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Li Y, Wu S, Huang J, Zhao L. Integration of physiological, miRNA-mRNA interaction and functional analysis reveals the molecular mechanism underlying hypoxia stress tolerance in crucian carp (Carassius auratus). FASEB J 2024; 38:e23722. [PMID: 38934365 DOI: 10.1096/fj.202302629rr] [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: 12/19/2023] [Revised: 04/23/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024]
Abstract
Hypoxia has become one of the most critical factors limiting the development of aquaculture. Crucian carp (Carassius auratus) is widely consumed fish in China, with excellent tolerance to hypoxic environment. However, the molecular mechanisms underlying hypoxia adaptation and tolerance in crucian carp remain unclear. Compared with the control, increased T-SOD, CAT, GSH-Px, T-AOC, ALT, and AST activities and MDA, TCHO, and TG contents, and decreased TP and ATP contents were observed after hypoxia stress. Based on RNA-seq, 2479 differentially expressed (DE) mRNAs and 60 DE miRNAs were identified, and numerous DE mRNAs involved in HIF signaling pathway (hif-1α, epo, vegfa, and ho), anaerobic metabolism (hk1/hk2, pfk, gapdh, pk, and ldh) and immune response (nlrp12, cxcr1, cxcr4, ccr9, and cxcl12) were significantly upregulated after hypoxia exposure. Integrated analysis found that ho, igfbp1, hsp70, and hk2 were predicted to be regulated by novel_867, dre-miR-125c-3p/novel_173, dre-miR-181b-5p, and dre-miR-338-5p/dre-miR-17a-3p, respectively, and targets of DE miRNAs were significantly enriched in MAPK signaling pathway, FoxO signaling pathway, and glycolysis/gluconeogenesis. Expression analysis showed that the mRNA levels of vegfa, epo, ho, hsp70, hsp90aa.1, igfbp1, ldh, hk1, pfk, pk, and gapdh exhibited a remarkable increase, whereas sdh and mdh were downregulated in the H3h, H12h, and H24h groups compared with the control. Furthermore, research found that hk2 is a target of dre-miR-17a-3p, overexpression of dre-miR-17a-3p significantly decreased the expression level of hk2, while the opposite results were obtained after dre-miR-17a-3p silencing. These results contribute to our understanding of the molecular mechanisms of hypoxia tolerance in crucian carp.
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Affiliation(s)
- Yongjuan Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- College of Science, Gansu Agricultural University, Lanzhou, China
| | - Shenji Wu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jinqiang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Lu Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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2
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Wu S, Huang J, Li Y. A novel hypoxic lncRNA, LOC110520012 sponges miR-206-y to regulate angiogenesis and liver cell proliferation in rainbow trout (Oncorhynchus mykiss) by targeting vegfaa. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116554. [PMID: 38878335 DOI: 10.1016/j.ecoenv.2024.116554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/28/2024] [Accepted: 06/04/2024] [Indexed: 06/25/2024]
Abstract
Long non-coding RNA (lncRNA) is a novel emerging type of competitive endogenous RNA (ceRNA) that performs key functions in multiple biological processes. However, little is known about the roles of lncRNA under hypoxia stress in fish. Here, vascular endothelial growth factor-Aa (vegfaa) was cloned in rainbow trout (Oncorhynchus mykiss), with the complete cDNA sequence of 2914 bp, encoding 218 amino acids. The molecular weight of the protein was approximately 25.33 kDa, and contained PDGF and VEGF_C domains. Time-course and spatial expression patterns revealed that LOC110520012 was a key regulator of rainbow trout in response to hypoxia stress, and LOC110520012, miR-206-y and vegfaa exhibited a ceRNA regulatory relationship in liver, gill, muscle and rainbow trout liver cells treated with acute hypoxia. Subsequently, the targeting relationship of LOC110520012 and vegfaa with miR-206-y was confirmed by dual-luciferase reporter analysis, and overexpression of LOC110520012 mediated the inhibition of miR-206-y expression in rainbow trout liver cells, while the opposite results were obtained after LOC110520012 silencing with siRNA. We also proved that vegfaa was a target of miR-206-y in vitro and in vivo, and the vegfaa expression and anti-proliferative effect on rainbow trout liver cells regulated by miR-206-y mimics could be reversed by LOC110520012. These results suggested that LOC110520012 can positively regulate vegfaa expression by sponging miR-206-y under hypoxia stress in rainbow trout, which facilitate in-depth understanding of the molecular mechanisms of fish adaptation and tolerance to hypoxia.
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Affiliation(s)
- Shenji Wu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jinqiang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Yongjuan Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; College of Science, Gansu Agricultural University, Lanzhou 730070, China
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3
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Wang X, Chen X, Sun X, Ao J. Comparative analysis of miRNAs and mRNAs in large yellow croaker head kidney cells (LYCK) provided novel insights into the redox regulation of fish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170503. [PMID: 38301776 DOI: 10.1016/j.scitotenv.2024.170503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/21/2023] [Accepted: 01/25/2024] [Indexed: 02/03/2024]
Abstract
Reactive oxygen species (ROS) over-production and oxidative stress resulted from climate change and environmental pollution seriously endangered global fish populations and healthy development of marine aquaculture. Peroxiredoxins (Prxs), a highly conserved family of thiol-specific antioxidants, can mitigate ROS and protect cells from oxidative stress. We previously demonstrated that large yellow croaker PrxIV (LcPrxIV) could not only regulate the pro-inflammatory responses, but also scavenge ROS. However, the underlying mechanism how LcPrxIV regulated immune response and redox homeostasis remains unknown. MicroRNAs (miRNAs) are non-coding RNAs that play important roles in the regulation of various biological processes. In this study, mRNA and miRNA expression profiles from LYCK-pcDNA3.1 and LYCK-PrxIV cells, with or without oxidative stress stimulated by H2O2 were evaluated using high-throughput sequencing. A series of differentially expressed miRNAs (DEMs) and differentially expressed genes (DEGs), as well as DEM-DEG pairs were identified from each two-group comparison, respectively. GO and KEGG functional analyses indicated that most significant DEGs were associated with signaling pathways related to oxidative stress and immune response. Subsequent DEM-DEG interaction analysis revealed that miR-731 and miR-1388 may be involved in both redox regulation and immune response via synergistic effect with LcPrxIV. Interestingly, miR-731 could regulate the expression of different down-stream DEGs under different stimulations of LcPrxIV over-expression, H2O2, or both. Moreover, miR-731 could cause the DEG, γ-glutamyl hydrolase (GGH), to be expressed in opposite ways under different stimulations. On the other hand, the expression of miR-1388 could be negatively or positively regulated under the stimulation of LcPrxIV over-expression with or without oxidative stress, thus regulating gene expression of different mRNAs. Based on these results, we speculate that LcPrxIV may participate in immune response or redox regulation by regulating the expression of different down-stream genes through controlling the expression level of a certain miRNA or by regulating the varieties of expressed miRNAs.
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Affiliation(s)
- Xianhui Wang
- Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, China
| | - Xinhua Chen
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoming Sun
- Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, China; School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China.
| | - Jingqun Ao
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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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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Shi L, Zhang A, Liu H, Wang H. Deletion of the foxO4 Gene Increases Hypoxia Tolerance in Zebrafish. Int J Mol Sci 2023; 24:ijms24108942. [PMID: 37240290 DOI: 10.3390/ijms24108942] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Oxygen homeostasis is an important organizing principle for understanding development, physiology, disease, and evolution. Under various physiological and pathological states, organisms experience oxygen deficiency or hypoxia. FoxO4 has been recognized as an important transcriptional regulator involved in a variety of cellular functions, including proliferation, apoptosis, differentiation, and stress resistance, but its role in hypoxia adaptation mechanisms in animals is not so clear. To explore the role of foxO4 in the hypoxia response, we detected the expression of foxO4 and the regulatory relationship between Hif1α and foxO4 under hypoxic conditions. It was found that the expression of foxO4 was up-regulated in ZF4 cells and zebrafish tissues after hypoxia treatment, and Hif1α could directly target the HRE of the foxO4 promoter to regulate foxO4 transcription, indicating that foxO4 was involved in the hypoxia response by the Hif1α-mediated pathway. Furthermore, we obtained foxO4 knockout zebrafish and found that the disruption of foxO4 increased the tolerance to hypoxia. Further research found that the oxygen consumption and locomotor activity of foxO4-/- zebrafish were lower than those of WT zebrafish, as was true for NADH content, NADH/NAD+ rate, and expression of mitochondrial respiratory chain complex-related genes. This suggests that disruption of foxO4 reduced the oxygen demand threshold of the organism, which explained why the foxO4-/- zebrafish were more tolerant to hypoxia than WT zebrafish. These results will provide a theoretical basis for further study of the role of foxO4 in the hypoxia response.
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Affiliation(s)
- Linlin Shi
- Key Lab of Freshwater Animal Breeding/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan 430070, China
| | - Axin Zhang
- Key Lab of Freshwater Animal Breeding/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong Liu
- Key Lab of Freshwater Animal Breeding/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Huanling Wang
- Key Lab of Freshwater Animal Breeding/Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
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Cao Q, Zhang H, Li T, He L, Zong J, Shan H, Huang L, Zhang Y, Liu H, Jiang J. Profiling miRNAs of Teleost Fish in Responses to Environmental Stress: A Review. BIOLOGY 2023; 12:biology12030388. [PMID: 36979079 PMCID: PMC10045198 DOI: 10.3390/biology12030388] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/11/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023]
Abstract
miRNAs are a class of endogenous and evolutionarily conserved noncoding short RNA molecules that post-transcriptionally regulate gene expression through sequence-specific interactions with mRNAs and are capable of controlling gene expression by binding to miRNA targets and interfering with the final protein output. The miRNAs of teleost were firstly reported in zebrafish development, but there are recent studies on the characteristics and functions of miRNAs in fish, especially when compared with mammals. Environmental factors including salinity, oxygen concentration, temperature, feed, pH, environmental chemicals and seawater metal elements may affect the transcriptional and posttranscriptional regulators of miRNAs, contributing to nearly all biological processes. The survival of aquatic fish is constantly challenged by the changes in these environmental factors. Environmental factors can influence miRNA expression, the functions of miRNAs and their target mRNAs. Progress of available information is reported on the environmental effects of the identified miRNAs, miRNA targets and the use of miRNAs in fish.
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Affiliation(s)
- Quanquan Cao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- MARBEC, University Montpellier, CNRS, IFREMER, IRD, 34090 Montpellier, France
- Correspondence: or (Q.C.); (H.L.); (J.J.); Tel./Fax: +86-28-86291010 (J.J.)
| | - Hailong Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tong Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lingjie He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiali Zong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongying Shan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lishi Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yupeng Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Haifeng Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: or (Q.C.); (H.L.); (J.J.); Tel./Fax: +86-28-86291010 (J.J.)
| | - Jun Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: or (Q.C.); (H.L.); (J.J.); Tel./Fax: +86-28-86291010 (J.J.)
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He Y, Liu Y, Yang Y, Liu Y, Jia X, Shen Y, Xu X, Li J. elk1/miR-462-731 Feedback Loop Regulates Macrophages Polarization and Phagocytosis in Grass Carp (Ctenopharyngodon idella). Front Immunol 2022; 13:946857. [PMID: 35911773 PMCID: PMC9330907 DOI: 10.3389/fimmu.2022.946857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNA clusters are microRNAs (miRNAs) that are distributed in close proximity on chromosomes. In this study, we report a miRNA cluster identified from grass carp (Ctenopharyngodon idella), miR-462-731, which plays a positive role in host antibacterial immunity. The expression of miR-462-731 was disrupted after infection by Aeromonas hydrophila. Transcription factor ETS transcription factor ELK1 was identified to bind to the promoter of the miR-462-731 cluster and suppress its expression. In addition, miR-731 negatively regulates the expression of elk1, forms an elk1/miR-462-731 double negative feedback loop. In addition, we found that miR-731 directly targets ezrin a (ezra), participates in inducing PI3K/AKT signaling in macrophage, to induce macrophage polarization to the M1 phenotype with stronger phagocytosis. Our results demonstrate a novel elk1/miR-462-731 feedback loop. The data deepen our understanding of the relationship between macrophage polarization and phagocytosis in teleost fish.
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Affiliation(s)
- Yan He
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yuting Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yuyue Yang
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Yang Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Xuewen Jia
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yubang Shen
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- *Correspondence: Xiaoyan Xu, ; Jiale Li,
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- *Correspondence: Xiaoyan Xu, ; Jiale Li,
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Hu T, Li D, Fan T, Zhao X, Chen Z. Circular RNA PUM1 performs as a competing endogenous RNA of microRNA-340-5p to mediate DEAD-box helicase 5 to mitigate cerebral ischemia-reperfusion injury. Bioengineered 2022; 13:11564-11578. [PMID: 35510394 PMCID: PMC9276027 DOI: 10.1080/21655979.2022.2068923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cerebral ischemia-reperfusion damages local brain tissue and impairs brain function, but its specific pathogenesis is still uncertain. Recent studies have clarified circPUM1 is aberrantly elevated in cerebral ischemia-reperfusion injury; however, circPUM1ʹs function in cerebral ischemia-reperfusion-induced neuronal injury remains ambiguous. The results illustrated circPUM1 and DEAD-box helicase 5 were decreased, but microRNA-340-5p was elevated in transient middle cerebral artery occlusion mice and oxygen glucose deprivation/reoxygenation-treated SH-SY5Y cells. Knockdown of circPUM1 aggravated the neuronal injury in transient middle cerebral artery occlusion mice and motivated glial cell activation, neuronal apoptosis and inflammation. Enhancing circPUM1 restrained oxygen glucose deprivation/reoxygenation-induced SH-SY5Y cell apoptosis, the release of lactate dehydrogenase and inflammatory factors, and activation of nuclear factor-kappaB pathway, while elevating microRNA-340-5p aggravated oxygen glucose deprivation/reoxygenation-induced cell damage. Functional rescue experiments exhibited that the impacts of knockdown or enhancement of circPUM1 were turned around by microRNA-340-5p downregulation and DEAD-box helicase 5 silencing, respectively. Moreover, it was demonstrated that circPUM1 competitively adsorbed microRNA-340-5p to mediate DEAD-box helicase 5. All in all, this study clarifies that circPUM1 mitigates cerebral ischemia-reperfusion-induced neuronal injury by targeting the microRNA-340-5p/DEAD-box helicase 5 axis.
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Affiliation(s)
- Teng Hu
- Department of Neurological Intervention, Dalian Municipal Central Hospital, Dalian City, China
| | - Di Li
- Department of Neurological Intervention, Dalian Municipal Central Hospital, Dalian City, China
| | - TiePing Fan
- Department of Neurological Intervention, Dalian Municipal Central Hospital, Dalian City, China
| | - XuSheng Zhao
- Department of Neurological Intervention, Dalian Municipal Central Hospital, Dalian City, China
| | - ZhongJun Chen
- Department of Neurological Intervention, Dalian Municipal Central Hospital, Dalian City, China
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Huang Y, Wang WF, Huang CX, Li XH, Liu H, Wang HL. miR-731 modulates the zebrafish heart morphogenesis via targeting Calcineurin/Nfatc3a pathway. Biochim Biophys Acta Gen Subj 2022; 1866:130133. [PMID: 35346765 DOI: 10.1016/j.bbagen.2022.130133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 03/18/2022] [Accepted: 03/23/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Zebrafish miR-731 is orthologous of human miR-425, which has been demonstrated to have cardio-protective roles by a variety of mechanisms. The miR-731 morphants show pericardium enlargement, and many DEGs (differentially expressed genes) are enriched in 'Cardiac muscle contraction' and 'Calcium signaling pathway', implying that miR-731 plays a potential role in heart function and development. However,the in vivo physiological role of miR-731 in the heart needs to be fully defined. METHODS Zebrafish miR-731 morphants were generated by morpholino knockdown, and miR-731 knockout zebrafish was generated by CRISRP/Cas9. We observed cardiac morphogenesis based on whole-mount in situ hybridization. Furthermore, RNA-seq and qRT-PCR were used to elucidate the molecular mechanism and analyze the gene expression. Double luciferase verification and Western blot were used to verify the target gene. RESULTS The depletion of miR-731 in zebrafish embryos caused the deficiency of cardiac development and function, which was associated with reduced heart rate, ventricular enlargement and heart looping disorder. In addition, mechanistic study demonstrated that Calcineurin/Nfatc3a signaling involved in miR-731 depletion induced abnormal cardiac function and developmental defects. CONCLUSION MiR-731 regulates cardiac function and morphogenesis through Calcineurin/Nfatc3a signaling. GENERAL SIGNIFICANCE Our studies highlight the potential importance of miR-731 in cardiac development.
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Affiliation(s)
- Yan Huang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Wei-Feng Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Chun-Xiao Huang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Xuan-Hui Li
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Hong Liu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Huan-Ling Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, Hubei, PR China.
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10
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Luo W, Wang J, Zhou Y, Pang M, Yu X, Tong J. Dynamic mRNA and miRNA expression of the head during early development in bighead carp (Hypophthalmichthys nobilis). BMC Genomics 2022; 23:168. [PMID: 35232381 PMCID: PMC8887032 DOI: 10.1186/s12864-022-08387-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 02/09/2022] [Indexed: 11/24/2022] Open
Abstract
Background Head of fish species, an exquisitely complex anatomical system, is important not only for studying fish evolution and development, but also for economic values. Currently, although some studies have been made on fish growth and body shapes, very limited information is available on the molecular mechanism of head development. Results In this study, RNA sequencing (RNA–Seq) and small RNA sequencing (sRNA–Seq) technologies were used to conduct integrated analysis for the head of bighead carp at different development stages, including 1, 3, 5, 15 and 30 Dph (days post hatch). By RNA-Seq data, 26 pathways related to growth and bone formation were identified as the main physiological processes during early development. Coupling this to sRNA–Seq data, we picked out six key pathways that may be responsible for head development, namely ECM receptor interaction, TNF signaling pathway, osteoclast differentiation, PI3K–Akt signaling pathway, Neuroactive ligand–receptor interaction and Jak–STAT signaling pathway. Totally, 114 important candidate genes from the six pathways were obtained. Then we found the top 20 key genes according to the degree value by cytohubba, which regulated cell growth, skeletal formation and blood homeostasis, such as pik3ca, pik3r1, egfr, vegfa, igf1 and itga2b. Finally, we also acquired 19 key miRNAs playing multiple roles in the perfection of various tissues in the head (such as brain, eye and mouth) and mineralization of head bone system, such as let–7e, miR–142a–5p, miR–144–3p, miR–23a–3p and miR–223. Conclusions Results of this study will be informative for genetic mechanisms of head development and also provide potential candidate targets for the interaction regulation during early growth in bighead carp. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08387-x.
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Affiliation(s)
- Weiwei Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Junru Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Ying Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Meixia Pang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.,Postdoctoral Innovation Practice Base, Shenzhen Polytechnic, Shenzhen, 518055, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
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11
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Wang Q, Li X, Sha H, Luo X, Zou G, Liang H. Identification of microRNAs in Silver Carp ( Hypophthalmichthys molitrix) Response to Hypoxia Stress. Animals (Basel) 2021; 11:ani11102917. [PMID: 34679939 PMCID: PMC8696637 DOI: 10.3390/ani11102917] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/28/2021] [Accepted: 10/06/2021] [Indexed: 12/31/2022] Open
Abstract
Simple Summary Hypoxia stress is one of the main problems in silver carp (Hypophthalmichthys molitrix) culture. Severe hypoxia stress can lead to damage and even death of silver carp. Therefore, it is very important to explore how silver carp adapt to and respond to hypoxia stress. MicroRNAs play an important role in a series of important life activities in organisms. In this study, the differentiallyexpressed miRNAs were screened from a mixed pool of liver, brain, heart and gill of silver carp under different levels of hypoxia stress by high-throughput sequencing. Our findings provided new insights to further study the miRNA regulatory mechanism and molecular characteristics of anoxic response in silver carp. Abstract Hypoxia is one of the serious stresses in fish culture, which can lead to physical and morphological changes, and cause injury and even death to fish. Silver carp (Hypophthalmichthys molitrix) is an important economic fish and widely distributed in China. MicroRNA is a kind of endogenous non-coding single-stranded small RNA, which is involved in cell development, and immune response and gene expression regulation. In this study, silver carp were kept in the closed containers for hypoxia treatment by spontaneous oxygen consumption. The samples of heart, brain, liver and gill were collected, and the total RNAs extracted separately from the four tissues were mixed in equal amounts according to the concentration. Afterwards, the RNA pool was constructed for high-throughput sequencing, and based on the small RNA sequencing, the differentially expressed microRNAs were identified. Furthermore, their target gene prediction and enrichment analyses were carried out. The results showed that a total of 229 known miRNAs and 391 putative novel miRNAs were identified, which provided valuable resources for further study on the regulatory mechanism of miRNAs in silver carp under hypoxia stress. The authors verified 16 differentially expressed miRNAs by qRT-PCR, and the results were consistent with small RNA sequencing (sRNA-seq). The predicted target genes number of differentially expressed miRNAs was 25,146. GO and KEGG functional enrichment analysis showed that these target genes were mainly involved in the adaption of hypoxia stress in silver carp through biological regulation, catalytic activity and apoptosis. This study provides references for further study of interaction between miRNAs and target genes, and the basic data for the response mechanism under hypoxia stress in silver carp.
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Affiliation(s)
- Qiaoxin Wang
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China;
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (H.S.); (X.L.)
| | - Xiaohui Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (H.S.); (X.L.)
| | - Hang Sha
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (H.S.); (X.L.)
| | - Xiangzhong Luo
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (H.S.); (X.L.)
| | - Guiwei Zou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (H.S.); (X.L.)
- Correspondence: (G.Z.); (H.L.); Tel.: +86-27-81780097 (H.L.)
| | - Hongwei Liang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (X.L.); (H.S.); (X.L.)
- Correspondence: (G.Z.); (H.L.); Tel.: +86-27-81780097 (H.L.)
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12
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Ahkin Chin Tai JK, Freeman JL. Zebrafish as an integrative vertebrate model to identify miRNA mechanisms regulating toxicity. Toxicol Rep 2020; 7:559-570. [PMID: 32373477 PMCID: PMC7195498 DOI: 10.1016/j.toxrep.2020.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/22/2020] [Accepted: 03/24/2020] [Indexed: 12/12/2022] Open
Abstract
Zebrafish are an established vertebrate model for toxicity studies. Zebrafish have a fully sequenced genome and the capability to create genetic models. Zebrafish have over 80 % homology for genes related to human disease. Functions of miRNAs in the zebrafish genome are being characterized. Zebrafish are ideal for mechanistic studies on how miRNAs regulate toxicity.
Zebrafish (Danio rerio) are an integrative vertebrate model ideal for toxicity studies. The zebrafish genome is sequenced with detailed characterization of all life stages. With their genetic similarity to humans, zebrafish models are established to study biological processes including development and disease mechanisms for translation to human health. The zebrafish genome, similar to other eukaryotic organisms, contains microRNAs (miRNAs) which function along with other epigenetic mechanisms to regulate gene expression. Studies have now established that exposure to toxins and xenobiotics can change miRNA expression profiles resulting in various physiological and behavioral alterations. In this review, we cover the intersection of miRNA alterations from toxin or xenobiotic exposure with a focus on studies using the zebrafish model system to identify miRNA mechanisms regulating toxicity. Studies to date have addressed exposures to toxins, particulate matter and nanoparticles, various environmental contaminants including pesticides, ethanol, and pharmaceuticals. Current limitations of the completed studies and future directions for this research area are discussed.
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Affiliation(s)
| | - Jennifer L Freeman
- School of Health Sciences, Purdue University, West Lafayette, IN 47907 USA
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13
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Wu TS, Lin YT, Huang YT, Yu FY, Liu BH. Ochratoxin A triggered intracerebral hemorrhage in embryonic zebrafish: Involvement of microRNA-731 and prolactin receptor. CHEMOSPHERE 2020; 242:125143. [PMID: 31675585 DOI: 10.1016/j.chemosphere.2019.125143] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
Ochratoxin A (OTA), a mycotoxin widely found in foodstuffs, reportedly damages multiple brain regions in developing rodents, but the corresponding mechanisms have not been elucidated. In this study, zebrafish embryos at 6 h post fertilization (hpf) were exposed to various concentrations of OTA and the phenomenon associated with intracerebral hemorrhage was observed at 72 hpf. Exposure of embryos to OTA significantly increased their hemorrhagic rate in a dose-dependent manner. Large numbers of extravagated erythrocytes were observed in the midbrain/hindbrain areas of Tg(fli-1a:EGFP; gata1:DsRed) embryos following exposure to OTA. OTA also disrupted the vascular patterning, especially the arch-shaped central arteries (CtAs), in treated embryos. Histological analysis revealed a cavity-like pattern in their hindbrain ventricles, implying the possibility of cerebral edema. OTA-induced intracerebral hemorrhage and CtA vessel defects were partially reversed by the presence of miR-731 antagomir or the overexpression of prolactin receptor a (prlra); prlra is a downstream target of miR-731. These results suggest that exposure to OTA has a negative effect on cerebral vasculature development by interfering with the miR-731/PRLR axis in zebrafish.
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Affiliation(s)
- Ting-Shuan Wu
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Ting Lin
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ying-Tzu Huang
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Feng-Yih Yu
- Department of Biomedical Sciences, Chung Shan Medical University, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan.
| | - Biing-Hui Liu
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan.
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14
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Huang Y, Huang CX, Wang WF, Liu H, Wang HL. Zebrafish miR-462-731 is required for digestive organ development. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 34:100679. [PMID: 32200130 DOI: 10.1016/j.cbd.2020.100679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs), as important regulators of post-transcriptional gene expression, play important roles in the occurrence and function of organs. In this study, morpholino (MO) knockdown of miR-462/miR-731 was used to investigate the potential mechanisms of the miR-462-731 cluster during zebrafish liver development. The results showed significant reduction of digestive organs, especially liver and exocrine pancreas after the miR-462/miR-731 knockdown, and those phenotypes could be partially rescued by corresponding miRNA duplex. Acinar cells of the exocrine pancreas were also severely affected with pancreatic insufficiency. In particular, knockdown of miR-462 caused pancreas morphogenesis abnormity with specific bilateral exocrine pancreas. Additionally, it was found that miR-731 played a role in liver and exocrine pancreas development by directly targeting dkk3b, instead of the down-regulation of Wnt/β-catenin signaling. These findings contribute significantly to our understanding of molecular mechanisms of miR-462-731 cluster in development of digestive organs.
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Affiliation(s)
- Yan Huang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Chun-Xiao Huang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Wei-Feng Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Hong Liu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Huan-Ling Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, Hubei, PR China.
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15
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Liu Q, Yang J, Gong Y, Cai J, Zhang Z. Role of miR-731 and miR-2188-3p in mediating chlorpyrifos induced head kidney injury in common carp via targeting TLR and apoptosis pathways. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 215:105286. [PMID: 31479757 DOI: 10.1016/j.aquatox.2019.105286] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/22/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
Chlorpyrifos (CPF) is an environmental pollutant with increasing importance due to its high toxicity to fish and aquatic animals. In the present study, we divided 120 common carp (Cyprinus carpio L.) into two groups including control group and CPF group, CPF group was exposed to 14.5 μg/L CPF for 30 d. 17 miRNAs were differentially expressed in CPF group head kidney tissues according to the results of miRNAome analysis. In addition, histopathological examination and electron microscopy proved that CPF exposure could lead to damage of head kidney and obvious apoptosis characteristics. The possible target genes of miRNA were predicted using online target gene prediction websites, miRNAome sequencing, GO and KEGG enrichment. miRNAome results showed that expression of miR-731 and miR-2188-3p in CPF group was 0.48 time and 0.45 time as control group, respectively. qRT-PCR results proved the reality of miRNAome. During CPF exposure, mRNA expression of TLR pathway genes and its downstream genes involved in autophagy and apoptosis pathway including TLR1, TLR2, TLR7, TLR9, MyD88, IRAK1, IRAK4, IRF7, PI3K, AKT, mTOR, Caspase3, Caspase8 and Bax were differentially increased under CPF exposure, along with ATG13 and Bcl2 decreased at the same time. Western blot results indicated that apoptosis related protein Caspase3 and Caspase8 were differentially up-regulated in the CPF group. In summary, CPF exposure could induce apoptosis while inhibited autophagy in head kidney of common carp via the regulation of miR-2188-3p and miR-731 by targeting TLR pathway. These results provide new insights for unveiling the biological effects of CPF and miRNAs in common carp.
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Affiliation(s)
- Qi Liu
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Jie Yang
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Yafan Gong
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Jingzeng Cai
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, PR China
| | - Ziwei Zhang
- Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment, College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, PR China.
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16
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Ma F, Liu Z, Huang J, Li Y, Kang Y, Liu X, Wang J. High-throughput sequencing reveals microRNAs in response to heat stress in the head kidney of rainbow trout (Oncorhynchus mykiss). Funct Integr Genomics 2019; 19:775-786. [PMID: 31076931 DOI: 10.1007/s10142-019-00682-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 02/11/2019] [Accepted: 04/30/2019] [Indexed: 12/26/2022]
Abstract
Recently, the research of animal microRNAs (miRNAs) has attracted wide attention for its regulatory effect in the development process and the response to abiotic stresses. Rainbow trout is a commercially and cold water fish species, and usually encounters heat stress, which affects its growth and leads to a huge economic loss. But there were few investigations about the roles of miRNAs in heat stress in rainbow trout. In this study, miRNAs of rainbow trout which were involved in heat stress were identified by high-throughput sequencing of six small RNA libraries from head kidney tissues under control (18 °C) and heat-treated (24 °C) conditions. A total of 392 conserved miRNAs and 989 novel miRNAs were identified, of which 78 miRNAs were expressed in different response to heat stress. Ten of these miRNAs were further validated by quantitative real-time PCR. In addition to, including 393 negative correlation miRNA-target gene pairs, several important regulatory pathways were involved in heat stress of the potential target genes, including protein processing in endoplasmic reticulum, NOD-like receptor signaling pathway, and phagosome. Our data significantly advance understanding of heat stress regulatory mechanism of miRNA in the head kidney of rainbow trout, which provide a useful resource for the cultivation of rainbow trout.
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Affiliation(s)
- Fang Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhe Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Jinqiang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yongjuan Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yujun Kang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiaoxia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jianfu Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
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17
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Nie X, Chen Y, Tan J, Dai Y, Mao W, Qin G, Ye S, Sun J, Yang Z, Chen J. MicroRNA-221-3p promotes pulmonary artery smooth muscle cells proliferation by targeting AXIN2 during pulmonary arterial hypertension. Vascul Pharmacol 2019; 116:24-35. [DOI: 10.1016/j.vph.2017.07.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 05/13/2017] [Accepted: 07/06/2017] [Indexed: 12/23/2022]
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18
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Demin KA, Lakstygal AM, Alekseeva PA, Sysoev M, de Abreu MS, Alpyshov ET, Serikuly N, Wang D, Wang M, Tang Z, Yan D, Strekalova TV, Volgin AD, Amstislavskaya TG, Wang J, Song C, Kalueff AV. The role of intraspecies variation in fish neurobehavioral and neuropharmacological phenotypes in aquatic models. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 210:44-55. [PMID: 30822702 DOI: 10.1016/j.aquatox.2019.02.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
Intraspecies variation is common in both clinical and animal research of various brain disorders. Relatively well-studied in mammals, intraspecies variation in aquatic fish models and its role in their behavioral and pharmacological responses remain poorly understood. Like humans and mammals, fishes show high variance of behavioral and drug-evoked responses, modulated both genetically and environmentally. The zebrafish (Danio rerio) has emerged as a particularly useful model organism tool to access neurobehavioral and drug-evoked responses. Here, we discuss recent findings and the role of the intraspecies variance in neurobehavioral, pharmacological and toxicological studies utilizing zebrafish and other fish models. We also critically evaluate common sources of intraspecies variation and outline potential strategies to improve data reproducibility and translatability.
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Affiliation(s)
- Konstantin A Demin
- Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia; Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Anton M Lakstygal
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Granov Russian Research Centre of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
| | - Polina A Alekseeva
- Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
| | - Maxim Sysoev
- Granov Russian Research Centre of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
| | - Murilo S de Abreu
- The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA; Bioscience Institute, University of Passo Fundo, Passo Fundo, RS, Brazil
| | | | - Nazar Serikuly
- School of Pharmacy, Southwest University, Chongqing, China
| | - DongMei Wang
- School of Pharmacy, Southwest University, Chongqing, China
| | - MengYao Wang
- School of Pharmacy, Southwest University, Chongqing, China
| | - ZhiChong Tang
- School of Pharmacy, Southwest University, Chongqing, China
| | - DongNi Yan
- School of Pharmacy, Southwest University, Chongqing, China
| | - Tatyana V Strekalova
- Department of Neuroscience, Maastricht University, Maastricht, Netherlands; Laboratory of Psychiatric Neurobiology and Department of Normal Physiology, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Andrey D Volgin
- Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia
| | | | - JiaJia Wang
- Research Institute of Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Cai Song
- Research Institute of Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Allan V Kalueff
- School of Pharmacy, Southwest University, Chongqing, China; Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia; The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA; Ural Federal University, Ekaterinburg, Russia; ZENEREI Research Center, Slidell, LA, USA; Laboratory of Biological Psychiatry, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Institute of Experimental Medicine, Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia; Granov Russian Research Centre of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia.
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19
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Goodale BC, Hampton TH, Ford EN, Jackson CE, Shaw JR, Stanton BA, King BL. Profiling microRNA expression in Atlantic killifish (Fundulus heteroclitus) gill and responses to arsenic and hyperosmotic stress. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 206:142-153. [PMID: 30476744 PMCID: PMC6298807 DOI: 10.1016/j.aquatox.2018.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
The Atlantic killifish (Fundulus heteroclitus), native to estuarine areas of the Atlantic coast of the United States, has become a valuable ecotoxicological model as a result of its ability to acclimate to rapid environmental changes and adapt to polluted habitats. MicroRNAs (miRNAs) are highly conserved small RNAs that regulate gene expression and play critical roles in stress responses in a variety of organisms. Global miRNA expression in killifish and the potential roles miRNA have in environmental acclimation have yet to be characterized. Accordingly, we profiled miRNA expression in killifish gill for the first time and identified a small group of highly expressed, well-conserved miRNAs as well as 16 novel miRNAs not yet identified in other organisms. Killifish respond to large fluctuations in salinity with rapid changes in gene expression and protein trafficking to maintain osmotic balance, followed by a secondary phase of gene and protein expression changes that enable remodeling of the gills. Arsenic, a major environmental toxicant, was previously shown to inhibit gene expression responses in killifish gill, as well the ability of killifish to acclimate to a rapid increase in salinity. Thus, we examined the individual and combined effects of salinity and arsenic on miRNA expression in killifish gill. Using small RNA sequencing, we identified 270 miRNAs expressed in killifish, and found that miR-135b was differentially expressed in response to arsenic and at 24 h following transfer to salt water. Predicted targets of miR-135b are involved in ion transport, cell motility and migration, GTPase mediated signal transduction and organelle assembly. Consistent with previous studies of these two environmental stressors, we found a significant interaction (i.e., arsenic dependent salinity effect), whereby killifish exposed to arsenic exhibited an opposite response in miR-135b expression at 24 h post hyperosmotic challenge compared to controls. By examining mRNA expression of predicted miRNA targets during salinity acclimation and arsenic exposure, we found that miR-135b targets were significantly more likely to decrease during salinity acclimation than non-targets. Our identification of a significant interaction effect of arsenic and salinity on miR-135b expression supports the hypothesis that arsenic alters upstream regulators of stress response networks, which may adversely affect the killifish response to osmotic stress. The characterization of miRNAs in this ecotoxicological model will be a valuable resource for future studies investigating the role of miRNAs in response to environmental stress.
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Affiliation(s)
- Britton C Goodale
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, United States.
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, United States
| | - Emily N Ford
- Department of Physical and Biological Sciences, Western New England University, Springfield, MA 01119, United States
| | - Craig E Jackson
- School of Public and Environmental Affairs, Indiana University, Bloomington, IN 47405, United States
| | - Joseph R Shaw
- School of Public and Environmental Affairs, Indiana University, Bloomington, IN 47405, United States
| | - Bruce A Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, United States
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, United States
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20
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The critical role of microRNAs in stress response: Therapeutic prospect and limitation. Pharmacol Res 2018; 142:294-302. [PMID: 30553824 DOI: 10.1016/j.phrs.2018.12.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 12/22/2022]
Abstract
Stress response refers to the systemic nonspecific response upon exposure to strong stimulation or chronic stress, such as severe trauma, shock, infection, burn, major surgery or improper environment, which disturb organisms and damage their physical and psychological health. However, the pathogenesis of stress induced disorder remains complicated and diverse under different stress exposure. Recently, studies have revealed a specific role of microRNAs (miRNAs) in regulating cellular function under different types of stress, suggesting a significant role in the treatment and prevention of stress-related diseases, such as stress ulcer, posttraumatic stress disorder, stress-induced cardiomyopathy and so on. This paper have reviewed the literature on microRNA related stress diseases in different databases including PubMed, Web of Science, and the MiRbase. It considers only peer-reviewed papers published in English between 2004 and 2018. This review summarizes new advances in principles and mechanisms of miRNAs regulating stress signalling pathway and the role of miRNAs in human stress diseases. This comprehensive review is to provide an integrated account of how different stresses affect miRNAs and how stress-miRNA pathways may, in turn, be linked with disease, which offers some potential strategies for stress disorder treatment. Furthermore, the limitation of current studies and challenges for clinical use are discussed.
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21
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Zebrafish miR-462-731 regulates hematopoietic specification and pu.1-dependent primitive myelopoiesis. Cell Death Differ 2018; 26:1531-1544. [PMID: 30459392 DOI: 10.1038/s41418-018-0234-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs (miRNAs) play significant roles in both embryonic hematopoiesis and hematological malignancy. Zebrafish miR-462-731 cluster is orthologous of miR-191-425 in human which regulates proliferation and tumorigenesis. In our previous work, miR-462-731 was found highly and ubiquitously expressed during early embryogenesis. In this study, by loss-of-function analysis (morpholino knockdown combined with CRISRP/Cas9 knockout) and mRNA profiling, we suggest that miR-462-731 is required for normal embryonic development by regulating cell survival. We found that loss of miR-462/miR-731 caused a remarkable decrease in the number of erythroid cells as well as an ectopic myeloid cell expansion at 48 hpf, suggesting a skewing of myeloid-erythroid lineage differentiation. Mechanistically, miR-462-731 provides an instructive input for pu.1-dependent primitive myelopoiesis through regulating etsrp/scl signaling combined with a novel pu.1/miR-462-731 feedback loop. On the other hand, morpholino (MO) knockdown of miR-462/miR-731 resulted in an expansion of posterior blood islands at 24 hpf, which is a mild ventralization phenotype resulted from elevation of BMP signaling. Rescue experiments with both BMP type I receptor inhibitor dorsomorphin and alk8 MO indicate that miR-462-731 acts upstream of alk8 within the BMP/Smad signaling pathway and functions as a novel endogenous BMP antagonist. Besides, an impairment of angiogenesis was observed in miR-462/miR-731 morphants. The specification of arteries and veins was also perturbed, as characterized by the irregular patterning of efnb2a and flt4 expression. Our study unveils a previously unrecognized role of miR-462-731 in BMP/Smad signaling mediated hematopoietic specification of mesodermal progenitors and demonstrates a miR-462-731 mediated regulatory mechanism driving primitive myelopoiesis in the ALPM. We also show a requirement for miR-462-731 in regulating arterial-venous specification and definitive hematopoietic stem cell (HSC) production. The current findings might provide further insights into the molecular mechanistic basis of miRNA regulation of embryonic hematopoiesis and hematological malignancy.
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Zebrafish models of epigenetic regulation of CNS functions. Brain Res Bull 2018; 142:344-351. [DOI: 10.1016/j.brainresbull.2018.08.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/22/2018] [Accepted: 08/30/2018] [Indexed: 12/12/2022]
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Chatterjee N, Gim J, Choi J. Epigenetic profiling to environmental stressors in model and non-model organisms: Ecotoxicology perspective. ENVIRONMENTAL HEALTH AND TOXICOLOGY 2018; 33:e2018015-0. [PMID: 30286591 PMCID: PMC6182246 DOI: 10.5620/eht.e2018015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/19/2018] [Indexed: 05/16/2023]
Abstract
Epigenetics, potentially heritable changes in genome function that occur without alterations to DNA sequence, is an important but understudied component of ecotoxicology studies. A wide spectrum of environmental challenge, such as temperature, stress, diet, toxic chemicals, are known to impact on epigenetic regulatory mechanisms. Although the role of epigenetic factors in certain biological processes, such as tumourigenesis, has been heavily investigated, in ecotoxicology field, epigenetics still have attracted little attention. In ecotoxicology, potential role of epigenetics in multi- and transgenerational phenomenon to environmental stressors needs to be unrevealed. Natural variation in the epigenetic profiles of species in responses to environmental stressors, nature of dose-response relationships for epigenetic effects, and how to incorporate this information into ecological risk assessment should also require attentions. In this review, we presented the available information on epigenetics in ecotoxicological context. For this, we have conducted a systemic review on epigenetic profiling in response to environmental stressors, mostly chemical exposure, in model organisms, as well as, in ecotoxicologically relevant wildlife species.
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Affiliation(s)
- Nivedita Chatterjee
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdaero, Dondaemun-gu, Seoul 02504, Republic of Korea
| | - Jiwan Gim
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdaero, Dondaemun-gu, Seoul 02504, Republic of Korea
| | - Jinhee Choi
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdaero, Dondaemun-gu, Seoul 02504, Republic of Korea
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Epigenetics in teleost fish: From molecular mechanisms to physiological phenotypes. Comp Biochem Physiol B Biochem Mol Biol 2018; 224:210-244. [PMID: 29369794 DOI: 10.1016/j.cbpb.2018.01.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 01/08/2018] [Accepted: 01/16/2018] [Indexed: 02/07/2023]
Abstract
While the field of epigenetics is increasingly recognized to contribute to the emergence of phenotypes in mammalian research models across different developmental and generational timescales, the comparative biology of epigenetics in the large and physiologically diverse vertebrate infraclass of teleost fish remains comparatively understudied. The cypriniform zebrafish and the salmoniform rainbow trout and Atlantic salmon represent two especially important teleost orders, because they offer the unique possibility to comparatively investigate the role of epigenetic regulation in 3R and 4R duplicated genomes. In addition to their sequenced genomes, these teleost species are well-characterized model species for development and physiology, and therefore allow for an investigation of the role of epigenetic modifications in the emergence of physiological phenotypes during an organism's lifespan and in subsequent generations. This review aims firstly to describe the evolution of the repertoire of genes involved in key molecular epigenetic pathways including histone modifications, DNA methylation and microRNAs in zebrafish, rainbow trout, and Atlantic salmon, and secondly, to discuss recent advances in research highlighting a role for molecular epigenetics in shaping physiological phenotypes in these and other teleost models. Finally, by discussing themes and current limitations of the emerging field of teleost epigenetics from both theoretical and technical points of view, we will highlight future research needs and discuss how epigenetics will not only help address basic research questions in comparative teleost physiology, but also inform translational research including aquaculture, aquatic toxicology, and human disease.
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Discovery of microRNAs associated with the antiviral immune response of Atlantic cod macrophages. Mol Immunol 2017; 93:152-161. [PMID: 29190475 DOI: 10.1016/j.molimm.2017.11.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/13/2017] [Accepted: 11/17/2017] [Indexed: 02/08/2023]
Abstract
MicroRNAs (miRNAs) are known to play important immunoregulatory roles in teleosts, although miRNAs involved in the antiviral immune response of Atlantic cod (Gadus morhua) were previously uncharacterised. Using deep sequencing and qPCR, the present study was conducted to identify miRNAs responsive to the viral mimic, polyriboinosinic polyribocytidylic acid (pIC) in Atlantic cod macrophages. Macrophage samples isolated from Atlantic cod (n=3) and treated with pIC or phosphate buffered saline (PBS control) for 24 and 72h were used for miRNA profiling. Following deep sequencing, DESeq2 analyses identified four (miR-731-3p, miR-125b-3-3p, miR-150-3p and miR-462-3p) and two (miR-2188-3p and miR-462-3p) significantly differentially expressed miRNAs at 24 and 72h post-stimulation (HPS), respectively. Sequencing-identified miRNAs were subjected to qPCR validation using a larger number of biological replicates (n=6) exposed to pIC or PBS over time (i.e. 12, 24, 48 and 72 HPS). As in sequencing, miR-731-3p, miR-462-3p and miR-2188-3p showed significant up-regulation by pIC. The sequencing results were not qPCR-validated for miR-125b-3-3p and miR-150-3p as up- and down-regulated miRNAs at 24 HPS, respectively; however, qPCR results showed significant up-regulation in response to pIC stimulation at later time points (i.e. 48 and/or 72 HPS). We also used qPCR to assess the expression of other miRNAs that were previously shown as immune responsive in other vertebrates. qPCR results at 48 and/or 72 HPS revealed that miR-128-3-5p, miR-214-1-5p and miR-451-3p were induced by pIC, whereas miR-30b-3p and miR-199-1-3p expression were repressed in response to pIC. The present study identified ten pIC-stimulated miRNAs, suggesting them as important in antiviral immune responses of Atlantic cod macrophages. Some pIC-responsive miRNAs identified in this study were predicted to target putative immune-related genes of Atlantic cod (e.g. miR-30b-3p targeting herc4), although the regulatory functions of these miRNAs need to be validated by future studies.
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Huang CH, Chen N, Huang CX, Zhang B, Wu M, He L, Liu H, Tang R, Wang WM, Wang HL. Involvement of the miR-462/731 cluster in hypoxia response in Megalobrama amblycephala. FISH PHYSIOLOGY AND BIOCHEMISTRY 2017; 43:863-873. [PMID: 28280952 DOI: 10.1007/s10695-017-0341-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 01/04/2017] [Indexed: 05/20/2023]
Abstract
MicroRNAs (miRNAs) are non-coding small RNAs showing both evolutionarily conserved and unique features and are involved in nearly all biological processes. In the present study, the role played by miR-462/731 cluster miRNAs in hypoxia response in Megalobrama amblycephala, an important freshwater fish, was investigated. The M. amblycephala miR-462/731 cluster locus and their 5' flanking sequences were sequenced and analyzed. In M. amblycephala and other teleost fish species, the mature sequences of miR-462 and miR-731 were identical and hypoxia-responsive elements (HREs) were identified upstream of the miR-462/731 loci. The two miRNAs were significantly induced in the liver, spleen, gill, muscle, and brain after hypoxia treatment. The expression of both miRNAs was also upregulated in cells that received treatment which mimicked hypoxia. Furthermore, reporter assay revealed that M. amblycephala HREs can be activated by hypoxia. Taken together, the 462/731 cluster may play a role in the regulation of the hypoxia response in M. amblycephala.
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Affiliation(s)
- Cui-Hong Huang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Nan Chen
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Chun-Xiao Huang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Bao Zhang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Meng Wu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Lei He
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Hong Liu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, 430070, Wuhan, People's Republic of China
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Rong Tang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, 430070, Wuhan, People's Republic of China
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Wei-Min Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Huan-Ling Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China.
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, 430070, Wuhan, People's Republic of China.
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fishery, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China.
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Li YW, Chiang KY, Li YH, Wu SY, Liu W, Lin CR, Wu JL. MiR-145 mediates zebrafish hepatic outgrowth through progranulin A signaling. PLoS One 2017; 12:e0177887. [PMID: 28531199 PMCID: PMC5439702 DOI: 10.1371/journal.pone.0177887] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/04/2017] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRs) are mRNA-regulatory molecules that fine-tune gene expression and modulate both processes of development and tumorigenesis. Our previous studies identified progranulin A (GrnA) as a growth factor which induces zebrafish hepatic outgrowth through MET signaling. We also found that miR-145 is one of potential fine-tuning regulators of GrnA involved in embryonic hepatic outgrowth. The low level of miR-145 seen in hepatocarinogenesis has been shown to promote pathological liver growth. However, little is known about the regulatory mechanism of miR-145 in embryonic liver development. In this study, we demonstrate a significant decrease in miR-145 expression during hepatogenesis. We modulate miR-145 expression in zebrafish embryos by injection with a miR-145 mimic or a miR-145 hairpin inhibitor. Altered embryonic liver outgrowth is observed in response to miR-145 expression modulation. We also confirm a critical role of miR-145 in hepatic outgrowth by using whole-mount in situ hybridization. Loss of miR-145 expression in embryos results in hepatic cell proliferation, and vice versa. Furthermore, we demonstrate that GrnA is a target of miR-145 and GrnA-induced MET signaling is also regulated by miR-145 as determined by luciferase reporter assay and gene expression analysis, respectively. In addition, co-injection of GrnA mRNA with miR-145 mimic or MO-GrnA with miR-145 inhibitor restores the liver defects caused by dysregulation of miR-145 expression. In conclusion, our findings suggest an important role of miR-145 in regulating GrnA-dependent hepatic outgrowth in zebrafish embryonic development.
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Affiliation(s)
- Ya-Wen Li
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Keng-Yu Chiang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- Department of Life science, National Taiwan University, Taipei, Taiwan
| | - Yen-Hsing Li
- Department of Chemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Sung-Yu Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Wangta Liu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Lipid Science and Aging Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chia-Ray Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Jen-Leih Wu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
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The zebrafish miR-125c is induced under hypoxic stress via hypoxia-inducible factor 1α and functions in cellular adaptations and embryogenesis. Oncotarget 2017; 8:73846-73859. [PMID: 29088751 PMCID: PMC5650306 DOI: 10.18632/oncotarget.17994] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/06/2017] [Indexed: 12/15/2022] Open
Abstract
Hypoxia is a unique environmental stress. Hypoxia inducible factor-lα (HIF-lα) is a major transcriptional regulator of cellular adaptations to hypoxic stress. MicroRNAs (miRNAs) as posttranscriptional gene expression regulators occupy a crucial role in cell survival under low-oxygen environment. Previous evidences suggested that miR-125c is involved in hypoxia adaptation, but its precise biological roles and the regulatory mechanism underlying hypoxic responses remain unknown. The present study showed that zebrafish miR-125c is upregulated by hypoxia in a Hif-lα-mediated manner in vitro and in vivo. Dual-luciferase assay revealed that cdc25a is a novel target of miR-125c. An inverse correlation between miR-125c and cdc25a was further confirmed in vivo, suggesting miR-125c as a crucial physiological inhibitor of cdc25a which responds to cellular hypoxia. Overexpression of miR-125c suppressed cell proliferation, led to cell cycle arrest at the G1 phase in ZF4 cells and induced apoptotic responses during embryo development. More importantly, miR-125c overexpression resulted in severe malformation and reduction of motility during zebrafish embryonic development. Taken together, we conclude that miR-125c plays a pivotal role in cellular adaptations to hypoxic stress at least in part through the Hif-1α/miR-125c/cdc25a signaling and has great impact on zebrafish early embryonic development.
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Dynamics of miRNA transcriptome during gonadal development of zebrafish. Sci Rep 2017; 7:43850. [PMID: 28262836 PMCID: PMC5338332 DOI: 10.1038/srep43850] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/31/2017] [Indexed: 12/28/2022] Open
Abstract
Studies in non-teleost vertebrates have found microRNAs (miRNAs) to be essential for proper gonadal development. However, comparatively little is known about their role during gonadal development in teleost fishes. So far in zebrafish, a model teleost, transcript profiling throughout gonadal development has not been established because of a tiny size of an organ in juvenile stages and its poor distinguishability from surrounding tissues. We performed small RNA sequencing on isolated gonads of See-Thru-Gonad line, from the undifferentiated state at 3 weeks post fertilization (wpf) to fully mature adults at 24 wpf. We identified 520 gonadal mature miRNAs; 111 of them had significant changes in abundance over time, while 50 miRNAs were either testis- or ovary-enriched significantly in at least one developmental stage. We characterized patterns of miRNA abundance over time including isomiR variants. We identified putative germline versus gonadal somatic miRNAs through differential small RNA sequencing of isolated gametes versus the whole gonads. This report is the most comprehensive analysis of the miRNA repertoire in zebrafish gonads during the sexual development to date and provides an important database from which functional studies can be performed.
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Huang CX, Chen N, Wu XJ, He Y, Huang CH, Liu H, Wang WM, Wang HL. Zebrafish let-7b acts downstream of hypoxia-inducible factor-1α to assist in hypoxia-mediated cell proliferation and cell cycle regulation. Life Sci 2017; 171:21-29. [PMID: 28077310 DOI: 10.1016/j.lfs.2017.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/06/2017] [Accepted: 01/06/2017] [Indexed: 01/13/2023]
Abstract
AIMS Hypoxia-inducible factor-1α (HIF-1α) is a transcriptional regulator of cellular responses to hypoxic stress. MicroRNAs (miRNAs) play an essential role in hypoxia-mediated cellular responses. Previous studies have identified some let-7 family members as hypoxia-regulated miRNAs (HRMs). In the present study, we aimed to investigate whether zebrafish let-7b/7f contribute cellular hypoxic response in a Hif-1α-dependent manner. MAIN METHODS Stable suppression of zebrafish hif-1α was achieved by microinjection of an optimized short-hairpin RNA (shRNA) expression vector. Next-generation sequencing was conducted to characterize miRNA and mRNA expression profiles. MiRNA promoter analysis and target detection was performed by dual-luciferase assay. Quantitative real-time PCR (qRT-PCR) and western blot were used to determine the expression of let-7b/7f, Hif-1α and Foxh1. Proliferation of ZF4 cells was examined using Cell Counting Kit-8 (CCK-8) and cell cycle progression was analyzed by flow cytometry assay. KEY FINDINGS Correlation between 7 miRNAs and 76 putative targets was identified based on integrated analysis of miRNA-mRNA profiles. Let-7b and let-7f were further considered as potential HRMs, with let-7b further validated as Hif-1α up-regulated. In addition, Forkhead-box H1 (Foxh1) was confirmed as a bona fide downstream target of let-7b. Furthermore, overexpression of both let-7b and let-7f repressed cell proliferation through blocking cell cycle progression of the G1-S transition. SIGNIFICANCE Our findings for the first time suggest zebrafish let-7b acts downstream of Hif-1α to assist in hypoxia-mediated cell proliferation and cell cycle regulation at least in part through the downregulation of foxh1. We also identified 4 novel potential HIF-1α-regulated miRNAs in zebrafish.
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Affiliation(s)
- Chun-Xiao Huang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, China
| | - Nan Chen
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, China
| | - Xin-Jie Wu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, China
| | - Yan He
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, China
| | - Cui-Hong Huang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, China
| | - Hong Liu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, China
| | - Wei-Min Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, China
| | - Huan-Ling Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agricultural University, Wuhan, China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, China.
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