151
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Anastasiadi D, Vandeputte M, Sánchez-Baizán N, Allal F, Piferrer F. Dynamic epimarks in sex-related genes predict gonad phenotype in the European sea bass, a fish with mixed genetic and environmental sex determination. Epigenetics 2018; 13:988-1011. [PMID: 30265213 PMCID: PMC6284782 DOI: 10.1080/15592294.2018.1529504] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/10/2018] [Accepted: 09/22/2018] [Indexed: 12/13/2022] Open
Abstract
The integration of genomic and environmental influences into methylation patterns to bring about a phenotype is of central interest in developmental epigenetics, but many details are still unclear. The sex ratios of the species used here, the European sea bass, are determined by genetic and temperature influences. We created four families from parents known to produce offspring with different sex ratios, exposed larvae to masculinizing temperatures and examined, in juvenile gonads, the DNA methylation of seven genes related to sexual development by a targeted sequencing approach. The genes most affected by both genetics and environment were cyp19a1a and dmrt1, with contrasting sex-specific methylation and temperature responses. The relationship between cyp19a1a methylation and expression is relevant to the epigenetic regulation of vertebrate sex, and we report the evidence of such relationship only below a methylation threshold, ~ 80%, and that it was sex-specific: negatively correlated in females but positively correlated in males. From parents to offspring, the methylation in gonads was midway between oocytes and sperm, with bias towards oocytes for amh-r2, er-β2, fsh-r and cyp19a1a. In contrast, dmrt1 levels resembled those of sperm. The methylation of individual CpGs from foxl2, er-β2 and nr3c1 were conserved from parents to offspring, whereas those of cyp19a1a, dmrt1 and amh-r2 were affected by temperature. Utilizing a machine-learning procedure based on the methylation levels of a selected set of CpGs, we present the first, to our knowledge, system based on epigenetic marks capable of predicting sex in an animal with ~ 90% accuracy and discuss possible applications.
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Affiliation(s)
- Dafni Anastasiadi
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Marc Vandeputte
- MARBEC, Univ. Montpellier, Ifremer-CNRS-IRD, Palavas-les-Flots, France
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Núria Sánchez-Baizán
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - François Allal
- MARBEC, Univ. Montpellier, Ifremer-CNRS-IRD, Palavas-les-Flots, France
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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152
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Dong Z, Zhang N, Liu Y, Xu W, Cui Z, Shao C, Chen S. Expression analysis and characterization of zglp1 in the Chinese tongue sole (Cynoglossus semilaevis). Gene 2018; 683:72-79. [PMID: 30312653 DOI: 10.1016/j.gene.2018.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/23/2018] [Accepted: 10/01/2018] [Indexed: 10/28/2022]
Abstract
Zinc finger GATA like protein-1 (ZGLP1) is a nuclear zinc finger protein that regulates the interaction between somatic cells and germ cells during gonad developmental process in mammals. In this study, the zglp1 of Chinese tongue sole, Cynoglossus semilaevis (cysezglp1), was cloned and characterized for the first time in fish. Cysezglp1 had an open reading frame with five exons and was located to chromosome 9. The open reading frame of cysezglp1 consisted of 1692 nucleotides and encoded a 583 amino acid polypeptide. The predicted protein contained two zinc finger structures (Znf1 and Znf2), one of which was highly homologous to the GATA-type zinc finger domain. Multiple sequence alignment showed that Znf1 was conserved across different species while Znf2 was more divergent. Through quantitative Real-time PCR (qRT-PCR), we found that cysezglp1 was predominantly expressed in gonads, and the expression level of the ovary was significantly higher than that of the testis. We compared expression level in different embryonic stages and found that cysezglp1 mRNAs were mainly expressed in the fertilized egg to the cleavage stage, subsequently declining in the blastula stage. Cysezglp1 expression was not detected from the gastrulation stage onward. In the ovary, cysezglp1 expression was detected at 120 days after hatching and expression gradually increased with the maturation of the ovary. In situ hybridization showed that the cysezglp1 was mainly expressed in oocytes. Taken together, our results suggest that cysezglp1 may play an important role in the process of oogenesis in Chinese tongue sole.
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Affiliation(s)
- Zhongdian Dong
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, CAFS, Qingdao 266071, China
| | - Ning Zhang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, CAFS, Qingdao 266071, China
| | - Yang Liu
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, CAFS, Qingdao 266071, China; Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Wenteng Xu
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, CAFS, Qingdao 266071, China; Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Zhongkai Cui
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, CAFS, Qingdao 266071, China; Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Changwei Shao
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, CAFS, Qingdao 266071, China; Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, 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, CAFS, Qingdao 266071, China; Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China.
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153
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Hill PL, Burridge CP, Ezaz T, Wapstra E. Conservation of Sex-Linked Markers among Conspecific Populations of a Viviparous Skink, Niveoscincus ocellatus, Exhibiting Genetic and Temperature-Dependent Sex Determination. Genome Biol Evol 2018; 10:1079-1087. [PMID: 29659810 PMCID: PMC5905450 DOI: 10.1093/gbe/evy042] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2018] [Indexed: 12/18/2022] Open
Abstract
Sex determination systems are exceptionally diverse and have undergone multiple and independent evolutionary transitions among species, particularly reptiles. However, the mechanisms underlying these transitions have not been established. Here, we tested for differences in sex-linked markers in the only known reptile that is polymorphic for sex determination system, the spotted snow skink, Niveoscincus ocellatus, to quantify the genomic differences that have accompanied this transition. In a highland population, sex is determined genetically, whereas in a lowland population, offspring sex ratio is influenced by temperature. We found a similar number of sex-linked loci in each population, including shared loci, with genotypes consistent with male heterogamety (XY). However, population-specific linkage disequilibrium suggests greater differentiation of sex chromosomes in the highland population. Our results suggest that transitions between sex determination systems can be facilitated by subtle genetic differences.
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Affiliation(s)
- Peta L Hill
- School of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania, Australia
| | | | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Erik Wapstra
- School of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania, Australia
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154
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Metzger DCH, Schulte PM. The DNA Methylation Landscape of Stickleback Reveals Patterns of Sex Chromosome Evolution and Effects of Environmental Salinity. Genome Biol Evol 2018; 10:775-785. [PMID: 29420714 PMCID: PMC5841383 DOI: 10.1093/gbe/evy034] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2018] [Indexed: 12/12/2022] Open
Abstract
Epigenetic mechanisms such as DNA methylation are a key component of dosage compensation on sex chromosomes and have been proposed as an important source of phenotypic variation influencing plasticity and adaptive evolutionary processes, yet little is known about the role of DNA methylation in an ecological or evolutionary context in vertebrates. The threespine stickleback (Gasterosteus aculeatus) is an ecological and evolutionary model system that has been used to study mechanisms involved in the evolution of adaptive phenotypes in novel environments as well as the evolution heteromorphic sex chromosomes and dosage compensation in vertebrates. Using whole genome bisulfite sequencing, we compared genome-wide DNA methylation patterns between threespine stickleback males and females and between stickleback reared at different environmental salinities. Apparent hypermethylation of the younger evolutionary stratum of the stickleback X chromosome in females relative to males suggests a potential role of DNA methylation in the evolution of heteromorphic sex chromosomes. We also demonstrate that rearing salinity has genome-wide effects on DNA methylation levels, which has the potential to lead to the accumulation of epigenetic variation between natural populations in different environments.
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Affiliation(s)
- David C H Metzger
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Patricia M Schulte
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
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155
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Trukhina AV, Lukina NA, Smirnov AF. Hormonal Sex Inversion and Some Aspects of Its Genetic Determination in Chicken. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418090144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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156
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Domingos JA, Budd AM, Banh QQ, Goldsbury JA, Zenger KR, Jerry DR. Sex-specific dmrt1 and cyp19a1 methylation and alternative splicing in gonads of the protandrous hermaphrodite barramundi. PLoS One 2018; 13:e0204182. [PMID: 30226860 PMCID: PMC6143260 DOI: 10.1371/journal.pone.0204182] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 09/03/2018] [Indexed: 01/06/2023] Open
Abstract
Epigenetics is involved in sex differentiation of gonochoristic and hermaphroditic fish species, whereby two genes dmrt1 (pro-male) and cyp19a1 (pro-female) are known to play major roles. Barramundi, Lates calcarifer, is an important tropical aquaculture species that undergo natural and permanent male to female sex change, a process for which the exact underlying molecular mechanisms are still unknown. To elucidate whether DNA methylation is involved in sex control of barramundi, a next-generation bisulfite amplicon sequencing approach was used to target 146 CpG sites within proximal promoters and first exons of seven sex-related genes (dmrt1, cyp19a1, amh, foxl2, nr5a2, sox8 and sox9) of 24 testis and 18 ovaries of captive and wild adult barramundi. Moreover, comparative expression profiles of the key dmrt1 and cyp19a1 genes were further investigated using RT-qPCR and Sanger sequencing approaches, whereas expression levels of remaining targeted genes were based on available literature for the species. Results showed that cyp19a1 and amh were more methylated in males, whereas dmrt1 and nr5a2 were more methylated in females (P < 0.001), with no gender differences found for foxl2, sox8 or sox9 genes (P > 0.05). Sex-biased promoter DNA methylation was inversely related to gene expression only for dmrt1 and nr5a2, and directly related to amh expression, whereas no differences in cyp19a1 expression were found between testes and ovaries. Notably, unique sex-specific alternative splicing of dmrt1 and cyp19a1 were discovered, whereby males lacked the full-length aromatase coding cyp19a1 mRNA due to partial or total exon splicing, and females lacked the dmrt1 exon containing the DM-domain sequence. This study advances the current knowledge aiming to elucidate the genetic mechanisms within male and female gonads of this large protandrous hermaphrodite by providing the first evidence of epigenetics and alternative splicing simultaneously affecting key genes (cyp19a1 and dmrt1) central to sex differentiation pathways.
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Affiliation(s)
- Jose A. Domingos
- Tropical Futures Institute, James Cook University Singapore, Singapore
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- * E-mail:
| | - Alyssa M. Budd
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Quyen Q. Banh
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Julie A. Goldsbury
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Dean R. Jerry
- Tropical Futures Institute, James Cook University Singapore, Singapore
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
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157
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Meng L, Xu W, Zhu Y, Zhang N, Shao C, Liu Y, Chen S. Molecular characterization and expression analysis of strbp in Chinese tongue sole (Cynoglossus semilaevis). Theriogenology 2018; 118:225-232. [DOI: 10.1016/j.theriogenology.2018.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 12/11/2022]
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158
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Wang FL, Yan LX, Shi HJ, Liu XY, Zheng QY, Sun LN, Wang DS. Genome-wide identification, evolution of DNA methyltransferases and their expression during gonadal development in Nile tilapia. Comp Biochem Physiol B Biochem Mol Biol 2018; 226:73-84. [PMID: 30170023 DOI: 10.1016/j.cbpb.2018.08.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 11/18/2022]
Abstract
DNA methyltransferases (dnmts) are responsible for DNA methylation and play important roles in organism development. In this study, seven dnmts genes (dnmt1, dnmt2, dnmt3aa, dnmt3ab, dnmt3ba, dnmt3bb.1, dnmt3bb.2) were identified in Nile tilapia. Comprehensive analyses of dnmts were performed using available genome databases from representative animal species. Phylogenetic analysis revealed that the dnmts family were highly conserved in teleosts. Based on transcriptome data from eight adult tilapia tissues, the dnmts were found to be dominantly expressed in the head kidney, testis and ovary. Analyses of the gonadal transcriptome data in different developmental stages revealed that all dnmts were expressed in both ovary and testis, and four de novo dnmts (dnmt3aa, dnmt3ab, dnmt3bb.1, dnmt3bb.2) showed higher expression in the testis than in the ovary. Furthermore, during sex reversal induced by Fadrozole, the expression of these four de novo dnmts increased significantly in treated group compared to female control group. By in situ hybridization, the seven dnmts were found to be expressed mainly in phase I and II oocytes of the ovary and spermatocytes of the testis. When gonads were incubated with a methyltransferase inhibitor (5-AzaCdR) in vitro, the expression of dnmts genes were down-regulated significantly, while the expression of cyp19a1a (a key gene in female pathway) and dmrt1 (a key gene in male pathway) increased significantly. Our results revealed the conservation of dnmts during evolution and indicated a potential role of dnmts in epigenetic regulation of gonadal development.
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Affiliation(s)
- Fei-Long Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Long-Xia Yan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Hong-Juan Shi
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Xing-Yong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Qiao-Yuan Zheng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China
| | - Li-Na Sun
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China.
| | - De-Shou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, 400715 Chongqing, PR China.
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159
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New locus reveals the genetic architecture of sex reversal in the Chinese tongue sole (Cynoglossus semilaevis). Heredity (Edinb) 2018; 121:319-326. [PMID: 30093666 PMCID: PMC6134077 DOI: 10.1038/s41437-018-0126-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/19/2018] [Accepted: 07/06/2018] [Indexed: 11/08/2022] Open
Abstract
Sex reversal in insects, amphibians, reptiles, and fishes is a complicated and interesting biological phenomenon. Sex reversal changes the sex ratio of populations and may complicate breeding schemes. In the Chinese tongue sole (Cynoglossus semilaevis), genetic females may change into pseudomales, thereby increasing aquaculture costs because of the lower growth rate of the males than that of the females. Here we identify a new locus associated with sex reversal; this single nucleotide polymorphism (SNP) is located in the third intron of the doublesex and mab-3 related transcription factor 1 (Dmrt1) gene on the Z chromosome (named Cyn_Z_8564889) and has two alleles, A and G. Cyn_Z_8564889 regulates sex reversal interactively with our previously detected SNP (Cyn_Z_6676874), with the genetic females simultaneously carrying the T allele of Cyn_Z_6676874 and the A allele of Cyn_Z_8564889 changing into pseudomales. Other Dmrt1 polymorphisms were detected, which formed two haplotypes. Two SNPs in the second exon of Dmrt1 result in amino acid changes, suggesting that Dmrt1 is essential in sex reversal. We also verified that pseudomales produce no or little W sperm. The interaction and linkage between Cyn_Z_6676874 and Cyn_Z_8564889 and the absence of W sperm from pseudomales unravel the genetic architecture of sex reversal in C. semilaevis.
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160
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Li XY, Liu XL, Zhu YJ, Zhang J, Ding M, Wang MT, Wang ZW, Li Z, Zhang XJ, Zhou L, Gui JF. Origin and transition of sex determination mechanisms in a gynogenetic hexaploid fish. Heredity (Edinb) 2018; 121:64-74. [PMID: 29391565 PMCID: PMC5997666 DOI: 10.1038/s41437-017-0049-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 12/23/2017] [Indexed: 12/31/2022] Open
Abstract
Most vertebrates reproduce sexually, and plastic sex determination mechanisms including genotypic sex determination (GSD) and environmental sex determination (ESD) have been extensively revealed. However, why sex determination mechanisms evolve diversely and how they correlate with diverse reproduction strategies remain largely unclear. Here, we utilize the superiority of a hexaploid gibel carp (Carassius gibelio) that is able to reproduce by unisexual gynogenesis and contains a rare but diverse proportion of males to investigate these puzzles. A total of 2248 hexaploid specimens were collected from 34 geographic wild populations throughout mainland China, in which 24 populations were revealed to contain 186 males with various incidences ranging from 1.2 to 26.5%. Subsequently, the proportion of temperature-dependent sex determination (TSD) was revealed to be positively correlated to average annual temperature in wild populations, and male incidence in lab gynogenetic progenies was demonstrated to increase with the increasing of larval rearing temperature. Meanwhile, extra microchromosomes were confirmed to play genotypic male determination role as previously reported. Thereby, GSD and TSD were found to coexist in gibel carp, and the proportions of GSD were observed to be much higher than that of TSD in sympatric wild populations. Our findings uncover a potential new mechanism in the evolution of sex determination system in polyploid vertebrates with unisexual gynogenesis ability, and also reveal a possible association of sex determination mechanism transition between TSD and GSD and reproduction mode transition between unisexual gynogenesis and bisexual reproduction.
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Affiliation(s)
- Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiao-Li Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yao-Jun Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jun Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, China
| | - Miao Ding
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ming-Tao Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, 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, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, China.
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161
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Anastasiadi D, Esteve-Codina A, Piferrer F. Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species. Epigenetics Chromatin 2018; 11:37. [PMID: 29958539 PMCID: PMC6025724 DOI: 10.1186/s13072-018-0205-1] [Citation(s) in RCA: 240] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation is one of the main epigenetic mechanisms for the regulation of gene expression in eukaryotes. In the standard model, methylation in gene promoters has received the most attention since it is generally associated with transcriptional silencing. Nevertheless, recent studies in human tissues reveal that methylation of the region downstream of the transcription start site is highly informative of gene expression. Also, in some cell types and specific genes it has been found that methylation of the first intron, a gene feature typically rich in enhancers, is linked with gene expression. However, a genome-wide, tissue-independent, systematic comparative analysis of the relationship between DNA methylation in the first intron and gene expression across vertebrates has not been explored yet. RESULTS The most important findings of this study are: (1) using different tissues from a modern fish, we show a clear genome-wide, tissue-independent quasi-linear inverse relationship between DNA methylation of the first intron and gene expression. (2) This relationship is conserved across vertebrates, since it is also present in the genomes of a model pufferfish, a model frog and different human tissues. Among the gene features, tissues and species interrogated, the first intron's negative correlation with the gene expression was most consistent. (3) We identified more tissue-specific differentially methylated regions (tDMRs) in the first intron than in any other gene feature. These tDMRs have positive or negative correlation with gene expression, indicative of distinct mechanisms of tissue-specific regulation. (4) Lastly, we identified CpGs in transcription factor binding motifs, enriched in the first intron, the methylation of which tended to increase with the distance from the first exon-first intron boundary, with a concomitant decrease in gene expression. CONCLUSIONS Our integrative analysis clearly reveals the important and conserved role of the methylation level of the first intron and its inverse association with gene expression regardless of tissue and species. These findings not only contribute to our basic understanding of the epigenetic regulation of gene expression but also identify the first intron as an informative gene feature regarding the relationship between DNA methylation and gene expression where future studies should be focused.
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Affiliation(s)
- Dafni Anastasiadi
- Institute of Marine Sciences (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Francesc Piferrer
- Institute of Marine Sciences (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain.
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162
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Li XY, Gui JF. An epigenetic regulatory switch controlling temperature-dependent sex determination in vertebrates. SCIENCE CHINA-LIFE SCIENCES 2018; 61:996-998. [PMID: 29946868 DOI: 10.1007/s11427-018-9314-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China. .,University of Chinese Academy of sciences, Beijing, 100049, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China. .,University of Chinese Academy of sciences, Beijing, 100049, China.
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163
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Garcia-Moreno SA, Plebanek MP, Capel B. Epigenetic regulation of male fate commitment from an initially bipotential system. Mol Cell Endocrinol 2018; 468:19-30. [PMID: 29410272 PMCID: PMC6084468 DOI: 10.1016/j.mce.2018.01.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 12/21/2022]
Abstract
A fundamental goal in biology is to understand how distinct cell types containing the same genetic information arise from a single stem cell throughout development. Sex determination is a key developmental process that requires a unidirectional commitment of an initially bipotential gonad towards either the male or female fate. This makes sex determination a unique model to study cell fate commitment and differentiation in vivo. We have focused this review on the accumulating evidence that epigenetic mechanisms contribute to the bipotential state of the fetal gonad and to the regulation of chromatin accessibility during and immediately downstream of the primary sex-determining switch that establishes the male fate.
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Affiliation(s)
| | | | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA.
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164
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Beal A, Rodriguez-Casariego J, Rivera-Casas C, Suarez-Ulloa V, Eirin-Lopez JM. Environmental Epigenomics and Its Applications in Marine Organisms. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/13836_2018_28] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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165
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Zhu YJ, Li XY, Zhang J, Li Z, Ding M, Zhang XJ, Zhou L, Gui JF. Distinct sperm nucleus behaviors between genotypic and temperature-dependent sex determination males are associated with replication and expression-related pathways in a gynogenetic fish. BMC Genomics 2018; 19:437. [PMID: 29866041 PMCID: PMC5987661 DOI: 10.1186/s12864-018-4823-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/24/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coexistence and transition of diverse sex determination strategies have been revealed in some ectothermic species, but the variation between males caused by different sex determination strategies and the underlying mechanism remain unclear. Here, we used the gynogenetic gibel carp (Carassius gibelio) with both genotypic sex determination (GSD) and temperature-dependent sex determination (TSD) strategies to illustrate this issue. RESULTS We found out that males of GSD and TSD in gibel carp had similar morphology, testicular histology, sperm structure and sperm vitality. However, when maternal individuals were mated with males of GSD, sperm nucleus swelling and fusing with the female pronucleus were observed in the fertilized eggs. On the contrary, when maternal individuals were mated with males of TSD, sperm nucleus remained in the condensed status throughout the whole process. Subsequently, semen proteomics analysis unveiled that DNA replication and gene expression-related pathways were inhibited in the sperm from males of TSD compared to males of GSD, and most differentially expressed proteins associated with DNA replication, transcription and translation were down-regulated. Moreover, via BrdU incorporation and immunofluorescence detection, male nucleus replication was revealed to be present in the fertilized eggs by the sperm from males of GSD, but absent in the fertilized eggs by the sperm from males of TSD. CONCLUSIONS These findings indicate that DNA replication and gene expression-related pathways are associated with the distinct sperm nucleus development behaviors in fertilized eggs in response to the sperm from males of GSD and TSD. And this study is the first attempt to screen the differences between males determined via GSD and TSD in gynogenetic species, which might give a hint for understanding evolutionary adaption of diverse sex determination mechanisms in unisexual vertebrates.
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Affiliation(s)
- Yao-Jun Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jun Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Miao Ding
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China. .,Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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166
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Affiliation(s)
| | - Clare E Holleley
- Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia.
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167
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Ge C, Ye J, Weber C, Sun W, Zhang H, Zhou Y, Cai C, Qian G, Capel B. The histone demethylase KDM6B regulates temperature-dependent sex determination in a turtle species. Science 2018; 360:645-648. [DOI: 10.1126/science.aap8328] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/13/2018] [Indexed: 12/14/2022]
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168
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Bókony V, Kövér S, Nemesházi E, Liker A, Székely T. Climate-driven shifts in adult sex ratios via sex reversals: the type of sex determination matters. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0325. [PMID: 28760766 DOI: 10.1098/rstb.2016.0325] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2017] [Indexed: 01/09/2023] Open
Abstract
Sex reversals whereby individuals of one genetic sex develop the phenotype of the opposite sex occur in ectothermic vertebrates with genetic sex-determination systems that are sensitive to extreme temperatures during sexual differentiation. Recent rises in global temperatures have led researchers to predict that sex reversals will become more common, resulting in the distortion of many populations' sex ratios. However, it is unclear whether susceptibility to climate-driven sex-ratio shifts depends on the type of sex determination that varies across species. First, we show here using individual-based theoretical models that XX/XY (male-heterogametic) and ZZ/ZW (female-heterogametic) sex-determination systems can respond differentially to temperature-induced sex reversals. Interestingly, the impacts of climate warming on adult sex ratio (ASR) depend on the effects of both genotypic and phenotypic sex on survival and reproduction. Second, we analyse the temporal changes of ASR in natural amphibian populations using data from the literature, and find that ASR shifted towards males in ZZ/ZW species over the past 60 years, but did not change significantly in XX/XY species. Our results highlight the fact that we need a better understanding of the interactions between genetic and environmental sex-determining mechanisms to predict the responses of ectotherms to climate change and the associated extinction risks.This article is part of the themed issue 'Adult sex ratios and reproductive decisions: a critical re-examination of sex differences in human and animal societies'.
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Affiliation(s)
- Veronika Bókony
- Lendület Evolutionary Ecology Research Group, Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Herman Ottó út 15, 1022 Budapest, Hungary
| | - Szilvia Kövér
- Department of Ecology, University of Veterinary Medicine, Rottenbiller u. 50, 1077 Budapest, Hungary
| | - Edina Nemesházi
- Lendület Evolutionary Ecology Research Group, Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Herman Ottó út 15, 1022 Budapest, Hungary.,Department of Ecology, University of Veterinary Medicine, Rottenbiller u. 50, 1077 Budapest, Hungary
| | - András Liker
- Department of Limnology, University of Pannonia, Pf. 158, 8201 Veszprém, Hungary.,MTA-PE Evolutionary Ecology Research Group, University of Pannonia, Pf. 158, 8201 Veszprém, Hungary
| | - Tamás Székely
- Department of Biology and Biochemistry, Milner Centre for Evolution, University of Bath, Bath BA2 7AY, UK
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169
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Gonad Transcriptome Analysis of High-Temperature-Treated Females and High-Temperature-Induced Sex-Reversed Neomales in Nile Tilapia. Int J Mol Sci 2018; 19:ijms19030689. [PMID: 29495590 PMCID: PMC5877550 DOI: 10.3390/ijms19030689] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/25/2018] [Accepted: 02/26/2018] [Indexed: 12/11/2022] Open
Abstract
Background: Nowadays, the molecular mechanisms governing TSD (temperature-dependent sex determination) or GSD + TE (genotypic sex determination + temperature effects) remain a mystery in fish. Methods: We developed three all-female families of Nile tilapia (Oreochromis niloticus), and the family with the highest male ratio after high-temperature treatment was used for transcriptome analysis. Results: First, gonadal histology analysis indicated that the histological morphology of control females (CF) was not significantly different from that of high-temperature-treated females (TF) at various development stages. However, the high-temperature treatment caused a lag of spermatogenesis in high-temperature-induced neomales (IM). Next, we sequenced the transcriptome of CF, TF, and IM Nile tilapia. 79, 11,117, and 11,000 differentially expressed genes (DEGs) were detected in the CF–TF, CF–IM, and TF–IM comparisons, respectively, and 44 DEGs showed identical expression changes in the CF–TF and CF–IM comparisons. Principal component analysis (PCA) indicated that three individuals in CF and three individuals in TF formed a cluster, and three individuals in IM formed a distinct cluster, which confirmed that the gonad transcriptome profile of TF was similar to that of CF and different from that of IM. Finally, six sex-related genes were validated by qRT-PCR. Conclusions: This study identifies a number of genes that may be involved in GSD + TE, which will be useful for investigating the molecular mechanisms of TSD or GSD + TE in fish.
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170
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Tsakogiannis A, Manousaki T, Lagnel J, Sterioti A, Pavlidis M, Papandroulakis N, Mylonas CC, Tsigenopoulos CS. The transcriptomic signature of different sexes in two protogynous hermaphrodites: Insights into the molecular network underlying sex phenotype in fish. Sci Rep 2018; 8:3564. [PMID: 29476120 PMCID: PMC5824801 DOI: 10.1038/s41598-018-21992-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 02/14/2018] [Indexed: 01/22/2023] Open
Abstract
Sex differentiation is a puzzling problem in fish due to the variety of reproductive systems and the flexibility of their sex determination mechanisms. The Sparidae, a teleost family, reflects this remarkable diversity of sexual mechanisms found in fish. Our aim was to capture the transcriptomic signature of different sexes in two protogynous hermaphrodite sparids, the common pandora Pagellus erythrinus and the red porgy Pagrus pagrus in order to shed light on the molecular network contributing to either the female or the male phenotype in these organisms. Through RNA sequencing, we investigated sex-specific differences in gene expression in both species' brains and gonads. The analysis revealed common male and female specific genes/pathways between these protogynous fish. Whereas limited sex differences found in the brain indicate a sexually plastic tissue, in contrast, the great amount of sex-biased genes observed in gonads reflects the functional divergence of the transformed tissue to either its male or female character. Α common "crew" of well-known molecular players is acting to preserve either sex identity of the gonad in these fish. Lastly, this study lays the ground for a deeper understanding of the complex process of sex differentiation in two species with an evolutionary significant reproductive system.
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Affiliation(s)
- A Tsakogiannis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - T Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece
| | - J Lagnel
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece
| | - A Sterioti
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece
| | - M Pavlidis
- Department of Biology, University of Crete, Heraklion, Greece
| | - N Papandroulakis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece
| | - C C Mylonas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece
| | - C S Tsigenopoulos
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, Greece.
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171
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Epigenetics in teleost fish: From molecular mechanisms to physiological phenotypes. Comp Biochem Physiol B Biochem Mol Biol 2018; 224:210-244. [PMID: 29369794 DOI: 10.1016/j.cbpb.2018.01.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 01/08/2018] [Accepted: 01/16/2018] [Indexed: 02/07/2023]
Abstract
While the field of epigenetics is increasingly recognized to contribute to the emergence of phenotypes in mammalian research models across different developmental and generational timescales, the comparative biology of epigenetics in the large and physiologically diverse vertebrate infraclass of teleost fish remains comparatively understudied. The cypriniform zebrafish and the salmoniform rainbow trout and Atlantic salmon represent two especially important teleost orders, because they offer the unique possibility to comparatively investigate the role of epigenetic regulation in 3R and 4R duplicated genomes. In addition to their sequenced genomes, these teleost species are well-characterized model species for development and physiology, and therefore allow for an investigation of the role of epigenetic modifications in the emergence of physiological phenotypes during an organism's lifespan and in subsequent generations. This review aims firstly to describe the evolution of the repertoire of genes involved in key molecular epigenetic pathways including histone modifications, DNA methylation and microRNAs in zebrafish, rainbow trout, and Atlantic salmon, and secondly, to discuss recent advances in research highlighting a role for molecular epigenetics in shaping physiological phenotypes in these and other teleost models. Finally, by discussing themes and current limitations of the emerging field of teleost epigenetics from both theoretical and technical points of view, we will highlight future research needs and discuss how epigenetics will not only help address basic research questions in comparative teleost physiology, but also inform translational research including aquaculture, aquatic toxicology, and human disease.
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172
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Díaz N, Piferrer F. Estrogen exposure overrides the masculinizing effect of elevated temperature by a downregulation of the key genes implicated in sexual differentiation in a fish with mixed genetic and environmental sex determination. BMC Genomics 2017; 18:973. [PMID: 29254503 PMCID: PMC5735924 DOI: 10.1186/s12864-017-4345-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 11/21/2017] [Indexed: 12/30/2022] Open
Affiliation(s)
- Noelia Díaz
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Passeig Marítim, 37-49, E-08003, Barcelona, Spain.,Present address: Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Passeig Marítim, 37-49, E-08003, Barcelona, Spain.
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173
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Ribas L, Vanezis K, Imués MA, Piferrer F. Treatment with a DNA methyltransferase inhibitor feminizes zebrafish and induces long-term expression changes in the gonads. Epigenetics Chromatin 2017; 10:59. [PMID: 29216900 PMCID: PMC5721477 DOI: 10.1186/s13072-017-0168-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/30/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The role of epigenetic modifications such as DNA methylation during vertebrate sexual development is far from being clear. Using the zebrafish model, we tested the effects of one of the most common DNA methyltransferase (dnmt) inhibitor, 5-aza-2'-deoxycytidine (5-aza-dC), which is approved for the treatment of acute myeloid leukaemia and is under active investigation for the treatment of solid tumours. Several dose-response experiments were carried out during two periods, including not only the very first days of development (0-6 days post-fertilization, dpf), as done in previous studies, but also, and as a novelty, the period of gonadal development (10-30 dpf). RESULTS Early treatment with 5-aza-dC altered embryonic development, delayed hatching and increased teratology and mortality, as expected. The most striking result, however, was an increase in the number of females, suggesting that alterations induced by 5-aza-dC treatment can affect sexual development as well. Results were confirmed when treatment coincided with gonadal development. In addition, we also found that the adult gonadal transcriptome of 5-aza-dC-exposed females included significant changes in the expression of key reproduction-related genes (e.g. cyp11a1, esr2b and figla), and that several pro-female-related pathways such as the Fanconi anaemia or the Wnt signalling pathways were downregulated. Furthermore, an overall inhibition of genes implicated in epigenetic regulatory mechanisms (e.g. dnmt1, dicer, cbx4) was also observed. CONCLUSIONS Taken together, our results indicate that treatment with a DNA methylation inhibitor can also alter the sexual development in zebrafish, with permanent alterations of the adult gonadal transcriptome, at least in females. Our results show the importance of DNA methylation for proper control of sexual development, open new avenues for the potential control of sex ratios in fish (aquaculture, population control) and call attention to possibly hidden long-term effects of dnmt therapy when used, for example, in the treatment of prepuberal children affected by some types of cancer.
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Affiliation(s)
- Laia Ribas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Passeig Marítim, 37-45, 08003, Barcelona, Spain
| | - Konstantinos Vanezis
- Imperial Centre for Translational and Experimental Medicine, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Marco Antonio Imués
- Departamento de Recursos Hidrobiológicos, Universidad de Nariño, Torobajo, Pasto, Colombia
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Passeig Marítim, 37-45, 08003, Barcelona, Spain.
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174
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Gavery MR, Roberts SB. Epigenetic considerations in aquaculture. PeerJ 2017; 5:e4147. [PMID: 29230373 PMCID: PMC5723431 DOI: 10.7717/peerj.4147] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/17/2017] [Indexed: 12/14/2022] Open
Abstract
Epigenetics has attracted considerable attention with respect to its potential value in many areas of agricultural production, particularly under conditions where the environment can be manipulated or natural variation exists. Here we introduce key concepts and definitions of epigenetic mechanisms, including DNA methylation, histone modifications and non-coding RNA, review the current understanding of epigenetics in both fish and shellfish, and propose key areas of aquaculture where epigenetics could be applied. The first key area is environmental manipulation, where the intention is to induce an ‘epigenetic memory’ either within or between generations to produce a desired phenotype. The second key area is epigenetic selection, which, alone or combined with genetic selection, may increase the reliability of producing animals with desired phenotypes. Based on aspects of life history and husbandry practices in aquaculture species, the application of epigenetic knowledge could significantly affect the productivity and sustainability of aquaculture practices. Conversely, clarifying the role of epigenetic mechanisms in aquaculture species may upend traditional assumptions about selection practices. Ultimately, there are still many unanswered questions regarding how epigenetic mechanisms might be leveraged in aquaculture.
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Affiliation(s)
- Mackenzie R Gavery
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Steven B Roberts
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, WA, USA
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175
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Kuc C, Richard DJ, Johnson S, Bragg L, Servos MR, Doxey AC, Craig PM. Rainbow trout exposed to benzo[a]pyrene yields conserved microRNA binding sites in DNA methyltransferases across 500 million years of evolution. Sci Rep 2017; 7:16843. [PMID: 29203905 PMCID: PMC5715007 DOI: 10.1038/s41598-017-17236-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/22/2017] [Indexed: 12/24/2022] Open
Abstract
The objective of this study was to examine the regulation of DNA methylation following acute (24 h) and prolonged (14 d) exposure to low (1 ng/L) and high (10 ng/L) benzo[a]pyrene. However, with the recent release of the rainbow trout genome, we were able to conduct a more detailed analysis regarding the regulation of the enzymes involved in DNA methylation; DNA methyltransferases (DNMTs). Bioinformatic approaches were used to identify candidate microRNA (miRNA) that potentially bind to the DNMT1 and DNMT3a 3′UTR. Results indicated a significant decrease in global methylation in both liver and muscle, with an associated decrease in DNA methyltransferase activity and DNMT3a transcript abundance. There was a significant increase in one specific candidate miRNA (miR29a) that was predicted to bind to DNMT3a. Taking a comparative genomics approach, the binding sites of miR29a to the DNMT3a 3′UTR was compared across species, spanning fish to mammals, and revealed a highly conserved binding motif that has been maintained since the vertebrate ancestor, approximately 500 million years ago. This research establishes that miRNA act as an essential mediator between the environment and DNA methylation patterns via DNMTs, which is further confirmed by a genomic regulatory mechanism that has been deeply conserved throughout evolution.
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Affiliation(s)
- Christopher Kuc
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.,Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Daniel J Richard
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Samantha Johnson
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.,Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Leslie Bragg
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Paul M Craig
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
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176
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Drinan DP, Loher T, Hauser L. Identification of Genomic Regions Associated With Sex in Pacific Halibut. J Hered 2017; 109:326-332. [DOI: 10.1093/jhered/esx102] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/07/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daniel P Drinan
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, Washington
| | - Timothy Loher
- International Pacific Halibut Commission, Seattle, Washington
| | - Lorenz Hauser
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, Washington
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177
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Molecular characterization of Pod1 during sex development in Chinese tongue sole (Cynoglossus semilaevis). Biochem Biophys Res Commun 2017; 494:714-718. [PMID: 29106955 DOI: 10.1016/j.bbrc.2017.10.126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 10/24/2017] [Indexed: 12/11/2022]
Abstract
Pod1 encodes a Class II bHLH transcription factor involved in the development of a number of tissues such as gonad, spleen, lungs and heart. However, to date, little is known about its function in teleosts. In this study, we cloned and characterized Pod1 gene from Cynoglossus semilaevis. This gene contains three exons and two introns, with the full-length cDNA of 918 nucleotides that encodes a 183 amino acid protein with a conserved bHLH domain. Realtime quantitative PCR revealed that Pod1 was predominantly expressed in the testes of C. semilaevis. In different stages of testes development, Pod1 expression was undetectable up to 120 days after hatching (dah), and then increased at 210 dah and 1 year after hatching (yah). Furthermore, in situ hybridization (ISH) analysis revealed that Pod1 was mainly localized in the germ cells of testes, but was not detected in ovarian cells; which suggested its possible functions in spermatogenesis of C. semilaevis. The methylation profile analysis of Pod1 genomic sequence in the gonads showed that the differences in their putative promoter regions of Pod1 among ovary, male and pseudo-male testes were not obvious. Thus, further research might be needed to evaluate whether Pod1 expression is regulated by epigenetic level.
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178
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Cavalieri V, Spinelli G. Environmental epigenetics in zebrafish. Epigenetics Chromatin 2017; 10:46. [PMID: 28982377 PMCID: PMC5629768 DOI: 10.1186/s13072-017-0154-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/27/2017] [Indexed: 02/06/2023] Open
Abstract
It is widely accepted that the epigenome can act as the link between environmental cues, both external and internal, to the organism and phenotype by converting the environmental stimuli to phenotypic responses through changes in gene transcription outcomes. Environmental stress endured by individual organisms can also enforce epigenetic variations in offspring that had never experienced it directly, which is termed transgenerational inheritance. To date, research in the environmental epigenetics discipline has used a wide range of both model and non-model organisms to elucidate the various epigenetic mechanisms underlying the adaptive response to environmental stimuli. In this review, we discuss the advantages of the zebrafish model for studying how environmental toxicant exposures affect the regulation of epigenetic processes, especially DNA methylation, which is the best-studied epigenetic mechanism. We include several very recent studies describing the state-of-the-art knowledge on this topic in zebrafish, together with key concepts in the function of DNA methylation during vertebrate embryogenesis.
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Affiliation(s)
- Vincenzo Cavalieri
- Laboratory of Molecular Biology and Functional Genomics, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Edificio 16, 90128, Palermo, Italy. .,Zebrafish Laboratory, Advanced Technologies Network (ATeN) Center, University of Palermo, Viale delle Scienze Edificio 18, 90128, Palermo, Italy.
| | - Giovanni Spinelli
- Laboratory of Molecular Biology and Functional Genomics, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Edificio 16, 90128, Palermo, Italy.
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179
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Anastasiadi D, Díaz N, Piferrer F. Small ocean temperature increases elicit stage-dependent changes in DNA methylation and gene expression in a fish, the European sea bass. Sci Rep 2017; 7:12401. [PMID: 28963513 PMCID: PMC5622125 DOI: 10.1038/s41598-017-10861-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 08/16/2017] [Indexed: 01/24/2023] Open
Abstract
In natural fish populations, temperature increases can result in shifts in important phenotypic traits. DNA methylation is an epigenetic mechanism mediating phenotypic changes. However, whether temperature increases of the magnitude predicted by the latest global warming models can affect DNA methylation is unknown. Here, we exposed European sea bass to moderate temperature increases in different periods within the first two months of age. We show that increases of even 2 °C in larvae significantly changed global DNA methylation and the expression of ecologically-relevant genes related to DNA methylation, stress response, muscle and organ formation, while 4 °C had no effect on juveniles. Furthermore, DNA methylation changes were more marked in larvae previously acclimated to a different temperature. The expression of most genes was also affected by temperature in the larvae but not in juveniles. In conclusion, this work constitutes the first study of DNA methylation in fish showing that temperature increases of the magnitude predicted by the latest global warming models result in stage-dependent alterations in global DNA methylation and gene expression levels. This study, therefore, provides insights on the possible consequences of climate change in fish mediated by genome-wide epigenetic modifications.
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Affiliation(s)
- Dafni Anastasiadi
- Institute of Marine Sciences (ICM-CSIC), Passeig Marítim, 37-49, 08003, Barcelona, Spain
| | - Noelia Díaz
- Institute of Marine Sciences (ICM-CSIC), Passeig Marítim, 37-49, 08003, Barcelona, Spain.,Max Planck Institute for Molecular Biomedicine, Regulatory Genomics Lab, Röntgenstraße 20, 48149, Münster, Germany
| | - Francesc Piferrer
- Institute of Marine Sciences (ICM-CSIC), Passeig Marítim, 37-49, 08003, Barcelona, Spain.
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180
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Goikoetxea A, Todd EV, Gemmell NJ. Stress and sex: does cortisol mediate sex change in fish? Reproduction 2017; 154:R149-R160. [PMID: 28890443 DOI: 10.1530/rep-17-0408] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/24/2017] [Accepted: 09/08/2017] [Indexed: 12/30/2022]
Abstract
Cortisol is the main glucocorticoid (GC) in fish and the hormone most directly associated with stress. Recent research suggests that this hormone may act as a key factor linking social environmental stimuli and the onset of sex change by initiating a shift in steroidogenesis from estrogens to androgens. For many teleost fish, sex change occurs as a usual part of the life cycle. Changing sex is known to enhance the lifetime reproductive success of these fish and the modifications involved (behavioral, gonadal and morphological) are well studied. However, the exact mechanism behind the transduction of the environmental signals into the molecular cascade that underlies this singular process remains largely unknown. We here synthesize current knowledge regarding the role of cortisol in teleost sex change with a focus on two well-described transformations: temperature-induced masculinization and socially regulated sex change. Three non-mutually exclusive pathways are considered when describing the potential role of cortisol in mediating teleost sex change: cross-talk between GC and androgen pathways, inhibition of aromatase expression and upregulation of amh (the gene encoding anti-Müllerian hormone). We anticipate that understanding the role of cortisol in the initial stages of sex change will further improve our understanding of sex determination and differentiation across vertebrates, and may lead to new tools to control fish sex ratios in aquaculture.
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Affiliation(s)
| | - Erica V Todd
- Department of AnatomyUniversity of Otago, Dunedin, New Zealand
| | - Neil J Gemmell
- Department of AnatomyUniversity of Otago, Dunedin, New Zealand
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181
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Effects of different dietary DHA:EPA ratios on gonadal steroidogenesis in the marine teleost, tongue sole (Cynoglossus semilaevis). Br J Nutr 2017; 118:179-188. [PMID: 28831954 DOI: 10.1017/s0007114517001891] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The present study was conducted to investigate the effects of dietary DHA and EPA on gonadal steroidogenesis in mature females and males, with a feeding trial on tongue sole, a typical marine teleost with sexual dimorphism. Three experimental diets differing basically in DHA:EPA ratio, that is, 0·68 (diet D:E-0·68), 1·09 (D:E-1·09) and 2·05 (D:E-2·05), were randomly assigned to nine tanks of 3-year-old tongue sole (ten females and fifteen males in each tank). The feeding trail lasted for 90 d before and during the spawning season. Fish were reared in a flowing seawater system and fed to apparent satiation twice daily. Compared with diet D:E-0·68, diet D:E-1·09 significantly enhanced the oestradiol production in females, whereas diet D:E-2·05 significantly enhanced the testosterone production in males. In ovaries, diet D:E-1·09 induced highest mRNA expression of follicle-stimulating hormone receptor (FSHR), steroidogenic acute regulatory protein, 17α-hydroxylase (P450c17) and 3β-hydroxysteroid dehydrogenase (3β-HSD). In testes, diet 2·05 resulted in highest mRNA expression of FSHR, cholesterol side-chain cleavage enzyme, P450c17 and 3β-HSD. Fatty acid profiles in fish tissues reflected closely those of diets. Female fish had more gonadal EPA content but less DHA content than male fish, whereas there was a reverse observation in liver. In conclusion, the dietary DHA:EPA ratio, possibly combined with the dietary EPA:arachidonic acid ratio, differentially regulated sex steroid hormone synthesis in mature female and male tongue soles. Females seemed to require more EPA but less DHA for the gonadal steroidogenesis than males. The results are beneficial to sex-specific nutritive strategies in domestic teleost.
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182
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Vertebrate sex determination: evolutionary plasticity of a fundamental switch. Nat Rev Genet 2017; 18:675-689. [DOI: 10.1038/nrg.2017.60] [Citation(s) in RCA: 253] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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183
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The destiny of the resistance/susceptibility against GCRV is controlled by epigenetic mechanisms in CIK cells. Sci Rep 2017; 7:4551. [PMID: 28674382 PMCID: PMC5495752 DOI: 10.1038/s41598-017-03990-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 05/08/2017] [Indexed: 12/23/2022] Open
Abstract
Hemorrhagic disease caused by grass carp reovirus (GCRV) has severely threatened the grass carp (Ctenopharyngodon idella) cultivation industry. It is noteworthy that the resistance against GCRV infection was reported to be inheritable, and identified at both individual and cellular levels. Therefore, this work was inspired and dedicated to unravel the molecular mechanisms of fate decision post GCRV infection in related immune cells. Foremost, the resistant and susceptible CIK (C. idella kidney) monoclonal cells were established by single cell sorting, subculturing and infection screening successively. RNA-Seq, MeDIP-Seq and small RNA-Seq were carried out with C1 (CIK cells), R2 (resistant cells) and S3 (susceptible cells) groups. It was demonstrated that genome-wide DNA methylation, mRNA and microRNA expression levels in S3 were the highest among three groups. Transcriptome analysis elucidated that pathways associated with antioxidant activity, cell proliferation regulation, apoptosis activity and energy consuming might contribute to the decision of cell fates post infection. And a series of immune-related genes were identified differentially expressed across resistant and susceptible groups, which were negatively modulated by DNA methylation or microRNAs. To conclude, this study systematically uncovered the regulatory mechanism on the resistance from epigenetic perspective and provided potential biomarkers for future studies on resistance breeding.
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184
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Hatching enzymes disrupt aberrant gonadal degeneration by the autophagy/apoptosis cell fate decision. Sci Rep 2017; 7:3183. [PMID: 28600501 PMCID: PMC5466654 DOI: 10.1038/s41598-017-03314-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/25/2017] [Indexed: 11/19/2022] Open
Abstract
Environmental stressors, gonadal degenerative diseases and tumour development can significantly alter the oocyte physiology, and species fertility and fitness. To expand the molecular understanding about oocyte degradation, we isolated several spliced variants of Japanese anchovy hatching enzymes (AcHEs; ovastacin homologue) 1 and 2, and analysed their potential in oocyte sustenance. Particularly, AcHE1b, an ovary-specific, steroid-regulated, methylation-dependent, stress-responsive isoform, was neofunctionalized to regulate autophagic oocyte degeneration. AcHE1a and 2 triggered apoptotic degeneration in vitellogenic and mature oocytes, respectively. Progesterone, starvation, and high temperature elevated the total degenerating oocyte population and AcHE1b transcription by hyper-demethylation. Overexpression, knockdown and intracellular zinc ion chelation study confirmed the functional significance of AcHE1b in autophagy induction, possibly to mitigate the stress effects in fish, via ion-homeostasis. Our finding chronicles the importance of AcHEs in stress-influenced apoptosis/autophagy cell fate decision and may prove significant in reproductive failure assessments, gonadal health maintenance and ovarian degenerative disease therapy.
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185
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Trautner JH, Reiser S, Blancke T, Unger K, Wysujack K. Metamorphosis and transition between developmental stages in European eel (Anguilla anguilla, L.) involve epigenetic changes in DNA methylation patterns. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2017; 22:139-145. [DOI: 10.1016/j.cbd.2017.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 12/24/2022]
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186
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Fan Z, Zou Y, Jiao S, Tan X, Wu Z, Liang D, Zhang P, You F. Significant association of cyp19a promoter methylation with environmental factors and gonadal differentiation in olive flounder Paralichthys olivaceus. Comp Biochem Physiol A Mol Integr Physiol 2017; 208:70-79. [DOI: 10.1016/j.cbpa.2017.02.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 01/09/2017] [Accepted: 02/15/2017] [Indexed: 11/29/2022]
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187
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Radhakrishnan S, Literman R, Mizoguchi B, Valenzuela N. MeDIP-seq and nCpG analyses illuminate sexually dimorphic methylation of gonadal development genes with high historic methylation in turtle hatchlings with temperature-dependent sex determination. Epigenetics Chromatin 2017; 10:28. [PMID: 28533820 PMCID: PMC5438563 DOI: 10.1186/s13072-017-0136-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/12/2017] [Indexed: 12/15/2022] Open
Abstract
Background DNA methylation alters gene expression but not DNA sequence and mediates some cases of phenotypic plasticity. Temperature-dependent sex determination (TSD) epitomizes phenotypic plasticity where environmental temperature drives embryonic sexual fate, as occurs commonly in turtles. Importantly, the temperature-specific transcription of two genes underlying gonadal differentiation is known to be induced by differential methylation in TSD fish, turtle and alligator. Yet, how extensive is the link between DNA methylation and TSD remains unclear. Here we test for broad differences in genome-wide DNA methylation between male and female hatchling gonads of the TSD painted turtle Chrysemys picta using methyl DNA immunoprecipitation sequencing, to identify differentially methylated candidates for future study. We also examine the genome-wide nCpG distribution (which affects DNA methylation) in painted turtles and test for historic methylation in genes regulating vertebrate gonadogenesis. Results Turtle global methylation was consistent with other vertebrates (57% of the genome, 78% of all CpG dinucleotides). Numerous genes predicted to regulate turtle gonadogenesis exhibited sex-specific methylation and were proximal to methylated repeats. nCpG distribution predicted actual turtle DNA methylation and was bimodal in gene promoters (as other vertebrates) and introns (unlike other vertebrates). Differentially methylated genes, including regulators of sexual development, had lower nCpG content indicative of higher historic methylation. Conclusions Ours is the first evidence suggesting that sexually dimorphic DNA methylation is pervasive in turtle gonads (perhaps mediated by repeat methylation) and that it targets numerous regulators of gonadal development, consistent with the hypothesis that it may regulate thermosensitive transcription in TSD vertebrates. However, further research during embryogenesis will help test this hypothesis and the alternative that instead, most differential methylation observed in hatchlings is the by-product of sexual differentiation and not its cause. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0136-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Srihari Radhakrishnan
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011 USA.,Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011 USA
| | - Robert Literman
- Ecology and Evolutionary Biology Program, Iowa State University, Ames, IA 50011 USA.,Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011 USA
| | - Beatriz Mizoguchi
- Interdepartmental Genetics and Genomics Program, Iowa State University, Ames, IA 50011 USA.,Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011 USA
| | - Nicole Valenzuela
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011 USA
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188
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Ge C, Ye J, Zhang H, Zhang Y, Sun W, Sang Y, Capel B, Qian G. Dmrt1 induces the male pathway in a turtle species with temperature-dependent sex determination. Development 2017; 144:2222-2233. [PMID: 28506988 DOI: 10.1242/dev.152033] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/28/2017] [Indexed: 01/31/2023]
Abstract
The molecular mechanism underlying temperature-dependent sex determination (TSD) has been a long-standing mystery; in particular, the thermosensitive genetic triggers for gonadal sex differentiation are largely unknown. Here, we have characterized a conserved DM domain gene, Dmrt1, in the red-eared slider turtle Trachemys scripta (T. scripta), which exhibits TSD. We found that Dmrt1 has a temperature-dependent, sexually dimorphic expression pattern, preceding gonadal sex differentiation, and is capable of responding rapidly to temperature shifts and aromatase inhibitor treatment. Most importantly, loss- and gain-of-function analyses provide solid evidence that Dmrt1 is both necessary and sufficient to initiate male development in T. scripta Furthermore, the DNA methylation dynamics of the Dmrt1 promoter are tightly correlated with temperature and could mediate the impact of temperature on sex determination. Collectively, our findings demonstrate that Dmrt1 is a candidate master male sex-determining gene in this TSD species, consistent with the idea that DM domain genes are conserved during the evolution of sex determination mechanisms.
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Affiliation(s)
- Chutian Ge
- Zhejiang Provincial Top Key Discipline of Biological Engineering, Zhejiang Wanli University, Ningbo 315100, China
| | - Jian Ye
- HangZhou Aquacultural Technique Extending Centre, Hangzhou 310001, China
| | - Haiyan Zhang
- Zhejiang Provincial Top Key Discipline of Biological Engineering, Zhejiang Wanli University, Ningbo 315100, China
| | - Yi Zhang
- Zhejiang Provincial Top Key Discipline of Biological Engineering, Zhejiang Wanli University, Ningbo 315100, China
| | - Wei Sun
- Zhejiang Provincial Top Key Discipline of Biological Engineering, Zhejiang Wanli University, Ningbo 315100, China
| | - Yapeng Sang
- Zhejiang Provincial Top Key Discipline of Biological Engineering, Zhejiang Wanli University, Ningbo 315100, China
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Guoying Qian
- Zhejiang Provincial Top Key Discipline of Biological Engineering, Zhejiang Wanli University, Ningbo 315100, China
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189
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Identification and analysis of the β-catenin1 gene in half-smooth tongue sole (Cynoglossus semilaevis). PLoS One 2017; 12:e0176122. [PMID: 28489928 PMCID: PMC5425175 DOI: 10.1371/journal.pone.0176122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/05/2017] [Indexed: 12/17/2022] Open
Abstract
β-catenin is a key signalling molecule in the canonical Wnt pathway, which plays a role in cell adhesion, embryogenesis and sex determination. However, little is known about its function in teleosts. We cloned and characterized the full-length β-catenin1 gene from half-smooth tongue sole (Cynoglossus semilaevis), which was designated CS-β-catenin1. The CS-β-catenin1 cDNA consists of 2,346 nucleotides and encodes a protein with 782 amino acids. Although CS-β-catenin1 was transcribed in the gonads of both sexes, the level was significantly higher in ovaries compared to testes. Furthermore, the mRNA level of CS-β-catenin1 was significantly upregulated at 160 days and constantly increased until 2 years of age. In situ hybridization revealed that CS-β-catenin1 mRNA was mainly localized in oocyte cells, especially in stage I, II and III oocytes. When CS-β-catenin1 expression was inhibited by injection of quercetin in the ovaries, levels of CS-Figla and CS-foxl2 mRNA were significantly down-regulated, and CS-dmrt1 was up-regulated, which suggested that CS-β-catenin1 is a potential upstream gene of CS-Figla and is involved in the development of the ovaries, i.e., folliculogenesis.
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190
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Tamagawa K, Makino T, Kawata M. The Effects of CpG Densities around Transcription Start Sites on Sex-Biased Gene Expression in Poecilia reticulata. Genome Biol Evol 2017; 9:1204-1211. [PMID: 28453630 PMCID: PMC5554587 DOI: 10.1093/gbe/evx083] [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] [Accepted: 04/25/2017] [Indexed: 11/14/2022] Open
Abstract
As most genes are shared between females and males, DNA methylation is assumed to play a crucial role in sex-biased gene expression. DNA methylation exclusively occurs at CpG dinucleotides, and therefore, we would expect that CpG density around transcription start sites (TSSs) relate to sex-biased gene expression. Here we investigated the relationship between CpG densities around TSSs and the ratio of gene expression levels between sexes in the guppy (Poecilia reticulata), which displays remarkable sexual dimorphisms. We found that genes with sex-biased gene expression had different CpG densities downstream of TSSs compared with genes lacking sex-biased gene expression. Intriguingly, male-biased expression genes with intermediate CpG density downstream of TSSs exhibited greater differences in gene expression between sexes in the gonad and tail. Our findings suggested the possibility that CpGs around TSSs, especially in the downstream regions, play a crucial role in sex-biased gene expression through DNA methylation.
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Affiliation(s)
- Katsunori Tamagawa
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | - Takashi Makino
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | - Masakado Kawata
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
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191
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Peat JR, Ortega-Recalde O, Kardailsky O, Hore TA. The elephant shark methylome reveals conservation of epigenetic regulation across jawed vertebrates. F1000Res 2017; 6:526. [PMID: 28580133 PMCID: PMC5437953 DOI: 10.12688/f1000research.11281.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/12/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Methylation of CG dinucleotides constitutes a critical system of epigenetic memory in bony vertebrates, where it modulates gene expression and suppresses transposon activity. The genomes of studied vertebrates are pervasively hypermethylated, with the exception of regulatory elements such as transcription start sites (TSSs), where the presence of methylation is associated with gene silencing. This system is not found in the sparsely methylated genomes of invertebrates, and establishing how it arose during early vertebrate evolution is impeded by a paucity of epigenetic data from basal vertebrates. METHODS We perform whole-genome bisulfite sequencing to generate the first genome-wide methylation profiles of a cartilaginous fish, the elephant shark Callorhinchus milii. Employing these to determine the elephant shark methylome structure and its relationship with expression, we compare this with higher vertebrates and an invertebrate chordate using published methylation and transcriptome data. Results: Like higher vertebrates, the majority of elephant shark CG sites are highly methylated, and methylation is abundant across the genome rather than patterned in the mosaic configuration of invertebrates. This global hypermethylation includes transposable elements and the bodies of genes at all expression levels. Significantly, we document an inverse relationship between TSS methylation and expression in the elephant shark, supporting the presence of the repressive regulatory architecture shared by higher vertebrates. CONCLUSIONS Our demonstration that methylation patterns in a cartilaginous fish are characteristic of higher vertebrates imply the conservation of this epigenetic modification system across jawed vertebrates separated by 465 million years of evolution. In addition, these findings position the elephant shark as a valuable model to explore the evolutionary history and function of vertebrate methylation.
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Affiliation(s)
- Julian R Peat
- Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand
| | | | - Olga Kardailsky
- Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand
| | - Timothy A Hore
- Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand
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192
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Sun Z, Hao T, Tian J. Identification of exosomes and its signature miRNAs of male and female Cynoglossus semilaevis. Sci Rep 2017; 7:860. [PMID: 28408738 PMCID: PMC5429842 DOI: 10.1038/s41598-017-00884-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/16/2017] [Indexed: 12/20/2022] Open
Abstract
Exosomes are small membrane particles which are widely found in various cell lines and physiological fluids in mammalian. MicroRNAs (miRNAs) enclosed in exosomes have been identified as proper signatures for many diseases and response to therapies. However, the composition of exosomes and enclosed miRNAs in fishes has not been investigated. Cynoglossus semilaevis is an important commercial flatfish with ambiguous distinction between males and females before sex maturation, which leads to screening difficulty in reproduction and cultivation. An effective detection method was required for sex differentiation of C. semilaevis. In this work, we successfully identified exosomes in C. semilaevis serum. The analysis of nucleotide composition showed that miRNA dominated in exosomes. Thereafter the miRNA profiles in exosomes from males and females were sequenced and compared to identify the signature miRNAs corresponding to sex differentiation. The functions of signature miRNAs were analyzed by target matching and annotation. Furthermore, 7 miRNAs with high expression in males were selected from signature miRNAs as the markers for sex identification with their expression profiles verified by real time quantitative PCR. Exosomes were first found in fish serum in this work. Investigation of marker miRNAs supplies an effective index for the filtration of male and female C. semilaevis in cultivation.
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Affiliation(s)
- Zhanpeng Sun
- College of Life Sciences, Zhejiang University, Zhejiang, 310058, P.R. China
| | - Tong Hao
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin, 300387, P.R. China.
| | - Jinze Tian
- Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Sciences, Tianjin Normal University, Tianjin, 300387, P.R. China
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193
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Santi S, Rougeot C, Toguyeni A, Gennotte V, Kebe I, Melard C. Temperature Preference and Sex Differentiation in African Catfish, Clarias gariepinus. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2017; 327:28-37. [DOI: 10.1002/jez.2066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 02/02/2017] [Accepted: 02/05/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Saïdou Santi
- Aquaculture Research and Education Center (CEFRA); University of Liège; Tihange Belgium
- Natural Resources and Environmental Sciences Research and Studies Laboratory (LERNSE); Institute of Rural Development (IDR); Polytechnic University of Bobo-Dioulasso; Bobo-Dioulasso; Burkina Faso
| | - Carole Rougeot
- Aquaculture Research and Education Center (CEFRA); University of Liège; Tihange Belgium
| | - Aboubacar Toguyeni
- Natural Resources and Environmental Sciences Research and Studies Laboratory (LERNSE); Institute of Rural Development (IDR); Polytechnic University of Bobo-Dioulasso; Bobo-Dioulasso; Burkina Faso
| | - Vincent Gennotte
- Aquaculture Research and Education Center (CEFRA); University of Liège; Tihange Belgium
| | - Ibrahima Kebe
- Aquaculture Research and Education Center (CEFRA); University of Liège; Tihange Belgium
| | - Charles Melard
- Aquaculture Research and Education Center (CEFRA); University of Liège; Tihange Belgium
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194
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Genome editing reveals dmrt1 as an essential male sex-determining gene in Chinese tongue sole (Cynoglossus semilaevis). Sci Rep 2017; 7:42213. [PMID: 28205594 PMCID: PMC5311979 DOI: 10.1038/srep42213] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/06/2017] [Indexed: 12/30/2022] Open
Abstract
Chinese tongue sole is a marine fish with ZW sex determination. Genome sequencing suggested that the Z-linked dmrt1 is a putative male determination gene, but direct genetic evidence is still lacking. Here we show that TALEN of dmrt1 efficiently induced mutations of this gene. The ZZ dmrt1 mutant fish developed ovary-like testis, and the spermatogenesis was disrupted. The female-related genes foxl2 and cyp19a1a were significantly increased in the gonad of the ZZ dmrt1 mutant. Conversely, the male-related genes Sox9a and Amh were significantly decreased. The dmrt1 deficient ZZ fish grew much faster than ZZ male control. Notably, we obtained an intersex ZW fish with a testis on one side and an ovary on the other side. This fish was chimeric for a dmrt1 mutation in the ovary, and wild-type dmrt1 in the testis. Our data provide the first functional evidence that dmrt1 is a male determining gene in tongue sole.
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195
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Single Locus Maintains Large Variation of Sex Reversal in Half-Smooth Tongue Sole ( Cynoglossus semilaevis). G3-GENES GENOMES GENETICS 2017; 7:583-589. [PMID: 28007836 PMCID: PMC5295603 DOI: 10.1534/g3.116.036822] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sex determination is a fundamental biological process for individual sex development and population sex ratios. However, for some species, the primary sex might be altered during development, and individuals can develop into the opposite sex. Sex reversal may happen in insects, reptiles, amphibians, and fishes. In half-smooth tongue sole (Cynoglossus semilaevis), some genetically female fish irreversibly reverse to pseudomales, resulting in higher costs in aquaculture owing to a lower growth rate of male fish during a 2-yr growth period. Here, we identified a locus with large controlling effect on sex reversal in the half-smooth tongue sole through genome-wide association study with high-density single nucleotide polymorphisms (SNPs). This SNP is located at the third intron of the F-box and leucine rich repeat protein 17 (FBXL17) gene on the Z chromosome, and it has two alleles, A and T. Genetic females with ZAW genotypes will never reverse into phenotypic males, but those with ZTW genotypes can sometimes undergo sex reversal. This SNP explains 82.7% of the genetic variation, or 58.4% of the phenotypic variation. Based on our results, a reproductive management program could be developed to improve the phenotypic female ratio in aquaculture, and elucidate the mechanism of sex reversal in half-smooth tongue sole. We expect that these findings will have a substantial impact on the population management in many harvested species where sex reversal occurs.
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196
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Heat-induced masculinization in domesticated zebrafish is family-specific and yields a set of different gonadal transcriptomes. Proc Natl Acad Sci U S A 2017; 114:E941-E950. [PMID: 28115725 DOI: 10.1073/pnas.1609411114] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Understanding environmental influences on sex ratios is important for the study of the evolution of sex-determining mechanisms and for evaluating the effects of global warming and chemical pollution. Fishes exhibit sexual plasticity, but the underlying mechanisms of environmental effects on their reproduction are unclear even in the well-established teleost research model, the zebrafish. Here we established the conditions to study the effects of elevated temperature on zebrafish sex. We showed that sex ratio response to elevated temperature is family-specific and typically leads to masculinization (female-to-male sex reversal), resulting in neomales. These results uncovered genotype-by-environment interactions that support a polygenic sex determination system in domesticated (laboratory) zebrafish. We found that some heat-treated fish had gene expression profiles similar to untreated controls of the same sex, indicating that they were resistant to thermal effects. Further, most neomales had gonadal transcriptomes similar to that of regular males. Strikingly, we discovered heat-treated females that displayed a normal ovarian phenotype but with a "male-like" gonadal transcriptome. Such major transcriptomic reprogramming with preserved organ structure has never been reported. Juveniles were also found to have a male-like transcriptome shortly after exposure to heat. These findings were validated by analyzing the expression of genes and signaling pathways associated with sex differentiation. Our results revealed a lasting thermal effect on zebrafish gonads, suggesting new avenues for detection of functional consequences of elevated temperature in natural fish populations in a global warming scenario.
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197
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XU W, CHEN S. Genomics and genetic breeding in aquatic animals: progress and prospects. FRONTIERS OF AGRICULTURAL SCIENCE AND ENGINEERING 2017; 4:305. [DOI: 10.15302/j-fase-2017154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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198
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Baroiller JF, D'Cotta H. The Reversible Sex of Gonochoristic Fish: Insights and Consequences. Sex Dev 2016; 10:242-266. [PMID: 27907925 DOI: 10.1159/000452362] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2016] [Indexed: 01/06/2023] Open
Abstract
Fish sex reversal is a means to understand sex determination and differentiation, but it is also used to control sex in aquaculture. This review discusses sex reversal in gonochoristic fish, with the coexistence of genetic and environmental influences. The different periods of fish sensitivity to sex reversal treatments are presented with the mechanisms implicated. The old players of sex differentiation are revisited with transcriptome data and loss of function studies following hormone- or temperature-induced sex reversal. We also discuss whether cortisol is the universal mediator of sex reversal in fish due to its implication in ovarian meiosis and 11KT increase. The large plasticity in fish for sex reversal is also evident in the brain, with a reversibility existing even in adulthood. Studies on epigenetics are presented, since it links the environment, gene expression, and sex reversal, notably the association of DNA methylation in sex reversal. Manipulations with exogenous factors reverse the primary sex in many fish species under controlled conditions, but several questions arise on whether this can occur under wild conditions and what is the ecological significance. Cases of sex reversal in wild fish populations are shown and their fitness and future perspectives are discussed.
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199
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Todd EV, Liu H, Muncaster S, Gemmell NJ. Bending Genders: The Biology of Natural Sex Change in Fish. Sex Dev 2016; 10:223-241. [PMID: 27820936 DOI: 10.1159/000449297] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Indexed: 11/19/2022] Open
Abstract
Sexual fate is no longer seen as an irreversible deterministic switch set during early embryonic development but as an ongoing battle for primacy between male and female developmental trajectories. That sexual fate is not final and must be actively maintained via continuous suppression of the opposing sexual network creates the potential for flexibility into adulthood. In many fishes, sexuality is not only extremely plastic, but sex change is a usual and adaptive part of the life cycle. Sequential hermaphrodites begin life as one sex, changing sometime later to the other, and include species capable of protandrous (male-to-female), protogynous (female-to-male), or serial (bidirectional) sex change. Natural sex change involves coordinated transformations across multiple biological systems, including behavioural, anatomical, neuroendocrine, and molecular axes. We here review the biological processes underlying this amazing transformation, focussing particularly on its molecular basis, which remains poorly understood, but where new genomic technologies are significantly advancing our understanding of how sex change is initiated and progressed at the molecular level. Knowledge of how a usually committed developmental process remains plastic in sequentially hermaphroditic fishes is relevant to understanding the evolution and functioning of sexual developmental systems in vertebrates generally, as well as pathologies of sexual development in humans.
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Affiliation(s)
- Erica V Todd
- Department of Anatomy, University of Otago, Dunedin, New Zealand
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200
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Holleley CE, Sarre SD, O'Meally D, Georges A. Sex Reversal in Reptiles: Reproductive Oddity or Powerful Driver of Evolutionary Change? Sex Dev 2016; 10:279-287. [DOI: 10.1159/000450972] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2016] [Indexed: 12/16/2022] Open
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