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Comparative Analysis of miRNA-mRNA Regulation in the Testes of Gobiocypris rarus following 17α-Methyltestosterone Exposure. Int J Mol Sci 2023; 24:ijms24044239. [PMID: 36835651 PMCID: PMC9968023 DOI: 10.3390/ijms24044239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/23/2023] Open
Abstract
17α-Methyltestosterone (17MT), a synthetic organic compound commonly found in sewage waters, can affect reproduction in aquatic animals, such as tilapia and yellow catfish. In the present study, male Gobiocypris rarus were exposed to 25, 50, and 100 ng/L of 17α-methyltestosterone (17MT) for 7 days. We first analyzed miRNA- and RNA-seq results to determine miRNA-target gene pairs and then developed miRNA-mRNA interactive networks after 17MT administration. Total weights, total lengths, and body lengths were not significantly different between the test groups and control groups. The paraffin slice method was applied to testes of G. rarus in the MT exposure and control groups. We found that there were more mature sperm (S) and fewer secondary spermatocytes (SSs) and spermatogonia (SGs) in the testes of control groups. As 17MT concentration increased, fewer and fewer mature sperm (S) were observed in the testes of male G. rarus. The results showed that FSH, 11-KT, and E2 were significantly higher in individuals exposed to 25 ng/L 17MT compared with the control groups. VTG, FSH, LH, 11-KT, and E2 were significantly lower in the 50 ng/L 17MT exposure groups compared to the control groups. VTG, FSH, LH, 11-KT, E2, and T were significantly lower in the groups exposed to 100 ng/L 17MT. High-throughput sequencing revealed 73,449 unigenes, 1205 known mature miRNAs, and 939 novel miRNAs in the gonads of G. rarus. With miRNA-seq, 49 (MT25-M vs. Con-M), 66 (MT50-M vs. Con-M), and 49 (MT100-M vs. Con-M) DEMs were identified in the treatment groups. Five mature miRNAs (miR-122-x, miR-574-x, miR-430-y, lin-4-x, and miR-7-y), as well as seven differentially expressed genes (soat2, inhbb, ihhb, gatm, faxdc2, ebp, and cyp1a1), which may be associated with testicular development, metabolism, apoptosis, and disease response, were assayed using qRT-PCR. Furthermore, miR-122-x (related to lipid metabolism), miR-430-y (embryonic development), lin-4-x (apoptosis), and miR-7-y (disease) were differentially expressed in the testes of 17MT-exposed G. rarus. This study highlights the role of miRNA-mRNA pairs in the regulation of testicular development and immune response to disease and will facilitate future studies on the miRNA-RNA-associated regulation of teleost reproduction.
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Zhu C, Liu G, Gu X, Yin J, Xia A, Han M, Zhang T, Jiang Q. Effect of quercetin on muscle growth and antioxidant status of the dark sleeper Odontobutis potamophila. Front Genet 2022; 13:938526. [PMID: 35957695 PMCID: PMC9358148 DOI: 10.3389/fgene.2022.938526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Quercetin is a flavanol beneficial in reducing fat, promoting muscle growth, and Anti-oxidation. To study its effects in freshwater fish, the full-length cDNA of the follistatin (FST) and myostatin (MSTN) genes of the dark sleeper Odontobutis potamophila were cloned for the first time. Juvenile individual O. potamophila was exposed to quercetin at one of four concentrations (0, 2.5, 5, and 10 mg/L) for 21 days. The expression level of MSTN which inhibits muscle growth in the quercetin solution was lower than in the unexposed control group. The genes that promote muscle growth are in TGF-β superfamily like FST, TGF-β1 (transforming growth factor-beta 1), and Myogenic regulatory factors (MRFs) like Myf5 (myogenic factor 5), MyoD (myogenic differentiation), MyoG (myogenin), were higher than in the control group. Apolipoprotein and growth hormone receptor transcription levels in the quercetin-treated fish were significantly lower than in the control group. The concentrations of triglyceride, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol in the muscle tissue decreased, and the lipid-lowering function of quercetin was also demonstrated at the biochemical level. In this study, we analyzed the mRNA levels of AKT, Keap1 (kelch-like ECH-associated protein 1), Nrf2 (NF-E2-related factor 2) oxidation-related genes in the Nrf2/ARE antioxidant pathway, and Malondialdehyde (MDA), catalase (CAT) activity and glutathione (GSH) content in the hepatopancreas of O. potamophila after quercetin treatment, the mRNA expression of AKT, Nrf2 and CAT activity and GSH content are higher than in the control group. Quercetin enhances antioxidant properties and positively affects muscle growth. The results showed that quercetin has no significant effects on the growth performance of O. potamophila, but is effective in increasing muscle growth rate and lowering muscle fat content.
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Affiliation(s)
- Chenxi Zhu
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Guoxing Liu
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiankun Gu
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
- The Lowtemperature Germplasm Bank of Important Economic Fish of Jiangsu Provincial Science and TechnologyResources (Agricultural Germplasm Resources) Coordination Service Platform, Freshwater Fisheries Research Institute of JiangsuProvince, NanjingChina
| | - Jiawen Yin
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
- The Lowtemperature Germplasm Bank of Important Economic Fish of Jiangsu Provincial Science and TechnologyResources (Agricultural Germplasm Resources) Coordination Service Platform, Freshwater Fisheries Research Institute of JiangsuProvince, NanjingChina
| | - Aijun Xia
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
- The Lowtemperature Germplasm Bank of Important Economic Fish of Jiangsu Provincial Science and TechnologyResources (Agricultural Germplasm Resources) Coordination Service Platform, Freshwater Fisheries Research Institute of JiangsuProvince, NanjingChina
| | - Mingming Han
- Biology Program, School of Distance Education, Universiti Sains Malaysia, Minden, Malaysia
| | - Tongqing Zhang
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
- The Lowtemperature Germplasm Bank of Important Economic Fish of Jiangsu Provincial Science and TechnologyResources (Agricultural Germplasm Resources) Coordination Service Platform, Freshwater Fisheries Research Institute of JiangsuProvince, NanjingChina
| | - Qichen Jiang
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
- The Lowtemperature Germplasm Bank of Important Economic Fish of Jiangsu Provincial Science and TechnologyResources (Agricultural Germplasm Resources) Coordination Service Platform, Freshwater Fisheries Research Institute of JiangsuProvince, NanjingChina
- *Correspondence: Qichen Jiang,
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Liu G, Li J, Jiang Z, Zhu X, Gao X, Jiang Q, Wang J, Wei W, Zhang X. Pathogenicity of Aeromonas veronii causing mass mortalities of Odontobutis potamophila and its induced host immune response. FISH & SHELLFISH IMMUNOLOGY 2022; 125:180-189. [PMID: 35561950 DOI: 10.1016/j.fsi.2022.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/03/2022] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Aeromonas veronii is a freshwater bacterium associated with many diseases in aquatic animals. However, few cases of A. veronii infection were reported in Odontobutis potamophila, which has been becoming a promising fish species in China in recent years. In this study, the dominant bacteria were isolated from diseased O. potamophila showing signs of hemorrhage on fins, ulceration on the dorsal and abdomen. The representative isolate Stl3-1was identified as A. veronii based on analysis of its morphological, physiological, and biochemical features, as well as 16S rRNA and gyrB gene sequences. The median lethal dosage (LD50) of the isolate Stl3-1 for O. potamophila was determined as 4.5 × 105 CFU/mL. Histopathological analysis revealed that the isolate Stl3-1caused considerable histological lesions in the fish, including tissue cell degeneration, necrosis, and inflammatory cell infiltrating. Detection of virulence-related genes showed that A. veronii Stl3-1 was positive for exu, ompA, lip, flaH, hlyA, aer, flgM, tapA, act, flgA, gcaT and flgN. Additionally, quantitive real-time PCR (qRT-PCR) was also undertaken to analyses the host defensive response in O. potamophila infected by A. veronii. The immune-related gene expressions in O. potamophila during experimental infection were monitored at different point of time, and the results showed that the expression levels of MHC II, Myd88, TLR, and SOD were significantly up-regulated in liver, gill, spleen, and head kidney. The results revealed that A. veronii was a pathogen causing mass mortalities of O. potamophila and will contribute to better understanding the host defensive response against A. veronii infection.
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Affiliation(s)
- Guoxing Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China; Research Center of Characteristic Fish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, 210017, China
| | - Jie Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Ziyan Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Xinhai Zhu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Xiaojian Gao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Qun Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Jun Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Wanhong Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Xiaojun Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
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Zhao H, Zhang L, Li Q, Zhao Z, Duan Y, Huang Z, Ke H, Liu C, Li H, Liu L, Du J, Wei Z, Mou C, Zhou J. Integrated analysis of the miRNA and mRNA expression profiles in Leiocassis longirostris at gonadal maturation. Funct Integr Genomics 2022; 22:655-667. [PMID: 35467220 DOI: 10.1007/s10142-022-00857-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 03/09/2022] [Accepted: 03/22/2022] [Indexed: 11/04/2022]
Abstract
Leiocassis longirostris is a commercially important fish species that shows a sexually dimorphic growth pattern. A lack of molecular data from the gonads of this species has hindered research and selective breeding efforts. In this study, we conducted a comprehensive analysis of the expression profile of miRNA and mRNA to explore their regulatory roles in the gonadal maturation stage of L. longirostris. We identified 60 differentially expressed miRNAs and 20,752 differentially expressed genes by sequencing. A total of 90 miRNAs and 21 target genes involved in gonad development and sex determination were identified. Overall, the results of this study enhance our understanding of the molecular mechanisms underlying sex determination and differentiation and provide valuable genomic information for the selective breeding of L. longirostris.
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Affiliation(s)
- Han Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611731, Sichuan, China
| | - Lu Zhang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611731, Sichuan, China
| | - Qiang Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611731, Sichuan, China
| | - Zhongmeng Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611731, Sichuan, China
| | - Yuanliang Duan
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611731, Sichuan, China
| | - Zhipeng Huang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611731, Sichuan, China
| | - Hongyu Ke
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611731, Sichuan, China
| | - Chao Liu
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611731, Sichuan, China
| | - Huadong Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611731, Sichuan, China
| | - Lu Liu
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611731, Sichuan, China
| | - Jun Du
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611731, Sichuan, China
| | - Zhen Wei
- Leiocassis Longirostris Foundation Seed Farm, Sichuan Province, China
| | - Chengyan Mou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611731, Sichuan, China
| | - Jian Zhou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611731, Sichuan, China.
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Zhong H, Guo Z, Xiao J, Zhang H, Luo Y, Liang J. Comprehensive Characterization of Circular RNAs in Ovary and Testis From Nile Tilapia. Front Vet Sci 2022; 9:847681. [PMID: 35464370 PMCID: PMC9019548 DOI: 10.3389/fvets.2022.847681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/09/2022] [Indexed: 11/16/2022] Open
Abstract
Circular RNA (circRNA) is an endogenous biomolecule in eukaryotes. It has tissue- and cell-specific expression patterns and can act as a microRNA sponge or competitive endogenous RNA. Although circRNA has been found in several species in recent years, the expression profiles in fish gonad are still not fully understood. We detected the expression of circRNA in the ovary, testis, and sex-changed gonad of tilapia by high-throughput deep sequencing, and circRNA-specific computing tools. A total of 20,607 circRNAs were obtained, of which 141 were differentially expressed in the testis and ovary. Among these circRNAs, 135 circRNAs were upregulated and 6 circRNAs were downregulated in female fish. In addition, GO annotation and KEGG pathway analysis of the host genes of circRNAs indicated that these host genes were mainly involved in adherens junction, androgen production, and reproductive development, such as ZP3, PLC, delta 4a, ARHGEF10, and HSD17b3. It is worth noting that we found that circRNAs in tilapia gonads have abundant miRNA-binding sites. Among them, 935 circRNAs have a regulatory effect on miR-212, 856 circRNAs have a regulatory effect on miR-200b-3p, and 529 circRNAs have a regulatory effect on miR-200b-5p. Thus, our findings provide a new evidence for circRNA–miRNA networks in the gonads in tilapia.
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Affiliation(s)
- Huan Zhong
- Hunan Research Center of Engineering Technology for Utilization of Distinctive Aquatic Resource, College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Zhongbao Guo
- Guangxi Tilapia Genetic Breeding Center, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Jun Xiao
- Guangxi Tilapia Genetic Breeding Center, Guangxi Academy of Fishery Sciences, Nanning, China
- *Correspondence: Jun Xiao
| | - Hong Zhang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, China
| | - Yongju Luo
- Guangxi Tilapia Genetic Breeding Center, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Junneng Liang
- Guangxi Tilapia Genetic Breeding Center, Guangxi Academy of Fishery Sciences, Nanning, China
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6
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Li J, Zhang G, Yin D, Li Y, Zhang Y, Cheng J, Zhang K, Ji J, Wang T, Jia Y, Yin S. Integrated application of multi-omics strategies provides insights into the environmental hypoxia response in Pelteobagrus vachelli muscle. Mol Cell Proteomics 2022; 21:100196. [PMID: 35031490 PMCID: PMC8938323 DOI: 10.1016/j.mcpro.2022.100196] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 11/07/2021] [Accepted: 01/05/2022] [Indexed: 11/28/2022] Open
Abstract
Increasing pressures on aquatic ecosystems because of pollutants, nutrient enrichment, and global warming have severely depleted oxygen concentrations. This sudden and significant lack of oxygen has resulted in persistent increases in fish mortality rates. Revealing the molecular mechanism of fish hypoxia adaptation will help researchers to find markers for hypoxia induced by environmental stress. Here, we used a multiomics approach to identify several hypoxia-associated miRNAs, mRNAs, proteins, and metabolites involved in diverse biological pathways in the muscles of Pelteobagrus vachelli. Our findings revealed significant hypoxia-associated changes in muscles over 4 h of hypoxia exposure and discrete tissue-specific patterns. We have previously reported that P. vachelli livers exhibit increased anaerobic glycolysis, heme synthesis, erythropoiesis, and inhibit apoptosis when exposed to hypoxia for 4 h. However, the opposite was observed in muscles. According to our comprehensive analysis, fishes show an acute response to hypoxia, including activation of catabolic pathways to generate more energy, reduction of biosynthesis to decrease energy consumption, and shifting from aerobic to anaerobic metabolic contributions. Also, we found that hypoxia induced muscle dysfunction by impairing mitochondrial function, activating inflammasomes, and apoptosis. The hypoxia-induced mitochondrial dysfunction enhanced oxidative stress, apoptosis, and further triggered interleukin-1β production via inflammasome activation. In turn, interleukin-1β further impaired mitochondrial function or apoptosis by suppressing downstream mitochondrial biosynthesis–related proteins, thus resulting in a vicious cycle of inflammasome activation and mitochondrial dysfunction. Our findings contribute meaningful insights into the molecular mechanisms of hypoxia, and the methods and study design can be utilized across different fish species. First multiomics analysis of mRNA, miRNA, protein, and metabolite in fishes. Liver and muscle were tissue-specific induced by hypoxia. About 70 genes and 16 miRNAs related to hypoxia adaptation were detected. Hypoxia affects muscle function by mediating energy metabolism via HIF pathway.
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Affiliation(s)
- Jie Li
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China; Key Laboratory for Physiology Biochemistry and Application, Heze University, Heze, 274015, China
| | - Guosong Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China; Key Laboratory for Physiology Biochemistry and Application, Heze University, Heze, 274015, China.
| | - Danqing Yin
- School of Computer Science, University of Sydney, Sydney, 2006, Australia
| | - Yao Li
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yiran Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Jinghao Cheng
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Kai Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Jie Ji
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Tao Wang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yongyi Jia
- Zhejiang Institute of Freshwater Fisheries, Huzhou, 313001, China
| | - Shaowu Yin
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, China.
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7
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Liu S, Yang Q, Chen Y, Liu Q, Wang W, Song J, Zheng Y, Liu W. Integrated Analysis of mRNA- and miRNA-Seq in the Ovary of Rare Minnow Gobiocypris rarus in Response to 17α-Methyltestosterone. Front Genet 2021; 12:695699. [PMID: 34421998 PMCID: PMC8375321 DOI: 10.3389/fgene.2021.695699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
17α-Methyltestosterone (MT) is a synthetic androgen. The objective of this study was to explore the effects of exogenous MT on the growth and gonadal development of female rare minnow Gobiocypris rarus. Female G. rarus groups were exposed to 25–100 ng/L of MT for 7 days. After exposure for 7 days, the total weight and body length were significantly decreased in the 50-ng/L MT groups. The major oocytes in the ovaries of the control group were vitellogenic oocytes (Voc) and cortical alveolus stage oocytes (Coc). In the MT exposure groups, some fish had mature ovaries with a relatively lower proportion of mature oocytes, and the diameter of the perinucleolar oocytes (Poc) was decreased compared with those of the control group. Ovarian VTG, FSH, LH, 11-KT, E2, and T were significantly increased after exposure to 50 ng/L of MT for 7 days. Unigenes (73,449), 24 known mature microRNAs (miRNAs), and 897 novel miRNAs in the gonads of G. rarus were found using high-throughput sequencing. Six mature miRNAs (miR-19, miR-183, miR-203, miR-204, miR-205, and miR-96) as well as six differentially expressed genes (fabp3, mfap4, abca1, foxo3, tgfb1, and zfp36l1) that may be associated with ovarian development and innate immune response were assayed using qPCR. Furthermore, the miR-183 cluster and miR-203 were differentially expressed in MT-exposed ovaries of the different G. rarus groups. This study provides some information about the role of miRNA–mRNA pairs in the regulation of ovarian development and innate immune system, which will facilitate future studies of the miRNA–RNA-associated regulation of teleost reproduction.
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Affiliation(s)
- Shaozhen Liu
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Qiong Yang
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Yue Chen
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Qing Liu
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Weiwei Wang
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Jing Song
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Yao Zheng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Wenzhong Liu
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
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Ma Z, Yang J, Zhang Q, Xu C, Wei J, Sun L, Wang D, Tao W. miR-133b targets tagln2 and functions in tilapia oogenesis. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110637. [PMID: 34147671 DOI: 10.1016/j.cbpb.2021.110637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/08/2021] [Accepted: 06/16/2021] [Indexed: 10/21/2022]
Abstract
microRNAs (miRNAs) are important components of non-coding RNAs that participate in diverse life activities by regulating gene expression at the post transcriptional level through base complementary pairing with 3'UTRs of target mRNAs. miR-133b is a member of the miR-133 family, which play important roles in muscle differentiation and tumorigenesis. Recently, miR-133b was reported to affect estrogen synthesis by targeting foxl2 in mouse, while its role in fish reproduction remains to be elucidated. In the present study, we isolated the complete sequence of miR-133b, which was highly expressed in tilapia ovary at 30 and 90 dah (days after hatching) and subsequently decreased at 120 to 150 dah by qPCR. Interestingly, only a few oogonia were remained in the antagomir-133b treated tilapia ovary, while phase I and II oocytes were observed in the ovaries of the control group. Unexpectedly, the expression of foxl2 and cyp19a1a, as well as estradiol levels in serum were increased in the treated group. Furthermore, tagln2, an important factor for oogenesis, was predicted as the target gene of miR-133b, which was confirmed by dual luciferase reporter vector experiments. miR-133b and tagln2 were co-expressed in tilapia ovaries. Taken together, miR-133b may be involved in the early oogenesis of tilapia by regulating tagln2 expression. This study enriches the understanding of miR-133b function during oogenesis and lays a foundation for further study of the regulatory network during oogenesis.
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Affiliation(s)
- Zhisheng Ma
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jing Yang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Qingqing Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Chunmei Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jing Wei
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Lina Sun
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
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Luo BY, Xiong XY, Liu X, He XY, Qiu GF. Identification and characterization of sex-biased and differentially expressed miRNAs in gonadal developments of the Chinese mitten crab, Eriocheir sinensis. Mol Reprod Dev 2021; 88:217-227. [PMID: 33655621 DOI: 10.1002/mrd.23459] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 12/25/2020] [Accepted: 02/02/2021] [Indexed: 01/02/2023]
Abstract
MicroRNA (miRNA) is a posttranscriptional downregulator that plays a vital role in a wide variety of biological processes. In this study, we constructed five ovarian and testicular small RNA libraries using two somatic libraries as reference controls for the identification of sex-biased miRNAs and gonadal differentially expressed miRNAs (DEMs) of the Chinese mitten crab, Eriocheir sinensis. A total of 535 known and 243 novel miRNAs were identified, including 312 sex-biased miRNAs and 402 gonadal DEMs. KEGG pathway analysis showed that DEM target genes were statistically enriched in MAPK, Wnt, and GnRH signaling pathway, and so on. A number of the sex-biased miRNAs target genes associated with sex determination/differentiation, such as IAG, Dsx, Dmrt1, and Fem1, while others target the genes related to gonadal development, such as P450s, Wnt, Ef1, and Tra-2c. Dual-luciferase reporter assay in vitro further confirmed that miR-34 and let-7b can downregulate IAG expression, miR-9-5p, let-7d, let-7b, and miR-8915 can downregulate Dsx. Taken together, these data strongly suggest a potential role for the sex-biased miRNAs in sex determination/differentiation and gonadal development in the crab.
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Affiliation(s)
- Bi-Yun Luo
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Xin-Yi Xiong
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Xue Liu
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Xue-Ying He
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Gao-Feng Qiu
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
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10
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Jia Y, Zheng J, Liu S, Li F, Chi M, Cheng S, Gu Z. A Chromosome-Level Genome Assembly of the Dark Sleeper Odontobutis potamophila. Genome Biol Evol 2021; 13:6134080. [PMID: 33576781 PMCID: PMC7883661 DOI: 10.1093/gbe/evaa271] [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] [Accepted: 12/22/2020] [Indexed: 01/20/2023] Open
Abstract
The dark sleeper, Odontobutis potamophila, is a commercially valuable fish that widely distributed in China and Southeast Asia countries. The phenomenon of sexual dimorphism in growth is conspicuous, which the males grow substantially larger and faster than the females. However, the high-quality genome resources for gaining insight into sex-determining mechanisms to develop sex-control breeding are still lacking. Here, a chromosomal-level genome assembly of O. potamophila was generated from a combination of Illumina reads, 10× Genomics sequencing, and Hi-C chromatin interaction sequencing. The assembled genome was 1,134.62 Mb with a contig N50 of 22.25 Mb and a scaffold N50 of 24.85 Mb, representing 94.4% completeness (Benchmarking Universal Single-Copy Orthologs). Using Hi-C data, 96.49% of the total contig bases were anchored to the 22 chromosomes, with a contig N50 of 22.25 Mb and a scaffold N50 of 47.68 Mb. Approximately 54.18% of the genome were identified as repetitive elements, and 23,923 protein-coding genes were annotated in the genome. The assembled genome can be used as a valuable resource for molecular breeding and functional studies of O. potamophila in the future.
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Affiliation(s)
- Yongyi Jia
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Jianbo Zheng
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Shili Liu
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Fei Li
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Meili Chi
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Shun Cheng
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Zhimi Gu
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
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11
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Identification and characterization of miRNA expression profiles across five tissues in giant panda. Gene 2020; 769:145206. [PMID: 33059030 DOI: 10.1016/j.gene.2020.145206] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/15/2020] [Accepted: 09/29/2020] [Indexed: 12/29/2022]
Abstract
microRNA (miRNA) is a small endogenous noncoding RNA molecule that plays multiple roles in regulating most biological processes. However, for China's national treasure giant panda, a world-famous rare and protected species, reports of its miRNA have been found only in blood and breast milk. To explore the miRNA expression differences between different giant panda tissues, here, we generated the miRNA profiles of five tissues (heart, liver, spleen, lung, and kidney) from four giant pandas with Illumina Hiseq 2500 platform, and filtered the differentially expressed miRNAs (DEmiRs) in each tissue, predicted the target genes of miRNA from each tissue based on the DEmiRs. Then, the GO and KEGG enrichment analysis were conducted using the target genes predicted from DEmiRs in each tissue. The RNA-seq generated an average of 0.718 GB base per sample. A total of 1,256 known miRNAs and 12 novel miRNAs were identified, and there were 215, 131, 185, 83, and 126 tissue-specific DEmiRs filtered in the heart, liver, spleen, lung, and kidney, respectively, including miR-1b-5p, miR-122-5p, miR-143, miR-126-5p, and miR-10b-5p, respectively. The predicted target genes, including MYL2, LRP5, MIF, CFD, and PEBP1 in the heart, liver, spleen, lung, and kidney, respectively, were closely associated with tissue-specific biological functions. The enrichment analysis results of target genes showed tissue-specific characteristics, such as the significantly enriched GO terms extracellular matrix in the heart and insulin-like growth factor binding in the liver. The miRNA profiles of the heart, liver, spleen, lung, and kidney of giant panda have been reported in this study, it reveals the miRNA expression differences between different tissues of the giant panda, and provides valuable genetic resources for the further related molecular genetic research of the rare and protected species giant panda and other mammals.
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12
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Identification and Comparison of microRNAs in the Gonad of the Yellowfin Seabream ( Acanthopagrus Latus). Int J Mol Sci 2020; 21:ijms21165690. [PMID: 32784462 PMCID: PMC7461063 DOI: 10.3390/ijms21165690] [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: 07/02/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/14/2022] Open
Abstract
Yellowfin seabream (Acanthopagrus latus) is a commercially important fish in Asian coastal waters. Although natural sex reversal has been described in yellowfin seabream, the mechanisms underlying sexual differentiation and gonadal development in this species remain unclear. MicroRNAs (miRNAs) have been shown to play crucial roles in gametogenesis and gonadal development. Here, two libraries of small RNAs, constructed from the testes and ovaries of yellowfin seabream, were sequenced. Across both gonads, we identified 324 conserved miRNAs and 92 novel miRNAs: 67 ovary-biased miRNAs, including the miR-200 families, the miR-29 families, miR-21, and miR-725; and 88 testis-biased miRNAs, including the let-7 families, the miR-10 families, miR-7, miR-9, and miR-202-3p. GO (Gene Ontology) annotations and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses of putative target genes indicated that many target genes were significantly enriched in the steroid biosynthesis pathway and in the reproductive process. Our integrated miRNA-mRNA analysis demonstrated a putative negatively correlated expression pattern in yellowfin seabream gonads. This study profiled the expression patterns of sex-biased miRNAs in yellowfin seabream gonads, and provided important molecular resources that will help to clarify the miRNA-mediated post-transcriptional regulation of sexual differentiation and gonadal development in this species.
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13
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Identification of miRNA-mRNA Crosstalk in Respiratory Syncytial Virus- (RSV-) Associated Pediatric Pneumonia through Integrated miRNAome and Transcriptome Analysis. Mediators Inflamm 2020; 2020:8919534. [PMID: 32410870 PMCID: PMC7211260 DOI: 10.1155/2020/8919534] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/03/2020] [Accepted: 03/28/2020] [Indexed: 12/13/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the most common respiratory virus and is associated with pediatric pneumonia, causing bronchiolitis and significant mortality in infants and young children. MicroRNAs (miRNAs) are endogenous noncoding small RNAs that function in gene regulation and are associated with host immune response and disease progression. In the present study, we profiled the global transcriptome and miRNAome of whole blood samples from children with mild or severe RSV-associated pneumonia, aiming to identify the potential biomarkers and investigate the molecular mechanisms of severe RSV-associated pediatric pneumonia. We found that expression profiles of whole blood microRNAs and mRNAs were altered and distinctly different in children with severe RSV-associated pneumonia. In particular, the four most significantly upregulated miRNAs in children with severe RSV-associated pneumonia were hsa-miR-1271-5p, hsa-miR-10a-3p, hsa-miR-125b-5p, and hsa-miR-30b-3p. The severe RSV-associated pneumonia-specific differentially expressed miRNA target interaction network was also contrasted. These target genes were further analyzed with Gene Ontology enrichment analysis. We found that most of the target genes were involved in inflammatory and immune responses, including the NF-κB signaling pathway, the MAPK signaling pathway, and T cell receptor signaling. Our findings will contribute to the identification of biomarkers and new drug design strategies to treat severe RSV-associated pediatric pneumonia.
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14
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Yu Q, Peng C, Ye Z, Tang Z, Li S, Xiao L, Liu S, Yang Y, Zhao M, Zhang Y, Lin H. An estradiol-17β/miRNA-26a/cyp19a1a regulatory feedback loop in the protogynous hermaphroditic fish, Epinephelus coioides. Mol Cell Endocrinol 2020; 504:110689. [PMID: 31891771 DOI: 10.1016/j.mce.2019.110689] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 12/27/2022]
Abstract
Cyp19a1a is a key gene responsible for the production of estradiol-17β (E2), the main functional estrogen and a major downstream regulator of reproduction in teleost fish. It is widely known that CYP19 gene expression, aromatase activity, and E2 production can influence gonadal differentiation and sex reversal in teleost fish, but the feedback mechanisms whereby E2 regulates cyp19a1a remain poorly understood, especially regarding the potential roles of endogenous small RNA molecules (miRNAs). Here, we identified miR-26a-5p as a regulatory factor of its predicted target gene (cyp19a1a). In vitro and in vivo studies showed that miR-26a-5p can decrease cyp19a1a expression. Furthermore, high doses of E2 act as a repressor of miR-26a-5p. This study proposes a regulatory feedback loop whereby E2 regulates cyp19a1a through miR-26a-5p, and suggests that this positive feedback is an important aspect of the control of E2 production.
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Affiliation(s)
- Qi Yu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266373, China; Southern Marine Science and Engineering Guangdong Laboratory (ZhanJiang), Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Cheng Peng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, PR China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260, China
| | - Zhifeng Ye
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, PR China
| | - Zhujing Tang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, PR China
| | - Shuisheng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (ZhanJiang), Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Ling Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (ZhanJiang), Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Su Liu
- Marine Fisheries Development Center of Guangdong Province, Huizhou, 516081, China
| | - Yuqing Yang
- Marine Fisheries Development Center of Guangdong Province, Huizhou, 516081, China
| | - Mi Zhao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, PR China.
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266373, China; Southern Marine Science and Engineering Guangdong Laboratory (ZhanJiang), Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China; Marine Fisheries Development Center of Guangdong Province, Huizhou, 516081, China.
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, PR China
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15
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Chen Y, Zhang M, Jin X, Tao H, Wang Y, Peng B, Fu C, Yu L. Transcriptional reprogramming strategies and miRNA-mediated regulation networks of Taxus media induced into callus cells from tissues. BMC Genomics 2020; 21:168. [PMID: 32070278 PMCID: PMC7029464 DOI: 10.1186/s12864-020-6576-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 02/11/2020] [Indexed: 11/10/2022] Open
Abstract
Background Taxus cells are a potential sustainable and environment-friendly source of taxol, but they have low survival ratios and slow grow rates. Despite these limitations, Taxus callus cells induced through 6 months of culture contain more taxol than their parent tissues. In this work, we utilized 6-month-old Taxus media calli to investigate their regulatory mechanisms of taxol biosynthesis by applying multiomics technologies. Our results provide insights into the adaptation strategies of T. media by transcriptional reprogramming when induced into calli from parent tissues. Results Seven out of 12 known taxol, most of flavonoid and phenylpropanoid biosynthesis genes were significantly upregulated in callus cells relative to that in the parent tissue, thus indicating that secondary metabolism is significantly strengthened. The expression of genes involved in pathways metabolizing biological materials, such as amino acids and sugars, also dramatically increased because all nutrients are supplied from the medium. The expression level of 94.1% genes involved in photosynthesis significantly decreased. These results reveal that callus cells undergo transcriptional reprogramming and transition into heterotrophs. Interestingly, common defense and immune activities, such as “plant–pathogen interaction” and salicylic acid- and jasmonic acid-signaling transduction, were repressed in calli. Thus, it’s an intelligent adaption strategy to use secondary metabolites as a cost-effective defense system. MiRNA- and degradome-sequencing results showed the involvement of a precise regulatory network in the miRNA-mediated transcriptional reprogramming of calli. MiRNAs act as direct regulators to enhance the metabolism of biological substances and repress defense activities. Given that only 17 genes of secondary metabolite biosynthesis were effectively regulated, miRNAs are likely to play intermediate roles in the biosynthesis of secondary metabolites by regulating transcriptional factors (TFs), such as ERF, WRKY, and SPL. Conclusion Our results suggest that increasing the biosynthesis of taxol and other secondary metabolites is an active regulatory measure of calli to adapt to heterotrophic culture, and this alteration mainly involved direct and indirect miRNA-induced transcriptional reprogramming. These results expand our understanding of the relationships among the metabolism of biological substances, the biosynthesis of secondary metabolites, and defense systems. They also provide a series of candidate miRNAs and transcription factors for taxol biosynthesis.
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Affiliation(s)
- Ying Chen
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, People's Republic of China.,Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, People's Republic of China.,Hubei Engineering Research Center for Edible and Medicinal Resources, Wuhan, 430074, People's Republic of China
| | - Meng Zhang
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, People's Republic of China.,Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, People's Republic of China.,Hubei Engineering Research Center for Edible and Medicinal Resources, Wuhan, 430074, People's Republic of China
| | - Xiaofei Jin
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, People's Republic of China.,Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, People's Republic of China.,Hubei Engineering Research Center for Edible and Medicinal Resources, Wuhan, 430074, People's Republic of China
| | - Haoran Tao
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, People's Republic of China.,Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, People's Republic of China.,Hubei Engineering Research Center for Edible and Medicinal Resources, Wuhan, 430074, People's Republic of China
| | - Yamin Wang
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, People's Republic of China.,Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, People's Republic of China.,Hubei Engineering Research Center for Edible and Medicinal Resources, Wuhan, 430074, People's Republic of China
| | - Bo Peng
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, People's Republic of China.,Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, People's Republic of China.,Hubei Engineering Research Center for Edible and Medicinal Resources, Wuhan, 430074, People's Republic of China
| | - Chunhua Fu
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, People's Republic of China. .,Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, People's Republic of China. .,Hubei Engineering Research Center for Edible and Medicinal Resources, Wuhan, 430074, People's Republic of China.
| | - Longjiang Yu
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, People's Republic of China.,Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, People's Republic of China.,Hubei Engineering Research Center for Edible and Medicinal Resources, Wuhan, 430074, People's Republic of China
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Lobo IKC, Nascimento ÁRD, Yamagishi MEB, Guiguen Y, Silva GFD, Severac D, Amaral ADC, Reis VR, Almeida FLD. Transcriptome of tambaqui Colossoma macropomum during gonad differentiation: Different molecular signals leading to sex identity. Genomics 2020; 112:2478-2488. [PMID: 32027957 DOI: 10.1016/j.ygeno.2020.01.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/11/2020] [Accepted: 01/31/2020] [Indexed: 12/13/2022]
Abstract
Tambaqui (Colossoma macropomum) is the major native species in Brazilian aquaculture, and we have shown that females exhibit a higher growth compared to males, opening up the possibility for the production of all-female population. To date, there is no information on the sex determination and differentiation molecular mechanisms of tambaqui. In the present study, transcriptome sequencing of juvenile trunks was performed to understand the molecular network involved in the gonadal sex differentiation. The results showed that before differentiation, components of the Wnt/β-catenin pathway, fox and fst genes imprint female sex development, whereas antagonistic pathways (gsk3b, wt1 and fgfr2), sox9 and genes for androgen synthesis indicate male differentiation. Hence, in undifferentiated tambaqui, the Wnt/β-catenin exerts a role on sex differentiation, either upregulated in female-like individuals, or antagonized in male-like individuals.
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Affiliation(s)
| | | | | | - Yann Guiguen
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France.
| | | | - Dany Severac
- MGX, Univ Montpellier, CNRS, INSERM, Montpellier, France.
| | - Aldessandro da Costa Amaral
- Programa de Pós-graduação em Ciências Pesqueiras nos Trópicos, Universidade Federal do Amazonas, Manaus, Brazil
| | - Vanessa Ribeiro Reis
- Programa de Pós-graduação em Biotecnologia, Universidade Federal do Amazonas, Manaus, Brazil
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17
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Wang T, Zhu W, Zhang H, Wen X, Yin S, Jia Y. Integrated analysis of proteomics and metabolomics reveals the potential sex determination mechanism in Odontobutis potamophila. J Proteomics 2019; 208:103482. [PMID: 31401171 DOI: 10.1016/j.jprot.2019.103482] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/28/2019] [Accepted: 08/05/2019] [Indexed: 02/06/2023]
Abstract
Odontobutis potamophila is a valuable species for aquaculture in China, which shows asexually dimorphic growth pattern. In this study, the integrated proteomics and metabolomics were used to analyze the sex determination mechanism. A total of 2781 significantly different regulated proteins were identified by proteomics and 2693 significantly different expressed metabolites were identified by metabolomics. Among them, 2560 proteins and 1701 metabolites were significantly up-regulated in testes, whereas 221 proteins and 992 metabolites were significantly up-regulated in ovaries. Venn diagram analysis showed 513 proteins were differentially regulated at both protein and metabolite levels. Correlation analysis of differentially-regulated proteins and metabolites were identified by Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway analysis. The results showed lipid metabolism plays an important role in sex determination. The metabolites decanoyl-CoA, leukotriene, 3-dehydrosphinganine, and arachidonate were the biomarkers in testes, whereas estrone and taurocholate were the biomarkers in ovaries. Interaction networks of the significant differentially co-regulated proteins and metabolites in the process of lipid metabolism showed arachidonic acid metabolism and steroid hormone biosynthesis were the most important pathways in sex determination. The findings of this study provide valuable information for selective breeding of O. potamophila. SIGNIFICANCE OF THE STUDY: The male O. potamophila grows substantially larger and at a quicker rate than the female. Thus, males have greater economic value than females. However, limited research was done to analyze the sex determination mechanism of O. potamophila, which seriously hindered the development of whole-male O. potamophila breeding. In this study, four key proteins (Ctnnb1, Piwil1, Hsd17b1, and Dnali1), six most important biomarkers (decanoyl-CoA, leukotriene, 3-dehydrosphinganine, arachidonate, estrone, and taurocholate) and two key pathways (arachidonic acid metabolism and steroid hormone biosynthesis) in sex determination of O. potamophila were found by integrated application of iTRAQ and LC-MS techniques. The results give valuable information for molecular breeding of O. potamophila in aquaculture.
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Affiliation(s)
- Tao Wang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Wenxu Zhu
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Hongyan Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Xin Wen
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Shaowu Yin
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China.
| | - Yongyi Jia
- Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China.
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18
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Zhang G, Li J, Zhang J, Liang X, Zhang X, Wang T, Yin S. Integrated Analysis of Transcriptomic, miRNA and Proteomic Changes of a Novel Hybrid Yellow Catfish Uncovers Key Roles for miRNAs in Heterosis. Mol Cell Proteomics 2019; 18:1437-1453. [PMID: 31092672 PMCID: PMC6601203 DOI: 10.1074/mcp.ra118.001297] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/09/2019] [Indexed: 01/14/2023] Open
Abstract
Heterosis is a complex biological phenomenon in which hybridization produces offspring that exhibit superior phenotypic characteristics compared with the parents. Heterosis is widely utilized in agriculture, for example in fish farming; however, its underlying molecular basis remains elusive. To gain a comprehensive and unbiased molecular understanding of fish heterosis, we analyzed the mRNA, miRNA, and proteomes of the livers of three catfish species, Pelteobagrus fulvidraco, P. vachelli, and their hybrid, the hybrid yellow catfish "Huangyou-1" (P. fulvidraco ♀ × P. vachelli ♂). Using next-generation sequencing and mass spectrometry, we show that the nonadditive, homoeolog expression bias and expression level dominance pattern were readily identified at the transcriptional, post-transcriptional, or protein levels, providing the evidence for the widespread presence of dominant models during hybridization. A number of predicted miRNA-mRNA-protein pairs were found and validated by qRT-PCR and PRM assays. Furthermore, several diverse key pathways were identified, including immune defense, metabolism, digestion and absorption, and cell proliferation and development, suggesting the vital mechanisms involved in the generation of the heterosis phenotype in progenies. We propose that the high parental expression of genes/proteins (growth, nutrition, feeding, and disease resistance) coupled with low parental miRNAs of the offspring, are inherited from the mother or father, thus indicating that the offspring were enriched with the advantages of the father or mother. We provide new and important information about the molecular mechanisms of heterosis, which represents a significant step toward a more complete elucidation of this phenomenon.
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Affiliation(s)
- Guosong Zhang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; §Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong 274015, China
| | - Jie Li
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Jiajia Zhang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Xia Liang
- §Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong 274015, China
| | - Xinyu Zhang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Tao Wang
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Shaowu Yin
- From the ‡College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;; ¶Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China.
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Shu Y, Zhang H, Cai Q, Tang D, Wang G, Liu T, Lv B, Wu H. Integrated mRNA and miRNA expression profile analyses reveal the potential roles of sex-biased miRNA-mRNA pairs in gonad tissues of the Chinese concave-eared torrent frog (Odorrana tormota). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 332:69-80. [PMID: 30964604 DOI: 10.1002/jez.b.22851] [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: 08/07/2018] [Revised: 02/21/2019] [Accepted: 03/20/2019] [Indexed: 12/20/2022]
Abstract
The Chinese concave-eared torrent frog (Odorrana tormota) is typically sexually dimorphic. Females are significantly less common than males in the wild. Until now, the molecular mechanisms of reproduction and sex differentiation of frogs remain unclear. Here, we integrated mRNA and microRNA (miRNA) expression profiles to reveal the molecular mechanisms of reproduction and sex differentiation in O. tormota. We identified 234 differentially expressed miRNAs (DEMs) and 18,551 differentially expressed transcripts. Of these, 12,053 mRNAs and 64 miRNAs were upregulated in testes, and 6,498 mRNAs and 170 miRNAs were upregulated in ovaries. Integrated analysis of the miRNA and mRNA expression profiles predicted 75,602 potential miRNA-mRNA interaction sites, with 42,065 negative miRNA-mRNA interactions. We found 36 differentially expressed genes (DEGs) related to reproduction and sex differentiation, of which 15 DEGs formed 92 negative miRNA-mRNA interactions with 34 known DEMs. Thus, miRNAs may play other important roles in O. tormota. Furthermore, Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed reproductive-related processes, such as the gonadotropinreleasing hormone signaling pathway and ovarian steroidogenesis. Based on functional annotation and the literature, the retinoic acid signaling pathway, the SOX9-AMH pathway, and the process of spermatogenesis may be involved in the molecular mechanisms of reproduction and sex differentiation in O. tormota, and may be regulated by miRNAs. The miRNA-mRNA pairs described may provide further understanding of the regulatory mechanisms associated with reproduction and sex differentiation, and the molecular mechanism of reproduction in O. tormota.
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Affiliation(s)
- Yilin Shu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Huijuan Zhang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Qijia Cai
- Key Laboratory of Algal Biology of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Dong Tang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Gang Wang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Ting Liu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Bihua Lv
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hailong Wu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China
- College of Life Sciences, Anhui Normal University, Wuhu, China
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Abdelmoneim A, Abdu A, Chen S, Sepúlveda MS. Molecular signaling pathways elicited by 17α-ethinylestradiol in Japanese medaka male larvae undergoing gonadal differentiation. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 208:187-195. [PMID: 30682621 DOI: 10.1016/j.aquatox.2019.01.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/10/2019] [Accepted: 01/15/2019] [Indexed: 06/09/2023]
Abstract
Estrogenic contaminants released into water bodies are potentially affecting the reproduction of aquatic organisms. Exposure to 17α-ethinylestradiol (EE2), a synthetic estrogen agonist commonly found in sewage effluents, has been shown to cause gonadal changes in male gonochoristic fish ranging from gonadal intersex to complete sex reversal. Although these gonadal changes have been well studied in Japanese medaka Oryzias latipes, the molecular mechanisms behind them are poorly understood. Our objective was to study the signaling pathways elicited by exposure to different concentrations of EE2 in this species. Embryos and larvae were sexed by the presence of leucophores and dmy expression (only in males). Male medaka were exposed to two EE2 concentrations (30 and 300 ng/L) during their gonadal differentiation period (7-22 dpf). The transcriptome of larvae was analyzed using RNA sequencing followed by pathway analysis. Genes involved in sex differentiation and gonadal development (e.g., cldn19, ctbp1, hsd17b4) showed a female-like expression pattern in EE2-exposed males with some genes changing in expression in an EE2 concentration-dependent manner. However, not all genes known to be involved in sex differentiation and gonadal development (e.g., wnt4b) were altered by EE2. Several of the prominently affected signaling pathways involved genes associated with steroidogenesis, steroid receptor signaling and steroid metabolism, such as cyp2b3, cyp3b40, cyp1a, hsd17b4. We also report on novel genes and pathways affected that might play a role in gonadal changes, including several genes associated with FXR/RXR and LXR/RXR activation networks. This study is the first to examine the transcriptomic changes in male fish resulting from exposure to EE2 during the gonadal differentiation period, providing new insights on the signaling pathways involved in the development of gonadal changes in gonochoristic fish.
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Affiliation(s)
- Ahmed Abdelmoneim
- Department of Forestry & Natural Resources and Bindley Biological Sciences, Purdue University, West Lafayette, IN, USA; Department of Veterinary Forensic Medicine & Toxicology, Assiut University, Assiut, Egypt
| | - Amira Abdu
- Department of Forestry & Natural Resources and Bindley Biological Sciences, Purdue University, West Lafayette, IN, USA; Department of Parasitology, Assiut University, Assiut, Egypt
| | - Shuai Chen
- Department of Forestry & Natural Resources and Bindley Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Maria S Sepúlveda
- Department of Forestry & Natural Resources and Bindley Biological Sciences, Purdue University, West Lafayette, IN, USA.
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21
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Yong Huang, Chen H, Gao X, Sun X. Identification and Сharacteristics of Conserved miRNA in Testis Tissue from Chinese Giant Salamander (Andrias davidianus) by Deep Sequencing. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s106816201902016x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Breakpoint mapping at nucleotide resolution in X-autosome balanced translocations associated with clinical phenotypes. Eur J Hum Genet 2019; 27:760-771. [PMID: 30700833 DOI: 10.1038/s41431-019-0341-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/17/2018] [Accepted: 01/04/2019] [Indexed: 12/22/2022] Open
Abstract
Precise breakpoint mapping of balanced chromosomal rearrangements is crucial to identify disease etiology. Ten female patients with X-autosome balanced translocations associated with phenotypic alterations were evaluated, by mapping and sequencing their breakpoints. The rearrangements' impact on the expression of disrupted genes, and inferred mechanisms of formation in each case were assessed. For four patients that presented one of the chromosomal breaks in heterochromatic and highly repetitive segments, we combined cytogenomic methods and short-read sequencing to characterize, at nucleotide resolution, breakpoints that occurred in reference genome gaps. Most of rearrangements were possibly formed by non-homologous end joining and have breakpoints at repeat elements. Seven genes were found to be disrupted in six patients. Six of the affected genes showed altered expression, and the functional impairment of three of them were considered pathogenic. One gene disruption was considered potentially pathogenic, and three had uncertain clinical significance. Four patients presented no gene disruptions, suggesting other pathogenic mechanisms. Four genes were considered potentially affected by position effect and the expression abrogation of one of them was confirmed. This study emphasizes the importance of breakpoint-junction characterization at nucleotide resolution in balanced rearrangements to reveal genetic mechanisms associated with the patients' phenotypes, mechanisms of formation that originated the rearrangements, and genomic nature of disrupted DNA sequences.
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Chen L, Huang R, Zhu D, Yang C, He L, Li Y, Liao L, Zhu Z, Wang Y. Deep sequencing of small RNAs from 11 tissues of grass carp Ctenopharyngodon idella and discovery of sex-related microRNAs. JOURNAL OF FISH BIOLOGY 2019; 94:132-141. [PMID: 30471229 DOI: 10.1111/jfb.13875] [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: 03/22/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
This research identified 169 known microRNAs (miRNAs), 380 novel miRNAs, and 30,538 targets in 11 tissues (blood, brain, derma, gill, heart, intestine, kidney, liver, muscle, pronephros, and spleen) from grass carp Ctenopharyngodon idella with high-throughput sequencing (HTS). Transcripts per million (TPM) expression analysis detected 41 brain-enriched miRNAs (accounting for 61.19% of all tissue-enriched miRNAs). Real-time quantitative PCR (RT-qPCR) confirmed that 21 of 24 randomly selected tissue-enriched miRNAs from the TPM analysis were indeed tissue-enriched (P < 0.05), suggesting the HTS and TPM analyses were reliable. Nine of the 41 brain-enriched miRNAs are complementary to members of the double-sex and mab-3 related transcription factor family (dmrt) involved in sex differentiation. RT-qPCR revealed that cid-miR-138 was more highly expressed in testis than in ovary (P < 0.01), while the reverse was true for target gene dmrt4a (P < 0.01). This opposite expression pattern suggested the direct participation of cid-miR-138-dmrt4a in neuroendocrine mechanisms related to brain-pituitary networks during sex development. The discovery of miRNAs from 11 C. idella tissues expands the available fish miRNA database, and enhances our understanding of the role of sex-related miRNAs in tissue differentiation and maintenance of specific tissue functions in fishes.
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Affiliation(s)
- Liangming Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rong Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Denghui Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Libo He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yongming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Lanjie Liao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zuoyan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yaping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Identification and characteristics of muscle growth-related microRNA in the Pacific abalone, Haliotis discus hannai. BMC Genomics 2018; 19:915. [PMID: 30545311 PMCID: PMC6293614 DOI: 10.1186/s12864-018-5347-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/03/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Pacific abalone, Haliotis discus hannai, is the most important cultivated abalone in China. Improving abalone muscle growth and increasing the rate of growth are important genetic improvement programs in this industry. MicroRNAs are important small noncoding RNA molecules that regulate post-transcription gene expression. However, no miRNAs have been reported to regulate muscle growth in H. discus hannai. RESULTS we profiled six small RNA libraries for three large abalone individuals (L_HD group) and three small individuals (S_HD group) using RNA sequencing technology. A total of 205 miRNAs, including 200 novel and 5 known miRNAs, were identified. In the L_HD group, 3 miRNAs were up-regulated and 7 were down-regulated compared to the S_HD specimens. Bioinformatics analysis of miRNA target genes revealed that miRNAs participated in the regulation of cellular metabolic processes, the regulation of biological processes, the Wnt signaling pathway, ECM-receptor interaction, and the MAPK signaling pathway, which are associated with regulating growth. Bone morphogenetic protein 7 (BMP7) was verified as a target gene of hdh-miR-1984 by a luciferase reporter assay and we examined the expression pattern in different developmental stages. CONCLUSION This is the first study to demonstrate that miRNAs are related to the muscle growth of H. discus hannai. This information could be used to study the mechanisms of abalone muscle growth. These DE-miRNAs may be useful as molecular markers for functional genomics and breeding research in abalone and closely related species.
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Zhu W, Wang T, Zhao C, Wang D, Zhang X, Zhang H, Chi M, Yin S, Jia Y. Evolutionary conservation and divergence of Vasa, Dazl and Nanos1 during embryogenesis and gametogenesis in dark sleeper (Odontobutis potamophila). Gene 2018; 672:21-33. [PMID: 29885464 DOI: 10.1016/j.gene.2018.06.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 06/04/2018] [Accepted: 06/05/2018] [Indexed: 11/17/2022]
Abstract
Germline-specific genes, Vasa, Dazl and Nanos1, have highly conserved functions in germline development and fertility across animal phyla. In this study, the full-length sequences of Opvasa, Opdazl and Opnanos1 were cloned and characterized from the dark sleeper (Odontobutis potamophila). Gonad-specific expression patterns of Opvasa and Opdazl were confirmed in adult tissues by quantitative real-time PCR (qRT-PCR). Different from Opvasa and Opdazl, the expression of Opnanos1 was ubiquitously detected in all examined tissues except for the liver and spleen. Time-course dynamic expressions during embryogenesis were assessed, and all three genes (Opvasa, Opdazl and Opnanos1) persisted at a high level until gastrulation. qRT-PCR and Western blotting analyses revealed that all three genes were highly expressed throughout gametogenesis. In testis, the expressions of all three genes at the mRNA and protein levels were down-regulated during spermatogenesis. In ovary, different expression patterns were found, and all three genes had a differential role in translational regulation during oogenesis. The expressions of Opvasa, Opdazl and Opnanos1 at the mRNA but not the protein level were high in stage IV. Different expression patterns were found in premeiotic gonads treated by HPG axis hormones (HCG and LHRH-A). Immunolocalization analysis demonstrated that in testis, Opvasa, Opdazl and Opnanos1 were detected in spermatogonia and spermatocytes but absent in the meiotic products, such as spermatids and spermatozoa. In ovary, Opvasa, Opdazl and Opnanos1 persisted at a high level throughout oogenesis. These findings indicated that Opvasa, Opdazl and Opnanos1 played an important role in mitotic and early meiotic phases of oogenesis and spermatogenesis, and they functioned as maternal factors in early embryogenesis. Their proteins could be used as three new markers for germ cells during gametogenesis in O. potamophila gonad. Our data laid a good foundation for improving the breeding efficiency of O. potamophila.
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Affiliation(s)
- Wenxu Zhu
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Tao Wang
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Cheng Zhao
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Dan Wang
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Xinyu Zhang
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Hongyan Zhang
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Meili Chi
- Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China
| | - Shaowu Yin
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China.
| | - Yongyi Jia
- Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China.
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