 in the testis of Chinese tongue sole showed that it is mainly expressed in the cytoplasm of Sertoli cells. We determined that ssa-mir-196a-4 interacted with lgr8 by bioinformatics analysis using miRanda software. According to the dual-luciferase gene reporter assay, lgr8 is a direct target of ssa-mir-196a-4. Overexpression of ssa-mir-196a-4 in the cells of the testis cell line of Chinese tongue sole decreased the expression levels of lgr8 messenger RNA (mRNA) and protein by targeting its coding sequence (CDS) region. These results suggest that ssa-mir-196a-4 acts as a post-transcriptional regulator of lgr8 and plays an important role in developing testes of Chinese tongue sole.

Digging into bivalve miRNAomes: between conservation and innovation

Bivalves are a diverse mollusc group of economic and ecological importance. An evident resilience to pollution, parasites and extreme environments makes some bivalve species important models for studying adaptation and immunity. Despite substantial progress in sequencing projects of bivalves, information on non-coding genes and gene-regulatory aspects is still lacking. Here, we review the current repertoire of bivalve microRNAs (miRNAs), important regulators of gene expression in Metazoa. We exploited available short non-coding RNA (sncRNA) data for Pinctada martensii, Crassostrea gigas, Corbicula fluminea, Tegillarca granosa and Ruditapes philippinarum, and we produced new sncRNA data for two additional bivalves, the Mediterranean mussel Mytilus galloprovincialis and the blood clam Scapharca broughtonii. We found substantial heterogeneity and incorrect annotations of miRNAs; hence, we reannotated conserved miRNA families using recently established criteria for bona fide microRNA annotation. We found 106 miRNA families missing in the previously published bivalve datasets and 89 and 87 miRNA complements were identified in the two additional species. The overall results provide a homogeneous and evolutionarily consistent picture of miRNAs in bivalves and enable future comparative studies. The identification of two bivalve-specific miRNA families sheds further light on the complexity of transcription and its regulation in bivalve molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

MiR-92 Family Members Form a Cluster Required for Notochord Tubulogenesis in Urochordate Ciona savignyi

MicroRNAs are frequently clustered in the genome and polycistronically transcribed, regulating targeted genes in diverse signaling pathways. The miR-17-92 cluster is a typical miRNA cluster, playing crucial roles in the organogenesis and homeostasis of physiological processes in vertebrates. Here, we identified three miRNAs (csa-miR-92a, csa-miR-92b, and csa-miR-92c) that belonged to the miR-92 family and formed a miRNA cluster in the genome of a urochordate marine ascidian Ciona savignyi. Except for miR-92a and miR-92b, other homologs of the vertebrate miR-17-92 cluster members could not be identified in the Ciona genome. We further found that the mature sequences of urochordate miR-92 family members were highly conserved compared with the vertebrate species. The expression pattern revealed that three miR-92 family members had consistent expression levels in adult tissues and were predominantly expressed in heart and muscle tissue. We further showed that, at the embryonic and larval stages, csa-miR-92c was expressed in the notochord of embryos during 18–31 h post fertilization (hpf) by in situ hybridization. Knockout of csa-miR-92c resulted in the disorganization of notochord cells and the block of lumen coalescence in the notochord. Fibroblast growth factor (FGF), mitogen-activated protein kinase (MAPK), and wingless/integrated (Wnt)/planar cell polarity (PCP) signaling pathways might be involved in the regulatory processes, since a large number of core genes of these pathways were the predicted target genes of the miR-92 family. Taken together, we identified a miR-92 cluster in urochordate Ciona and revealed the expression patterns and the regulatory roles of its members in organogenesis. Our results provide expression and phylogenetic data on the understanding of the miR-92 miRNA cluster’s function during evolution.

Integrated analysis of miRNAome and transcriptome reveals miRNA-mRNA network regulation in Vibrio alginolyticus infected thick shell mussel Mytilus coruscus

The thick shell mussel Mytilus coruscus has developed into a model species for studying the interaction between molluscs and environmental stimuli. Herein, integrated analysis of miRNAome and transcriptome was performed to reveal miRNA-mRNA network regulation in Vibrio alginolyticus infected M. coruscus. There have detected some histological abnormalities in digestive gland and gills of V. alginolyticus challenged mussels, ascertaining the effective irritation by the present bacterial strain. A total of 265 novel miRNAs were finally predicted, of which 26 were differentially expressed miRNAs (DEMs). Additionally, 667 differentially expressed genes (DEGs) were detected, which may be potentially associated with innate immune response to V. alginolyticus infection. A regulatory network linked to 22 important pathways and 16 DEMs and 34 OGs was constructed. Some traditional immune-related signaling pathways such as toll-like receptor signaling pathway (TLR) signaling pathway, transforming growth factor-beta (TGF-beta) signaling pathway, peroxisome, phagosome, lysosome, mammalian target of rapamyoin (mTOR) signaling pathway were linked to specific miRNAs and genes in this network. Further, interactional relationship between certain miRNAs and TLR pathway was dissected, which the results predicted that a number of TLRs and TLR-associated signaling genes including TLR1, TLR2, TLR4, TLR6, IRAK1, TRAF6, MAPK, and IL-17 were negatively regulated by novel_miR_11, novel_miR_145, novel_miR_196, novel_miR_5, novel_miR_163 and novel_miR_217 in the TLR pathway. Additionally, interactional relationship between novel_miR_145 and TLR2 was validated by laboratory experiment. The integrated analysis of mRNA and microRNA deep sequencing data exhibited a sophisticated miRNA-mRNA regulation network in M. coruscus in response to V. alginolyticus challenge, which shed a new light on the underlying mechanism of molluscan confronting bacterial infection.

Discovery and functional understanding of MiRNAs in molluscs: a genome-wide profiling approach

Small non-coding RNAs play a pivotal role in gene regulation, repression of transposable element and viral activity in various organisms. Among the various categories of these small non-coding RNAs, microRNAs (miRNAs) guide post-translational gene regulation in cellular development, proliferation, apoptosis, oncogenesis, and differentiation. Here, we performed a genome-wide computational prediction of miRNAs to improve the understanding of miRNA observation and function in molluscs. As an initial step, hundreds of conserved miRNAs were predicted in 35 species of molluscs through genome scanning. Afterwards, the miRNAs' population, isoforms, organization, and function were characterized in detail. Furthermore, the key miRNA biogenesis factors, including AGO2, DGCR8, DICER, DROSHA, TRABP2, RAN, and XPO5, were elucidated based on homologue sequence searching. We also summarized the miRNAs' function in biomineralization, immune and stress response, as well as growth and development in molluscs. Because miRNAs play a vital role in various lifeforms, this study will provide insight into miRNA biogenesis and function in molluscs, as well as other invertebrates.

The functional roles of the non-coding RNAs in molluscs

This review focus on the current knowledge of non-coding RNAs (ncRNAs) in molluscs. In this review, we provide an overview of long ncRNAs (lncRNA), microRNAs (miRNA) and piwi-interacting RNAs (piRNA), followed by evidence for the regulation of ncRNAs in variety of biological process in molluscs, including development, biomineralization and innate immune response. This review advances our understanding on the roles of ncRNAs in molluscs and suggest the future direction to fully understand the epigenetic regulatory network of molluscs.

Hypoxia-induced miR-92a regulates p53 signaling pathway and apoptosis by targeting calcium-sensing receptor in genetically improved farmed tilapia (Oreochromis niloticus)

miR-92a miRNAs are immune molecules that regulate apoptosis (programmed cell death) during the immune response. Apoptosis helps to maintain the dynamic balance in tissues of fish under hypoxia stress. The aim of this study was to explore the role and potential mechanisms of miR-92a in the liver of tilapia under hypoxia stress. We first confirmed that CaSR (encoding a calcium-sensing receptor) is a target gene of miR-92a in genetically improved farmed tilapia (GIFT) using luciferase reporter gene assays. In GIFT under hypoxia stress, miR-92a was up-regulated and CaSR was down-regulated in a time-dependent manner. Knocked-down CaSR expression led to inhibited expression of p53, TP53INP1, and caspase-3/8, reduced the proportion of apoptotic hepatocytes, and decreased the activity of calcium ions induced by hypoxia in hepatocytes. GIFT injected in the tail vein with an miR-92a agomir showed up-regulation of miR-92a and down-regulation of CaSR, p53, TP53INP1, and caspase-3/8 genes in the liver, resulting in lower serum aspartate aminotransferase and alanine aminotransferase activities under hypoxia stress. These findings suggest that stimulation of miR-92a interferes with hypoxia-induced apoptosis in hepatocytes of GIFT by targeting CaSR, thereby alleviating liver damage. These results provide new insights into the adaptation mechanisms of GIFT to hypoxia stress.

Deep sequencing of small RNAs reveals the repertoire of miRNAs and piRNAs in Biomphalaria glabrata

BACKGROUND

Biomphalaria glabrata snails are widely distributed in schistosomiasis endemic areas like America and Caribe, displaying high susceptibility to infection by Schistosoma mansoni. After the availability of B. glabrata genome and transcriptome data, studies focusing on genetic markers and small non-coding RNAs have become more relevant. The small RNAs have been considered important through their ability to finely regulate the gene expression in several organisms, thus controlling the functions like cell growth, metabolism, and susceptibility/resistance to infection.

OBJECTIVE

The present study aims on identification and characterisation of the repertoire of small non-coding RNAs in B. glabrata (Bgl-small RNAs).

METHODS

By using small RNA sequencing, bioinformatics tools and quantitative reverse transcription polymerase chain reaction (RT-qPCR), we identified, characterised, and validated the presence of small RNAs in B. glabrata.

FINDINGS

89 mature miRNAs were identified and five of them were classified as Mollusk-specific. When compared to model organisms, sequences of B. glabrata miRNAs showed a high degree of conservation. In addition, several target genes were predicted for all the mature miRNAs identified. Furthermore, piRNAs were identified in the genome of B. glabrata for the first time. The B. glabrata piRNAs showed strong conservation of uridine as first nucleotide at 5’ end, besides adenine at 10th position. Our results showed that B. glabrata has diverse repertoire of circulating ncRNAs, several which might be involved in mollusk susceptibility to infection, due to their potential roles in the regulation of S. mansoni development.

MAIN CONCLUSIONS

Further studies are necessary in order to confirm the role of the Bgl-small RNAs in the parasite/host relationship thus opening new perspectives on interference of small RNAs in the organism development and susceptibility to infection.

MicroRNAs involved in innate immunity regulation in the sea cucumber: A review

The sea cucumber is one of the most economically significant echinoderms. The immunity against exogenous stimulation of sea cucumber is of great academic and economic importance. MicroRNAs (miRNAs) are a class of short endogenous non-coding RNAs (ncRNAs) that are considered as vital regulators of both innate and adaptive immune responses in most eukaryotes. In sea cucumbers, some miRNAs (such as miR-133, miR-137, and miR-2008, among others) that participate in the regulation of innate immunity have been recently identified and characterized. This review focuses on those known miRNAs and their corresponding target genes that participate in the regulation of the complement system, Toll-like receptor (TLR) pathway, reactive oxygen species (ROS) production and apoptosis pathways in sea cucumbers. Moreover, we cover immune-related miRNA investigations in sea cucumbers that provide insights into developing more miRNA-based biomarkers and therapeutic strategies for sea cucumber diseases.

Genetic features of Haliotis discus hannai by infection of vibrio and virus

BACKGROUND

Haliotis discus hannai more commonly referred to as the Pacific Abalone is of significant commercial and economical value in South Korea, with it being the second largest producer in the world. Despite this significance there is a lack of genetic studies with regards to the species. Most existing studies focused mainly on environmental factors.

OBJECTIVE

To provide a comprehensive review describing the genetic feature of Haliotis discus hannai by infection of vibrio and virus.

METHODS

This review summarized the immune response in the Haliotis spp. with regards to immunological genes such as Cathepsin B, C-type lectin and Toll-like receptors. Genetic studies with regards to transposable elements and miRNAs are few and far between. A study identified LTR retrotransposon Ty3/gypsy in the species. As to miRNA, a single study identified numerous miRNAs in the Haliotis discus hannai.

CONCLUSION

This paper sought to provide an overview of genetic perspective with regards to immune response genes, transposable elements and miRNAs.

P38 is involved in immune response by regulating inflammatory cytokine expressions in the Pacific oyster Crassostrea gigas

P38 mitogen-activated protein kinases are serine/threonine protein kinases reportedly involved in the innate immunity of vertebrates and invertebrates. In the present study, a P38 homolog (CgP38) was characterized from the Pacific oyster Crassostrea gigas. The full-length cDNA of CgP38 was of 1515 bp containing a 1101 bp open reading frame. A serine/threonine protein kinase (S_TKc) domain with a conserved Thr-Gly-Tyr motif and an ATRW substrate-binding site was found in the deduced amino acid sequence of CgP38. CgP38 shared a close evolutionary relationship with ChP38 from the Hong Kong oyster Crassostrea hongkongensis. The transcript levels of CgP38 in hemocytes increased significantly from 12 h to 48 h after lipopolysaccharide (LPS) stimulation and from 12 h to 24 h after Vibrio splendidus stimulation. The phosphorylation level of CgP38 in oyster hemocytes increased significantly at 2 h after LPS stimulation. CgP38 positively regulated the expression of interleukins, such as CgIL17-1, CgIL17-2, CgIL17-3, CgIL17-4 and CgIL17-6, and tumor necrosis factor CgTNF after LPS or V. splendidus stimulation. These results suggested that CgP38 participated in oyster immune response by regulating the expressions of inflammatory cytokines.

MicroRNA-664-5p promotes myoblast proliferation and inhibits myoblast differentiation by targeting serum response factor and Wnt1

MicroRNAs (miRNAs) are noncoding RNAs that regulate gene expression at the post-transcriptional level and are involved in the regulation of the formation, maintenance, and function of skeletal muscle. Using miRNA sequencing and bioinformatics analysis, we previously found that the miRNA miR-664-5p is significantly differentially expressed in longissimus dorsi muscles of Rongchang pigs. However, the molecular mechanism by which miR-664-5p regulates myogenesis remains unclear. In this study, using flow cytometry, 5-ethynyl-2'-deoxyuridine staining, and cell count and immunofluorescent assays, we found that cell-transfected miR-664-5p mimics greatly promoted proliferation of C2C12 mouse myoblasts by increasing the proportion of cells in the S- and G₂-phases and up-regulating the expression of cell cycle genes. Moreover, miR-664-5p inhibited myoblast differentiation by down-regulating myogenic gene expression. In contrast, miR-664-5p inhibitor repressed myoblast proliferation and promoted myoblast differentiation. Mechanistically, using dual-luciferase reporter gene experiments, we demonstrated that miR-664-5p directly targets the 3'-UTR of serum response factor (SRF) and Wnt1 mRNAs. We also observed that miR-664-5p inhibits both mRNA and protein levels of SRF and Wnt1 during myoblast proliferation and myogenic differentiation, respectively. Furthermore, the activating effect of miR-664-5p on myoblast proliferation was attenuated by SRF overexpression, and miR-664-5p repressed myogenic differentiation by diminishing the accumulation of nuclear β-catenin. Of note, miR-664-5p's inhibitory effect on myogenic differentiation was abrogated by treatment with Wnt1 protein, the key activator of the Wnt/β-catenin signaling pathway. Collectively, our findings suggest that miR-664-5p controls SRF and canonical Wnt/β-catenin signaling pathways in myogenesis.

MicroRNA-210 alleviates oxidative stress-associated cardiomyocyte apoptosis by regulating BNIP3

Oxidative stress-induced myocardial apoptosis and necrosis are involved in ischemia/reperfusion (I/R) injury. This study was performed to investigate microRNA (miR)-210's role in oxidative stress-related myocardial damage. The expression of miR-210 was upregulated in myocardial tissues of I/R rats, while that of Bcl-2 adenovirus E1B 19kDa-interacting protein 3 (BNIP3) was downregulated. To simulate in vivo oxidative stress, H9c2 cells were treated with H₂O₂ for 48 h. MiR-210 level was increased upon H₂O₂ stimulation, peaked at 8 h, and then decreased. An opposite expression pattern of BNIP3 was observed. BNIP3 was demonstrated as a direct target of miR-210 via luciferase reporter assay. H₂O₂-induced cell apoptosis was attenuated by miR-210 mimics, whereas aggravated by miR-210 inhibitor. MiR-210 knockdown-induced cell apoptosis in presence of H₂O₂ was attenuated by BNIP3 siRNA. Our work demonstrates that miR-210 plays a protective role in H₂O₂-induced cardiomyocyte apoptosis at least by regulating the pro-apoptotic BNIP3.

Inhibition of miR-92d-3p enhances inflammation responses in genetically improved farmed tilapia (GIFT, Oreochromis niloticus) with Streptococcus iniae infection by modulating complement C3

MicroRNAs (miRNAs) are small, non-coding RNAs that regulate target gene expression by binding to the 3'-untranslated regions (3'-UTRs) of their target mRNAs. The miR-92 family is an important miRNA family, which was discovered to be related to regulation of tumor proliferation, apoptosis, invasion, and metastasis. Inhibition of miR-92d-3p was found previously in head kidney of genetically improved farmed tilapia (GIFT, Oreochromis niloticus) exposed to Streptococcus iniae infection. In this study, we found that miR-92d-3p regulated complement C3 mRNA levels by binding to its 3'-UTR by 3'-UTR luciferase reporter assay, and reduced miR-92d-3p expression resulted in increased C3 mRNA levels. We detected a negative relationship between the expression levels of miR-92d-3p and C3 in GIFT injected with miRNA antagomir. We performed in vivo functional analysis by miR-92d-3p silencing. Inhibition of miR-92d-3p levels in GIFT head kidney caused a significant increase in C3 expression, which consequently increased the white blood cell counts and interleukin-1β, tumor necrosis factor-α, and interferon-γ mRNA levels, all of which may help to activate the inflammatory response in GIFT post-infection with S. iniae. Our findings indicate that miR-92d-3p regulated C3 levels by binding with the C3 mRNA 3'-UTR, and this interaction affected S. iniae infection induction and the immune response in GIFT. We concluded that miR-92d-3p plays an important role in modulating the inflammatory response in GIFT head kidney. Our findings may contribute to understanding the mechanisms of miRNA-mediated gene regulation in tilapia in response to S. iniae infection.