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Gu Y, Jin CX, Tong ZH, Jiang T, Yao FC, Zhang Y, Huang J, Song FB, Sun JL, Luo J. Expression of genes related to gonadal development and construction of gonadal DNA methylation maps of Trachinotus blochii under hypoxia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173172. [PMID: 38740210 DOI: 10.1016/j.scitotenv.2024.173172] [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: 01/03/2024] [Revised: 04/12/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
Chronic hypoxia can affect the growth and metabolism of fish and potentially impact gonadal development through epigenetic regulation. Trachinotus blochii (Golden pompano) is widely cultured near the coast and is sensitive to low oxygen conditions. We found that hypoxia and reoxygenation processes acted on multiple targets on the HPG axis, leading to endocrine disorders. Changes in the expression of key genes in the brain (gnrh), pituitary (fsh and lh), ovaries (cyp19a1a, foxl2, and er), and testes (dmrt1, ar, sox9, and gsdf) were associated with significant decreases in estrogen and testosterone levels. Hypoxia and reoxygenation lead to changes in DNA methylation levels in the gonads. Hypoxia upregulated the expression of dnmt1, dnmt3a, dnmt3b, tet1, and tet2 in females and dnmt3a and dnmt3b in males, while reoxygenation down-regulated the expression of dnmt1, dnmt3a, dnmt3b, tet1, and tet2 in males. Whole genome methylation sequencing showed that the number of differentially methylated regions was highest on chromosome 10 (5192) and lowest on chromosome 24 (275). Differentially methylated genes in females and males, as well as between males and females, were enriched in the oxytocin signaling pathway, fatty acid metabolism pathway, and HIF-1a pathway. In summary, hypoxia and reoxygenation can induce endocrine disorders, affect the expression of HPG axis genes, change the methylation pattern and modification pattern of gonad DNA, and then have potential effects on gonad development.
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Affiliation(s)
- Yue Gu
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Chun Xiu Jin
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Zai Hui Tong
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Tian Jiang
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Fu Cheng Yao
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Yu Zhang
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Jie Huang
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Fei Biao Song
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Jun Long Sun
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China.
| | - Jian Luo
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China.
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Habibi E, Miller MR, Schreier A, Campbell MA, Hung TC, Gille D, Baerwald M, Finger AJ. Single generation epigenetic change in captivity and reinforcement in subsequent generations in a delta smelt (Hypomesus transpacificus) conservation hatchery. Mol Ecol 2024:e17449. [PMID: 38967124 DOI: 10.1111/mec.17449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 05/24/2024] [Accepted: 06/14/2024] [Indexed: 07/06/2024]
Abstract
A refugial population of the endangered delta smelt (Hypomesus transpacificus) has been maintained at the Fish Conservation and Culture Laboratory (FCCL) at UC Davis since 2008. Despite intense genetic management, fitness differences between wild and cultured fish have been observed at the FCCL. To investigate the molecular underpinnings of hatchery domestication, we used whole-genome bisulfite sequencing to quantify epigenetic differences between wild and hatchery-origin delta smelt. Differentially methylated regions (DMRs) were identified from 104 individuals by comparing the methylation patterns in different generations of hatchery fish (G1, G2, G3) with their wild parents (G0). We discovered a total of 132 significant DMRs (p < .05) between G0 and G1, 132 significant DMRs between G0 and G2, and 201 significant DMRs between G0 and G3. Our results demonstrate substantial differences in methylation patterns emerged between the wild and hatchery-reared fish in the early generations in the hatchery, with a higher proportion of hypermethylated DMRs in hatchery-reared fish. The rearing environment was found to be a stronger predictor of individual clustering based on methylation patterns than family, sex or generation. Our study indicates a reinforcement of the epigenetic status with successive generations in the hatchery environment, as evidenced by an increase in methylation in hypermethylated DMRs and a decrease in methylation in hypomethylated DMRs over time. Lastly, our results demonstrated heterogeneity in inherited methylation pattern in families across generations. These insights highlight the long-term consequences of hatchery practices on the epigenetic landscape, potentially impacting wild fish populations.
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Affiliation(s)
- Ensieh Habibi
- Department of Animal Science, University of California Davis, Davis, California, USA
| | - Michael R Miller
- Department of Animal Science, University of California Davis, Davis, California, USA
| | - Andrea Schreier
- Department of Animal Science, University of California Davis, Davis, California, USA
| | - Matthew A Campbell
- Department of Animal Science, University of California Davis, Davis, California, USA
| | - Tien-Chieh Hung
- Fish Conservation and Culture Laboratory, Biological and Agricultural Engineering Department, University of California Davis, Davis, California, USA
| | - Daphne Gille
- California Department of Water Resources, Division of Integrated Science and Engineering, West Sacramento, California, USA
| | - Melinda Baerwald
- California Department of Water Resources, Division of Integrated Science and Engineering, West Sacramento, California, USA
| | - Amanda J Finger
- Department of Animal Science, University of California Davis, Davis, California, USA
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Zhang Y, Wang Y, Liu Q, Wang H, Wang Q, Shao C. The Role of Z Chromosome Localization Gene psmd9 in Spermatogenesis of Cynoglossus semilaevis. Int J Mol Sci 2024; 25:6372. [PMID: 38928079 PMCID: PMC11203642 DOI: 10.3390/ijms25126372] [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: 03/19/2024] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Proteasome 26S Subunit, Non-ATPase 9 (psmd9) plays an important role in the balance of protamine and the stability of the nucleolar structure during spermatogenesis. In this study, we cloned the psmd9 of Cynoglossus semilaevis and analyzed its expression pattern. psmd9 was identified on the Z chromosome of C. semilaevis, which is considered an interesting candidate gene for spermatogenesis. qRT-PCR and FISH experiments showed that the psmd9 gene was significantly highly expressed in the testes. It is worth noting that the expression level of psmd9 in male fish testes is significantly higher than that in pseudomales. In order to further explore the role of psmd9 in spermatogenesis, a male testicular cell line was used as the experimental material. The results of the psmd9-RNAi and overexpression experiments showed that psmd9 had a synergistic effect with spermatogenesis-related genes dnd1, cfap69, dnah3 and dnajb13, but had an antagonistic effect with ccne2. Our findings offer a scientific foundation for comprehending the role of psmd9 in the spermatogenesis regulatory network of C. semilaevis.
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Affiliation(s)
- Yuman Zhang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Y.Z.); (Y.W.); (Q.L.); (H.W.)
| | - Yue Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Y.Z.); (Y.W.); (Q.L.); (H.W.)
| | - Qian Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Y.Z.); (Y.W.); (Q.L.); (H.W.)
| | - Hongyan Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Y.Z.); (Y.W.); (Q.L.); (H.W.)
| | - Qian Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Y.Z.); (Y.W.); (Q.L.); (H.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Changwei Shao
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Y.Z.); (Y.W.); (Q.L.); (H.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
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Xu S, Xie B, Liu H, Liu J, Wang M, Zhong L, Zhou J, Wen Z, Zhang L, Chen X, Zhang S. 5 mC modification of steroid hormone biosynthesis-related genes orchestrates feminization of channel catfish induced by high-temperature. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 356:124310. [PMID: 38838810 DOI: 10.1016/j.envpol.2024.124310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/01/2024] [Accepted: 06/03/2024] [Indexed: 06/07/2024]
Abstract
To elucidate the mechanism behind channel catfish feminization induced by high temperature, gonad samples were collected from XY pseudo-females and wild-type females and subjected to high-throughput sequencing for Whole-Genome-Bisulfite-Seq (WGBS) and transcriptome sequencing (RNA-Seq). The analysis revealed 50 differentially methylated genes between wild-type females and XY pseudo-females, identified through the analysis of KEGG pathways and GO enrichment in the promoter of the genome and differentially methylated regions (DMRs). Among these genes, multiple differential methylation sites observed within the srd5a2 gene. Repeatability tests confirmed 7 differential methylation sites in the srd5a2 gene in XY pseudo-females compared to normal males, with 1 specific differential methylation site (16608174) distinguishing XY pseudo-females from normal females. Interestingly, the expression of these genes in the transcriptome showed no difference between wild-type females and XY pseudo-females. Our study concluded that methylation of the srd5a2 gene sequence leads to decreased expression, which inhibits testosterone synthesis while promoting the synthesis of 17β-estradiol from testosterone. This underscores the significance of the srd5a2 gene in the sexual differentiation of channel catfish, as indicated by the ipu00140 KEGG pathway analysis.
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Affiliation(s)
- Siqi Xu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210027, China; Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China
| | - Bingjie Xie
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210027, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Hongyan Liu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210027, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Ju Liu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210027, China
| | - Minghua Wang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210027, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Liqiang Zhong
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210027, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Jian Zhou
- Fisheries Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 611731, China
| | - Zhengyong Wen
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang Normal University, Neijiang 641100, China
| | - Lu Zhang
- Fisheries Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 611731, China
| | - Xiaohui Chen
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210027, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China; College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Shiyong Zhang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210027, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China; College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China.
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Cheng X, Jiang W, Wang Q, Liu K, Dai W, Liu Y, Shao C, Li Q. Unveiling Gene Expression Dynamics during Early Embryogenesis in Cynoglossus semilaevis: A Transcriptomic Perspective. Life (Basel) 2024; 14:505. [PMID: 38672775 PMCID: PMC11050975 DOI: 10.3390/life14040505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Commencing with sperm-egg fusion, the early stages of metazoan development include the cleavage and formation of blastula and gastrula. These early embryonic events play a crucial role in ontogeny and are accompanied by a dramatic remodeling of the gene network, particularly encompassing the maternal-to-zygotic transition. Nonetheless, the gene expression dynamics governing early embryogenesis remain unclear in most metazoan lineages. We conducted transcriptomic profiling on two types of gametes (oocytes and sperms) and early embryos (ranging from the four-cell to the gastrula stage) of an economically valuable flatfish-the Chinese tongue sole Cynoglossus semilaevis (Pleuronectiformes: Cynoglossidae). Comparative transcriptome analysis revealed that large-scale zygotic genome activation (ZGA) occurs in the blastula stage, aligning with previous findings in zebrafish. Through the comparison of the most abundant transcripts identified in each sample and the functional analysis of co-expression modules, we unveiled distinct functional enrichments across different gametes/developmental stages: actin- and immune-related functions in sperms; mitosis, transcription inhibition, and mitochondrial function in oocytes and in pre-ZGA embryos (four- to 1000-cell stage); and organ development in post-ZGA embryos (blastula and gastrula). These results provide insights into the intricate transcriptional regulation of early embryonic development in Cynoglossidae fish and expand our knowledge of developmental constraints in vertebrates.
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Affiliation(s)
- Xinyi Cheng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China;
- BGI Research, Wuhan 430074, China;
| | - Wei Jiang
- BGI Research, Shenzhen 518083, China;
| | - Qian Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Q.W.); (K.L.); (Y.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Kaiqiang Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Q.W.); (K.L.); (Y.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Wei Dai
- BGI Research, Wuhan 430074, China;
| | - Yuyan Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Q.W.); (K.L.); (Y.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Changwei Shao
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Q.W.); (K.L.); (Y.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qiye Li
- BGI Research, Wuhan 430074, China;
- BGI Research, Shenzhen 518083, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Yue B, Wang HY, Huang Y, Li S, Ma W, Liu Q, Shao C. Molecular functional characterization of the setdb1 and its potential target gene sox5 illuminate the histone modification-mediated orchestration of gonadal development in Chinese tongue sole (Cynoglossus semilaevis). Gene 2024; 901:148199. [PMID: 38253299 DOI: 10.1016/j.gene.2024.148199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/31/2023] [Accepted: 01/19/2024] [Indexed: 01/24/2024]
Abstract
SET (SuVar3-9, Enhancer of Zeste, Trithorax) domain bifurcated histone lysine methyltransferase 1, setdb1, is the predominant histone lysine methyltransferase catalyzing H3K9me3. Prior studies have illustrated that setdb1 and H3K9me3 critically regulate sex differentiation and gametogenesis. However, the molecular details by which setdb1 is involved in these processes in fish have been poorly reported. Here, we cloned and characterized the setdb1 ORF (open reading frame) sequence from Chinese tongue sole (Cynoglossus semilaevis). The setdb1 ORF sequence was 3,669 bp, encoding a 1,222-amino-acid protein. Phylogenetic analysis showed that setdb1 was structurally conserved. qRT-PCR revealed that setdb1 had a high expression level in the testes at 12 mpf (months post fertilization). Single-cell RNA-seq data at 24 mpf indicated that setdb1 was generally expressed in spermatogenic cells at each stage except for sperm and was centrally expressed in oogonia. H3K9me3 modification was observed in gonads with the immunofluorescence technique. Furthermore, the overexpression experiment suggested that sox5 was a candidate target of setdb1. sox5 was abundantly expressed in male and pseudomale gonads at 24 mpf. Single-cell RNA-seq data showed that sox5 was mainly expressed in spermatogonia and its expression gradually declined with differentiation. Taken together, our findings imply that setdb1 regulates sox5 transcription in gonads, which provides molecular clues into histone modification-mediated orchestration of sex differentiation and gametogenesis.
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Affiliation(s)
- Bowen Yue
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Hong-Yan Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Yingyi Huang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Shuo Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Wenxiu Ma
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Qian Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Changwei Shao
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China.
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Xia YQ, Yang Y, Liu YY, Cheng JX, Liu Y, Li CH, Liu PF. DNA Methylation Analysis Reveals Potential Mechanism in Takifugu rubripes Against Cryptocaryon irritans Infection. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:288-305. [PMID: 38446292 DOI: 10.1007/s10126-024-10296-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/02/2024] [Indexed: 03/07/2024]
Abstract
Takifugu rubripes (T. rubripes) is a valuable commercial fish, and Cryptocaryon irritans (C. irritans) has a significant impact on its aquaculture productivity. DNA methylation is one of the earliest discovered ways of gene epigenetic modification and also an important form of modification, as well as an essential type of alteration that regulates gene expression, including immune response. To further explore the anti-infection mechanism of T. rubripes in inhibiting this disease, we determined genome-wide DNA methylation profiles in the gill of T. rubripes using whole-genome bisulfite sequencing (WGBS) and combined with RNA sequence (RNA-seq). A total of 4659 differentially methylated genes (DMGs) in the gene body and 1546 DMGs in the promoter between the infection and control group were identified. And we identified 2501 differentially expressed genes (DEGs), including 1100 upregulated and 1401 downregulated genes. After enrichment analysis, we identified DMGs and DEGs of immune-related pathways including MAPK, Wnt, ErbB, and VEGF signaling pathways, as well as node genes prkcb, myca, tp53, and map2k2a. Based on the RNA-Seq results, we plotted a network graph to demonstrate the relationship between immune pathways and functional related genes, in addition to gene methylation and expression levels. At the same time, we predicted the CpG island and transcription factor of four immune-related key genes prkcb and mapped the gene structure. These unique discoveries could be helpful in the understanding of C. irritans pathogenesis, and the candidate genes screened may serve as optimum methylation-based biomarkers that can be utilized for the correct diagnosis and therapy T. rubripes in the development of the ability to resist C. irritans infection.
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Affiliation(s)
- Yu-Qing Xia
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, People's Republic of China
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
| | - Yi Yang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
- College of Marine Technology and Environment, Dalian Ocean University, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
| | - Yan-Yun Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
- College of Marine Technology and Environment, Dalian Ocean University, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
| | - Jian-Xin Cheng
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
- College of Life Science, Liaoning Normal University, Dalian, 116081, People's Republic of China
| | - Ying Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, People's Republic of China
| | - Cheng-Hua Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, People's Republic of China.
| | - Peng-Fei Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China.
- College of Marine Technology and Environment, Dalian Ocean University, 52 Heishijiao Street, Dalian, 116023, People's Republic of China.
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Lema SC, Luckenbach JA, Yamamoto Y, Housh MJ. Fish reproduction in a warming world: vulnerable points in hormone regulation from sex determination to spawning. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220516. [PMID: 38310938 PMCID: PMC10838641 DOI: 10.1098/rstb.2022.0516] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 12/11/2023] [Indexed: 02/06/2024] Open
Abstract
Reproduction in fishes is sensitive to temperature. Elevated temperatures and anomalous 'heat waves' associated with climate change have the potential to impact fish reproductive performance and, in some cases, even induce sex reversals. Here we examine how thermal sensitivity in the hormone pathways regulating reproduction provides a framework for understanding impacts of warmer conditions on fish reproduction. Such effects will differ depending on evolved variation in temperature sensitivity of endocrine pathways regulating reproductive processes of sex determination/differentiation, gametogenesis and spawning, as well as how developmental timing of those processes varies with reproductive ecology. For fish populations unable to shift geographical range, persistence under future climates may require changes in temperature responsiveness of the hormone pathways regulating reproductive processes. How thermal sensitivity in those hormone pathways varies among populations and species, how those pathways generate temperature maxima for reproduction, and how rapidly reproductive thermal tolerances can change via adaptation or transgenerational plasticity will shape which fishes are most at risk for impaired reproduction under rising temperatures. This article is part of the theme issue 'Endocrine responses to environmental variation: conceptual approaches and recent developments'.
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Affiliation(s)
- Sean C. Lema
- Biological Sciences Department, Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, CA 93430, USA
| | - J. Adam Luckenbach
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112, USA
- Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
| | - Yoji Yamamoto
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Minato-ku, Tokyo 108-8477, Japan
| | - Madeline J. Housh
- Biological Sciences Department, Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, CA 93430, USA
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9
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Bókony V, Kalina C, Ujhegyi N, Mikó Z, Lefler KK, Vili N, Gál Z, Gabor CR, Hoffmann OI. Does stress make males? An experiment on the role of glucocorticoids in anuran sex reversal. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2024; 341:172-181. [PMID: 38155497 DOI: 10.1002/jez.2772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/30/2023]
Abstract
Environmentally sensitive sex determination may help organisms adapt to environmental change but also makes them vulnerable to anthropogenic stressors, with diverse consequences for population dynamics and evolution. The mechanisms translating environmental stimuli to sex are controversial: although several fish experiments supported the mediator role of glucocorticoid hormones, results on some reptiles challenged it. We tested this hypothesis in amphibians by investigating the effect of corticosterone on sex determination in agile frogs (Rana dalmatina). This species is liable to environmental sex reversal whereby genetic females develop into phenotypic males. After exposing tadpoles during sex determination to waterborne corticosterone, the proportion of genetic females with testes or ovotestes increased from 11% to up to 32% at 3 out of 4 concentrations. These differences were not statistically significant except for the group treated with 10 nM corticosterone, and there was no monotonous dose-effect relationship. These findings suggest that corticosterone is unlikely to mediate sex reversal in frogs. Unexpectedly, animals originating from urban habitats had higher sex-reversal and corticosterone-release rates, reduced body mass and development speed, and lower survival compared to individuals collected from woodland habitats. Thus, anthropogenic environments may affect both sex and fitness, and the underlying mechanisms may vary across ectothermic vertebrates.
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Affiliation(s)
- Veronika Bókony
- Department of Evolutionary Ecology, Plant Protection Institute, HUN-REN Centre for Agricultural Research, Budapest, Hungary
- Department of Zoology, University of Veterinary Medicine Budapest, Budapest, Hungary
| | - Csenge Kalina
- Department of Zoology, University of Veterinary Medicine Budapest, Budapest, Hungary
| | - Nikolett Ujhegyi
- Department of Evolutionary Ecology, Plant Protection Institute, HUN-REN Centre for Agricultural Research, Budapest, Hungary
| | - Zsanett Mikó
- Department of Evolutionary Ecology, Plant Protection Institute, HUN-REN Centre for Agricultural Research, Budapest, Hungary
| | - Kinga Katalin Lefler
- Department of Aquaculture, Institute of Agricultural and Environmental Safety, Hungarian University of Agriculture and Life Science, Gödöllő, Hungary
| | - Nóra Vili
- Department of Zoology, University of Veterinary Medicine Budapest, Budapest, Hungary
| | - Zoltán Gál
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Science, Gödöllő, Hungary
| | - Caitlin R Gabor
- Department of Biology, Texas State University, San Marcos, Texas, USA
| | - Orsolya Ivett Hoffmann
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Science, Gödöllő, Hungary
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10
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Sun Y, Li X, Mai J, Xu W, Wang J, Zhang Q, Wang N. Three Copies of zbed1 Specific in Chromosome W Are Essential for Female-Biased Sexual Size Dimorphism in Cynoglossus semilaevis. BIOLOGY 2024; 13:141. [PMID: 38534411 DOI: 10.3390/biology13030141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024]
Abstract
The sex chromosome, especially specific in one sex, generally determines sexual size dimorphism (SSD), a phenomenon with dimorphic sexual difference in the body size. For Cynoglossus semilaevis, a flatfish in China, although the importance of chromosome W and its specific gene zbed1 in female-biased SSD have been suggested, its family members and regulation information are still unknown. At present, three zbed1 copies gene were identified on chromosome W, with no gametologs. Phylogenetic analysis for the ZBED family revealed an existence of ZBED9 in the fish. Nine members were uncovered from C. semilaevis, clustering into three kinds, ZBED1, ZBED4 and ZBEDX, which is less than the eleven kinds of ZBED members in mammals. The predominant expression of zbed1 in the female brain and pituitary tissues was further verified by qPCR. Transcription factor c/ebpα could significantly enhance the transcriptional activity of zbed1 promoter, which is opposite to its effect on the male determinant factor-dmrt1. When zbed1 was interfered with, piwil1, esr2 and wnt7b were up-regulated, while cell-cycle-related genes, including cdk4 and ccng1, were down-regulated. Thus, zbed1 is involved in cell proliferation by regulating esr2, piwil1, cell cycle and the Wnt pathway. Further research on their interactions would be helpful to understand fish SSD.
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Affiliation(s)
- Yuqi Sun
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xihong Li
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Jiaqi Mai
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Wenteng Xu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Jiacheng Wang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Qi Zhang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China
| | - Na Wang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
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11
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Kitano J, Ansai S, Takehana Y, Yamamoto Y. Diversity and Convergence of Sex-Determination Mechanisms in Teleost Fish. Annu Rev Anim Biosci 2024; 12:233-259. [PMID: 37863090 DOI: 10.1146/annurev-animal-021122-113935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Sexual reproduction is prevalent across diverse taxa. However, sex-determination mechanisms are so diverse that even closely related species often differ in sex-determination systems. Teleost fish is a taxonomic group with frequent turnovers of sex-determining mechanisms and thus provides us with great opportunities to investigate the molecular and evolutionary mechanisms underlying the turnover of sex-determining systems. Here, we compile recent studies on the diversity of sex-determination mechanisms in fish. We demonstrate that genes in the TGF-β signaling pathway are frequently used for master sex-determining (MSD) genes. MSD genes arise via two main mechanisms, duplication-and-transposition and allelic mutations, with a few exceptions. We also demonstrate that temperature influences sex determination in many fish species, even those with sex chromosomes, with higher temperatures inducing differentiation into males in most cases. Finally, we review theoretical models for the turnover of sex-determining mechanisms and discuss what questions remain elusive.
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Affiliation(s)
- Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan;
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan;
| | - Yusuke Takehana
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan;
| | - Yoji Yamamoto
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan;
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12
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Sun D, Yu H, Kong L, Liu S, Xu C, Li Q. The role of DNA methylation reprogramming during sex determination and sex reversal in the Pacific oyster Crassostrea gigas. Int J Biol Macromol 2024; 259:128964. [PMID: 38219938 DOI: 10.1016/j.ijbiomac.2023.128964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/19/2023] [Accepted: 12/14/2023] [Indexed: 01/16/2024]
Abstract
DNA methylation is instrumental in vertebrate sex reversal. However, the mechanism of DNA methylation regulation regarding sex reversal in invertebrates is unclear. In this study, we used whole genome bisulfite sequencing (WGBS) to map single-base resolution methylation profiles of the Pacific oyster, including female-to-male (FMa-to-FMb) and male-to-female (MFa-to-MFb) sex reversal, as well as sex non-reversed males and females (MMa-to-MMb and FFa-to-FFb). The results showed that global DNA methylation levels increase during female-to-male sex reversals, with a particular increase in the proportion of high methylation levels (mCGs >0.75) and a decrease in the proportion of intermediate methylation levels (0.25 < mCGs <0.75). This increase in DNA methylation was mainly associated with the elevated expression of DNA methylase genes. Genome-wide methylation patterns of females were accurately remodeled to those of males after sex reversal, while the opposite was true for the male-to-female reversal. Those findings directly indicate that alterations in DNA methylation play a significant role in sex reversal in Pacific oysters. Comparative analysis of the DNA methylomes of pre- and post- sex reversal gonadal tissues (FMb-vs-FMa or MFb-vs-MFa) revealed that differentially methylated genes were mainly involved in the biological processes of sex determination or gonadal development. However critical genes such as Dmrt1, Foxl2 and Sox-like, which are involved in the putative sex determination pathway in Pacific oysters, showed almost an absence of methylation modifications, varying greatly from vertebrates. Additionally, comparative analysis of the DNA methylomes of sexual reversal and sex non-reversal (FMa-vs-FFa or MFa-vs-MMa) revealed that heat shock protein genes, such as Hsp68-like and Hsp70B, were important for the occurrence of sex reversal. These findings shed light on the epigenetic mechanisms underlying the maintenance of gonadal plasticity and the reversal of organ architecture in oysters.
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Affiliation(s)
- Dongfang Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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13
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Zhang Y, Lu Y, Xu F, Zhang X, Wu Y, Zhao J, Luo Q, Liu H, Chen K, Fei S, Cui X, Sun Y, Ou M. Molecular Characterization, Expression Pattern, DNA Methylation and Gene Disruption of Figla in Blotched Snakehead ( Channa maculata). Animals (Basel) 2024; 14:491. [PMID: 38338134 PMCID: PMC10854511 DOI: 10.3390/ani14030491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Figla is one of the earliest expressed genes in the oocyte during ovarian development. In this study, Figla was characterized in C. maculata, one of the main aquaculture species in China, and designated as CmFigla. The length of CmFigla cDNA was 1303 bp, encoding 197 amino acids that contained a conserved bHLH domain. CmFigla revealed a female-biased expression patterns in the gonads of adult fish, and CmFigla expression was far higher in ovaries than that in testes at all gonadal development stages, especially at 60~180 days post-fertilization (dpf). Furthermore, a noteworthy inverse relationship was observed between CmFigla expression and the methylation of its promoter in the adult gonads. Gonads at 90 dpf were used for in situ hybridization (ISH), and CmFigla transcripts were mainly concentrated in oogonia and the primary oocytes in ovaries, but undetectable in the testes. These results indicated that Figla would play vital roles in the ovarian development in C. maculata. Additionally, the frame-shift mutations of CmFigla were successfully constructed through the CRISPR/Cas9 system, which established a positive foundation for further investigation on the role of Figla in the ovarian development of C. maculata. Our study provides valuable clues for exploring the regulatory mechanism of Figla in the fish ovarian development and maintenance, which would be useful for the sex control and reproduction of fish in aquaculture.
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Affiliation(s)
- Yang Zhang
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; (Y.Z.); (Y.L.); (X.C.)
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Yuntao Lu
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; (Y.Z.); (Y.L.); (X.C.)
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Feng Xu
- Chongqing Fisheries Technical Extension Center, Chongqing 404100, China;
| | - Xiaotian Zhang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Yuxia Wu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Jian Zhao
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Qing Luo
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Haiyang Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Kunci Chen
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Shuzhan Fei
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
| | - Xiaojuan Cui
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; (Y.Z.); (Y.L.); (X.C.)
| | - Yuandong Sun
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; (Y.Z.); (Y.L.); (X.C.)
| | - Mi Ou
- School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China; (Y.Z.); (Y.L.); (X.C.)
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (X.Z.); (Y.W.); (J.Z.); (Q.L.); (H.L.); (K.C.); (S.F.)
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14
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Li L, Li X, Chen Y, Yang Y, Wang N, Xu W. Identification and Functional Analysis of Cynoglossus semilaevis Z-Linked E3 Ubiquitin Ligase rnf34. Animals (Basel) 2024; 14:311. [PMID: 38275772 PMCID: PMC10812492 DOI: 10.3390/ani14020311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
The high proportion of males in C. semilaevis hinders their industrial development. The genetic ZW individual can become a pseudomale by sex reversal. And the pseudomale can produce Z-sperm (with epigenetic information to cause sex reversal) while W-sperm is absent, which leads to an even higher male proportion in offspring. Recently, with the development of transcriptomic technologies, research on spermatogenesis in C. semilaevis has been focused on the ubiquitination pathway. In this study, we analyzed the function of the ubiquitin ligase rnf34 gene on the Z chromosome. A qPCR experiment showed that its expression level in the gonad was the highest among different tissues. In the ovary, the expression gradually increased with development from 40 days post-hatching (dph) to 1.5 years post-hatching (yph). In the testis, rnf34 showed increased expression from 40 dph to 6 months post-hatching (mpf) and stabilized up until 1.5 ypf. In situ hybridization showed that the mRNA of rnf34 was mainly distributed in the germ cells of the testis and the ovary. In vivo siRNA-mediated knockdown of the rnf34 gene in male fish affected the expression of a series of genes related to sex differentiation and spermatogenesis. These results provide genetic data on the molecular mechanisms of gonadal development and spermatogenesis in C. semilaevis.
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Affiliation(s)
- Lu Li
- School of Fishery, Zhejiang Ocean University, Zhoushan 316022, China
- Function Laboratory for Marine Science and Food Production Process, Laoshan Laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China
| | - Xihong Li
- Function Laboratory for Marine Science and Food Production Process, Laoshan Laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China
| | - Yadong Chen
- Function Laboratory for Marine Science and Food Production Process, Laoshan Laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China
| | - Yingming Yang
- Function Laboratory for Marine Science and Food Production Process, Laoshan Laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China
| | - Na Wang
- Function Laboratory for Marine Science and Food Production Process, Laoshan Laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China
| | - Wenteng Xu
- Function Laboratory for Marine Science and Food Production Process, Laoshan Laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China
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15
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Fagbémi MNA, Nivelle R, Muller M, Mélard C, Lalèyè P, Rougeot C. Effect of high temperatures on sex ratio and differential expression analysis (RNA-seq) of sex-determining genes in Oreochromis niloticus from different river basins in Benin. ENVIRONMENTAL EPIGENETICS 2024; 9:dvad009. [PMID: 38487307 PMCID: PMC10939319 DOI: 10.1093/eep/dvad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/09/2023] [Accepted: 01/10/2024] [Indexed: 03/17/2024]
Abstract
The high temperature sex reversal process leading to functional phenotypic masculinization during development has been widely described in Nile tilapia (Oreochromis n iloticus) under laboratory or aquaculture conditions and in the wild. In this study, we selected five wild populations of O. niloticus from different river basins in Benin and produced twenty full-sib families of mixed-sex (XY and XX) by natural reproduction. Progenies were exposed to room temperature or high (36.5°C) temperatures between 10 and 30 days post-fertilization (dpf). In control groups, we observed sex ratios from 40% to 60% males as expected, except for 3 families from the Gobé region which showed a bias towards males. High temperature treatment significantly increased male rates in each family up to 88%. Transcriptome analysis was performed by RNA-sequencing (RNA-seq) on brains and gonads from control and treated batches of six families at 15 dpf and 40 dpf. Analysis of differentially expressed genes, differentially spliced genes, and correlations with sex reversal was performed. In 40 dpf gonads, genes involved in sex determination such as dmrt1, cyp11c1, amh, cyp19a1b, ara, and dax1 were upregulated. In 15 dpf brains, a negative correlation was found between the expression of cyp19a1b and the reversal rate, while at 40 dpf a negative correlation was found between the expression of foxl2, cyp11c1, and sf1 and positive correlation was found between dmrt1 expression and reversal rate. Ontology analysis of the genes affected by high temperatures revealed that male sex differentiation processes, primary male sexual characteristics, autophagy, and cilium organization were affected. Based on these results, we conclude that sex reversal by high temperature treatment leads to similar modifications of the transcriptomes in the gonads and brains in offspring of different natural populations of Nile tilapia, which thus may activate a common cascade of reactions inducing sex reversal in progenies.
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Affiliation(s)
- Mohammed Nambyl A Fagbémi
- Aquaculture Research and Education Centre (CEFRA), Liège University, query author on which is prefered, 10 Chemin de la Justice B-4500, Tihange, Belgium
- Laboratory of Hydrobiology and Aquaculture (LHA), Faculty of Agricultural Sciences, University of Abomey-Calavi, 01 BP: 526, Cotonou, Benin
| | - Renaud Nivelle
- Aquaculture Research and Education Centre (CEFRA), Liège University, query author on which is prefered, 10 Chemin de la Justice B-4500, Tihange, Belgium
- Laboratory for Organogenesis and Regeneration (LOR), Interdisciplinary Research Institute in Biomedical Sciences (GIGA-I3), Liège University, Sart Tilman, Liège, Belgium
| | - Marc Muller
- Laboratory for Organogenesis and Regeneration (LOR), Interdisciplinary Research Institute in Biomedical Sciences (GIGA-I3), Liège University, Sart Tilman, Liège, Belgium
| | - Charles Mélard
- Aquaculture Research and Education Centre (CEFRA), Liège University, query author on which is prefered, 10 Chemin de la Justice B-4500, Tihange, Belgium
| | - Philippe Lalèyè
- Laboratory of Hydrobiology and Aquaculture (LHA), Faculty of Agricultural Sciences, University of Abomey-Calavi, 01 BP: 526, Cotonou, Benin
| | - Carole Rougeot
- Aquaculture Research and Education Centre (CEFRA), Liège University, query author on which is prefered, 10 Chemin de la Justice B-4500, Tihange, Belgium
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16
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Guirandy N, Simon O, Geffroy B, Daffe G, Daramy F, Houdelet C, Gonzalez P, Pierron F. Gamma irradiation-induced offspring masculinization is associated with epigenetic changes in female zebrafish. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 269:115790. [PMID: 38086259 DOI: 10.1016/j.ecoenv.2023.115790] [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: 08/19/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 01/12/2024]
Abstract
Sex ratio variation is a key topic in ecology, because of its direct effects on population dynamics and thus, on animal conservation strategies. Among factors affecting sex ratio, types of sex determination systems have a central role, since some species could have a sex determined by genetic factors, environmental factors or a mix of those two. Yet, most studies on the factors affecting sex determination have focused on temperature or endocrine-disrupting chemicals (EDCs), and much less is known regarding other factors. Exposure to gamma irradiation was found to trigger offspring masculinization in zebrafish. Here we aimed at deciphering the potential mechanisms involved, by focusing on stress (i.e. cortisol) and epigenetic regulation of key genes involved in sex differentiation in fish. Cortisol levels in exposed and control (F0) zebrafish females' gonads were similar. However, irradiation increased the DNA methylation level of foxl2a and cyp19a1a in females of the F0 and F1 generation, respectively, while no effects were detected in testis. Overall, our results suggest that parental exposure could alter offspring sex ratio, at least in part by inducing methylation changes in ovaries.
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Affiliation(s)
- Noëmie Guirandy
- IRSN/PSE-ENV/SRTE/LECO, Centre de Cadarache-B.P. 3 - Bat 183, 13115 St Paul Lez Durance, France.
| | - Olivier Simon
- IRSN/PSE-ENV/SRTE/LECO, Centre de Cadarache-B.P. 3 - Bat 183, 13115 St Paul Lez Durance, France
| | - Benjamin Geffroy
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Guillemine Daffe
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
| | - Flore Daramy
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
| | - Camille Houdelet
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Patrice Gonzalez
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
| | - Fabien Pierron
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
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17
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Hou M, Wang Q, Zhao R, Cao Y, Zhang J, Sun X, Yu S, Wang K, Chen Y, Zhang Y, Li J. Analysis of Chromatin Accessibility and DNA Methylation to Reveal the Functions of Epigenetic Modifications in Cyprinus carpio Gonads. Int J Mol Sci 2023; 25:321. [PMID: 38203492 PMCID: PMC10778764 DOI: 10.3390/ijms25010321] [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: 11/27/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
Epigenetic modifications are critical in precisely regulating gene expression. The common carp (Cyprinus carpio) is an economically important fish species, and females exhibit faster growth rates than males. However, the studies related to epigenetic modifications in the common carp gonads are limited. In this study, we conducted the Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) and Bisulfite sequencing (BS-seq) to explore the roles of epigenetic modifications in the common carp gonads. We identified 84,207 more accessible regions and 77,922 less accessible regions in ovaries compared to testes, and some sex-biased genes showed differential chromatin accessibility in their promoter regions, such as sox9a and zp3. Motif enrichment analysis showed that transcription factors (TFs) associated with embryonic development and cell proliferation were heavily enriched in ovaries, and the TFs Foxl2 and SF1 were only identified in ovaries. We also analyzed the possible regulations between chromatin accessibility and gene expression. By BS-seq, we identified 2087 promoter differentially methylated genes (promoter-DMGs) and 5264 gene body differentially methylated genes (genebody-DMGs) in CG contexts. These genebody-DMGs were significantly enriched in the Wnt signaling pathway, TGF-beta signaling pathway, and GnRH signaling pathway, indicating that methylation in gene body regions could play an essential role in sex maintenance, just like methylation in promoter regions. Combined with transcriptomes, we revealed that the expression of dmrtb1-like, spag6, and fels was negatively correlated with their methylation levels in promoter regions. Our study on the epigenetic modifications of gonads contributes to elucidating the molecular mechanism of sex differentiation and sex maintenance in the common carp.
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Affiliation(s)
- Mingxi Hou
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (R.Z.); (Y.C.); (J.Z.); (X.S.); (S.Y.); (Y.Z.)
| | - Qi Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (R.Z.); (Y.C.); (J.Z.); (X.S.); (S.Y.); (Y.Z.)
| | - Ran Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (R.Z.); (Y.C.); (J.Z.); (X.S.); (S.Y.); (Y.Z.)
| | - Yiming Cao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (R.Z.); (Y.C.); (J.Z.); (X.S.); (S.Y.); (Y.Z.)
| | - Jin Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (R.Z.); (Y.C.); (J.Z.); (X.S.); (S.Y.); (Y.Z.)
| | - Xiaoqing Sun
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (R.Z.); (Y.C.); (J.Z.); (X.S.); (S.Y.); (Y.Z.)
| | - Shuangting Yu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (R.Z.); (Y.C.); (J.Z.); (X.S.); (S.Y.); (Y.Z.)
- Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kaikuo Wang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; (K.W.); (Y.C.)
| | - Yingjie Chen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; (K.W.); (Y.C.)
| | - Yan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (R.Z.); (Y.C.); (J.Z.); (X.S.); (S.Y.); (Y.Z.)
| | - Jiongtang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (R.Z.); (Y.C.); (J.Z.); (X.S.); (S.Y.); (Y.Z.)
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18
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Yao ZL, Fang QF, Li JY, Zhou M, Du S, Chen HJ, Wang H, Jiang SJ, Wang X, Zhao Y, Ji XS. Alternative splicing of histone demethylase Kdm6bb mediates temperature-induced sex reversal in the Nile tilapia. Curr Biol 2023; 33:5057-5070.e5. [PMID: 37995698 DOI: 10.1016/j.cub.2023.10.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/05/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023]
Abstract
Sex determination in many fish species is remarkably plastic and temperature sensitive. Nile tilapia display a genetic sex-determination system (XX/XY). However, high-temperature treatment during critical thermosensitive periods can induce XX females into XXm pseudo-males, and this phenomenon is termed temperature-induced sex reversal (TISR). To investigate the molecular mechanism of TISR in Nile tilapia, we performed Iso-seq analysis and found a dramatic effect of high temperature on gene alternative splicing (AS). Kdm6bb histone demethylase showed a novel AS at intron 5 that generates Kdm6bb_tv1 transcripts without intron 5 and Kdm6bb_tv2 with intron 5. Kdm6bb_tv1 encodes a full-length protein while Kdm6bb_tv2 encodes a truncated protein. Expression analysis revealed that intron 5 splicing of Kdm6bb is male and gonad biased at larval stage, and only gonad biased at adult stage. High-temperature treatment induced intron 5 splicing in the gonads of XX and XY fish, resulting in increased Kdm6bb_tv1 expression. To directly test the role of Kdm6bb_tv1 in Nile tilapia TISR, we knocked out expression of Kdm6bb_tv1. However, Kdm6bb_tv1-/- homozygous mutants showed embryonic lethality. Overexpression of Kdm6bb_tv1, but not Kdm6bb_tv2, induced sex reversal of XX females into pseudo-males. Overexpression of Kdm6bb_tv1, as with high-temperature treatment, modified the promotor region of Gsdf and Dmrt1 by demethylating the trimethylated lysine 27 of histone 3 (H3K27me3), thereby increasing expression. Collectively, these studies demonstrate that AS of Kdm6bb intron 5 increases the expression of Kdm6bb_tv1, which acts as a direct link between high temperature and activation of Gsdf and Dmrt1 expression, leading to male sex determination.
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Affiliation(s)
- Zhi Lei Yao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Qing Feng Fang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Jia Yue Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Min Zhou
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Shaojun Du
- Department of Biochemistry and Molecular Biology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Hong Ju Chen
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Hui Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Shi-Jin Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Xiao Wang
- Library, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Yan Zhao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China.
| | - Xiang Shan Ji
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271018, Shandong, China; Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian 271018, Shandong, China.
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19
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Pierron F, Daramy F, Heroin D, Daffe G, Barré A, Bouchez O, Nikolski M. Sex-specific DNA methylation and transcription of zbtb38 and effects of gene-environment interactions on its natural antisense transcript in zebrafish. Epigenetics 2023; 18:2260963. [PMID: 37782752 PMCID: PMC10547075 DOI: 10.1080/15592294.2023.2260963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/06/2023] [Indexed: 10/04/2023] Open
Abstract
There is increasing evidence for the involvement of epigenetics in sex determination, maintenance, and plasticity, from plants to humans. In our previous work, we reported a transgenerational feminization of a zebrafish population for which the first generation was exposed to cadmium, a metal with endocrine disrupting effects. In this study, starting from the previously performed whole methylome analysis, we focused on the zbtb38 gene and hypothesized that it could be involved in sex differentiation and Cd-induced offspring feminization. We observed sex-specific patterns of both DNA methylation and RNA transcription levels of zbtb38. We also discovered that the non-coding exon 3 of zbtb38 encodes for a natural antisense transcript (NAT). The activity of this NAT was found to be influenced by both genetic and environmental factors. Furthermore, increasing transcription levels of this NAT in parental gametes was highly correlated with offspring sex ratios. Since zbtb38 itself encodes for a transcription factor that binds methylated DNA, our results support a non-negligible role of zbtb38 not only in orchestrating the sex-specific transcriptome (i.e., sex differentiation) but also, via its NAT, offspring sex ratios.
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Affiliation(s)
| | - Flore Daramy
- Univ Bordeaux, CNRS, Bordeaux INP, Pessac, France
| | | | | | - Aurélien Barré
- Univ Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, France
| | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Macha Nikolski
- Univ Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, France
- Univ Bordeaux, CNRS, IBGC, Bordeaux, France
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20
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Shen Y, Jiang H, Canario AV, Chen T, Liu Y, Yang G, Meng X, Zhao J, Chen X. The fusion gene hsf5-rnf43 in Nile tilapia: A potential regulator in the maintenance of testis function and sexual differentiation. iScience 2023; 26:108284. [PMID: 38026183 PMCID: PMC10679895 DOI: 10.1016/j.isci.2023.108284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/27/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
We identified that the genes heat shock transcription factor 5 (hsf5) and ring finger protein 43 (rnf43) happened fusion in Nile tilapia (Oreochromis niloticus), called hsf5-rnf43, and provided the characteristic and functional analysis of hsf5-rnf43 gene in fish for the first time. Analysis of spatiotemporal expression showed that hsf5-rnf43 was specifically expressed in the testis and located in primary spermatocytes of adult Nile tilapia and gradually increased during testis development from 5 to 180 days after hatching. We also found DNA methylation regulated sex-biased expression of hsf5-rnf43 in the early development of Nile tilapia, and was affected by high temperature during the thermosensitive period of Nile tilapia sex differentiation. Therefore, we first reported that the fusion gene hsf5-rnf43 was sex-biased expressed in the testis regulated by DNA methylation and affected by high temperature, which may be involved in the maintenance of testis function and sex differentiation of Nile tilapia.
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Affiliation(s)
- Yawei Shen
- College of Fisheries, Henan Normal University, Xinxiang 453007, Henan, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Hewei Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Adelino V.M. Canario
- CCMAR/CIMAR Centre for Marine Sciences, University of Algarve, Campus de Gambelas, Faro 8005-139, Portugal
| | - Tiantian Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yufei Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Guokun Yang
- College of Fisheries, Henan Normal University, Xinxiang 453007, Henan, China
| | - Xiaolin Meng
- College of Fisheries, Henan Normal University, Xinxiang 453007, Henan, China
| | - Jinliang Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaowu Chen
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
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21
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Yu Y, Chen M, Shen ZG. Molecular biological, physiological, cytological, and epigenetic mechanisms of environmental sex differentiation in teleosts: A systematic review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 267:115654. [PMID: 37918334 DOI: 10.1016/j.ecoenv.2023.115654] [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: 08/23/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/04/2023]
Abstract
Human activities have been exerting widespread stress and environmental risks in aquatic ecosystems. Environmental stress, including temperature rise, acidification, hypoxia, light pollution, and crowding, had a considerable negative impact on the life histology of aquatic animals, especially on sex differentiation (SDi) and the resulting sex ratios. Understanding how the sex of fish responds to stressful environments is of great importance for understanding the origin and maintenance of sex, the dynamics of the natural population in the changing world, and the precise application of sex control in aquaculture. This review conducted an exhaustive search of the available literature on the influence of environmental stress (ES) on SDi. Evidence has shown that all types of ES can affect SDi and universally result in an increase in males or masculinization, which has been reported in 100 fish species and 121 cases. Then, this comprehensive review aimed to summarize the molecular biology, physiology, cytology, and epigenetic mechanisms through which ES contributes to male development or masculinization. The relationship between ES and fish SDi from multiple aspects was analyzed, and it was found that environmental sex differentiation (ESDi) is the result of the combined effects of genetic and epigenetic factors, self-physiological regulation, and response to environmental signals, which involves a sophisticated network of various hormones and numerous genes at multiple levels and multiple gradations in bipotential gonads. In both normal male differentiation and ES-induced masculinization, the stress pathway and epigenetic regulation play important roles; however, how they co-regulate SDi is unclear. Evidence suggests that the universal emergence or increase in males in aquatic animals is an adaptation to moderate ES. ES-induced sex reversal should be fully investigated in more fish species and extensively in the wild. The potential aquaculture applications and difficulties associated with ESDi have also been addressed. Finally, the knowledge gaps in the ESDi are presented, which will guide the priorities of future research.
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Affiliation(s)
- Yue Yu
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan, PR China
| | - Min Chen
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan, PR China
| | - Zhi-Gang Shen
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan, PR China.
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22
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Valdivieso A, Caballero-Huertas M, Moraleda-Prados J, Piferrer F, Ribas L. Exploring the Effects of Rearing Densities on Epigenetic Modifications in the Zebrafish Gonads. Int J Mol Sci 2023; 24:16002. [PMID: 37958987 PMCID: PMC10647740 DOI: 10.3390/ijms242116002] [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: 09/19/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Rearing density directly impacts fish welfare, which, in turn, affects productivity in aquaculture. Previous studies have indicated that high-density rearing during sexual development in fish can induce stress, resulting in a tendency towards male-biased sex ratios in the populations. In recent years, research has defined the relevance of the interactions between the environment and epigenetics playing a key role in the final phenotype. However, the underlying epigenetic mechanisms of individuals exposed to confinement remain elucidated. By using zebrafish (Danio rerio), the DNA methylation promotor region and the gene expression patterns of six genes, namely dnmt1, cyp19a1a, dmrt1, cyp11c1, hsd17b1, and hsd11b2, involved in the DNA maintenance methylation, reproduction, and stress were assessed. Zebrafish larvae were subjected to two high-density conditions (9 and 66 fish/L) during two periods of overlapping sex differentiation of this species (7 to 18 and 18 to 45 days post-fertilization, dpf). Results showed a significant masculinization in the populations of fish subjected to high densities from 18 to 45 dpf. In adulthood, the dnmt1 gene was differentially hypomethylated in ovaries and its expression was significantly downregulated in the testes of fish exposed to high-density. Further, the cyp19a1a gene showed downregulation of gene expression in the ovaries of fish subjected to elevated density, as previously observed in other studies. We proposed dnmt1 as a potential testicular epimarker and the expression of ovarian cyp19a1a as a potential biomarker for predicting stress originated from high densities during the early stages of development. These findings highlight the importance of rearing densities by long-lasting effects in adulthood conveying cautions for stocking protocols in fish hatcheries.
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Affiliation(s)
- Alejandro Valdivieso
- IHPE, Université de Montpellier, CNRS, IFREMER, Université de Perpignan Via Domitia, 34090 Montpellier, France
| | - Marta Caballero-Huertas
- CIRAD, UMR ISEM, 34398 Montpellier, France;
- ISEM, Université de Montpellier, CIRAD, CNRS, IRD, EPHE, 34090 Montpellier, France
| | - Javier Moraleda-Prados
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (ICM-CSIC), 08003 Barcelona, Spain; (J.M.-P.); (F.P.)
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (ICM-CSIC), 08003 Barcelona, Spain; (J.M.-P.); (F.P.)
| | - Laia Ribas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (ICM-CSIC), 08003 Barcelona, Spain; (J.M.-P.); (F.P.)
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23
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Zhu T, Kong M, Yu Y, Schartl M, Power DM, Li C, Ma W, Sun Y, Li S, Yue B, Li W, Shao C. Exosome delivery to the testes for dmrt1 suppression: A powerful tool for sex-determining gene studies. J Control Release 2023; 363:275-289. [PMID: 37726035 DOI: 10.1016/j.jconrel.2023.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/21/2023]
Abstract
Exosomes are endosome-derived extracellular vesicles about 100 nm in diameter. They are emerging as promising delivery platforms due to their advantages in biocompatibility and engineerability. However, research into and applications for engineered exosomes are still limited to a few areas of medicine in mammals. Here, we expanded the scope of their applications to sex-determining gene studies in early vertebrates. An integrated strategy for constructing the exosome-based delivery system was developed for efficient regulation of dmrt1, which is one of the most widely used sex-determining genes in metazoans. By combining classical methods in molecular biology and the latest technology in bioinformatics, isomiR-124a was identified as a dmrt1 inhibitor and was loaded into exosomes and a testis-targeting peptide was used to modify exosomal surface for efficient delivery. Results showed that isomiR-124a was efficiently delivered to the testes by engineered exosomes and revealed that dmrt1 played important roles in maintaining the regular structure and function of testis in juvenile fish. This is the first de novo development of an exosome-based delivery system applied in the study of sex-determining gene, which indicates an attractive prospect for the future applications of engineered exosomes in exploring more extensive biological conundrums.
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Affiliation(s)
- Tengfei Zhu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Wenhaizhong Road 168, Qingdao 266237, China
| | - Ming Kong
- College of Marine Life Science, Ocean University of China, Yushan Road 5, Qingdao 266003, China
| | - Yingying Yu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Guangyun Road 33, Foshan 528225, China
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, Sanderring 2, Würzburg 97074, Germany; The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Deborah Mary Power
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Algarve, Faro 8005-139, Portugal
| | - Chen Li
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao 266071, China; Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affair, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao 266072, China
| | - Wenxiu Ma
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Wenhaizhong Road 168, Qingdao 266237, China
| | - Yanxu Sun
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Wenhaizhong Road 168, Qingdao 266237, China
| | - Shuo Li
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Wenhaizhong Road 168, Qingdao 266237, China
| | - Bowen Yue
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Wenhaizhong Road 168, Qingdao 266237, China
| | - Weijing Li
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Wenhaizhong Road 168, Qingdao 266237, China
| | - Changwei Shao
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Wenhaizhong Road 168, Qingdao 266237, China.
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24
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Bond DM, Ortega-Recalde O, Laird MK, Hayakawa T, Richardson KS, Reese FCB, Kyle B, McIsaac-Williams BE, Robertson BC, van Heezik Y, Adams AL, Chang WS, Haase B, Mountcastle J, Driller M, Collins J, Howe K, Go Y, Thibaud-Nissen F, Lister NC, Waters PD, Fedrigo O, Jarvis ED, Gemmell NJ, Alexander A, Hore TA. The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes. Nat Commun 2023; 14:6364. [PMID: 37848431 PMCID: PMC10582058 DOI: 10.1038/s41467-023-41784-8] [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: 12/12/2022] [Accepted: 09/13/2023] [Indexed: 10/19/2023] Open
Abstract
Combining genome assembly with population and functional genomics can provide valuable insights to development and evolution, as well as tools for species management. Here, we present a chromosome-level genome assembly of the common brushtail possum (Trichosurus vulpecula), a model marsupial threatened in parts of their native range in Australia, but also a major introduced pest in New Zealand. Functional genomics reveals post-natal activation of chemosensory and metabolic genes, reflecting unique adaptations to altricial birth and delayed weaning, a hallmark of marsupial development. Nuclear and mitochondrial analyses trace New Zealand possums to distinct Australian subspecies, which have subsequently hybridised. This admixture allowed phasing of parental alleles genome-wide, ultimately revealing at least four genes with imprinted, parent-specific expression not yet detected in other species (MLH1, EPM2AIP1, UBP1 and GPX7). We find that reprogramming of possum germline imprints, and the wider epigenome, is similar to eutherian mammals except onset occurs after birth. Together, this work is useful for genetic-based control and conservation of possums, and contributes to understanding of the evolution of novel mammalian epigenetic traits.
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Affiliation(s)
- Donna M Bond
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | | | - Melanie K Laird
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, 060-0808, Japan
| | - Kyle S Richardson
- Department of Anatomy, University of Otago, Dunedin, New Zealand
- Biology Department, University of Montana Western, Dillon, MT, 59725, USA
| | - Finlay C B Reese
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Bruce Kyle
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | | | | | | | - Amy L Adams
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Wei-Shan Chang
- School of Life and Environmental Science, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
- Health and Biosecurity, CSIRO, Canberra, ACT, Australia
| | - Bettina Haase
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | | | | | - Joanna Collins
- Tree of Life, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Yasuhiro Go
- Graduate School of Information Science, Hyogo University, Hyogo, Japan
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Aichi, Japan
- Department of System Neuroscience, National Institute for Physiological Sciences, Aichi, Japan
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Nicholas C Lister
- School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Paul D Waters
- School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Erich D Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, 10065, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Alana Alexander
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Timothy A Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand.
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25
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Shen X, Yan H, Li W, Zhou H, Wang J, Zhang Q, Zhang L, Liu Q, Liu Y. Estrodiol-17β and aromatase inhibitor treatment induced alternations of genome-wide DNA methylation pattern in Takifugu rubripes gonads. Gene 2023; 882:147641. [PMID: 37460000 DOI: 10.1016/j.gene.2023.147641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/12/2023] [Accepted: 07/12/2023] [Indexed: 07/28/2023]
Abstract
Estradiol-17β (E2) and aromatase inhibitor (AI) exposure can change the phenotypic sex of fish gonads. To investigated whether alterations in DNA methylation is involved in this process, the level of genome-wide DNA methylation in Takifugu rubripes gonads was quantitatively analyzed during the E2-induced feminization and AI-induced masculinization processes in this study. The methylation levels of the total cytosine (C) in control-XX(C-XX), control-XY (C-XY), E2-treated-XY (E-XY) and AI-treated-XX (AI-XX) were 9.11%, 9.19%, 8.63% and 9.23%, respectively. In the C-XX vs C-XY comparison, 4,196 differentially methylated regions (DMRs) overlapped with the gene body of 2,497 genes and 608 DMRs overlapped with the promoter of 575 genes. In the E-XY vs C-XY comparison, 6,539 DMRs overlapped with the gene body of 3,416 genes and 856 DMRs overlapped with the promoter of 776 genes. In the AI-XX vs C-XX comparison, 2,843 DMRs overlapped with the gene body of 1,831 genes and 461 DMRs overlapped with the promoter of 421 genes. Gonadal genomic methylation mainly occurred at CG sites and the genes that overlapped with DMRs on CG context were most enriched in the signaling pathways related to gonad differentiation, such as the Wnt, TGF-β, MAPK, CAM and GnRH pathways. The DNA methylation levels of steroid synthesis genes and estrogen receptor genes promoter or gene body were negative correlated with their expression. After bisulfite sequencing verification, the DNA methylation level of the amhr2 promoter in XY was increased after E2 treatment, which consistent with the data from the genome-wide DNA methylation sequencing. In C-XY group, the expression of amhr2 was significantly higher than that in E-XY (p < 0.05). Additionally, dnmt1, which is responsible for methylation maintenance, expressed at similar level in four groups (p > 0.05). dnmt3, tet2, and setd1b, which were responsible for methylation modification, expressed at significantly higher levels in E-XY compared to the C-XY (p < 0.05). Dnmt3 and tet2 were expressed at significantly higher levels in AI-XX than that in C-XX (p < 0.05). These results indicated that E2 and AI treatment lead to the aberrant genome-wide DNA methylation level and expression level of dnmt3, tet2, and setd1b in T. rubripes gonad.
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Affiliation(s)
- Xufang Shen
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Life Sciences, Liaoning Normal University, Dalian, Liaoning 116029, China
| | - Hongwei Yan
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China.
| | - Weiyuan Li
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Marine Science and Environment Engineering, Dalian Ocean University, 116023 Dalian, Liaoning, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China
| | - Huiting Zhou
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China
| | - Jia Wang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China
| | - Qi Zhang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China
| | - Lei Zhang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Marine Science and Environment Engineering, Dalian Ocean University, 116023 Dalian, Liaoning, China
| | - Qi Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Marine Science and Environment Engineering, Dalian Ocean University, 116023 Dalian, Liaoning, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China.
| | - Ying Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China
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Li X, Li L, Cui Z, Li M, Xu W. Phosphoproteomics Reveal New Candidates in Abnormal Spermatogenesis of Pseudomales in Cynoglossus semilaevis. Int J Mol Sci 2023; 24:11430. [PMID: 37511189 PMCID: PMC10380018 DOI: 10.3390/ijms241411430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/05/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Phosphorylation is a post-translational modification that contributes to versatile protein functions in spermatogenesis, and the variations they generate usually results in abnormal spermatogenesis or sperm dysfunction. The sex-reversal phenomenon exists in Chinese tongue sole under certain conditions such that individuals with a ZW genotype can acquire a male phenotype and are thus called pseudomales. Pseudomale tongue sole can reach sexual maturity but produce only Z-type sperm, and the Z sperm carries paternal epigenetic information. Whether phosphorylation plays a role in the sperm abnormality of pseudomales is unknown. In this study, a phosphoproteomic analysis was performed to compare protein phosphorylation profiles between pseudomale and male testes. Altogether, we identified 14,253 phosphopeptides matching with 4843 proteins, with 1329 differentially phosphorylated peptides corresponding to 1045 differentially phosphorylated proteins (DPPs). Phosphorylation at 781 sites was upregulated and at 548 sites was downregulated. Four motifs were identified among differentially phosphorylated peptides, which were "SP", "SD", "RxxS", and "TP". Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that the cell cycle and DNA/RNA processing were significantly enriched with the genes encoding DPPs. To analyze DPP function in depth, a protein-protein interaction network was constructed, and Ran-binding protein 2 was found to play a central role in spermatogenesis by regulating several processes such as the cell cycle, eukaryotic translation, ubiquitination, and minichromosome maintenance. In kinase-associated network analyses, two "mitogen-activated protein kinase (Mapk)-centered" clusters were identified that may account for abnormal spermatogenesis in pseudomales. One cluster was centered on Mapk6, which predominantly regulated the cell cycle by interacting with several cyclin-dependent kinases, and the other was centered on the "testis-expressed kinase 1-like (Tesk1l)/Pim1l-Mapk4l- testis-expressed 14 (Tex14)" kinase cascade, which might contribute to spermatogenesis by regulating β-catenin. Taken together, these data suggested the new candidates involved in pseudomale sperm abnormalities and provided clues to discover the phosphorylated regulatory mechanism underlying tongue sole spermatogenesis.
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Affiliation(s)
- Xihong Li
- Function Laboratory for Marine Science and Food Production Process, Laoshan Laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China
| | - Lu Li
- Function Laboratory for Marine Science and Food Production Process, Laoshan Laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China
- School of Fishery, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zhongkai Cui
- Function Laboratory for Marine Science and Food Production Process, Laoshan Laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China
| | - Ming Li
- Function Laboratory for Marine Science and Food Production Process, Laoshan Laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China
| | - Wenteng Xu
- Function Laboratory for Marine Science and Food Production Process, Laoshan Laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China
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27
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Sun D, Yu H, Li Q. Starvation-induced changes in sex ratio involve alterations in sex-related gene expression and methylation in Pacific oyster Crassostrea gigas. Comp Biochem Physiol B Biochem Mol Biol 2023; 267:110863. [PMID: 37164224 DOI: 10.1016/j.cbpb.2023.110863] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/06/2023] [Accepted: 05/06/2023] [Indexed: 05/12/2023]
Abstract
Aquatic animals are subject to varying degrees of starvation stress in their natural habitats due to food limitations. Consequently, starvation is a crucial environmental factor for sex determination in many species; however, limited research has been conducted on the effects of starvation on sex determination in shellfish. Here, four full sibling families of Pacific oysters were established and subjected to starvation stress. The results demonstrated that starvation caused the sex ratio (female to male) to change from 1:0.78 to 1:1.44 and resulted in a delay in gonadal development. Further studies revealed that the expression levels of DNA methylation-related genes Dnmt1 (DNA methyltransferase 1), Dnmt3a/b (DNA methyltransferase 3a/b) and Tet3 (tet methylcytosine dioxygenase 3) decreased under starvation stress. Conversely, the upregulation of Dmrt1 (doublesex and mab-3 related transcription factor 1), a gene typically associated with males, in females suggests that the increased proportion of males may be linked to starvation-induced high expression of this particular gene. In addition, the gene Dgkd (diacylglycerol kinase delta), which is involved in the regulation of second messenger protein kinase C, was differentially methylated between males and females, with the methylation level of this gene gradually increasing with male development, while the methylation level of this gene decreased under starvation stress. Correlation analysis of Dgkd methylation levels with expression levels showed a negative correlation between DNA methylation and gene expression. Finally dual fluorescence reporter experiments confirmed that DNA methylation suppressed Dgkd expression in vitro. In summary, the results suggest that starvation may regulate Dgkd gene expression through DNA methylation and thus affect Dmrt1 expression, thereby causing sex reversal in the Pacific oyster. The outcomes resolved how environmental factors are involved in sex reversal from an epigenetic perspective and provided a theoretical basis for sex control breeding in the Pacific oyster.
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Affiliation(s)
- Dongfang Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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28
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Tang J, Song A, Pan L, Miao J, Li Z, Zhou Y. Study of DNA methylation of hsd17β, er and reproductive endocrine disrupting effects in female Chlamys farreri under benzo[a]pyrene stress. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 328:121667. [PMID: 37080513 DOI: 10.1016/j.envpol.2023.121667] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
Benzo[a]pyrene (B[a]P) is one kind of persistent organic pollutants (POPs) in the marine environment which has multiple toxic effects. However, epigenetic studies correlated with reproductive endocrine disruption in invertebrates have not been explored. In our study, Chlamys farreri in the mature stage were exposed to B[a]P (0, 0.4, 2 and 10 μg/L) for 5 and 10 d to explore the effects on reproductive endocrine and DNA methylation. The results proved that B[a]P stress significantly restrained the growth of mature oocytes, reduced the content of sex hormones, and affected the expression of genes related to ovarian development. Histological observation showed that the ovarian microstructure was damaged. The detection of SAM/SAH, dnmts, GNMT in the ovary showed that the level of global DNA methylation fluctuated. Significant hypermethylation of the hsd17β promoter region in the ovary was associated with a significant downregulation of its gene expression. In summary, our results suggested that exposure to B[a]P might affect DNA methylation to regulate key reproductive genes, interfere with the synthesis of sex hormones, and inhibit ovarian development. These findings provide a basis for a better understanding of how epigenetic mechanisms are involved in the response of marine invertebrates to POPs stress, opening up new avenues for incorporating environmental epigenetic approaches into marine invertebrate management and conservation plans.
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Affiliation(s)
- Jian Tang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Aimin Song
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Luqing Pan
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
| | - Jingjing Miao
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Zeyuan Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yueyao Zhou
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
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29
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González-Rodríguez P, Füllgrabe J, Joseph B. The hunger strikes back: an epigenetic memory for autophagy. Cell Death Differ 2023:10.1038/s41418-023-01159-4. [PMID: 37031275 DOI: 10.1038/s41418-023-01159-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/10/2023] Open
Abstract
Historical and demographical human cohorts of populations exposed to famine, as well as animal studies, revealed that exposure to food deprivation is associated to lasting health-related effects for the exposed individuals, as well as transgenerational effects in their offspring that affect their diseases' risk and overall longevity. Autophagy, an evolutionary conserved catabolic process, serves as cellular response to cope with nutrient starvation, allowing the mobilization of an internal source of stored nutrients and the production of energy. We review the evidence obtained in multiple model organisms that support the idea that autophagy induction, including through dietary regimes based on reduced food intake, is in fact associated to improved health span and extended lifespan. Thereafter, we expose autophagy-induced chromatin remodeling, such as DNA methylation and histone posttranslational modifications that are known heritable epigenetic marks, as a plausible mechanism for transgenerational epigenetic inheritance of hunger.
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Affiliation(s)
- Patricia González-Rodríguez
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jens Füllgrabe
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Bertrand Joseph
- Institute of Environmental Medicine, Toxicology Unit, Karolinska Institutet, Stockholm, Sweden.
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30
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Arafah M, Aldawood N, Alrezaki A, Nahdi S, Alwasel S, Mansour L, Harrath AH. Prenatal exposure to acrylamide differently affected the sex ratio, aromatase and apoptosis in female adult offspring of two subsequent generations. Physiol Res 2023; 72:59-69. [PMID: 36545876 PMCID: PMC10069810 DOI: 10.33549/physiolres.934975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
In the present study, we investigated the effect of acrylamide (ACR) exposure during pregnancy on the ovary of female adult offspring of two subsequent generations. Sixty-day-old Wistar albino female rats were given different doses of ACR (2.5 and 10 mg/kg/day) from day 6 of pregnancy until giving birth. Females from the first generation (AF1) were fed ad libitum, and thereafter, a subgroup was euthanized at 8 weeks of age and ovary samples were obtained. The remaining females were maintained until they reached sexual maturity (50 days old) and then treated in the same way as the previous generation to obtain the second generation of females (AF2). The histopathological examination indicated a high frequency of corpora lutea along with an increased number of antral follicles that reached the selectable stage mainly at a dose of 2.5 mg/kg/day. Interestingly, ACR exposure significantly increased the mRNA levels of CYP19 gene and its corresponding CYP19 protein expression in AF1 females. The TUNEL assay showed a significantly high rate of apoptosis in stromal cells except for dose of 2.5 mg/kg/day. However, in AF2 females, ACR exposure significantly increased the number of degenerating follicles and cysts while the number of growing follicles was reduced. Moreover, in both ACR-treated groups, estradiol-producing enzyme CYP19A gene and its corresponding protein were significantly reduced, and an excessive apoptosis was produced. We concluded that the ovarian condition of AF1 females had considerable similarity to the typical early perimenopausal stage, whereas that of AF2 females was similar to the late perimenopausal stage in women.
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Affiliation(s)
- M Arafah
- Department of Pathology, College of Medicine, King Saud University, Riyadh, Kingdom of Saudi Arabia; Department of Zoology, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia.
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31
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Liu Q, Wang Y, Tan L, Ma W, Zhao X, Shao C, Wang Q. The Role of the Heat Shock Cognate Protein 70 Genes in Sex Determination and Differentiation of Chinese Tongue Sole ( Cynoglossus semilaevis). Int J Mol Sci 2023; 24:ijms24043761. [PMID: 36835170 PMCID: PMC9964925 DOI: 10.3390/ijms24043761] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023] Open
Abstract
Fish sex determination can be affected by environmental temperature. This process relies on temperature-sensitive proteins such as heat shock proteins (HSPs). Our previous work found that heat shock cognate proteins (HSCs) may participate in high-temperature associated sex reversal of Chinese tongue sole (Cynoglossus semilaevis). However, the role of hsc genes in responding to high temperature and affecting sex determination/differentiation remains unclear. Here, by using C. semilaevis as model, we identified hsc70 and hsc70-like. hsc70 was abundant in the gonads with a testicular-higher expression at all gonadal development stages except for 6 months post fertilization (mpf). Intriguingly, hsc70-like showed higher expression in testes from 6 mpf on. Both long-term heat treatment during the temperature-sensitive sex-determining period and short-term heat stress at the end of this period caused different expression of hsc70/hsc70-like between sexes. The dual-luciferase assay results also suggested that these genes can respond to high temperature rapidly in vitro. Heat treatment of C. semilaevis testis cells overexpressed with hsc70/hsc70-like could affect the expression of sex-related genes sox9a and cyp19a1a. Our results indicated that hsc70 and hsc70-like were key regulators linking external high-temperature signals with sex differentiation in vivo and provide a new idea for understanding the mechanism by which high temperature affects sex determination/differentiation in teleosts.
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Affiliation(s)
- Qian Liu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Re-search Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Yue Wang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Re-search Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Leilei Tan
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Re-search Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Jiangsu Key Laboratory of Marine Biological Resources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Wenxiu Ma
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Re-search Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xiaona Zhao
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Re-search Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Changwei Shao
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Re-search Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- Correspondence: (C.S.); (Q.W.); Tel.: +86-139-6962-5483 (C.S.); Tel.: +86-187-6521-7669 (Q.W.)
| | - Qian Wang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Re-search Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- Correspondence: (C.S.); (Q.W.); Tel.: +86-139-6962-5483 (C.S.); Tel.: +86-187-6521-7669 (Q.W.)
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32
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Valdivieso A, Anastasiadi D, Ribas L, Piferrer F. Development of epigenetic biomarkers for the identification of sex and thermal stress in fish using DNA methylation analysis and machine learning procedures. Mol Ecol Resour 2023; 23:453-470. [PMID: 36305237 PMCID: PMC10098837 DOI: 10.1111/1755-0998.13725] [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: 07/31/2021] [Revised: 09/28/2022] [Accepted: 10/14/2022] [Indexed: 01/04/2023]
Abstract
The sex ratio is a key ecological demographic parameter crucial for population viability. However, the epigenetic mechanisms operating during gonadal development regulating gene expression and the sex ratio remain poorly understood. Moreover, there is interest in the development of epigenetic markers associated with a particular phenotype or as sentinels of environmental effects. Here, we profiled DNA methylation and gene expression of 10 key genes related to sex development and stress, including steroidogenic enzymes, and growth and transcription factors. We provide novel information on the sex-related differences and on the influence of elevated temperature on these genes in zebrafish, a species with mixed genetic and environmental influences on sex ratios. We identified both positive (e.g., amh, cyp11c and hsd11b2) and negative (e.g., cyp11a1 and dmrt1) correlations in unexposed males, and negative correlation (amh) in exposed females between DNA methylation and gene expression levels. Further, we combined DNA methylation analysis with machine learning procedures and found a series of informative CpGs capable not only of correctly identifying sex (based on cyp19a1a DNA methylation levels) but also of identifying whether males and females had been exposed to abnormally elevated temperature when young (based on amh and foxl2a DNA methylation levels, respectively). This was achieved in the absence of conspicuous morphological alterations of the gonads. These DNA methylation-based epigenetic biomarkers represent molecular resources that can correctly recapitulate past thermal history and pave the way for similar findings in other species to assess potential ecological effects of environmental disturbances in the context of climate change.
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Affiliation(s)
- Alejandro Valdivieso
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.,IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | - Dafni Anastasiadi
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.,The New Zealand Institute for Plant and Food Research Limited, Nelson, New Zealand
| | - Laia Ribas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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33
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Waters PD, Graves JAM, Whiteley SL, Georges A, Ruiz-Herrera A. Three dimensions of thermolabile sex determination. Bioessays 2023; 45:e2200123. [PMID: 36529688 DOI: 10.1002/bies.202200123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 10/14/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
The molecular mechanism of temperature-dependent sex determination (TSD) is a long-standing mystery. How is the thermal signal sensed, captured and transduced to regulate key sex genes? Although there is compelling evidence for pathways via which cells capture the temperature signal, there is no known mechanism by which cells transduce those thermal signals to affect gene expression. Here we propose a novel hypothesis we call 3D-TSD (the three dimensions of thermolabile sex determination). We postulate that the genome has capacity to remodel in response to temperature by changing 3D chromatin conformation, perhaps via temperature-sensitive transcriptional condensates. This could rewire enhancer-promoter interactions to alter the expression of key sex-determining genes. This hypothesis can accommodate monogenic or multigenic thermolabile sex-determining systems, and could be combined with upstream thermal sensing and transduction to the epigenome to commit gonadal fate.
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Affiliation(s)
- Paul D Waters
- Faculty of Science, School of Biotechnology and Biomolecular Science, UNSW Sydney, Sydney, NSW, Australia
| | - Jennifer A Marshall Graves
- Department of Environment and Genetics, La Trobe University, Bundoora, Australia.,Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Sarah L Whiteley
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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34
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Li L, He S, Lin MH, Zhang YP, Kuhl H, Liang XF. Whole-genome resequencing and bisulfite sequencing provide new insights into the feeding habit domestication in mandarin fish ( Siniperca chuatsi). Front Genet 2023; 13:1088081. [PMID: 36712873 PMCID: PMC9878154 DOI: 10.3389/fgene.2022.1088081] [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: 11/03/2022] [Accepted: 12/28/2022] [Indexed: 01/14/2023] Open
Abstract
Mandarin fish (Siniperca chuatsi) is one of the most economically important fish in China. However, it has the peculiar feeding habit that it feeds solely on live prey fish since first-feeding, while refuses dead prey fish or artificial diets. After the specific training procedure, partial individuals could accept dead prey fish and artificial diets. The genetic basis of individual difference in artificial diet feeding habit is still unknown. In the present study, the resequencing was performed between 10 individuals which could be domesticated to accept artificial diets and 10 individuals which could not. Through the selective sweep analysis based on heterozygosity (Hp) and population differentiation coefficient (Fst), 57 candidate windows were identified as the putative selected regions for feeding habit domestication of mandarin fish, involved in 149 genes. These genes were related to memory, vision and olfaction function, which could be potential targets of molecular marker assistant breeding of artificial diet feeding trait. Beside of the DNA sequence, we also explored the potential role of DNA methylation in feeding habit domestication in mandarin fish. Whole-genome bisulfite sequencing was performed between the individuals which could be domesticated to accept artificial diets and those could not. 5,976 differentially methylated regions were identified, referring to 3,522 genes, such as the genes involved in cAMP signaling pathway. The DNA methylation changes of these genes might contribute to the adaption of artificial diets in mandarin fish. In conclusion, the putative selected regions and the differentially methylated regions were identified in the whole genome, providing new insights into the feeding habit domestication from live prey fish to artificial diets in mandarin fish. And the involved genes were identified as the candidate genes for molecular breeding of artificial diet utilization in mandarin fish.
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Affiliation(s)
- Ling Li
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Shan He
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Ming-Hui Lin
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Yan-Peng Zhang
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Heiner Kuhl
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany,*Correspondence: Xu-Fang Liang, ; Heiner Kuhl,
| | - Xu-Fang Liang
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China,*Correspondence: Xu-Fang Liang, ; Heiner Kuhl,
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35
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Wang W, Yang Y, Tan S, Zhou T, Liu Y, Tian C, Bao L, Xing D, Su B, Wang J, Zhang Y, Liu S, Shi H, Gao D, Dunham R, Liu Z. Genomic imprinting-like monoallelic paternal expression determines sex of channel catfish. SCIENCE ADVANCES 2022; 8:eadc8786. [PMID: 36542716 PMCID: PMC9770954 DOI: 10.1126/sciadv.adc8786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
The X and Y chromosomes of channel catfish have the same gene contents. Here, we report allelic hypermethylation of the X chromosome within the sex determination region (SDR). Accordingly, the X-borne hydin-1 gene was silenced, whereas the Y-borne hydin-1 gene was expressed, making monoallelic expression of hydin-1 responsible for sex determination, much like genomic imprinting. Treatment with a methylation inhibitor, 5-aza-dC, erased the epigenetic marks within the SDR and caused sex reversal of genetic females into phenotypic males. After the treatment, hydin-1 and six other genes related to cell cycle control and proliferative growth were up-regulated, while three genes related to female sex differentiation were down-regulated in genetic females, providing additional support for epigenetic sex determination in catfish. This mechanism of sex determination provides insights into the plasticity of genetic sex determination in lower vertebrates and its connection with temperature sex determination where DNA methylation is broadly involved.
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Affiliation(s)
- Wenwen Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Yujia Yang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Suxu Tan
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Changxu Tian
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Lisui Bao
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - De Xing
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Baofeng Su
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Jinhai Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Yu Zhang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Huitong Shi
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Dongya Gao
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, USA
| | - Rex Dunham
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, USA
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36
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Transcriptomic Analysis Revealed Candidate Genes Involved in Pseudomale Sperm Abnormalities in Chinese Tongue Sole ( Cynoglossus semilaevis). BIOLOGY 2022; 11:biology11121716. [PMID: 36552227 PMCID: PMC9775080 DOI: 10.3390/biology11121716] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022]
Abstract
Chinese tongue sole (Cynoglossus semilaevis) has a ZZ/ZW sex determination system, but the genotypic female (ZW) can be sex-reversed into phenotypic males, namely, pseudomales. Pseudomale fish can produce only Z-type sperm but not W sperm. However, the molecular mechanism is unclear. To screen the key genes involved in pseudomale sperm abnormalities, we analysed the transcriptomic profiles of pseudomale and male sperm. In comparison to male sperm, 592 differentially expressed genes (DEGs) were identified in pseudomale sperm, including 499 upregulated and 93 downregulated genes. KEGG analysis indicated that the FoxO signalling pathway, especially the foxo3a and foxo6-like genes, may play an important role in spermatogenesis. The DEGs were mainly distributed on sex chromosomes, with 158 downregulated genes on the Z chromosome and 41 upregulated genes on the W chromosome. A specific area (14-15 M) on the Z chromosome was identified, which enriched eight DEGs inside the ~1 M region. In addition, there were five gene alleles on the sex chromosomes, which showed the opposite transcription pattern (upregulated for the W allele, downregulated for the Z allele). This study has provided valuable data for screening candidate genes involved in the pseudomale sperm abnormality.
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Wang HY, Liu X, Chen JY, Huang Y, Lu Y, Tan F, Liu Q, Yang M, Li S, Zhang X, Qin Y, Ma W, Yang Y, Meng L, Liu K, Wang Q, Fan G, Nóbrega RH, Liu S, Piferrer F, Shao C. Single-cell-resolution transcriptome map revealed novel genes involved in testicular germ cell progression and somatic cells specification in Chinese tongue sole with sex reversal. SCIENCE CHINA LIFE SCIENCES 2022; 66:1151-1169. [PMID: 36437386 DOI: 10.1007/s11427-021-2236-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022]
Abstract
Female-to-male sex reversals (pseudomales) are common in lower vertebrates and have been found in natural populations, which is a concern under rapid changes in environmental conditions. Pseudomales can exhibit altered spermatogenesis. However, the regulatory mechanisms underlying pseudomale spermatogenesis remain unclear. Here, we characterized spermatogenesis in Chinese tongue sole (Cynoglossus semilaevis), a species with genetic and environmental sex determination, based on a high-resolution single-cell RNA-seq atlas of cells derived from the testes of genotypic males and pseudomales. We identified five germ cell types and six somatic cell types and obtained a single-cell atlas of dynamic changes in gene expression during spermatogenesis in Chinese tongue sole, including alterations in pseudomales. We detected decreased levels of Ca2+ signaling pathway-related genes in spermatogonia, insufficient meiotic initiation in spermatocytes, and a malfunction of somatic niche cells in pseudomales. However, a cluster of CaSR genes and MAPK signaling factors were upregulated in undifferentiated spermatogonia of pseudomales. Additionally, we revealed that Z chromosome-specific genes, such as piwil2, dhx37, and ehmt1, were important for spermatogenesis. These results improve our understanding of reproduction after female-to-male sex-reversal and provide new insights into the adaptability of reproductive strategies in lower vertebrates.
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38
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Hu QL, Ye YX, Zhuo JC, Huang HJ, Li JM, Zhang CX. Chromosome-level Assembly, Dosage Compensation and Sex-biased Gene Expression in the Small Brown Planthopper, Laodelphax striatellus. Genome Biol Evol 2022; 14:evac160. [PMID: 36317697 PMCID: PMC9651030 DOI: 10.1093/gbe/evac160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2022] [Indexed: 01/19/2024] Open
Abstract
In insects, sex chromosome differentiation often results in unequal gene dosages between sexes. Dosage compensation mechanisms evolve to balance gene expression, but the degree and mechanism of regulation often vary by insect species. In hemipteran species, the small brown planthopper (SBPH), Laodelphax striatellus, is an injurious crop pest, with a sex chromosome type XX in females and XO in males. This species offers the opportunity to study dosage compensation and sex-biased gene expression. In this study, we generated a chromosome-level genome of SBPH using Oxford Nanopore Technologies and high-throughput chromatin conformation capture (Hi-C) technology. We also sequenced RNA-seq data from 16 tissue samples to annotate the genome and analyze gene dosage compensation. We finally obtained a 510.2 megabases (Mb) genome with 99.12% of the scaffolds anchored on 15 chromosomes (14 autosomes and 1 X chromosome) and annotated 16,160 protein-coding genes based on full-length cDNA sequencing data. Furthermore, we found complete dosage compensation in all L. striatellus somatic tissues, but lack of dosage compensation in gonad tissue testis. We also found that female-biased genes were significantly enriched on the X chromosome in all tissues, whereas male-biased genes in gonad tissues were enriched on autosomes. This study not only provides a high-quality genome assembly but also lays a foundation for a better understanding of the sexual regulatory network in hemipteran insects.
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Affiliation(s)
- Qing-Ling Hu
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yu-Xuan Ye
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
| | - Ji-Chong Zhuo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Hai-Jian Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Chuan-Xi Zhang
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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39
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van Gelderen TA, Montfort J, Álvarez-Dios JA, Thermes V, Piferrer F, Bobe J, Ribas L. Deciphering sex-specific miRNAs as heat-recorders in zebrafish. Sci Rep 2022; 12:18722. [PMID: 36333360 PMCID: PMC9636255 DOI: 10.1038/s41598-022-21864-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
In the last decade, a plethora of microRNAs (miRNAs) has been reported in a wide variety of physiological processes, including reproduction, in many aquatic organisms. However, miRNAome alterations occurred by environmental cues due to water temperature increment have not yet been elucidated. With the aim to identify epigenetic regulations mediated by miRNAs in the gonads in a climate change scenario, the animal model zebrafish (Danio rerio) were subjected to high temperatures during sex differentiation, a treatment that results in male-skewed sex ratios in the adulthood. Once the fish reached adulthood, gonads were sequenced by high-throughput technologies and a total of 23 and 1 differentially expressed miRNAs in ovaries and testes, respectively, were identified two months after the heat treatment. Most of these heat-recorder miRNAs were involved in human sex-related cancer and about 400 predicted-target genes were obtained, some with reproduction-related functions. Their synteny in the zebrafish genome was, for more than half of the predicted target genes, in the chromosomes 7, 2, 4, 3 and 11 in the ovaries, chromosome 4 being the place where the sex-associated-region (sar) is localized in wild zebrafish. Further, spatial localization in the gonads of two selected heat-recorder miRNAs (miR-122-5p and miR-146-5p) showed exclusive expression in the ovarian germ cells. The present study expands the catalog of sex-specific miRNAs and deciphers, for the first time, thermosensitive miRNAs in the zebrafish gonads that might be used as potential epimarkers to predict environmental past events.
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Affiliation(s)
- Tosca A van Gelderen
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (ICM-CSIC), 08003, Barcelona, Spain
- PhD Program in Genetics, Autonomous University of Barcelona, 08193, Bellaterra, Spain
| | - Jérôme Montfort
- Laboratoire de Physiologie et Génomique des Poissons, INRAE, Rennes, France
| | - José Antonio Álvarez-Dios
- Departamento de Matemática Aplicada, Facultad de Matemáticas, Universidad de Santiago de Compostela, 15781, Santiago de Compostela, Spain
| | - Violette Thermes
- Laboratoire de Physiologie et Génomique des Poissons, INRAE, Rennes, France
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (ICM-CSIC), 08003, Barcelona, Spain
| | - Julien Bobe
- Laboratoire de Physiologie et Génomique des Poissons, INRAE, Rennes, France
| | - Laia Ribas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (ICM-CSIC), 08003, Barcelona, Spain.
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40
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Liu Z, Zhou T, Gao D. Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture. Front Genet 2022; 13:994471. [PMID: 36406125 PMCID: PMC9666392 DOI: 10.3389/fgene.2022.994471] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/20/2022] [Indexed: 11/25/2022] Open
Abstract
Major progress has been made with genomic and genetic studies in aquaculture in the last decade. However, research on epigenetic regulation of aquaculture traits is still at an early stage. It is apparent that most, if not all, aquaculture traits are regulated at both genetic and epigenetic levels. This paper reviews recent progress in understanding of genetic and epigenetic regulation of important aquaculture traits such as growth, reproduction, disease resistance, and stress responses. Although it is challenging to make generalized statements, DNA methylation is mostly correlated with down-regulation of gene expression, especially when at promoters and enhancers. As such, methylation of growth factors and their receptors is negatively correlated with growth; hypomethylation of genes important for stress tolerance is correlated with increased stress tolerance; hypomethylation of genes important for male or female sex differentiation leads to sex differentiation into males or females, respectively. It is apparent that environmental regulation of aquaculture traits is mediated at the level of epigenetic regulation, and such environment-induced epigenetic changes appeared to be intergenerationally inherited, but evidences for transgenerational inheritance are still limited.
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Affiliation(s)
- Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States,*Correspondence: Zhanjiang Liu,
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Dongya Gao
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States
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41
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Gong G, Xiong Y, Xiao S, Li XY, Huang P, Liao Q, Han Q, Lin Q, Dan C, Zhou L, Ren F, Zhou Q, Gui JF, Mei J. Origin and chromatin remodeling of young X/Y sex chromosomes in catfish with sexual plasticity. Natl Sci Rev 2022; 10:nwac239. [PMID: 36846302 PMCID: PMC9945428 DOI: 10.1093/nsr/nwac239] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/22/2022] [Accepted: 10/21/2022] [Indexed: 11/15/2022] Open
Abstract
Assembly of a complete Y chromosome is a significant challenge in animals with an XX/XY sex-determination system. Recently, we created YY-supermale yellow catfish by crossing XY males with sex-reversed XY females, providing a valuable model for Y-chromosome assembly and evolution. Here, we assembled highly homomorphic Y and X chromosomes by sequencing genomes of the YY supermale and XX female in yellow catfish, revealing their nucleotide divergences with only less than 1% and with the same gene compositions. The sex-determining region (SDR) was identified to locate within a physical distance of 0.3 Mb by FST scanning. Strikingly, the incipient sex chromosomes were revealed to originate via autosome-autosome fusion and were characterized by a highly rearranged region with an SDR downstream of the fusion site. We found that the Y chromosome was at a very early stage of differentiation, as no clear evidence of evolutionary strata and classical structure features of recombination suppression for a rather late stage of Y-chromosome evolution were observed. Significantly, a number of sex-antagonistic mutations and the accumulation of repetitive elements were discovered in the SDR, which might be the main driver of the initial establishment of recombination suppression between young X and Y chromosomes. Moreover, distinct three-dimensional chromatin organizations of the Y and X chromosomes were identified in the YY supermales and XX females, as the X chromosome exhibited denser chromatin structure than the Y chromosome, while they respectively have significantly spatial interactions with female- and male-related genes compared with other autosomes. The chromatin configuration of the sex chromosomes as well as the nucleus spatial organization of the XX neomale were remodeled after sex reversal and similar to those in YY supermales, and a male-specific loop containing the SDR was found in the open chromatin region. Our results elucidate the origin of young sex chromosomes and the chromatin remodeling configuration in the catfish sexual plasticity.
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Affiliation(s)
- Gaorui Gong
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Xiong
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Shijun Xiao
- Jiaxing Key Laboratory for New Germplasm Breeding of Economic Mycology, Jiaxing 314000, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Peipei Huang
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China,School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Qian Liao
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingqing Han
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaohong Lin
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China,State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Cheng Dan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Fan Ren
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | | | - Jie Mei
- Corresponding author. E-mail:
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42
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Gong Z, Shi R, Chen S, Wang N. CircRNA Identification and CircRNA-miRNA-mRNA Network in Cynoglossus semilaevis Sexual Size Dimorphism. BIOLOGY 2022; 11:biology11101451. [PMID: 36290355 PMCID: PMC9598273 DOI: 10.3390/biology11101451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/14/2022]
Abstract
Sexual size dimorphism (SSD), which is the sexual differences in body size, has been widely reported in various species including fishes. For Chinese tongue sole (Cynoglossus semilaevis), a flatfish exhibiting typically female-biased SSD, little is known for its epigenetic regulation mechanism, especially the role of circRNAs. Here, we identified the differently expressed abundances of circRNAs in females, males, and pseudo-males to explore the potential functions of circRNAs in Chinese tongue sole SSD. In total, 14,745 novel circRNAs were screened, among which 1461 DE circRNAs were identified from the brain, gonad, liver, and muscle in female, male, and pseudo-male individuals. The ceRNA network was subsequently constructed, including 10 circRNAs, 26 mRNAs, and 11 miRNAs. These DE mRNAs were mainly related to the mRNA surveillance pathway, metabolic pathways, and cellular senescence. Importantly, the ceRNA network has revealed that several circRNAs such as novel_circ_004374 and novel_circ_014597 may regulate homeodomain interacting protein kinase 2 (hipk2) expression by sponging miR-130-x. It is also worth exploring whether or how novel_circ_008696 regulates SET Domain Containing 2, histone lysine methyltransferase (setd2), which in turn affects the epigenetic patterns of different sexual individuals. The present study not only enriches the knowledge on the potential roles of circRNA in the physiological process, but also provides new clues for the explanation of fish SSD. In future studies, the precise function and involvement of circRNAs in female-biased SSD will require more efforts.
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Affiliation(s)
- Zhihong Gong
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Rui Shi
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Songlin Chen
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Na Wang
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Correspondence:
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Identification and Expression Pattern of cyp26b1 Gene in Gonad of the Chinese Tongue Sole ( Cynoglossus semilaevis). Animals (Basel) 2022; 12:ani12192652. [PMID: 36230393 PMCID: PMC9559488 DOI: 10.3390/ani12192652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022] Open
Abstract
Simple Summary In fish, it is obvious that the asynchronous development of the gonads and sexual dimorphism limit the development of aquaculture, so the research into sex-differentiation and gonadal growth is very important. Due to the sexual reversal phenomenon (genetic females becoming phenotypic males), the Chinese tongue sole (Cynoglossus semilaevis) is a great model for investigating sex-differentiation. Herein, we report one gene involved in sex-differentiation and gonadal growth of the Chinese Tongue Sole. The gene cyp26b1 (cytochrome P450 family 26 subfamily b member 1) is a metabolizing Retinoic Acid (RA) enzyme. Since it regulates RA to control sex determination and differentiation, cyp26b1 is considered a critical part of mammals’ ovary-antagonizing and testis-determining downstream passageway of Sry (sex-determining region Y) and Sox9 (sry-box transcription factor 9). In fish, the related research is reported only on the Japanese flounder (Paralichthys olivaceus) and zebrafish (Danio rerio). In the current investigation, the identification and expression pattern of the cyp26b1 gene in the Chinese tongue sole suggested that cyp26b1 might impact sex-differentiation and gonadal development. Abstract As an RA-metabolizing enzyme, cyp26b1 has a substantial impact on RA-signaling pathways. The cyp26b1 gene from the Chinese tongue sole was cloned and identified in this investigation. The cyp26b1 ORF was 1536 bp in length and encoded a 512 amino acid protein. A quantitative real-time PCR (qPCR) indicated that the cyp26b1 expression is no significant sexual dimorphism in the gonads at the 80 days post-hatching (dph) stages. After 4 months post-hatching (mph), the expression of cyp26b1 showed sexual dimorphism and lower level of expression in the ovaries than in the testes. An in situ hybridization demonstrated that cyp26b1 mRNA was primarily located in the testis. Interestingly, the cyp26b1 mRNA probe was also detected in the ovaries. These results suggested that cyp26b1 participates in the sex-differentiation and gonadal development of the Chinese tongue sole.
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Yao M, Zhang S, Lu Q, Chen X, Zhang SY, Kong Y, Zhao J. Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward. Mol Ecol 2022; 31:5132-5164. [PMID: 35972241 DOI: 10.1111/mec.16659] [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: 03/18/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 12/15/2022]
Abstract
Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.
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Affiliation(s)
- Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Shan Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Qi Lu
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Xiaoyu Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Si-Yu Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Yueqiao Kong
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Jindong Zhao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
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45
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Valdivieso A, Wilson CA, Amores A, da Silva Rodrigues M, Nóbrega RH, Ribas L, Postlethwait JH, Piferrer F. Environmentally-induced sex reversal in fish with chromosomal vs. polygenic sex determination. ENVIRONMENTAL RESEARCH 2022; 213:113549. [PMID: 35618011 PMCID: PMC9620983 DOI: 10.1016/j.envres.2022.113549] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Sex ratio depends on sex determination mechanisms and is a key demographic parameter determining population viability and resilience to natural and anthropogenic stressors. There is increasing evidence that the environment can alter sex ratio even in genetically sex-determined species (GSD), as elevated temperature can cause female-to-male sex reversal (neomales). Alarmingly, neomales are being discovered in natural populations of several fish, amphibian and reptile species worldwide. Understanding the basis of neomale development is important for conservation biology. Among GSD species, it is unknown whether those with chromosomal sex determination (CSD), the most common system, will better resist the influence of high temperature than those with polygenic sex determination (PSD). Here, we compared the effects of elevated temperature in two wild zebrafish strains, Nadia (NA) and Ekkwill (EKW), which have CSD with a ZZ/ZW system, against the AB laboratory strain, which has PSD. First, we uncovered novel sex genotypes and the results showed that, at control temperature, the masculinization rate roughly doubled with the addition of each Z chromosome, while some ZW and WW fish of the wild strains became neomales. Surprisingly, we found that at elevated temperatures WW fish were just as likely as ZW fish to become neomales and that all strains were equally susceptible to masculinization. These results demonstrate that the Z chromosome is not essential for male development and that the dose of W buffers masculinization at the control temperature but not at elevated temperature. Furthermore, at the elevated temperature the testes of neomales, but not of normal males, contained more spermatozoa than at the control temperature. Our results show in an unprecedented way that, in a global warming scenario, CSD species may not necessarily be better protected against the masculinizing effect of elevated temperature than PSD species, and reveal genotype-by-temperature interactions in male sex determination and spermatogenesis.
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Affiliation(s)
- Alejandro Valdivieso
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | | | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Maira da Silva Rodrigues
- Reproductive and Molecular Biology Group, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, São Paulo, Brazil
| | - Rafael Henrique Nóbrega
- Reproductive and Molecular Biology Group, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, São Paulo, Brazil
| | - Laia Ribas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | | | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Spain.
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46
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Sánchez-Baizán N, Ribas L, Piferrer F. Improved biomarker discovery through a plot twist in transcriptomic data analysis. BMC Biol 2022; 20:208. [PMID: 36153614 PMCID: PMC9509653 DOI: 10.1186/s12915-022-01398-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 09/02/2022] [Indexed: 11/22/2022] Open
Abstract
Background Transcriptomic analysis is crucial for understanding the functional elements of the genome, with the classic method consisting of screening transcriptomics datasets for differentially expressed genes (DEGs). Additionally, since 2005, weighted gene co-expression network analysis (WGCNA) has emerged as a powerful method to explore relationships between genes. However, an approach combining both methods, i.e., filtering the transcriptome dataset by DEGs or other criteria, followed by WGCNA (DEGs + WGCNA), has become common. This is of concern because such approach can affect the resulting underlying architecture of the network under analysis and lead to wrong conclusions. Here, we explore a plot twist to transcriptome data analysis: applying WGCNA to exploit entire datasets without affecting the topology of the network, followed with the strength and relative simplicity of DEG analysis (WGCNA + DEGs). We tested WGCNA + DEGs against DEGs + WGCNA to publicly available transcriptomics data in one of the most transcriptomically complex tissues and delicate processes: vertebrate gonads undergoing sex differentiation. We further validate the general applicability of our approach through analysis of datasets from three distinct model systems: European sea bass, mouse, and human. Results In all cases, WGCNA + DEGs clearly outperformed DEGs + WGCNA. First, the network model fit and node connectivity measures and other network statistics improved. The gene lists filtered by each method were different, the number of modules associated with the trait of interest and key genes retained increased, and GO terms of biological processes provided a more nuanced representation of the biological question under consideration. Lastly, WGCNA + DEGs facilitated biomarker discovery. Conclusions We propose that building a co-expression network from an entire dataset, and only thereafter filtering by DEGs, should be the method to use in transcriptomic studies, regardless of biological system, species, or question being considered. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01398-w.
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47
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Govender P, Ghai M, Okpeku M. Sex-specific DNA methylation: impact on human health and development. Mol Genet Genomics 2022; 297:1451-1466. [PMID: 35969270 DOI: 10.1007/s00438-022-01935-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/28/2022] [Indexed: 11/26/2022]
Abstract
Human evolution has shaped gender differences between males and females. Over the years, scientific studies have proposed that epigenetic modifications significantly influence sex-specific differences. The evolution of sex chromosomes with epigenetics as the driving force may have led to one sex being more adaptable than the other when exposed to various factors over time. Identifying and understanding sex-specific differences, particularly in DNA methylation, will help determine how each gender responds to factors, such as disease susceptibility, environmental exposure, brain development and neurodegeneration. From a medicine and health standpoint, sex-specific methylation studies have shed light on human disease severity, progression, and response to therapeutic intervention. Interesting findings in gender incongruent individuals highlight the role of genetic makeup in influencing DNA methylation differences. Sex-specific DNA methylation studies will empower the biotechnology and pharmaceutical industry with more knowledge to identify biomarkers, design and develop sex bias drugs leading to better treatment in men and women based on their response to different diseases.
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Affiliation(s)
- Priyanka Govender
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Meenu Ghai
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa.
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
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48
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Zhou T, Chen G, Chen M, Wang Y, Zou G, Liang H. Tandem Mass Tag-Based Quantitative Proteomics Analysis of Gonads Reveals New Insight into Sexual Reversal Mechanism in Chinese Soft-Shelled Turtles. BIOLOGY 2022; 11:biology11071081. [PMID: 36101459 PMCID: PMC9312195 DOI: 10.3390/biology11071081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/10/2022] [Accepted: 07/15/2022] [Indexed: 11/16/2022]
Abstract
Chinese soft-shelled turtles display obvious sex dimorphism. The exogenous application of hormones (estradiol and methyltestosterone) can change the direction of gonadal differentiation of P. sinensis to produce sex reversed individuals. However, the molecular mechanism remains unclear. In this study, TMT-based quantitative proteomics analysis of four types of P. sinensis (female, male, pseudo-female, and pseudo-male) gonads were compared. Quantitative analysis of 6107 labeled proteins in the four types of P. sinensis gonads was performed. We identified 440 downregulated and 423 upregulated proteins between pseudo-females and males, as well as 394 downregulated and 959 upregulated proteins between pseudo-males and females. In the two comparisons, the differentially expressed proteins, including K7FKG1, K7GIQ2, COL4A6, K7F2U2, and K7FF80, were enriched in some important pathways, such as focal adhesion, endocytosis, apoptosis, extracellular matrix-receptor interaction, and the regulation of actin cytoskeleton, which were upregulated in pseudo-female vs. male and downregulated in pseudo-male vs. female. In pathways such as ribosome and spliceosome, the levels of RPL28, SRSF3, SNRNP40, and HNRNPK were increased from male to pseudo-female, while they decreased from female to pseudo-male. All differentially expressed proteins after sexual reversal were divided into six clusters, according to their altered levels in the four types of P. sinensis, and associated with cellular processes, such as embryonic development and catabolic process, that were closely related to sexual reversal. These data will provide clues for the sexual reversal mechanism in P. sinensis.
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Affiliation(s)
- Tong Zhou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (T.Z.); (G.C.); (M.C.); (Y.W.)
| | - Guobin Chen
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (T.Z.); (G.C.); (M.C.); (Y.W.)
- College of Fisheries and Life, Shanghai Ocean University, Shanghai 201306, China
| | - Meng Chen
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (T.Z.); (G.C.); (M.C.); (Y.W.)
| | - Yubin Wang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (T.Z.); (G.C.); (M.C.); (Y.W.)
- College of Fisheries and Life, Shanghai Ocean University, Shanghai 201306, China
| | - Guiwei Zou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (T.Z.); (G.C.); (M.C.); (Y.W.)
- Correspondence: (G.Z.); (H.L.); Tel.: +86-27-8178-0097 (H.L.)
| | - Hongwei Liang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (T.Z.); (G.C.); (M.C.); (Y.W.)
- Correspondence: (G.Z.); (H.L.); Tel.: +86-27-8178-0097 (H.L.)
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49
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Hosseini S, Trakooljul N, Hirschfeld M, Wimmers K, Simianer H, Tetens J, Sharifi AR, Brenig B. Epigenetic Regulation of Phenotypic Sexual Plasticity Inducing Skewed Sex Ratio in Zebrafish. Front Cell Dev Biol 2022; 10:880779. [PMID: 35912111 PMCID: PMC9334531 DOI: 10.3389/fcell.2022.880779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
The plasticity of sexual phenotype in response to environmental conditions results in biased sex ratios, and their variation has an effect on population dynamics. Epigenetic modifications can modulate sex ratio variation in species, where sex is determined by genetic and environmental factors. However, the role of epigenetic mechanisms underlying skewed sex ratios is far from being clear and is still an object of debate in evolutionary developmental biology. In this study, we used zebrafish as a model animal to investigate the effect of DNA methylation on sex ratio variation in sex-biased families in response to environmental temperature. Two sex-biased families with a significant difference in sex ratio were selected for genome-wide DNA methylation analysis using reduced representation bisulfite sequencing (RRBS). The results showed significant genome-wide methylation differences between male-biased and female-biased families, with a greater number of methylated CpG sites in testes than ovaries. Likewise, pronounced differences between testes and ovaries were identified within both families, where the male-biased family exhibited a higher number of methylated sites than the female-biased family. The effect of temperature showed more methylated positions in the high incubation temperature than the control temperature. We found differential methylation of many reproduction-related genes (e.g., sox9a, nr5a2, lhx8a, gata4) and genes involved in epigenetic mechanisms (e.g., dnmt3bb.1, dimt1l, hdac11, h1m) in both families. We conclude that epigenetic modifications can influence the sex ratio variation in zebrafish families and may generate skewed sex ratios, which could have a negative consequence for population fitness in species with genotype-environment interaction sex-determining system under rapid environmental changes.
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Affiliation(s)
- Shahrbanou Hosseini
- Molecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
- Functional Breeding Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
- Institute of Veterinary Medicine, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
- *Correspondence: Shahrbanou Hosseini, ; Nares Trakooljul,
| | - Nares Trakooljul
- Research Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Genomics Unit, Dummerstorf, Germany
- *Correspondence: Shahrbanou Hosseini, ; Nares Trakooljul,
| | - Marc Hirschfeld
- Molecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
- Institute of Veterinary Medicine, University of Goettingen, Göttingen, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Genomics Unit, Dummerstorf, Germany
| | - Henner Simianer
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
| | - Jens Tetens
- Functional Breeding Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
| | - Ahmad Reza Sharifi
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
| | - Bertram Brenig
- Molecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany
- Institute of Veterinary Medicine, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
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50
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Liu F, Xu H, Ni W, Wang Y, Hong X, Li W, Yu L, Chen C, Wei C, Liu X, Zhu X. Temporal variation in DNA methylation during gonadal development in a reptile with temperature-dependent sex determination. Biol Reprod 2022; 107:1217-1227. [PMID: 35835578 DOI: 10.1093/biolre/ioac142] [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: 01/12/2022] [Revised: 05/04/2022] [Accepted: 07/05/2022] [Indexed: 11/14/2022] Open
Abstract
DNA methylation plays a significant role in transducing external environmental signals to a cellular response in reptiles; however, whether the methylation patterns are conserved across species remains unclear. Here, we examined the genome-wide DNA methylation differentiation between male and female hatchling gonads of the temperature-dependent sex determination (TSD) Mauremys mutica (M. mutica) using methylation-dependent restriction-site associated DNA sequencing (MethylRAD-seq) to test differentially methylated genes underlying sexual development. Several categories, including heat shock genes (HSP90A, HSP30C), histone- (KDM8) and ubiquitin-related genes (TRIM39), kinases (WNK3) and gonad differentiation or gonadal development related genes (HSD17B8, HSD17B12), were identified as candidates for future study. Additionally, we identified several regulatory pathways potentially mediating TSD thermosensitivity such as the GnRH signaling pathway and calcium signaling pathway. These findings provide evidence that sexually dimorphic DNA methylation may be associated with sex determination or sex differentiation in TSD M. mutica.
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Affiliation(s)
- Fang Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038
| | - Haoyang Xu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038.,College of Life Science and Fisheries, Shanghai Ocean University, Shanghai, China, 201306
| | - Wei Ni
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038.,College of Life Science and Fisheries, Shanghai Ocean University, Shanghai, China, 201306
| | - Yakun Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038
| | - Xiaoyou Hong
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038
| | - Wei Li
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038
| | - Lingyun Yu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038
| | - Chen Chen
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038
| | - Chengqing Wei
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038
| | - Xiaoli Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038
| | - Xinping Zhu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 51038.,College of Life Science and Fisheries, Shanghai Ocean University, Shanghai, China, 201306
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