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Verleih M, Visnovska T, Nguinkal JA, Rebl A, Goldammer T, Andreassen R. The Discovery and Characterization of Conserved and Novel miRNAs in the Different Developmental Stages and Organs of Pikeperch ( Sander lucioperca). Int J Mol Sci 2023; 25:189. [PMID: 38203361 PMCID: PMC10778745 DOI: 10.3390/ijms25010189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Micro RNAs (miRNAs) are short non-coding RNAs that act as post-transcriptional gene expression regulators. Genes regulated in vertebrates include those affecting growth and development or stress and immune response. Pikeperch (Sander lucioperca) is a species that is increasingly being considered for farming in recirculation aquaculture systems. We characterized the pikeperch miRNA repertoire to increase the knowledge of the genomic mechanisms affecting performance and health traits by applying small RNA sequencing to different developmental stages and organs. There were 234 conserved and 8 novel miRNA genes belonging to 104 families. A total of 375 unique mature miRNAs were processed from these genes. Many mature miRNAs showed high relative abundances or were significantly more expressed at early developmental stages, like the miR-10 and miR-430 family, let-7, the miRNA clusters 106-25-93, and 17-19-92. Several miRNAs associated with immune responses (e.g., slu-mir-731-5p, slu-mir-2188-5p, and slu-mir-8159-5p) were enriched in the spleen. The mature miRNAs slu-mir-203a-3p and slu-mir-205-5p were enriched in gills. These miRNAs are similarly abundant in many vertebrates, indicating that they have shared regulatory functions. There was also a significantly increased expression of the disease-associated miR-462/miR-731 cluster in response to hypoxia stress. This first pikeperch miRNAome reference resource paves the way for future functional studies to identify miRNA-associated variations that can be utilized in marker-assisted breeding programs.
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Affiliation(s)
- Marieke Verleih
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (M.V.); (A.R.)
| | - Tina Visnovska
- Bioinformatics Core Facility, Oslo University Hospital, 0424 Oslo, Norway
| | - Julien A. Nguinkal
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany;
| | - Alexander Rebl
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (M.V.); (A.R.)
| | - Tom Goldammer
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (M.V.); (A.R.)
- Faculty of Agriculture and Environmental Sciences, University of Rostock, 18059 Rostock, Germany
| | - Rune Andreassen
- Department of Life Sciences and Health, OsloMet—Oslo Metropolitan University, 0167 Oslo, Norway;
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Houdelet C, Blondeau-Bidet E, Estevez-Villar M, Mialhe X, Hermet S, Ruelle F, Dutto G, Bajek A, Bobe J, Geffroy B. Circulating MicroRNAs Indicative of Sex and Stress in the European Seabass (Dicentrarchus labrax): Toward the Identification of New Biomarkers. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:749-762. [PMID: 37581865 DOI: 10.1007/s10126-023-10237-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/01/2023] [Indexed: 08/16/2023]
Abstract
MicroRNAs (miRNAs) constitute a new category of biomarkers. Studies on miRNAs in non-mammalian species have drastically increased in the last few years. Here, we explored the use of miRNAs as potential, poorly invasive markers, to identify sex and characterize acute stress in fish. The European seabass (Dicentrarchus labrax) was chosen as a model because of its rapid response to stress and its specific sex determination system, devoid of sexual chromosomes. We performed a small RNA-sequencing analysis in the blood plasma of male and female European seabass (mature and immature) as well as in the blood plasma of juveniles submitted to an acute stress and sampled throughout the recovery period (at 0 h, 0.5 h, 1.5 h and 6 h). In immature individuals, both miR-1388-3p and miR-7132a-5p were up-regulated in females, while miR-499a-5p was more abundant in males. However, no miRNAs were found to be differentially expressed between sexes in the blood plasma of mature individuals. For the acute stress analysis, five miRNAs (miR-155-5p, miR-200a-3p, miR-205-1-5p, miR-143-3p, and miR-223-3p) followed cortisol production over time. All miRNAs identified were tested and validated by RT-qPCR on sequenced samples. A complementary analysis on the 3'UTR sequences of the European seabass allowed to predict potential mRNA targets, some of them being particularly relevant regarding stress regulation, e.g., the glucocorticoid receptor 1 and the mineralocorticoid receptor. The present study provides new avenues and recommendations on the use of miRNAs as biomarkers of sex or stress of the European seabass, with potential application on other fish species.
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Affiliation(s)
- Camille Houdelet
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France
| | | | | | - Xavier Mialhe
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, Montpellier, France
| | - Sophie Hermet
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - François Ruelle
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France
| | - Gilbert Dutto
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France
| | - Aline Bajek
- Ecloserie Marine de Gravelines-Ichtus, Voie des Enrochements, F-59820, Gravelines, France
| | - Julien Bobe
- INRAE, UR1037, Fish Physiology and Genomic laboratory, F-35000, Rennes, France
| | - Benjamin Geffroy
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France.
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Tang R, Xu C, Zhu Y, Yan J, Yao Z, Zhou W, Gui L, Li M. Identification and expression analysis of sex biased miRNAs in chinese hook snout carp Opsariichthys bidens. Front Genet 2022; 13:990683. [PMID: 36118893 PMCID: PMC9478731 DOI: 10.3389/fgene.2022.990683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/08/2022] [Indexed: 12/22/2022] Open
Abstract
As an economically important fish, Opsariichthys bidens has obvious sexual dimorphism and strong reproductive capacity, but no epigenetics study can well explain its phenotypic variations. In recent years, many microRNAs involved in the regulation of reproductive development have been explored. In this study, the small RNA libraries of O. bidens on the testis and ovary were constructed and sequenced. A total of 295 known miRNAs were obtained and 100 novel miRNAs were predicted. By comparing testis and ovary libraries, 115 differentially expressed (DE) miRNAs were selected, of which 53 were up-regulated and 62 were down-regulated. A total of 64 GO items (padj < 0.01) and 206 KEGG pathways (padj < 0.01) were enriched in the target gene of miRNA. After that, the expression levels of nine DE miRNAs, including let-7a, miR-146b, miR-18c, miR-202-5p, miR-135c, miR-9-5p, miR-34c-3p, miR-460-5p and miR-338 were verified by qRT-PCR. Furthermore, bidirectional prediction of DE miRNAs and sex-related genes was carried out and the targeting correlation between miR-9-5p and nanos1 was verified by Dual-Luciferase reporter assay. Our findings identified the differentially expressed miRNA and paved the way to new possibilities for the follow-up study on the mechanism of miRNA-mRNA interaction in the gonads of O. bidens.
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Affiliation(s)
- Rongkang Tang
- Key Laboratory of Integrated Rice-fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Cong Xu
- Key Laboratory of Integrated Rice-fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Yefei Zhu
- Key Laboratory of Integrated Rice-fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jinpeng Yan
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Ziliang Yao
- Lishui Fishery Technical Extension Station, Lishui, Zhejiang, China
| | - Wenzong Zhou
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Lang Gui
- Key Laboratory of Integrated Rice-fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- *Correspondence: Lang Gui, ; Mingyou Li,
| | - Mingyou Li
- Key Laboratory of Integrated Rice-fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- *Correspondence: Lang Gui, ; Mingyou Li,
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Genome-wide identification of chicken bursae of Fabricius miRNAs in response to very virulent infectious bursal disease virus. Arch Virol 2022; 167:1855-1864. [PMID: 35752686 DOI: 10.1007/s00705-022-05496-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/19/2022] [Indexed: 11/02/2022]
Abstract
Infectious bursal disease virus (IBDV) can cause a highly contagious immunosuppressive disease in young chickens. MicroRNAs (miRNAs) are crucial regulators of gene expression and are involved in the pathogenesis of IBDV infection. To investigate the roles of miRNA in chicken bursae of Fabricius in response to very virulent IBDV (vvIBDV) infection, RNA sequencing was performed to compare the small RNA libraries from uninfected and vvIBDV-infected group which was infected for 3 days. A total of 77 differentially expressed (DE) miRNAs were identified in BF, of which 42 DE miRNAs were upregulated and 35 DE miRNAs were downregulated. A gene ontology analysis showed that genes associated with cellular processes, cells, and binding were enriched. Moreover, pathway analyses suggested that apoptosis, T cell receptor signaling pathways, and chemokine signaling pathways may be activated following vvIBDV infection. In addition, we predicted the target genes of DE miRNAs and constructed an miRNA-mRNA regulatory network. In total, 189 pairs of miRNA-target genes were identified, comprising 67 DE miRNAs and 73 mRNAs. In this network, gga-miR-1684b-3p was identified with the highest fold change, as well as gga-miR-1788-3p and gga-miR-3530-5p showed a high degree of change. The above three miRNAs were considered to play vital roles in vvIBDV-host interactions. This study was the first to perform a comprehensive analysis of DE miRNAs in the bursa of Fabricius in response to vvIBDV infection, and it provided new insights into molecular mechanisms underlying vvIBDV infection and pathogenesis.
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Chakraborty S, Woldemariam NT, Visnovska T, Rise ML, Boyce D, Santander J, Andreassen R. Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus. BIOLOGY 2022; 11:biology11010130. [PMID: 35053128 PMCID: PMC8773022 DOI: 10.3390/biology11010130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 12/28/2022]
Abstract
Simple Summary Lumpfish (Cyclopterus lumpus) is an emergent aquaculture species, and its miRNA repertoire is still unknown. miRNAs are critical post-transcriptional modulators of teleost gene expression. Therefore, a lumpfish reference miRNAome was characterized by small RNA sequencing and miRDeep analysis of samples from different organs and developmental stages. The resulting miRNAome, an essential reference for future expression analyses, consists of 443 unique mature miRNAs from 391 conserved and eight novel miRNA genes. Enrichment of specific miRNAs in particular organs and developmental stages indicates that some conserved lumpfish miRNAs regulate organ and developmental stage-specific functions reported in other teleosts. Abstract MicroRNAs (miRNAs) are endogenous small RNA molecules involved in the post-transcriptional regulation of protein expression by binding to the mRNA of target genes. They are key regulators in teleost development, maintenance of tissue-specific functions, and immune responses. Lumpfish (Cyclopterus lumpus) is becoming an emergent aquaculture species as it has been utilized as a cleaner fish to biocontrol sea lice (e.g., Lepeophtheirus salmonis) infestation in the Atlantic Salmon (Salmo salar) aquaculture. The lumpfish miRNAs repertoire is unknown. This study identified and characterized miRNA encoding genes in lumpfish from three developmental stages (adult, embryos, and larvae). A total of 16 samples from six different adult lumpfish organs (spleen, liver, head kidney, brain, muscle, and gill), embryos, and larvae were individually small RNA sequenced. Altogether, 391 conserved miRNA precursor sequences (discovered in the majority of teleost fish species reported in miRbase), eight novel miRNA precursor sequences (so far only discovered in lumpfish), and 443 unique mature miRNAs were identified. Transcriptomics analysis suggested organ-specific and age-specific expression of miRNAs (e.g., miR-122-1-5p specific of the liver). Most of the miRNAs found in lumpfish are conserved in teleost and higher vertebrates, suggesting an essential and common role across teleost and higher vertebrates. This study is the first miRNA characterization of lumpfish that provides the reference miRNAome for future functional studies.
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Affiliation(s)
- Setu Chakraborty
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, 0 Marine Lab Rd, St. John’s, NL A1C 5S7, Canada;
| | - Nardos T. Woldemariam
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet–Oslo Metropolitan University, Pilestredet 50, N-0130 Oslo, Norway;
| | - Tina Visnovska
- Bioinformatics Core Facility, Oslo University Hospital, 0372 Oslo, Norway;
| | - Matthew L. Rise
- Department of Ocean Sciences, Faculty of Sciences, Memorial University of Newfoundland, 0 Marine Lab Rd, St. John’s, NL A1C 5S7, Canada;
| | - Danny Boyce
- Dr. Joe Brown Aquatic Research Building (JBARB), Department of Ocean Sciences, Memorial University of Newfoundland, 0 Marine Lab Rd, St. John’s, NL A1C 5S7, Canada;
| | - Javier Santander
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, 0 Marine Lab Rd, St. John’s, NL A1C 5S7, Canada;
- Correspondence: (J.S.); (R.A.)
| | - Rune Andreassen
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet–Oslo Metropolitan University, Pilestredet 50, N-0130 Oslo, Norway;
- Correspondence: (J.S.); (R.A.)
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Tang X, Fu J, Shi Y, Guan W, Xu M. MicroRNAs and Related Cytokine Factors Quickly Respond in the Immune Response of Channel Catfish to Lipopolysaccharides and β-Glucan Stimulation. JOURNAL OF AQUATIC ANIMAL HEALTH 2021; 33:220-230. [PMID: 34160849 DOI: 10.1002/aah.10137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
MicroRNAs (miRNAs) are well-known as powerful regulators of gene expression, with their potential to serve for immunology widely researched in mammals and birds but rarely in fishes. To better understand fish immunology behavior, we herein investigated nine immune-related miRNAs that were reported in other animals, as well as five related cytokine factors and lysozyme (LZM) in the liver, anterior kidney, and spleen of Channel Catfish Ictalurus punctatus after being stimulated by lipopolysaccharides (LPS) and β-glucan. We also predicated the potential targets of these miRNAs via bioinformatics and further investigated nine of them via quantitative real-time PCR. Results showed that expressions of the nine miRNAs were quickly changed in varying extent after stimulation by LPS, especially for miR-122, miR-142a, miR-155, and miR-223, which were significantly changed in spleen, and the same occurred for the LZM and three cytokine factors TNF-α, IFN-γ and TLR2. Compared with LPS, although most of the miRNAs and the cytokine genes were also affected by β-glucan, the extent of the effect was weak. Bioinformatics analysis revealed many immune-related targets of the miRNAs, with some of them reported by previous studies. For the nine investigated target genes, seven targets (77.8%) were significantly upregulated after the stimulation of LPS. It therefore can be inferred that the immune-related miRNAs, LZM, and cytokine factors elicited quick immune responses of Channel Catfish to LPS stimulation as in other animals, but the regulation mechanism of miRNAs might be complex and diverse. This research will contribute to a better understanding will support further immunology research in fishes.
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Affiliation(s)
- Xuelian Tang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jinghua Fu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yifu Shi
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wanting Guan
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Minjun Xu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
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Zhou W, Xie Y, Li Y, Xie M, Zhang Z, Yang Y, Zhou Z, Duan M, Ran C. Research progress on the regulation of nutrition and immunity by microRNAs in fish. FISH & SHELLFISH IMMUNOLOGY 2021; 113:1-8. [PMID: 33766547 DOI: 10.1016/j.fsi.2021.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/17/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
MicroRNAs (miRNAs) are a class of highly conserved, endogenous non-coding single-stranded small RNA molecules with a length of 18-25 nucleotides. MiRNAs can negatively regulate the target gene through complementary pairing with the mRNA. It has been more than 20 years since the discovery of miRNA molecules, and many achievements have been made in fish research. This paper reviews the research progress in the regulation of fish nutrition and immunity by miRNAs in recent years. MiRNAs regulate the synthesis of long-chain polyunsaturated fatty acids, and are involved in the metabolism of glucose, lipids, as well as cholesterol in fish. Moreover, miRNAs play various roles in antibacterial and antiviral immunity of fish. They can promote the immune response of fish, but may also participate in the immune escape mechanism of bacteria or viruses. One important aspect of miRNAs regulation on fish immunity is mediated by targeting pattern recognition receptors and downstream signaling factors. Together, current results indicate that miRNAs are widely involved in the complex regulatory network of fish. Further studies on fish miRNAs may deepen our understanding of the regulatory network of fish nutrition and immunity, and have the potential to promote the development of microRNA-based products and detection reagents that can be applied in aquaculture industry.
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Affiliation(s)
- Wei Zhou
- Sino-Norway Joint Lab on Fish Gut Microbiota, Beijing, 100081, China
| | - Yadong Xie
- Sino-Norway Joint Lab on Fish Gut Microbiota, Beijing, 100081, China
| | - Yu Li
- Sino-Norway Joint Lab on Fish Gut Microbiota, Beijing, 100081, China
| | - Mingxu Xie
- Sino-Norway Joint Lab on Fish Gut Microbiota, Beijing, 100081, China
| | - Zhen Zhang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Yalin Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Zhigang Zhou
- Sino-Norway Joint Lab on Fish Gut Microbiota, Beijing, 100081, China
| | - Ming Duan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Chao Ran
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
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Yu S, Wang G, Liao J, Tang M, Chen J. Identifying and profiling the microRNAs associated with skin colour in the Muchuan black-bone chicken. ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1760151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Shigang Yu
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
| | - Gang Wang
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
| | - Juan Liao
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
| | - Mei Tang
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
| | - Jia Chen
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
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Liu J, Jia E, Shi H, Li X, Jiang G, Chi C, Liu W, Zhang D. Selection of reference genes for miRNA quantitative PCR and its application in miR-34a/Sirtuin-1 mediated energy metabolism in Megalobrama amblycephala. FISH PHYSIOLOGY AND BIOCHEMISTRY 2019; 45:1663-1681. [PMID: 31127447 DOI: 10.1007/s10695-019-00658-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/06/2019] [Indexed: 05/19/2023]
Abstract
MiRNAs are small, non-coding RNAs that downregulate gene expression at post-transcriptional levels. They have emerged as important regulators involved in metabolism, immunity, and cancer. Real-time quantitative PCR (RT-qPCR) is an effective and main method for quantifying target miRNA. For robust RT-qPCR method, suitable reference genes play crucial roles in data normalization. Blunt snout bream (Megalobrama amblycephala) is an economically important aquaculture species; however, no reference genes dedicated for qPCR method has been identified for this species so far. The objective of this study was to screen stable reference genes for miRNA RT-qPCR and demonstrated its application in energy metabolism in blunt snout bream. The stabilities of ten potential reference genes (miR-21-1-5p, miR-107a-3p, miR-222a-3p, miR-146a-5p, miR-101a-3p, miR-22a-3p, miR-103-3p, miR-456-3p, miR-221-3p, and U6 (RNU6A)) were evaluated in nine tissues (brain, muscle, liver, skin, spleen, heart, gill, intestine, and eye) under normal condition and in three tissues (liver, intestine, and spleen) under four stresses (heat stress, ammonia stress, bacterial challenge, and glycolipid stress). Using GeNorm, NormFinder, and RefFinder softwares, we discovered that different tissues and stresses are both important variability factors for the expression stability of miRNAs. After verifying miR-34a/Sirtuin-1 expressions in high-carbohydrate diet-induced blunt snout bream, we eventually identified that the most stable reference gene in this species was miR-221-3p, and the best combination of reference genes were miR-221-3p and miR-103-3p.
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Affiliation(s)
- Jie Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Erteng Jia
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Huajuan Shi
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Xiangfei Li
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Guangzhen Jiang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Cheng Chi
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Wenbin Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Dingdong Zhang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China.
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Kang H, Liang QJ, Hu R, Li ZH, Liu Y, Wang WN. Integrative mRNA-miRNA interaction analysis associated with the immune response of Epinephelus coioddes to Vibrio alginolyticus infection. FISH & SHELLFISH IMMUNOLOGY 2019; 90:404-412. [PMID: 31077847 DOI: 10.1016/j.fsi.2019.05.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/29/2019] [Accepted: 05/04/2019] [Indexed: 06/09/2023]
Abstract
MicroRNAs (miRNAs) are a kind of small non-coding RNAs that have been reported to play a vital role in mediating host-pathogen interactions. High-throughput sequencing technology was applied to identify and illuminate mRNAs and miRNAs from grouper infected with Vibrio alginolyticus. The KEGG pathway enrichment analysis showed that the most significate DEGs are associated with Toll-like receptor signaling pathway and NOD-like receptor signaling pathway. We obtained 374 known miRNAs and 116 novel miRNAs. During them, there are 31 up-regulated miRNAs and 93 down-regulated miRNAs. miRNA-mRNA GO and KEGG analysis show that there are 90 miRNAs associated with the immune system. The target genes of immune-related miRNAs (miR-142, miR-146, miR-150, miR-155, miR-203, miR-205, miR-24, miR-31) and genes (CD80, IL-2, AMPK, PI3K) in Epinephelus coioddes were predicted and validated. This study provides an opportunity to further understanding the molecular mechanisms especially the immune system of miRNA regulation in Epinephelus coioddes host-pathogen interactions.
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Affiliation(s)
- Huan Kang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China
| | - Qing-Jian Liang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China
| | - Rui Hu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China
| | - Zhong-Hua Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China
| | - Yuan Liu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China
| | - Wei-Na Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China.
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11
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Lan T, Chen YL, Gul Y, Zhao BW, Gao ZX. Comparative expression analysis of let-7 microRNAs during ovary development in Megalobrama amblycephala. FISH PHYSIOLOGY AND BIOCHEMISTRY 2019; 45:1101-1115. [PMID: 30835012 DOI: 10.1007/s10695-019-00624-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/21/2019] [Indexed: 06/09/2023]
Abstract
As a critical regulator of gene expression, let-7 family miRNAs have been reported to be involved in multiple physiological processes. In this study, in order to elucidate the putative regulatory effect of let-7 miRNAs during fish gonadal development and to identify which member is crucial for this regulation, the expression of ten members including let-7a/b/c/d/e/f/g/h/i/j were quantified in ovary, pituitary, and brain tissues during the different ovarian developmental stages of blunt snout bream Megalobrama amblycephala. According to the data from analysis of expression patterns, let-7a showed the highest expression value in almost all the tested ovaries, pituitaries, and brains, with let-7b and let-7d moderately expressed, following by other let-7 miRNAs. In terms of the differential expression levels of ten let-7 miRNAs at each developmental stage, the results showed that let-7a/b/d/f/h expression gradually increased during the ovary development from stage I to V and dropped significantly at the phase VI in ovary tissues. However, the expression of let-7a/b/e/f in pituitary increased during the ovary development from stage I to IV and declined at stage V. Among all the let-7 miRNAs, let-7a/b/d had the highest expression and their expression patterns were consistent with the gonad development of M. amblycephala. Furthermore, the mostly predicted target genes of let-7 miRNAs are significantly enriched in signaling pathways closely related to gonadal development through KEGG enrichment analysis. These results indicate that let-7 miRNA members, especially let-7a/b/d, may play important roles in the regulation of ovary development in M. amblycephala through negatively regulating expression of their target genes.
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Affiliation(s)
- Tian Lan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, 430070, China
| | - Yu-Long Chen
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, 430070, China
| | - Yasmeen Gul
- Department of Zoology, Government College Women University, Faisalabad, 38860, Pakistan
| | - Bo-Wen Zhao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, 430070, China
| | - Ze-Xia Gao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, 430070, China.
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12
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Bao L, Tian C, Liu S, Zhang Y, Elaswad A, Yuan Z, Khalil K, Sun F, Yang Y, Zhou T, Li N, Tan S, Zeng Q, Liu Y, Li Y, Li Y, Gao D, Dunham R, Davis K, Waldbieser G, Liu Z. The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish. BMC Biol 2019; 17:6. [PMID: 30683095 PMCID: PMC6346536 DOI: 10.1186/s12915-019-0627-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 01/09/2019] [Indexed: 11/30/2022] Open
Abstract
Background Sex determination mechanisms in teleost fish broadly differ from mammals and birds, with sex chromosomes that are far less differentiated and recombination often occurring along the length of the X and Y chromosomes, posing major challenges for the identification of specific sex determination genes. Here, we take an innovative approach of comparative genome analysis of the genomic sequences of the X chromosome and newly sequenced Y chromosome in the channel catfish. Results Using a YY channel catfish as the sequencing template, we generated, assembled, and annotated the Y genome sequence of channel catfish. The genome sequence assembly had a contig N50 size of 2.7 Mb and a scaffold N50 size of 26.7 Mb. Genetic linkage and GWAS analyses placed the sex determination locus within a genetic distance less than 0.5 cM and physical distance of 8.9 Mb. However, comparison of the channel catfish X and Y chromosome sequences showed no sex-specific genes. Instead, comparative RNA-Seq analysis between females and males revealed exclusive sex-specific expression of an isoform of the breast cancer anti-resistance 1 (BCAR1) gene in the male during early sex differentiation. Experimental knockout of BCAR1 gene converted genetic males (XY) to phenotypic females, suggesting BCAR1 as a putative sex determination gene. Conclusions We present the first Y chromosome sequence among teleost fish, and one of the few whole Y chromosome sequences among vertebrate species. Comparative analyses suggest that sex-specific isoform expression through alternative splicing may underlie sex determination processes in the channel catfish, and we identify BCAR1 as a potential sex determination gene. Electronic supplementary material The online version of this article (10.1186/s12915-019-0627-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lisui Bao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Changxu Tian
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yu Zhang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ahmed Elaswad
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zihao Yuan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Karim Khalil
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Fanyue Sun
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yujia Yang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ning Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Suxu Tan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qifan Zeng
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yueru Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yun Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dongya Gao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Rex Dunham
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Kenneth Davis
- USDA-ARS Warmwater Aquaculture Research Unit, P.O. Box 38, 141 Experiment Station Road, Stoneville, MS, 38776, USA
| | - Geoffrey Waldbieser
- USDA-ARS Warmwater Aquaculture Research Unit, P.O. Box 38, 141 Experiment Station Road, Stoneville, MS, 38776, USA
| | - Zhanjiang Liu
- Department of Biology, College of Art and Sciences, Syracuse University, Syracuse, NY, 13244, USA.
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13
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Zhao Y, Zhang A, Wang Y, Hu S, Zhang R, Qian S. Genome-wide identification of brain miRNAs in response to high-intensity intermittent swimming training in Rattus norvegicus by deep sequencing. BMC Mol Biol 2019; 20:3. [PMID: 30646850 PMCID: PMC6334412 DOI: 10.1186/s12867-019-0120-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 01/10/2019] [Indexed: 11/20/2022] Open
Abstract
Background Physical exercise can improve brain function by altering brain gene expression. The expression mechanisms underlying the brain’s response to exercise still remain unknown. miRNAs as vital regulators of gene expression may be involved in regulation of brain genes in response to exercise. However, as yet, very little is known about exercise-responsive miRNAs in brain. Results We constructed two comparative small RNA libraries of rat brain from a high-intensity intermittent swimming training (HIST) group and a normal control (NC) group. Using deep sequencing and bioinformatics analysis, we identified 2109 (1700 from HIST, 1691 from NC) known and 55 (50 from HIST, 28 from NC) novel candidate miRNAs. Among them, 34 miRNAs were identified as significantly differentially expressed in response to HIST, 16 were up-regulated and 18 were down-regulated. The results showed that all members of mir-200 family were strongly up-regulated, implying mir-200 family may play very important roles in HIST response mechanisms of rat brain. A total of 955 potential target genes of these 34 exercise-responsive miRNAs were identified from rat genes. Most of them are directly involved in the development and regulatory function of brain or nerve. Many acknowledged exercise-responsive brain genes such as Bdnf, Igf-1, Vgf, Ngf c-Fos, and Ntf3 etc. could be targeted by exercise-responsive miRNAs. Moreover, qRT-PCR and SABC immunohistochemical analysis further confirm the reliability of the expression of miRNAs and their targets. Conclusions This study demonstrated that physical exercise could induce differential expression of rat brain miRNAs and 34 exercise-responsive miRNAs were identified in rat brain. Our results suggested that exercise-responsive miRNAs could play important roles in regulating gene expression of rat brain in response to exercise. Electronic supplementary material The online version of this article (10.1186/s12867-019-0120-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yanhong Zhao
- College of Agriculture, Ludong University, Yantai, China.
| | - Anmin Zhang
- College of Sports, Yantai University, Yantai, China. .,Institute of Health Sciences, Shanxi University of Finance & Economics, Taiyuan, China.
| | - Yanfang Wang
- College of Life Sciences, Ludong University, Yantai, China
| | - Shuping Hu
- Institute of Health Sciences, Shanxi University of Finance & Economics, Taiyuan, China
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14
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Zhou T, Yuan Z, Tan S, Jin Y, Yang Y, Shi H, Wang W, Niu D, Gao L, Jiang W, Gao D, Liu Z. A Review of Molecular Responses of Catfish to Bacterial Diseases and Abiotic Stresses. Front Physiol 2018; 9:1113. [PMID: 30210354 PMCID: PMC6119772 DOI: 10.3389/fphys.2018.01113] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 07/25/2018] [Indexed: 12/11/2022] Open
Abstract
Catfish is one of the major aquaculture species in the United States. However, the catfish industry is threatened by several bacterial diseases such as enteric septicemia of catfish (ESC), columnaris disease and Aeromonas disease, as well as by abiotic stresses such as high temperature and low oxygen. Research has been conducted for several decades to understand the host responses to these diseases and abiotic stresses. With the development of sequencing technologies, and the application of genome-wide association studies in aquaculture species, significant progress has been made. This review article summarizes recent progress in understanding the molecular responses of catfish after bacterial infection and stress challenges, and in understanding of genomic and genetic basis for disease resistance and stress tolerance.
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Affiliation(s)
- Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Zihao Yuan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Suxu Tan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Yulin Jin
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Yujia Yang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Huitong Shi
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Wenwen Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Donghong Niu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Lei Gao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Wansheng Jiang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Dongya Gao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, United States
| | - Zhanjiang Liu
- Department of Biology, College of Art and Sciences, Syracuse University, Syracuse, NY, United States
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15
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Liu L, Zhu W, Liu J, Wang S, Jiang J. Identification and differential regulation of microRNAs during thyroid hormone-dependent metamorphosis in Microhyla fissipes. BMC Genomics 2018; 19:507. [PMID: 29954327 PMCID: PMC6025837 DOI: 10.1186/s12864-018-4848-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 05/31/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Anuran metamorphosis, which is obligatorily initiated and sustained by thyroid hormone (TH), is a dramatic example of extensive morphological, biochemical and cellular changes occurring during post-embryonic development. Thus, it provides an ideal model to understand the actions of the hormone and molecular mechanisms underlying these developmental and apoptotic processes. In addition to transcriptional factors, microRNAs (miRNAs) play key roles in diverse biological processes via post-transcriptional repression of mRNAs. However, the possible role of miRNAs in anuran metamorphosis is not well understood. Screening and identification of TH-responding miRNAs are required to reveal the integrated regulatory mechanisms of TH during metamorphosis. Given the specific role of TRs during M. fissipes metamorphosis and the characteristics of M. fissipes as an ideal model, Illumina sequencing technology was employed to get a full scope of miRNA in M. fissipes metamorphosis treated by T3. RESULTS Morphological and histological analysis revealed that 24 h T3 treatment M. fissipes tadpoles resembled that at the climax of natural metamorphosis. Thus, small RNA libraries were constructed from control and 24 h T3 treatment groups. A total of 164 conserved miRNAs and 36 predicted novel miRNAs were characterized. Furthermore, 5' first and ninth nucleotides of miRNAs were significantly enriched in U in our study. In all, 21 miRNAs were differentially expressed between the T3 and control groups (p < 0.01). A total of 10,206 unigenes were identified as target genes of these differentially expressed miRNAs. KEGG pathway analysis indicated that the most overrepresented miRNA target genes were enriched in the "PI3k-Akt signaling pathway". In addition, a network associated with the TH signaling pathway provides an opportunity to further understand the complex biological processes that occur in metamorphosis. CONCLUSIONS We identified a large number of miRNAs during M. fissipes metamorphosis, and 21 of them were differentially expressed in the two groups that represented two different metamorphic stages. These miRNAs may play important roles during metamorphosis. The study gives us clues for further studies of the mechanisms of anuran metamorphosis and provides a model to study the mechanism of TH-affected biological processes in humans.
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Affiliation(s)
- Lusha Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Wei Zhu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Jiongyu Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Shouhong Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
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16
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Lu J, Xu D, Shen Z, Lu L. Differential expression of miRNA in Carassius auratus gibelio in response to cyprinid herpesvirus 2 infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 82:1-6. [PMID: 29305165 DOI: 10.1016/j.dci.2017.12.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/28/2017] [Accepted: 12/29/2017] [Indexed: 06/07/2023]
Abstract
miRNAs (microRNAs), a small endogenous non-coding RNAs, play crucial roles in post-transcriptional regulator of genes expression in various biological processes. Cyprinid Herpesvirus-2 (CyHV-2) is a highly pathogenic member of the alloherpesviridae that causes acute mass mortalities in populations of Carassius auratus gibelio and Carassius auratus auratus. However, the molecular mechanisms underlying the pathogenicity of CyHV-2 have not been fully determined. Here, miRNA expression profiles were identified via high-throughput sequencing in the kidney of Carassius auratus gibelio infected or uninfected with CyHV-2. The results showed that a total number of 840 known miRNAs and 48 putative novel miRNAs were identified. Then we compared the expression patterns of miRNAs in the two groups, 23 miRNAs were significantly differentially expressed between the uninfected and infected groups. Further, the expressions of 23 miRNAs were validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR), the results showed that the expression patterns were basically the same with the sequencing. Prediction of targets of differentially expressed miRNAs revealed that the miRNAs participated in the regulation of multiple immune-related signaling pathways, including Chemokine signaling pathway, Apoptosis, Jak-STAT signaling pathway and MAPK signaling pathway. Taken together, these data provide insight into the regulatory mechanisms of miRNA and highlight the function of miRNA in the regulation of the immune response during the interaction between host and virus pathogens.
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Affiliation(s)
- Jianfei Lu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, PR China; Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, PR China
| | - Dan Xu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, PR China; Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, PR China; National Experimental Teaching Demonstration Center for Fishery Sciences, Shanghai Ocean University, Shanghai, PR China
| | - Zhaoyuan Shen
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, PR China; Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, PR China
| | - Liqun Lu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, PR China; Key Laboratory of Aquaculture Ministry for Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, PR China; National Experimental Teaching Demonstration Center for Fishery Sciences, Shanghai Ocean University, Shanghai, PR China.
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17
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He Y, Zhang Y, Li H, Zhang H, Li Z, Xiao L, Hu J, Ma Y, Zhang Q, Zhao X. Comparative Profiling of MicroRNAs Reveals the Underlying Toxicological Mechanism in Mice Testis Following Carbon Ion Radiation. Dose Response 2018; 16:1559325818778633. [PMID: 29977176 PMCID: PMC6024298 DOI: 10.1177/1559325818778633] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/13/2018] [Accepted: 02/13/2018] [Indexed: 01/07/2023] Open
Abstract
This study investigated the toxicity of heavy ion radiation to mice testis by microRNA (miRNA) sequencing and bioinformatics analyses. Testicular indices and histology were measured following enterocoelia irradiation with a 2 Gy carbon ion beam, with the testes exhibiting the most serious injuries at 4 weeks after carbon ion radiation (CIR) exposure. Illumina sequencing technology was used to sequence small RNA libraries of the control and irradiated groups at 4 weeks after CIR. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses implicated differential miRNAs in the regulation of target genes involved in metabolism, development, and reproduction. Here, 8 miRNAs, including miR-34c-5p, miR-138, and 6 let-7 miRNA family members previously reported in testis after radiation, were analyzed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) to validate miRNA sequencing data. The differentially expressed miRNAs described here provided a novel perspective for the role of miRNAs in testis toxicity following CIR.
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Affiliation(s)
- Yuxuan He
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Yong Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Hongyan Li
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Hong Zhang
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Zongshuai Li
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Longfei Xiao
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Junjie Hu
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Youji Ma
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Quanwei Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Xingxu Zhao
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
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Hu H, Shi Y, Zhang Y, Wu J, Asweto CO, Feng L, Yang X, Duan J, Sun Z. Comprehensive gene and microRNA expression profiling on cardiovascular system in zebrafish co-exposured of SiNPs and MeHg. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 607-608:795-805. [PMID: 28711009 DOI: 10.1016/j.scitotenv.2017.07.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/03/2017] [Accepted: 07/04/2017] [Indexed: 06/07/2023]
Abstract
Air pollution has been shown to increase cardiovascular diseases. However, little attention has been paid to the combined effects of PM and air pollutants on the cardiovascular system. To explore this, a high-throughput sequencing technology was used to determine combined effects of silica nanoparticles (SiNPs) and MeHg in zebrafish. Our study demonstrated that SiNPs and MeHg co-exposure could cause significant changes in mRNA and miRNA expression patterns in zebrafish. The differentially expressed (DE) genes in profiles 17 and 26 of STC analysis suggest that SiNPs and MeHg co-exposure had more proinflammatory and cardiovascular toxicity in zebrafish than single exposure. Major gene functions associated with cardiovascular system in the co-exposed zebrafish were discerned from the dynamic-gene-network, including stxbp1a, celf4, ahr1b and bai2. In addition, the prominently expressed pathway of cardiac muscle contraction was targeted by 3 DE miRNAs identified by the miRNA-pathway-network (dre-miR-7147, dre-miR-26a and dre-miR-375), which included 23 DE genes. This study presents a global view of the combined SiNPs and MeHg toxicity on the dynamic expression of both mRNAs and miRNAs in zebrafish, and could serve as fundamental research clues for future studies, especially on cardiovascular system toxicity.
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Affiliation(s)
- Hejing Hu
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Yanfeng Shi
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Yannan Zhang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Jing Wu
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Collins Otieno Asweto
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Lin Feng
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Xiaozhe Yang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Junchao Duan
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China.
| | - Zhiwei Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China.
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19
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Andreassen R, Høyheim B. miRNAs associated with immune response in teleost fish. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:77-85. [PMID: 28254620 DOI: 10.1016/j.dci.2017.02.023] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 02/25/2017] [Accepted: 02/26/2017] [Indexed: 06/06/2023]
Abstract
MicroRNAs (miRNAs) have been identified as important post transcriptional regulators of gene expression. In higher vertebrates, a subset of miRNAs has been identified as important regulators of a number of key genes in immune system gene networks, and this paper review recent studies on miRNAs associated with immune response in teleost fish. Challenge studies conducted in several species have identified differently expressed miRNAs associated with viral or bacterial infection. The results from these studies point out several miRNAs that are likely to have evolutionary conserved functions that are related to immune response in teleost fish. Changed expression levels of mature miRNAs from the five miRNA genes miRNA-462, miRNA-731, miRNA-146, miRNA-181 and miRNA-223 are observed following viral as well as bacterial infection in several teleost fish. Furthermore, significant changes in expression of mature miRNAs from the five genes miRNA-21, miRNA-155, miRNA-1388, miRNA-99 and miRNA-100 are observed in multiple studies of virus infected fish while changes in expression of mature miRNA from the three genes miRNA-122, miRNA-192 and miRNA-451 are observed in several studies of fish with bacterial infections. Interestingly, some of these genes are not present in higher vertebrates. The function of the evolutionary conserved miRNAs responding to infection depends on the target gene(s) they regulate. A few target genes have been identified while a large number of target genes have been predicted by in silico analysis. The results suggest that many of the targets are genes from the host's immune response gene networks. We propose a model with expected temporal changes in miRNA expression if they target immune response activators/effector genes or immune response inhibitors, respectively. The best way to understand the function of a miRNA is to identify its target gene(s), but as the amount of genome resources for teleost fish is limited, with less well characterized genomes and transcriptomes, identifying the true target genes of the miRNAs associated with the immune response is a challenge. Identifying such target genes by applying new methods and approaches will likely be the next important step to understand the function of the miRNAs associated with immune response in teleost fish.
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Affiliation(s)
- Rune Andreassen
- Department of Pharmacy and Biomedical and Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Pilestredet 50, N-0130 Oslo, Norway.
| | - Bjørn Høyheim
- Department of Basic Sciences and Aquatic Medicine, School of Veterinary Medicine, Norwegian University of Life Sciences, Ullevålsveien 72, 0454 Oslo, Norway.
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Tu J, Tian C, Zhao P, Sun J, Wang M, Fan Q, Yuan Y. Identification and profiling of growth-related microRNAs in Chinese perch (Siniperca chuatsi). BMC Genomics 2017; 18:489. [PMID: 28659132 PMCID: PMC5490230 DOI: 10.1186/s12864-017-3851-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 06/07/2017] [Indexed: 12/17/2022] Open
Abstract
Background MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play important roles in the regulation of diverse biological processes in eukaryotes. Chinese perch (Siniperca chuatsi) is one of the most economically important fish species widely cultured in China. Growth is an extremely important characteristic in fish. Individual differences in body size are common in Siniperca chuatsi, which significantly influence the aquaculture production of Siniperca chuatsi. However, the underline growth-related regulatory factors, such as miRNAs, are still unknown. Results To investigate the growth-related miRNAs in Siniperca chuatsi, two RNA libraries from four growth-related tissues (brain, pituitary, liver, and muscle) of Siniperca chuatsi at 6-month stage with relatively high or low growth rates (big-size group or small-size group) were obtained and sequenced using Solexa sequencing. A total of 252 known miRNAs and 12 novel miRNAs were identified. The expression patterns of these miRNAs in big-size group and small-size group were compared, and the results showed that 31 known and 5 novel miRNAs were differently expressed (DE). Furthermore, to verify the Solexa sequencing, five DE miRNAs were randomly selected and quantified by quantitative reverse transcription polymerase chain reaction (qRT-PCR). The results showed that their expression patterns were consistent with those of Solexa sequencing. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of target genes of DE miRNAs was performed. It showed that the target genes were involved in multiple biological processes including metabolic process, suggesting that metabolic process played an important role in growth of fish. Conclusions Siniperca chuatsi is a popular and economically important species in aquaculture. In this study, miRNAs in Siniperca chuatsi with different growth rates were identified, and their expression profiles were compared. The data provides the first large-scale miRNA profiles related to growth of Siniperca chuatsi, which is expected to contribute to a better understanding of the role of miRNAs in regulating the biological processes of growth and possibly useful for Siniperca chuatsi breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3851-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiagang Tu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Changxu Tian
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Peiqi Zhao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Junxiao Sun
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Min Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qixue Fan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yongchao Yuan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. .,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, Hubei, 430070, China.
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21
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Identification and comparative analysis of the pearl oyster Pinctada fucata hemocytes microRNAs in response to Vibrio alginolyticus infection. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0575-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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22
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Wu N, Zhu Q, Chen B, Gao J, Xu Z, Li D. High-throughput sequencing of pituitary and hypothalamic microRNA transcriptome associated with high rate of egg production. BMC Genomics 2017; 18:255. [PMID: 28335741 PMCID: PMC5364632 DOI: 10.1186/s12864-017-3644-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/18/2017] [Indexed: 01/21/2023] Open
Abstract
Background MicroRNAs exist widely in viruses, plants and animals. As endogenous small non-coding RNAs, miRNAs regulate a variety of biological processes. Tissue miRNA expression studies have discovered numerous functions for miRNAs in various tissues of chicken, but the regulation of miRNAs in chicken pituitary and hypothalamic development related to high and low egg-laying performance has remained unclear. Results In this study, using high-throughput sequencing technology, we sequenced two tissues (pituitary and hypothalamus) in 3 high- and 3 low-rate egg production Luhua chickens at the age of 300 days. By comparing low- and high-rate egg production chickens, 46 known miRNAs and 27 novel miRNAs were identified as differentially expressed (P < 0.05). Six differentially expressed known miRNAs, which are expressed in both tissues, were used in RT-qPCR validation and SNP detection. Among them, seven SNPs in two miRNA precursors (gga-miR-1684a and gga-miR-1434) were found that might enhance or reduce the production of the mature miRNAs. In addition, 124 and 30 reciprocally expressed miRNA-target pairs were identified by RNA-seq in pituitary and hypothalamic tissues, respectively and randomly selected candidate miRNA and miRNA-target pairs were validated by RT-qPCR in Jiuyuan black fowl. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation illustrated that a large number of egg laying-related pathways were enriched in the high-rate egg production chickens, including ovarian steroidogenesis and steroid hormone biosynthesis. Conclusions These differentially expressed miRNAs and their predicted target genes, especially identified reciprocally expressed miRNA-target pairs, advance the study of miRNA function and egg production associated miRNA identification. The analysis of the miRNA-related SNPs and their effects provided insights into the effects of SNPs on miRNA biogenesis and function. The data generated in this study will further our understanding of miRNA regulation mechanisms in the chicken egg-laying process. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3644-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nan Wu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000
| | - Qing Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000
| | - Binlong Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000
| | - Jian Gao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000
| | - Zhongxian Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, People's Republic of China, 610000.
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23
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Evolution of Fish Let-7 MicroRNAs and Their Expression Correlated to Growth Development in Blunt Snout Bream. Int J Mol Sci 2017; 18:ijms18030646. [PMID: 28300776 PMCID: PMC5372658 DOI: 10.3390/ijms18030646] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 03/12/2017] [Accepted: 03/13/2017] [Indexed: 12/12/2022] Open
Abstract
The lethal-7 (let-7) miRNA, known as one of the first founding miRNAs, is present in multiple copies in a genome and has diverse functions in animals. In this study, comparative genomic analysis of let-7 miRNAs members in fish species indicated that let-7 miRNA is a sequence conserved family in fish, while different species have the variable gene copy numbers. Among the ten members including let-7a/b/c/d/e/f/g/h/i/j, the let-7a precursor sequence was more similar to ancestral sequences, whereas other let-7 miRNA members were separate from the late differentiation of let-7a. The mostly predicted target genes of let-7 miRNAs are involved in biological process, especially developmental process and growth through Gene Ontology (GO) enrichment analysis. In order to identify the possible different functions of these ten miRNAs in fish growth development, their expression levels were quantified in adult males and females of Megalobrama amblycephala, as well as in 3-, 6-, and 12-months-old individuals with relatively slow- and fast-growth rates. These ten miRNAs had similar tissue expression patterns between males and females, with higher expression levels in the brain and pituitary than that in other tissues (p < 0.05). Among these miRNAs, the relative expression level of let-7a was the highest among almost all the tested tissues, followed by let-7b, let-7d and let-7c/e/f/g/h/i/j. As to the groups with different growth rates, the expression levels of let-7 miRNAs in pituitary and brain from the slow-growth group were always significantly higher than that in the fast-growth group (p < 0.05). These results suggest that let-7 miRNA members could play an important role in the regulation of growth development in M. amblycephala through negatively regulating expression of their target genes.
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Abdelrahman H, ElHady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao L, Beck B, Blackburn H, Bosworth B, Buchanan J, Chappell J, Daniels W, Dong S, Dunham R, Durland E, Elaswad A, Gomez-Chiarri M, Gosh K, Guo X, Hackett P, Hanson T, Hedgecock D, Howard T, Holland L, Jackson M, Jin Y, Khalil K, Kocher T, Leeds T, Li N, Lindsey L, Liu S, Liu Z, Martin K, Novriadi R, Odin R, Palti Y, Peatman E, Proestou D, Qin G, Reading B, Rexroad C, Roberts S, Salem M, Severin A, Shi H, Shoemaker C, Stiles S, Tan S, Tang KFJ, Thongda W, Tiersch T, Tomasso J, Prabowo WT, Vallejo R, van der Steen H, Vo K, Waldbieser G, Wang H, Wang X, Xiang J, Yang Y, Yant R, Yuan Z, Zeng Q, Zhou T. Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics 2017; 18:191. [PMID: 28219347 PMCID: PMC5319170 DOI: 10.1186/s12864-017-3557-1] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/06/2017] [Indexed: 12/31/2022] Open
Abstract
Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.
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Affiliation(s)
- Hisham Abdelrahman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Mohamed ElHady
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | | | - Standish Allen
- Aquaculture Genetics & Breeding Technology Center, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA
| | - Rafet Al-Tobasei
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Lisui Bao
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ben Beck
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Harvey Blackburn
- USDA-ARS-NL Wheat & Corn Collections at a Glance GRP, National Animal Germplasm Program, 1111 S. Mason St., Fort Collins, CO, 80521-4500, USA
| | - Brian Bosworth
- USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA
| | - John Buchanan
- Center for Aquaculture Technologies, 8395 Camino Santa Fe, Suite E, San Diego, CA, 92121, USA
| | - Jesse Chappell
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - William Daniels
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Sheng Dong
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Rex Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Evan Durland
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Ahmed Elaswad
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Marta Gomez-Chiarri
- Department of Fisheries, Animal & Veterinary Science, 134 Woodward Hall, 9 East Alumni Avenue, Kingston, RI, 02881, USA
| | - Kamal Gosh
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Perry Hackett
- Department of Genetics, Cell Biology and Development, 5-108 MCB, 420 Washington Avenue SE, Minneapolis, MN, 55455, USA
| | - Terry Hanson
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dennis Hedgecock
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Tiffany Howard
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Leigh Holland
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Molly Jackson
- Taylor Shellfish Farms, 130 SE Lynch RD, Shelton, WA, 98584, USA
| | - Yulin Jin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Karim Khalil
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Thomas Kocher
- Department of Biology, University of Maryland, 2132 Biosciences Research Building, College Park, MD, 20742, USA
| | - Tim Leeds
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Ning Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Lauren Lindsey
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Shikai Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zhanjiang Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
| | - Kyle Martin
- Troutlodge, 27090 Us Highway 12, Naches, WA, 98937, USA
| | - Romi Novriadi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ramjie Odin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Eric Peatman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dina Proestou
- USDA ARS NEA NCWMAC Shellfish Genetics at the University Rhode Island, 469 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Guyu Qin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Benjamin Reading
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695-7617, USA
| | - Caird Rexroad
- USDA ARS Office of National Programs, George Washington Carver Center Room 4-2106, 5601 Sunnyside Avenue, Beltsville, MD, 20705, USA
| | - Steven Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98105, USA
| | - Mohamed Salem
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Andrew Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, 50011, USA
| | - Huitong Shi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Craig Shoemaker
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Sheila Stiles
- USDOC/NOAA, National Marine Fisheries Service, NEFSC, Milford Laboratory, Milford, Connectcut, 06460, USA
| | - Suxu Tan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Kathy F J Tang
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Wilawan Thongda
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Terrence Tiersch
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA, 70820, USA
| | - Joseph Tomasso
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Wendy Tri Prabowo
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Roger Vallejo
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | | | - Khoi Vo
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Geoff Waldbieser
- USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA
| | - Hanping Wang
- Aquaculture Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, OH, 45661, USA
| | - Xiaozhu Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yujia Yang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Roger Yant
- Hybrid Catfish Company, 1233 Montgomery Drive, Inverness, MS, 38753, USA
| | - Zihao Yuan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qifan Zeng
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tao Zhou
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
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Agarwal S, Nagpure NS, Srivastava P, Kumar R, Pandey M, Srivastava S, Jena JK, Das P, Kushwaha B. In Silico Mining of Conserved miRNAs of Indian Catfish Clarias batrachus (Linnaeus, 1758) from the Contigs, ESTs, and BAC End Sequences. Appl Biochem Biotechnol 2016; 182:956-966. [DOI: 10.1007/s12010-016-2373-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 12/12/2016] [Indexed: 12/21/2022]
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Identification and Characterization of MicroRNAs in the Liver of Blunt Snout Bream (Megalobrama amblycephala) Infected by Aeromonas hydrophila. Int J Mol Sci 2016; 17:ijms17121972. [PMID: 27898025 PMCID: PMC5187772 DOI: 10.3390/ijms17121972] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 11/14/2016] [Accepted: 11/21/2016] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are small RNA molecules that play key roles in regulation of various biological processes. In order to better understand the biological significance of miRNAs in the context of Aeromonas hydrophila infection in Megalobrama amblycephala, small RNA libraries obtained from fish liver at 0 (non-infection), 4, and 24 h post infection (poi) were sequenced using Illumina deep sequencing technology. A total of 11,244,207, 9,212,958, and 7,939,157 clean reads were obtained from these three RNA libraries, respectively. Bioinformatics analysis identified 171 conserved miRNAs and 62 putative novel miRNAs. The existence of ten randomly selected novel miRNAs was validated by RT-PCR. Pairwise comparison suggested that 61 and 44 miRNAs were differentially expressed at 4 and 24 h poi, respectively. Furthermore, the expression profiles of nine randomly selected miRNAs were validated by qRT-PCR. MicroRNA target prediction, gene ontology (GO) annotation, and Kyoto Encylopedia of Genes and Genomes (KEGG) analysis indicated that a variety of biological pathways could be affected by A. hydrophila infection. Additionally, transferrin (TF) and transferrin receptor (TFR) genes were confirmed to be direct targets of miR-375. These results will expand our knowledge of the role of miRNAs in the immune response of M. amblycephala to A. hydrophila infection, and facilitate the development of effective strategies against A. hydrophila infection in M. amblycephala.
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Burgos-Aceves MA, Cohen A, Smith Y, Faggio C. Estrogen regulation of gene expression in the teleost fish immune system. FISH & SHELLFISH IMMUNOLOGY 2016; 58:42-49. [PMID: 27633675 DOI: 10.1016/j.fsi.2016.09.006] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 09/01/2016] [Accepted: 09/10/2016] [Indexed: 05/02/2023]
Abstract
Elucidating the mechanisms of estrogens-induced immunomodulation in teleost fish is of great importance due to the observed worldwide continuing decrease in pristine environments. However, little is know about the immunotoxicological consequences of exposure to these chemicals in fish, or of the mechanisms through which these effects are mediated. In this review, we summarize the results showing estrogens (natural or synthetic) acting through estrogen receptors and regulating specific target genes, also through microRNAs (miRNAs), leading to modulation of the immune functioning. The identification and characterization of miRNAs will provide new opportunities for functional genome research on teleost immune system and can also be useful when screening for novel molecule biomarkers for environmental pollution.
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Affiliation(s)
- Mario Alberto Burgos-Aceves
- Centro de Investigaciones Biológicas de Noroeste, S.C., Mar Bermejo 195, Col. Playa Palo de Sta. Rita, La Paz BCS, 23090, México
| | - Amit Cohen
- Genomic Data Analysis Unit, The Hebrew University of Jerusalem-Hadassah Medical School, P.O. Box 12272, Jerusalem 91120, Israel
| | - Yoav Smith
- Genomic Data Analysis Unit, The Hebrew University of Jerusalem-Hadassah Medical School, P.O. Box 12272, Jerusalem 91120, Israel
| | - Caterina Faggio
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres, 31, 98166 Messina, Italy.
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Wu N, Gaur U, Zhu Q, Chen B, Xu Z, Zhao X, Yang M, Li D. Expressed microRNA associated with high rate of egg production in chicken ovarian follicles. Anim Genet 2016; 48:205-216. [PMID: 27781291 DOI: 10.1111/age.12516] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2016] [Indexed: 01/28/2023]
Abstract
MicroRNA (miRNA) is a highly conserved class of small noncoding RNA about 19-24 nucleotides in length that function in a specific manner to post-transcriptionally regulate gene expression in organisms. Tissue miRNA expression studies have discovered a myriad of functions for miRNAs in various aspects, but a role for miRNAs in chicken ovarian tissue at 300 days of age has not hitherto been reported. In this study, we performed the first miRNA analysis of ovarian tissues in chickens with low and high rates of egg production using high-throughput sequencing. By comparing low rate of egg production chickens with high rate of egg production chickens, 17 significantly differentially expressed miRNAs were found (P < 0.05), including 11 known and six novel miRNAs. We found that all 11 known miRNAs were involved mainly in pathways of reproduction regulation, such as steroid hormone biosynthesis and dopaminergic synapse. Additionally, expression profiling of six randomly selected differentially regulated miRNAs were validated by quantitative real-time polymerase chain reaction (RT-qPCR). Some miRNAs, such as gga-miR-34b, gga-miR-34c and gga-miR-216b, were reported to regulate processes such as proliferation, cell cycle, apoptosis and metastasis and were expressed differentially in ovaries of chickens with high rates of egg production, suggesting that these miRNAs have an important role in ovary development and reproductive management of chicken. Furthermore, we uncovered that a significantly up-regulated miRNA-gga-miR-200a-3p-is ubiquitous in reproduction-regulation-related pathways. This miRNA may play a special central role in the reproductive management of chicken, and needs to be further studied for confirmation.
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Affiliation(s)
- N Wu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - U Gaur
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - Q Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - B Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - Z Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - X Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - M Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - D Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
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29
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Picone B, Rhode C, Roodt-Wilding R. Identification and characterization of miRNAs transcriptome in the South African abalone, Haliotis midae. Mar Genomics 2016; 31:9-12. [PMID: 27765454 DOI: 10.1016/j.margen.2016.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 09/30/2016] [Accepted: 10/13/2016] [Indexed: 12/13/2022]
Abstract
Aquatic animal diseases are one of the most important limitations to the growth of aquaculture. miRNAs represent an important class of small ncRNAs able to modulate host immune and stress responses. In Mollusca, a large phylum of invertebrates, miRNAs have been identified in several species. The current preliminary study identified known miRNAs from the South African abalone, Haliotis midae. The economic and ecological importance of abalone makes this species a suitable model for studying and understanding stress response in marine gastropods. Furthermore, the identification of miRNA, represents an alternative and powerful tool to combat infectious disease.
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Affiliation(s)
- Barbara Picone
- Department of Genetics, Stellenbosch University, van der Bijl Street, JC Smuts Building, Private Bag X1, Matieland 7602, South Africa.
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, van der Bijl Street, JC Smuts Building, Private Bag X1, Matieland 7602, South Africa.
| | - Rouvay Roodt-Wilding
- Department of Genetics, Stellenbosch University, van der Bijl Street, JC Smuts Building, Private Bag X1, Matieland 7602, South Africa.
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30
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Han J, Xu G, Xu T. The miiuy croaker microRNA transcriptome and microRNA regulation of RIG-I like receptor signaling pathway after poly(I:C) stimulation. FISH & SHELLFISH IMMUNOLOGY 2016; 54:419-426. [PMID: 27131903 DOI: 10.1016/j.fsi.2016.04.126] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/18/2016] [Accepted: 04/26/2016] [Indexed: 06/05/2023]
Abstract
MicroRNAs (miRNAs) as endogenous small non-coding RNAs play key regulatory roles in diverse biological processes via degrading the target mRNAs or inhibiting protein translation. Previously many researchers have reported the identification, characteristic of miRNAs and the interaction with its target gene. But, the study on the regulation of miRNAs to biological processes via regulatory the key signaling pathway was still limited. In order to comprehend the regulatory mechanism of miRNAs, two small RNA libraries from the spleen of miiuy croaker individuals with or without poly(I:C) infection were constructed. The 197 conserved miRNAs and 75 novel miRNAs were identified, and 14 conserved and 8 novel miRNAs appeared significant variations. Those differently expressed miRNAs relate to immune regulation of miiuy croaker. Furthermore, expressions of four differently expressed miRNAs were validated by qRT-PCR, and the result was consistent with sequencing data. The target genes of the differently expressed miRNAs in the two libraries were predicted, and some candidate target genes were involved in the RIG-I-like receptor (RLR) signaling pathway. The negative regulation of miRNAs to target genes were confirmed by comparing the expression pattern of miRNAs and their target genes. The results of regulating target genes were that firstly directly or indirectly activating the downstream signaling cascades and subsequent inducting the type I interferon, inflammatory cytokines and apoptosis. These studies could help us to deeper understand the roles of miRNAs played in the fish immune system, and provide a new way to investigate the defense mechanism of fish.
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Affiliation(s)
- Jingjing Han
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Guoliang Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China.
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31
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Wang B, Gan Z, Cai S, Wang Z, Yu D, Lin Z, Lu Y, Wu Z, Jian J. Comprehensive identification and profiling of Nile tilapia (Oreochromis niloticus) microRNAs response to Streptococcus agalactiae infection through high-throughput sequencing. FISH & SHELLFISH IMMUNOLOGY 2016; 54:93-106. [PMID: 27050313 DOI: 10.1016/j.fsi.2016.03.159] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 03/22/2016] [Accepted: 03/26/2016] [Indexed: 06/05/2023]
Abstract
MicroRNAs are a kind of small non-coding RNAs that participate in various biological processes. Deregulated microRNA expression is associated with several types of diseases. Tilapia (Oreochromis niloticus) is an important commercial fish species in China. To identify miRNAs and investigate immune-related miRNAs of O. niloticus, we applied high-throughput sequencing technology to identify and analyze miRNAs from tilapia infected with Streptococcus agalactiae at a timescale of 72 h divided into six different time points. The results showed that a total of 3009 tilapia miRNAs were identified, including in 1121 miRNAs which have homologues in the currently available databases and 1878 novel miRNAs. The expression levels of 218 tilapia miRNAs were significantly altered at 6 h-72 h post-bacterial infection (pi), and these miRNAs were therefore classified as differentially expressed tilapia miRNAs. For the 1121 differentially expressed tilapia miRNAs target 41961 genes. GO and KEGG enrichment analysis revealed that some target genes of tilapia miRNAs were grouped mainly into the categories of apoptotic process, signal pathway, and immune response. This is the first report of comprehensive identification of O. niloticus miRNAs being differentially regulated in spleen in normal conditions relating to S. agalactiae infection. This work provides an opportunity for further understanding of the molecular mechanisms of miRNA regulation in O. niloticus host-pathogen interactions.
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Affiliation(s)
- Bei Wang
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animala, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Insititutes, Zhanjiang, 524025, China
| | - Zhen Gan
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animala, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Insititutes, Zhanjiang, 524025, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Shuanghu Cai
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animala, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Insititutes, Zhanjiang, 524025, China
| | - Zhongliang Wang
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animala, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Insititutes, Zhanjiang, 524025, China
| | - Dapeng Yu
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animala, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Insititutes, Zhanjiang, 524025, China
| | - Ziwei Lin
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animala, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Insititutes, Zhanjiang, 524025, China
| | - Yishan Lu
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animala, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Insititutes, Zhanjiang, 524025, China
| | - Zaohe Wu
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animala, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Insititutes, Zhanjiang, 524025, China
| | - Jichang Jian
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animala, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Insititutes, Zhanjiang, 524025, China.
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32
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Integrated analysis of miRNA and mRNA expression profiles in tilapia gonads at an early stage of sex differentiation. BMC Genomics 2016; 17:328. [PMID: 27142172 PMCID: PMC4855716 DOI: 10.1186/s12864-016-2636-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/22/2016] [Indexed: 12/21/2022] Open
Abstract
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.
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33
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Andreassen R, Rangnes F, Sivertsen M, Chiang M, Tran M, Worren MM. Discovery of miRNAs and Their Corresponding miRNA Genes in Atlantic Cod (Gadus morhua): Use of Stable miRNAs as Reference Genes Reveals Subgroups of miRNAs That Are Highly Expressed in Particular Organs. PLoS One 2016; 11:e0153324. [PMID: 27128807 PMCID: PMC4851352 DOI: 10.1371/journal.pone.0153324] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 03/28/2016] [Indexed: 12/21/2022] Open
Abstract
Background Atlantic cod (Gadus morhua) is among the economically most important species in the northern Atlantic Ocean and a model species for studying development of the immune system in vertebrates. MicroRNAs (miRNAs) are an abundant class of small RNA molecules that regulate fundamental biological processes at the post-transcriptional level. Detailed knowledge about a species miRNA repertoire is necessary to study how the miRNA transcriptome modulate gene expression. We have therefore discovered and characterized mature miRNAs and their corresponding miRNA genes in Atlantic cod. We have also performed a validation study to identify suitable reference genes for RT-qPCR analysis of miRNA expression in Atlantic cod. Finally, we utilized the newly characterized miRNA repertoire and the dedicated RT-qPCR method to reveal miRNAs that are highly expressed in certain organs. Results The discovery analysis revealed 490 mature miRNAs (401 unique sequences) along with precursor sequences and genomic location of the miRNA genes. Twenty six of these were novel miRNA genes. Validation studies ranked gmo-miR-17-1—5p or the two-gene combination gmo-miR25-3p and gmo-miR210-5p as most suitable qPCR reference genes. Analysis by RT-qPCR revealed 45 miRNAs with significantly higher expression in tissues from one or a few organs. Comparisons to other vertebrates indicate that some of these miRNAs may regulate processes like growth, lipid metabolism, immune response to microbial infections and scar damage repair. Three teleost-specific and three novel Atlantic cod miRNAs were among the differentially expressed miRNAs. Conclusions The number of known mature miRNAs was considerably increased by our identification of miRNAs and miRNA genes in Atlantic cod. This will benefit further functional studies of miRNA expression using deep sequencing methods. The validation study showed that stable miRNAs are suitable reference genes for RT-qPCR analysis of miRNA expression. Applying RT-qPCR we have identified several miRNAs likely to have important regulatory functions in particular organs.
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Affiliation(s)
- Rune Andreassen
- Department of Pharmacy and Biomedical Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
- * E-mail:
| | - Fredrik Rangnes
- Department of Pharmacy and Biomedical Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
| | - Maria Sivertsen
- Department of Pharmacy and Biomedical Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
| | - Michelle Chiang
- Department of Pharmacy and Biomedical Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
| | - Michelle Tran
- Department of Pharmacy and Biomedical Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
| | - Merete Molton Worren
- Bioinformatics Core Facility, Institute for Medical Informatics, Oslo University Hospital, Oslo, Norway
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34
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Hong X, Qin J, Chen R, Yuan L, Zha J, Wang Z. Identification and characterization of novel and conserved microRNAs in several tissues of the Chinese rare minnow (Gobiocypris rarus) based on illumina deep sequencing technology. BMC Genomics 2016; 17:283. [PMID: 27066897 PMCID: PMC4828758 DOI: 10.1186/s12864-016-2606-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/28/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs), which comprise a large family of endogenous small non-coding RNA molecules, play important roles in the regulation of gene expression in various biological processes. The Chinese rare minnow (Gobiocypris rarus) is a Chinese native fish species and is used extensively as an experimental fish in China; however, relevant biological data, especially miRNA transcriptome data, have not been well documented. To discover conserved and potential novel miRNAs in Chinese rare minnows, a pool of equal amounts of RNA obtained from 6 different adult rare minnow tissues (brain, eye, gill, liver, muscle and heart) was sequenced using illumina deep sequencing technology. RESULTS In the present study, 26,930,553 raw reads, representing 2,118,439 unique high-quality reads, were obtained from the pooled small RNA library. Using bioinformatics analysis, 352 conserved and 112 novel Chinese rare minnow miRNAs were first discovered and characterized in this study. Moreover, we found extensive sequence variations (isomiRs) in rare minnow miRNAs, including internal miRNA isomiRs and terminal isomiRs at both the 5' and 3' ends and nucleotide variants. Six conserved and 4 novel miRNAs were selected and validated in 6 different adult rare minnow tissues using quantitative real-time PCR (qPCR). The results showed that miR-30a, miR-30b, and Novel-37 are ubiquitously expressed in a variety of tissues. miR-16a, miR-9, miR-125b, miR-34a, and Novel-69 were predominantly expressed in the brain. Novel-115 and Novel-7 were highly expressed in gills, but were relatively weakly expressed in other tissues. These results provided the expression patterns of miRNA genes in Chinese rare minnow. Finally, based on bioinformatics predictions, we mainly found that Novel-94 and Novel-1b-5p were simultaneously targeted to the 3'UTR of Dmrt1, which controls sex determination and/or sexual differentiation in a variety of metazoans at different sites. Novel-29b targeted the 3'UTR of Foxl2, which is involved in the maintenance of ovarian function and the transcriptional regulation of gonadal differentiation-related genes. Novel-62 and Novel-53 targeted the 3'UTR of ERbeta1 and ERbeta2 (which regulate the transcription of target genes), respectively. CONCLUSIONS Rare minnow is a widely used model for assessing the risk of environmental pollution in China. Identifying and characterizing rare minnow miRNA genes is necessary to discover the biological function of miRNAs and to screen for new molecule biomarkers to assess the risk of environmental pollution in the future.
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Affiliation(s)
- Xiangsheng Hong
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, People's Republic of China.,Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agriculture University, Wuhan, 430070, China
| | - Jianhui Qin
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agriculture University, Wuhan, 430070, China
| | - Rui Chen
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, People's Republic of China.,State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Lilai Yuan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, People's Republic of China.,State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Jinmiao Zha
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, People's Republic of China. .,Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Zijian Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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35
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Huang S, Cao X, Tian X, Wang W. High-Throughput Sequencing Identifies MicroRNAs from Posterior Intestine of Loach (Misgurnus anguillicaudatus) and Their Response to Intestinal Air-Breathing Inhibition. PLoS One 2016; 11:e0149123. [PMID: 26872032 PMCID: PMC4752256 DOI: 10.1371/journal.pone.0149123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/27/2016] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) exert important roles in animal growth, immunity, and development, and regulate gene expression at the post-transcriptional level. Knowledges about the diversities of miRNAs and their roles in accessory air-breathing organs (ABOs) of fish remain unknown. In this work, we used high-throughput sequencing to identify known and novel miRNAs from the posterior intestine, an important ABO, in loach (Misgurnus anguillicaudatus) under normal and intestinal air-breathing inhibited conditions. A total of 204 known and 84 novel miRNAs were identified, while 47 miRNAs were differentially expressed between the two small RNA libraries (i.e. between the normal and intestinal air-breathing inhibited group). Potential miRNA target genes were predicted by combining our transcriptome data of the posterior intestine of the loach under the same conditions, and then annotated using COG, GO, KEGG, Swissprot and Nr databases. The regulatory networks of miRNAs and their target genes were analyzed. The abundances of nine known miRNAs were validated by qRT-PCR. The relative expression profiles of six known miRNAs and their eight corresponding target genes, and two novel potential miRNAs were also detected. Histological characteristics of the posterior intestines in both normal and air-breathing inhibited group were further analyzed. This study contributes to our understanding on the functions and molecular regulatory mechanisms of miRNAs in accessory air-breathing organs of fish.
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Affiliation(s)
- Songqian Huang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 437000, Hubei, People’s Republic of China
| | - Xiaojuan Cao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 437000, Hubei, People’s Republic of China
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Hubei, People’s Republic of China
- * E-mail: (XC); (WW)
| | - Xianchang Tian
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 437000, Hubei, People’s Republic of China
| | - Weimin Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 437000, Hubei, People’s Republic of China
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Hubei, People’s Republic of China
- * E-mail: (XC); (WW)
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36
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Yuhong J, Leilei T, Fuyun Z, Hongyang J, Xiaowen L, Liying Y, Lei Z, Jingrong M, Jinpeng Y. Identification and characterization of immune-related microRNAs in blunt snout bream, Megalobrama amblycephala. FISH & SHELLFISH IMMUNOLOGY 2016; 49:470-492. [PMID: 26773859 DOI: 10.1016/j.fsi.2015.12.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 12/03/2015] [Accepted: 12/11/2015] [Indexed: 06/05/2023]
Abstract
MicroRNAs (miRNAs) play vital roles in diverse biological processes, including in immune response. Blunt snout bream (Megalobrama amblycephala) is a prevalent and important commercial endemic freshwater fish species in China's intensive polyculture systems. To identify immune-related miRNAs of M. amblycephala, two small RNA (sRNA) libraries from immune tissues with or without lipopolysaccharide (LPS) stimulation were constructed and sequenced using the high-throughput sequencing technology. Totally, 16,425,543 and 15,076,813 raw reads, corresponding to 14,156,755 and 13,445,869 clean reads, were obtained in the normal and infected libraries, respectively. A total of 324 miRNAs, including 218 known miRNAs and 106 putative novel miRNAs were identified by bioinformatic analysis. We analyzed differentially expressed miRNAs between two libraries using pairwise comparison. 113 (34.88%) miRNAs were found to be significantly differentially expressed between two libraries, with 63 (55.75%) exhibiting elevated expression in LPS stimulation sample. Thereinto, a number of known miRNAs were identified immune-related. Real-time quantitative PCR (RT-qPCR) were implemented for 12 miRNAs of two samples, and agreement was confirmed between the sequencing and RT-qPCR data. Target genes likely regulated by these differentially expressed miRNAs were predicted using computational prediction. The functional annotation of target genes by Gene Ontology enrichment (GO) and Kyoto Encyclopedia of Genes and Genomes pathway analysis (KEGG) indicated that a majority of differential miRNAs might involved in immune response. To our knowledge, this is the first comprehensive study of miRNAs in response to LPS stimulation in M. amblycephala, even in fish. These results deepened our understanding of the role of miRNAs in the intricate host's immune system, and should be useful to develop new control strategies for host immune defense against various bacterial invasions in M. amblycephala.
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Affiliation(s)
- Jiang Yuhong
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410017, China
| | - Tang Leilei
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410017, China
| | - Zhang Fuyun
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410017, China
| | - Jiang Hongyang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410017, China
| | - Liu Xiaowen
- Xiangya School of Medcine, Central South University, Changsha 410017, China
| | - Yang Liying
- Xiangya School of Medcine, Central South University, Changsha 410017, China
| | - Zhang Lei
- Xiangya School of Medcine, Central South University, Changsha 410017, China
| | - Mao Jingrong
- Xiangya School of Medcine, Central South University, Changsha 410017, China
| | - Yan Jinpeng
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410017, China.
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37
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Xu XY, Shen YB, Fu JJ, Yu HY, Huang WJ, Lu LQ, Li JL. MicroRNA-induced negative regulation of TLR-5 in grass carp, Ctenopharyngodon idella. Sci Rep 2016; 6:18595. [PMID: 26727169 PMCID: PMC4698583 DOI: 10.1038/srep18595] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/23/2015] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play crucial roles in numerous biological processes. However, the role of miRNAs in antibacterial defence in fish has not been fully determined. Here, we identified that nine miRNAs are differentially expressed in kidney between susceptible and resistant grass carp strains. Analysis of spatial and temporal miRNA expression patterns suggests that cid-miRn-115 and miR-142a-3p are potential regulators of anti-bacterial activity. Overexpressing of cid-miRn-115 and miR-142a-3p results in a visible change in Ctenopharyngodon idella kidney (CIK) cells immune effector activity. Bioinformatics analysis and overexpressing assay shows that cid-miRn-115 and miR-142a-3p directly regulate tlr5 expression. cid-miRn-115 and miR-142a-3p overexpressing leads to a significant decrease in tlr5 expression in CIK, thereby repressing its downstream genes, such as il-1β, il-8 and tnf-α. These findings provide a novel insight into the determination of anti-bacterial compounds in grass carp.
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Affiliation(s)
- Xiao-Yan Xu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China
| | - Yu-Bang Shen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China
| | - Jian-Jun Fu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China
| | - Hong-Yan Yu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China
| | - Wen-Ji Huang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China
| | - Li-Qun Lu
- National Pathogen Collection Center for Aquatic Animals, College of Fisheries and Life Science, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, PR China
| | - Jia-Le Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China.,E-Institute of Shanghai Universities, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, PR China
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Zhou Y, He Y, Wang C, Zhang X. Characterization of miRNAs from hydrothermal vent shrimp Rimicaris exoculata. Mar Genomics 2015; 24 Pt 3:371-8. [DOI: 10.1016/j.margen.2015.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 09/13/2015] [Accepted: 09/13/2015] [Indexed: 10/23/2022]
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39
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He L, Wang YL, Li Q, Yang HD, Duan ZL, Wang Q. Profiling microRNAs in the testis during sexual maturation stages in Eriocheir sinensis. Anim Reprod Sci 2015; 162:52-61. [DOI: 10.1016/j.anireprosci.2015.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/17/2015] [Accepted: 09/18/2015] [Indexed: 12/20/2022]
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40
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Schyth BD, Bela-ong DB, Jalali SAH, Kristensen LBJ, Einer-Jensen K, Pedersen FS, Lorenzen N. Two Virus-Induced MicroRNAs Known Only from Teleost Fishes Are Orthologues of MicroRNAs Involved in Cell Cycle Control in Humans. PLoS One 2015; 10:e0132434. [PMID: 26207374 PMCID: PMC4514678 DOI: 10.1371/journal.pone.0132434] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 06/16/2015] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are ~22 base pair-long non-coding RNAs which regulate gene expression in the cytoplasm of eukaryotic cells by binding to specific target regions in mRNAs to mediate transcriptional blocking or mRNA cleavage. Through their fundamental roles in cellular pathways, gene regulation mediated by miRNAs has been shown to be involved in almost all biological phenomena, including development, metabolism, cell cycle, tumor formation, and host-pathogen interactions. To address the latter in a primitive vertebrate host, we here used an array platform to analyze the miRNA response in rainbow trout (Oncorhynchus mykiss) following inoculation with the virulent fish rhabdovirus Viral hemorrhagic septicaemia virus. Two clustered miRNAs, miR-462 and miR-731 (herein referred to as miR-462 cluster), described only in teleost fishes, were found to be strongly upregulated, indicating their involvement in fish-virus interactions. We searched for homologues of the two teleost miRNAs in other vertebrate species and investigated whether findings related to ours have been reported for these homologues. Gene synteny analysis along with gene sequence conservation suggested that the teleost fish miR-462 and miR-731 had evolved from the ancestral miR-191 and miR-425 (herein called miR-191 cluster), respectively. Whereas the miR-462 cluster locus is found between two protein-coding genes (intergenic) in teleost fish genomes, the miR-191 cluster locus is found within an intron of a protein-coding gene (intragenic) in the human genome. Interferon (IFN)-inducible and immune-related promoter elements found upstream of the teleost miR-462 cluster locus suggested roles in immune responses to viral pathogens in fish, while in humans, the miR-191 cluster functionally associated with cell cycle regulation. Stimulation of fish cell cultures with the IFN inducer poly I:C accordingly upregulated the expression of miR-462 and miR-731, while no stimulatory effect on miR-191 and miR-425 expression was observed in human cell lines. Despite high sequence conservation, evolution has thus resulted in different regulation and presumably also different functional roles of these orthologous miRNA clusters in different vertebrate lineages.
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Affiliation(s)
- Brian Dall Schyth
- National Veterinary Institute, Technical University of Denmark, Frederiksberg C, Denmark
| | - Dennis Berbulla Bela-ong
- National Veterinary Institute, Technical University of Denmark, Frederiksberg C, Denmark
- Fish Health Section, Department of Animal Science, Aarhus University, Aarhus N, Denmark
| | | | - Lasse Bøgelund Juel Kristensen
- National Veterinary Institute, Technical University of Denmark, Frederiksberg C, Denmark
- Department of Molecular Biology and Genetics, University of Aarhus, Aarhus C, Denmark
| | | | - Finn Skou Pedersen
- Department of Molecular Biology and Genetics, University of Aarhus, Aarhus C, Denmark
| | - Niels Lorenzen
- Fish Health Section, Department of Animal Science, Aarhus University, Aarhus N, Denmark
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Torrado M, Franco D, Lozano-Velasco E, Hernández-Torres F, Calviño R, Aldama G, Centeno A, Castro-Beiras A, Mikhailov A. A MicroRNA-Transcription Factor Blueprint for Early Atrial Arrhythmogenic Remodeling. BIOMED RESEARCH INTERNATIONAL 2015; 2015:263151. [PMID: 26221584 PMCID: PMC4499376 DOI: 10.1155/2015/263151] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 12/27/2022]
Abstract
Spontaneous self-terminating atrial fibrillation (AF) is one of the most common heart rhythm disorders, yet the regulatory molecular mechanisms underlying this syndrome are rather unclear. MicroRNA (miRNA) transcriptome and expression of candidate transcription factors (TFs) with potential roles in arrhythmogenesis, such as Pitx2, Tbx5, and myocardin (Myocd), were analyzed by microarray, qRT-PCR, and Western blotting in left atrial (LA) samples from pigs with transitory AF established by right atrial tachypacing. Induced ectopic tachyarrhythmia caused rapid and substantial miRNA remodeling associated with a marked downregulation of Pitx2, Tbx5, and Myocd expression in atrial myocardium. The downregulation of Pitx2, Tbx5, and Myocd was inversely correlated with upregulation of the corresponding targeting miRNAs (miR-21, miR-10a/10b, and miR-1, resp.) in the LA of paced animals. Through in vitro transient transfections of HL-1 atrial myocytes, we further showed that upregulation of miR-21 did result in downregulation of Pitx2 in cardiomyocyte background. The results suggest that immediate-early miRNA remodeling coupled with deregulation of TF expression underlies the onset of AF.
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Affiliation(s)
- Mario Torrado
- Institute of Health Sciences, University of La Coruña, 15006 La Coruña, Spain
| | - Diego Franco
- Department of Experimental Biology, University of Jaén, Jaén, Spain
| | | | | | - Ramón Calviño
- University Hospital Center of La Coruña, La Coruña, Spain
| | | | | | | | - Alexander Mikhailov
- Institute of Health Sciences, University of La Coruña, 15006 La Coruña, Spain
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Wan SM, Yi SK, Zhong J, Nie CH, Guan NN, Chen BX, Gao ZX. Identification of MicroRNA for Intermuscular Bone Development in Blunt Snout Bream (Megalobrama amblycephala). Int J Mol Sci 2015; 16:10686-703. [PMID: 25970753 PMCID: PMC4463670 DOI: 10.3390/ijms160510686] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/17/2015] [Accepted: 05/05/2015] [Indexed: 01/08/2023] Open
Abstract
Intermuscular bone (IB), which occurs only in the myosepta of the lower teleosts, is attracting more attention of researchers due to its particular development and lack of genetic information. MicroRNAs (miRNAs) are emerging as important regulators for biological processes. In the present study, miRNAs from IBs and connective tissue (CT; encircled IBs) from six-month-old Megalobrama amblycephala were characterized and compared. The results revealed the sequences and expression levels of 218 known miRNA genes (belonging to 97 families). Of these miRNAs, 44 known microRNA sequences exhibited significant expression differences between the two libraries, with 24 and 20 differentially-expressed miRNAs exhibiting higher expression in the CT and IBs libraries, respectively. The expressions of 11 miRNAs were selected to validate in nine tissues. Among the high-ranked predicted gene targets, differentiation, cell cycle, metabolism, signal transduction and transcriptional regulation were implicated. The pathway analysis of differentially-expressed miRNAs indicated that they were abundantly involved in regulating the development and differentiation of IBs and CT. This study characterized the miRNA for IBs of teleosts for the first time, which provides an opportunity for further understanding of miRNA function in the regulation of IB development.
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Affiliation(s)
- Shi-Ming Wan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
| | - Shao-Kui Yi
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
| | - Jia Zhong
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
| | - Chun-Hong Nie
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ning-Nan Guan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Bo-Xiang Chen
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
- Animal Husbandry and Fisheries Research Center of Haid Group Co., Ltd., Guangzhou 511400, China.
| | - Ze-Xia Gao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
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Genome-wide identification and characterization of teleost-specific microRNAs within zebrafish. Gene 2015; 561:181-9. [DOI: 10.1016/j.gene.2015.02.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 01/29/2015] [Accepted: 02/02/2015] [Indexed: 02/01/2023]
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Wu S, Liu L, Zohaib A, Lin L, Yuan J, Wang M, Liu X. MicroRNA profile analysis of Epithelioma papulosum cyprini cell line before and after SVCV infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 48:124-128. [PMID: 25291211 DOI: 10.1016/j.dci.2014.09.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 06/03/2023]
Abstract
MicroRNAs (miRNAs) play significant roles in regulating almost all of the biological processes in eukaryotes. An accumulating body of evidence shows that miRNAs are associated with cellular changes following viral infection. Spring viremia of carp virus (SVCV) is the pathogen of Spring viremia of carp (SVC), which results in heavy losses in the cultured common carp (Cyprinus carpio) industry in many countries. To study the involvement of miRNAs during SVCV infection, we adopted the Solexa sequencing technology to sequence small RNA libraries from the Epithelioma papulosum cyprini (EPC) cell line before and after infection with SVCV. In this study, a total of 161 conserved and 26 novel miRNAs were identified. Subsequently, the expression patterns of these miRNAs were compared between the uninfected (control library, M) and SVCV-infected (infection library, E) libraries. In addition, to verify the Solexa sequencing results, the expression patterns of 14 randomly selected miRNAs were validated by qRT-PCR. The targets of the significantly differentially expressed miRNAs were then predicted, and the miRNAs that could directly target the SVCV genome were also predicted. No miRNA encoded by SVCV itself was detected. To the best of our knowledge, this study presents the first miRNA profiling assessment in association with fish rhabdovirus infection, and the data presented lay a foundation for further investigations to determine the roles of miRNAs in regulating the molecular mechanism during SVCV infection.
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Affiliation(s)
- Shusheng Wu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China
| | - Liyue Liu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China
| | - Ali Zohaib
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei, Wuhan 430070, China
| | - Li Lin
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China
| | - Junfa Yuan
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China
| | - Min Wang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xueqin Liu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan 430070, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
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45
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Johansen I, Andreassen R. Validation of miRNA genes suitable as reference genes in qPCR analyses of miRNA gene expression in Atlantic salmon (Salmo salar). BMC Res Notes 2014; 8:945. [PMID: 25533334 PMCID: PMC4308020 DOI: 10.1186/1756-0500-7-945] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 12/21/2022] Open
Abstract
Background MicroRNAs (miRNAs) are an abundant class of endogenous small RNA molecules that downregulate gene expression at the post-transcriptional level. They play important roles by regulating genes that control multiple biological processes, and recent years there has been an increased interest in studying miRNA genes and miRNA gene expression. The most common method applied to study gene expression of single genes is quantitative PCR (qPCR). However, before expression of mature miRNAs can be studied robust qPCR methods (miRNA-qPCR) must be developed. This includes identification and validation of suitable reference genes. We are particularly interested in Atlantic salmon (Salmo salar). This is an economically important aquaculture species, but no reference genes dedicated for use in miRNA-qPCR methods has been validated for this species. Our aim was, therefore, to identify suitable reference genes for miRNA-qPCR methods in Salmo salar. Results We used a systematic approach where we utilized similar studies in other species, some biological criteria, results from deep sequencing of small RNAs and, finally, experimental validation of candidate reference genes by qPCR to identify the most suitable reference genes. Ssa-miR-25-3p was identified as most suitable single reference gene. The best combinations of two reference genes were ssa-miR-25-3p and ssa-miR-455-5p. These two genes were constitutively and stably expressed across many different tissues. Furthermore, infectious salmon anaemia did not seem to affect their expression levels. These genes were amplified with high specificity, good efficiency and the qPCR assays showed a good linearity when applying a simple cybergreen miRNA-PCR method using miRNA gene specific forward primers. Conclusions We have identified suitable reference genes for miRNA-qPCR in Atlantic salmon. These results will greatly facilitate further studies on miRNA genes in this species. The reference genes identified are conserved genes that are identical in their mature sequence in many aquaculture species. Therefore, they may also be suitable as reference genes in other teleosts. Finally, the systematic approach used in our study successfully identified suitable reference genes, suggesting that this may be a useful strategy to apply in similar validation studies in other aquaculture species. Electronic supplementary material The online version of this article (doi:10.1186/1756-0500-7-945) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Rune Andreassen
- Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway.
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46
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Jing J, Wu J, Liu W, Xiong S, Ma W, Zhang J, Wang W, Gui JF, Mei J. Sex-biased miRNAs in gonad and their potential roles for testis development in yellow catfish. PLoS One 2014; 9:e107946. [PMID: 25229553 PMCID: PMC4168133 DOI: 10.1371/journal.pone.0107946] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/17/2014] [Indexed: 12/21/2022] Open
Abstract
Recently, YY super-male yellow catfish had been created by hormonal-induced sex reversal and sex-linked markers, which provides a promising research model for fish sex differentiation and gonad development, especially for testis development. MicroRNAs (miRNAs) have been revealed to play crucial roles in the gene regulation and gonad development in vertebrates. In this study, three small RNA libraries constructed from gonad tissues of XX female, XY male and YY super-male yellow catfish were sequenced. The sequencing data generated a total of 384 conserved miRNAs and 113 potential novel miRNAs, among which 23, 30 and 14 miRNAs were specifically detected in XX ovary, XY testis, and YY testis, respectively. We observed relative lower expression of several miR-200 family members, including miR-141 and miR-429 in YY testis compared with XY testis. Histological analysis indicated a higher degree of testis maturity in YY super-males compared with XY males, as shown by larger spermatogenic cyst, more spermatids and fewer spermatocytes in the spermatogenic cyst. Moreover, five miR-200 family members were significantly up-regulated in testis when treated by 17α-ethinylestradiol (EE2), high dose of which will impair testis development and cell proliferation. The down-regulation of miR-141 and 429 coincides with the progression of testis development in both yellow catfish and human. At last, the expression pattern of nine arbitrarily selected miRNAs detected by quantitative RT-PCR was consistent with the Solexa sequencing results. Our study provides a comprehensive miRNA transcriptome analysis for gonad of yellow catfish with different sex genotypes, and identifies a number of sex-biased miRNAs, some of that are potentially involved in testis development and spermatogenesis.
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Affiliation(s)
- Jing Jing
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Junjie Wu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Wei Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, China
| | - Shuting Xiong
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Wenge Ma
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jin Zhang
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Weimin Wang
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jian-Fang Gui
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, China
- * E-mail: (JFG); (JM)
| | - Jie Mei
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
- * E-mail: (JFG); (JM)
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Desvignes T, Beam MJ, Batzel P, Sydes J, Postlethwait JH. Expanding the annotation of zebrafish microRNAs based on small RNA sequencing. Gene 2014; 546:386-9. [PMID: 24835514 PMCID: PMC4130647 DOI: 10.1016/j.gene.2014.05.036] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/29/2014] [Accepted: 05/14/2014] [Indexed: 12/28/2022]
Abstract
MicroRNAs (miRs) are short non-coding RNAs that fine-tune the regulation of gene expression to coordinate a wide range of biological processes. Because of their role in the regulation of gene expression, miRs are essential players in development by acting on cell fate determination and progression towards cell differentiation and are increasingly relevant to human health and disease. Although the zebrafish Danio rerio is a major model for studies of development, genetics, physiology, evolution, and human biology, the annotation of zebrafish miR-producing genes remains limited. In the present work, we report deep sequencing data of zebrafish small RNAs from brain, heart, testis, and ovary. Results provide evidence for the expression of 56 un-annotated mir genes and 248 un-annotated mature strands, increasing the number of zebrafish mir genes over those already deposited in miRBase by 16% and the number of mature sequences by 63%. We also describe the existence of three pairs of mirror-mir genes and two mirtron genes, genetic features previously undescribed in non-mammalian vertebrates. This report provides information that substantially increases our knowledge of the zebrafish miRNome and will benefit the entire miR community.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
| | - Michael J Beam
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
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Qi P, Guo B, Zhu A, Wu C, Liu C. Identification and comparative analysis of the Pseudosciaena crocea microRNA transcriptome response to poly(I:C) infection using a deep sequencing approach. FISH & SHELLFISH IMMUNOLOGY 2014; 39:483-491. [PMID: 24945573 DOI: 10.1016/j.fsi.2014.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 06/06/2014] [Accepted: 06/09/2014] [Indexed: 06/03/2023]
Abstract
Two sRNA libraries with or without poly(I:C) infection of large yellow croaker Pseudosciaena crocea were constructed and sequenced using the high-throughput Illumina/Solexa deep sequencing technology. The high-throughput sequencing pipeline yielded 163,79,272 and 217,07,070 raw reads corresponding to 132,27,594 and 206,86,409 clean reads for the normal and infected libraries, respectively. Bioinfromatic analysis identified 534 miRNAs, of which, 158 miRNAs were known in miRBase 20.0 and the remaining 376 were not found homology to any known metazoan miRNAs, suggesting a possible species-specificity. We analyzed the significance of differently expressed miRNAs between two libraries using pairwise comparison. There was significant differential expression of 112 miRNAs (p < 0.001) between two libraries. Thereinto, a number of known miRNAs were identified immune-related. Real-time quantitative PCR experiments (RT-qPCR) were preformed for 6 miRNAs of the two samples, and agreement was found between the sequencing and RT-qPCR data. To our knowledge, this is the first comprehensive study of miRNAs in P. crocea and of expression analysis of P. crocea miRNAs in response to poly(I:C) infection, and many miRNAs were differentially regulated under normal and infection conditions. These findings deepened our understanding of the role of miRNAs in the intricate host's immune system, and should be useful to develop new control strategies for host immune defense against various foreign infection in P. crocea.
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Affiliation(s)
- Pengzhi Qi
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316004, China
| | - Baoying Guo
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316004, China
| | - Aiyi Zhu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316004, China
| | - Changwen Wu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316004, China.
| | - Changlin Liu
- Yellow Sea Fisheries Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
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Abstract
MicroRNAs (miRNAs) are transcriptional and posttranscriptional regulators involved in nearly all known biological processes in distant eukaryotic clades. Their discovery and functional characterization have broadened our understanding of biological regulatory mechanisms in animals and plants. They show both evolutionary conserved and unique features across Metazoa. Here, we present the current status of the knowledge about the role of miRNA in development, growth, and physiology of teleost fishes, in comparison to other vertebrates. Infraclass Teleostei is the most abundant group among vertebrate lineage. Fish are an important component of aquatic ecosystems and human life, being the prolific source of animal proteins worldwide and a vertebrate model for biomedical research. We review miRNA biogenesis, regulation, modifications, and mechanisms of action. Specific sections are devoted to the role of miRNA in teleost development, organogenesis, tissue differentiation, growth, regeneration, reproduction, endocrine system, and responses to environmental stimuli. Each section discusses gaps in the current knowledge and pinpoints the future directions of research on miRNA in teleosts.
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Affiliation(s)
| | - Igor Babiak
- Faculty of Aquaculture and Biosciences, University of Nordland, Bodø, Norway
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50
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Yi S, Lu D, Peng W, Wang T, Zhang Y, Lin H. Differential expression profiling of spleen microRNAs in response to two distinct type II interferons in Tetraodon nigroviridis. PLoS One 2014; 9:e96336. [PMID: 24800866 PMCID: PMC4011704 DOI: 10.1371/journal.pone.0096336] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 04/04/2014] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs are endogenous, small non-coding RNAs approximately 18-26 nucleotides in length that regulate target gene expression at the post-transcription level. Interferon-γ (IFN-γ) is a Th1 cytokine that is involved in both the innate and adaptive immune responses. We previously identified two IFN-γ genes in green-spotted puffer fish (Tetraodon nigroviridis). To determine whether miRNAs participate in IFN-γ-related immune responses, T. nigroviridis spleen cells were treated with recombinant IFN-γ isoforms, and a Solexa high-throughput sequencing method was used to identify miRNAs. In total, 1,556, 1,538 and 1,573 miRNAs were found in the three samples, and differentially expressed miRNAs were determined. In total, 398 miRNAs were differentially expressed after rIFN-γ1 treatment, and 438 miRNAs were differentially expressed after rIFN-γ2 treatment; additionally, 403 miRNAs were differentially expressed between the treatment groups. Ten differentially expressed miRNAs were chosen for validation using qRT-PCR. Target genes for the differentially expressed miRNAs were predicted, and GO and KEGG analyses were performed. This study provides basic knowledge regarding fish IFN-γ-induced miRNAs and offers clues for further studies into the mechanisms underlying fish IFN-γ-mediated immune responses.
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Affiliation(s)
- Shibai Yi
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
| | - Danqi Lu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
- * E-mail: (DL); (HL)
| | - Wan Peng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
| | - Ting Wang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
- * E-mail: (DL); (HL)
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