1
|
Perera E, Román-Padilla J, Hidalgo-Pérez JA, Huesa-Cerdán R, Yúfera M, Mancera JM, Martos-Sitcha JA, Martínez-Rodríguez G, Ortiz-Delgado JB, Navarro-Guillén C, Rodriguez-Casariego JA. Tissue explants as tools for studying the epigenetic modulation of the GH-IGF-I axis in farmed fish. Front Physiol 2024; 15:1410660. [PMID: 38966230 PMCID: PMC11222784 DOI: 10.3389/fphys.2024.1410660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/03/2024] [Indexed: 07/06/2024] Open
Abstract
Somatic growth in vertebrates is mainly controlled by the growth hormone (GH)/insulin-like growth factor I (IGF-I) axis. The role of epigenetic mechanisms in regulating this axis in fish is far from being understood. This work aimed to optimize and evaluate the use of short-term culture of pituitary and liver explants from a farmed fish, the gilthead seabream Sparus aurata, for studying epigenetic mechanisms involved in GH/IGF-I axis regulation. Our results on viability, structure, proliferation, and functionality of explants support their use in short-term assays. Pituitary explants showed no variation in gh expression after exposure to the DNA methylation inhibitor decitabine (5-Aza-2'-deoxycytidine; DAC), despite responding to DAC by changing dnmt3bb and tet1 expression, and TET activity, producing an increase in overall DNA hydroxymethylation. Conversely, in liver explants, DAC had no effects on dnmt s and tet s expression or activity, but modified the expression of genes from the GH-IGF-I axis. In particular, the expression of igfbp2a was increased and that of igfbp4, ghri and ghrii was decreased by DAC as well as by genistein, which is suggestive of impaired growth. While incubation of liver explants with S-adenosylmethionine (SAM) produced no clear effects, it is proposed that nutrients must ensure the methylation milieu within the liver in the fish to sustain proper growth, which need further in vivo verification. Pituitary and liver explants from S. aurata can be further used as described herein for the screening of inhibitors or activators of epigenetic regulators, as well as for assessing epigenetic mechanisms behind GH-IGF-I variation in farmed fish.
Collapse
Affiliation(s)
- Erick Perera
- Department of Marine Biology and Aquaculture, Instituto de Ciencias Marinas de Andalucía (ICMAN-CSIC), Spanish National Research Council (CSIC), Puerto Real, Spain
| | - Javier Román-Padilla
- Department of Biology, Faculty of Marine and Environmental Sciences, Instituto Universitario de Investigación Marina (INMAR), University of Cadiz, Campus de Excelencia Internacional del Mar (CEIMAR), Puerto Real, Spain
| | - Juan Antonio Hidalgo-Pérez
- Department of Marine Biology and Aquaculture, Instituto de Ciencias Marinas de Andalucía (ICMAN-CSIC), Spanish National Research Council (CSIC), Puerto Real, Spain
| | - Rubén Huesa-Cerdán
- Department of Marine Biology and Aquaculture, Instituto de Ciencias Marinas de Andalucía (ICMAN-CSIC), Spanish National Research Council (CSIC), Puerto Real, Spain
| | - Manuel Yúfera
- Department of Marine Biology and Aquaculture, Instituto de Ciencias Marinas de Andalucía (ICMAN-CSIC), Spanish National Research Council (CSIC), Puerto Real, Spain
| | - Juan Miguel Mancera
- Department of Biology, Faculty of Marine and Environmental Sciences, Instituto Universitario de Investigación Marina (INMAR), University of Cadiz, Campus de Excelencia Internacional del Mar (CEIMAR), Puerto Real, Spain
| | - Juan Antonio Martos-Sitcha
- Department of Biology, Faculty of Marine and Environmental Sciences, Instituto Universitario de Investigación Marina (INMAR), University of Cadiz, Campus de Excelencia Internacional del Mar (CEIMAR), Puerto Real, Spain
| | - Gonzalo Martínez-Rodríguez
- Department of Marine Biology and Aquaculture, Instituto de Ciencias Marinas de Andalucía (ICMAN-CSIC), Spanish National Research Council (CSIC), Puerto Real, Spain
| | - Juan Bosco Ortiz-Delgado
- Department of Marine Biology and Aquaculture, Instituto de Ciencias Marinas de Andalucía (ICMAN-CSIC), Spanish National Research Council (CSIC), Puerto Real, Spain
| | - Carmen Navarro-Guillén
- Department of Marine Biology and Aquaculture, Instituto de Ciencias Marinas de Andalucía (ICMAN-CSIC), Spanish National Research Council (CSIC), Puerto Real, Spain
| | - Javier A. Rodriguez-Casariego
- Environmental Epigenetics Laboratory, Institute of Environment, Florida International University, Miami, FL, United States
| |
Collapse
|
2
|
Zhang N, Zhang L, Peng Y, Fu F, Wang L, Mei Q, Wei Y. Yak IGFBP3 promotes hepatocyte proliferation through PI3K-Akt signaling pathway. Gene 2024; 917:148460. [PMID: 38604506 DOI: 10.1016/j.gene.2024.148460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/19/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
IGFBP3 (Insulin-like growth factor binding protein 3) constitutes a crucial constituent of the insulin-like growth factor (IGF), which are intimately associated with the organism's growth and development processes. Despite its significance, the precise function of IGFBP3 in yak liver development remains largely unexplored. In the present study, we systematically examined the expression profile of IGFBP3 in the liver tissues of yaks across various growth stages, elucidated its influence on the activity of yak hepatocytes, and probed its effects on murine liver development. A comparative analysis revealed that the expression of IGFBP3 was significantly higher in the liver tissue of 5-year-old yaks compared to their 15-month-old and 1-day-old counterparts (P < 0.01). To further validate its biological function, pET-28a-BgIGFBP3 prokaryotic expression vector was constructed. Upon exposing yak hepatocytes to varying concentrations of Bos grunniens (Bg) IGFBP3 protein, we observed augmented cellular activities and elevated colony formation rates. Moreover, our investigation revealed the upregulation of key genes within the PI3K-Akt signaling pathway, including ERBB2, IRS1, PIK3R1, AKT1, RAF1, MAP2K2, and MAPK3, in both yak hepatocyte cultures and murine models. These findings collectively indicate that BgIGFBP3 promotes the proliferation of yak hepatocytes and enhances murine liver development by modulating the PI3K-Akt signaling pathway. The functional relevance of BgIGFBP3 was substantiated through in vivo and in vitro experiments, thereby underscoring its potential as a regulatory factor in liver development processes.
Collapse
Affiliation(s)
- Nanchi Zhang
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
| | - Ling Zhang
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
| | - Ying Peng
- School of Computer Science and Engineering, Southwest Minzu University, Chengdu 610041, China
| | - Fang Fu
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
| | - Li Wang
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education, Southwest Minzu University, Chengdu 610041, China.
| | - Qundi Mei
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
| | - Yong Wei
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Sichuan Animal Sciences Academy, Chengdu 610066, China.
| |
Collapse
|
3
|
Cao L, Ma J, Chen P, Hou X, Yang N, Lu Y, Huang H. Exploring the influence of DNA methylation and single nucleotide polymorphisms of the Myostatin gene on growth traits in the hybrid grouper ( Epinephelus fuscoguttatus (female) × Epinephelus polyphekadion (male)). Front Genet 2024; 14:1277647. [PMID: 38259615 PMCID: PMC10801740 DOI: 10.3389/fgene.2023.1277647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Investigations into the correlation between growth characteristics and DNA methylation levels, along with genetic variations, can provide fundamental insights to enhance growth performance in groupers. The Myostatin (mstn) gene plays a vital role in regulating skeletal muscle development and growth. This study scrutinized the DNA methylation levels of the mstn gene across hybrid groupers (E. fuscoguttatus (♀) × E. polyphekadion (♂)) and their parental species, to evaluate its impact on growth attributes in grouper fish. The nucleotide sequence of the mstn gene was directly sequenced in the hybrid grouper, exhibiting different growth performance to identify the single nucleotide polymorphisms (SNPs) of the mstn gene and explore their correlation with growth characteristics. The findings revealed no significant differences in global DNA methylation levels within muscle tissue among the hybrid grouper and parents. However, significant differences in DNA methylation sites were discovered between the hybrid grouper and E. polyphekadion at sites 824 and 1521 (located at exon 2 and intron 2, respectively), and between E. fuscoguttatus and E. polyphekadion at site 1521. These variations could potentially influence the mRNA expression of the mstn gene. The study also identified that SNP g.1003 T > C in exon 2 of the mstn gene was significantly associated with various growth traits including body weight, total length, body length, head length, caudal peduncle height, and body height (p < 0.01). Specimens with the TT genotype at site 1003 demonstrated superior growth performance compared to those with the TC genotype. Furthermore, microstructural analyses of muscle tissue showed that the average area and diameter of muscle fibers in TT genotype individuals were significantly greater than those in TC genotype individuals. Therefore, this research provides robust evidence linking the DNA methylation level and polymorphisms of the mstn gene with growth traits, which could be beneficial for grouper breeding programs.
Collapse
Affiliation(s)
- Liu Cao
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- College of Fisheries and Life Sciences, Hainan Tropical Ocean University, Sanya, China
| | - Jun Ma
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- College of Fisheries and Life Sciences, Hainan Tropical Ocean University, Sanya, China
| | - Pan Chen
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- College of Fisheries and Life Sciences, Hainan Tropical Ocean University, Sanya, China
| | - Xingrong Hou
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- College of Fisheries and Life Sciences, Hainan Tropical Ocean University, Sanya, China
| | - Ning Yang
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- College of Fisheries and Life Sciences, Hainan Tropical Ocean University, Sanya, China
| | - Yan Lu
- College of Fisheries and Life Sciences, Hainan Tropical Ocean University, Sanya, China
| | - Hai Huang
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- College of Fisheries and Life Sciences, Hainan Tropical Ocean University, Sanya, China
| |
Collapse
|
4
|
Hughes JM, Guerriere KI, Popp KL, Castellani CM, Pasiakos SM. Exercise for optimizing bone health after hormone-induced increases in bone stiffness. Front Endocrinol (Lausanne) 2023; 14:1219454. [PMID: 37790607 PMCID: PMC10544579 DOI: 10.3389/fendo.2023.1219454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/17/2023] [Indexed: 10/05/2023] Open
Abstract
Hormones and mechanical loading co-regulate bone throughout the lifespan. In this review, we posit that times of increased hormonal influence on bone provide opportunities for exercise to optimize bone strength and prevent fragility. Examples include endogenous secretion of growth hormones and sex steroids that modulate adolescent growth and exogenous administration of osteoanabolic drugs like teriparatide, which increase bone stiffness, or its resistance to external forces. We review evidence that after bone stiffness is increased due to hormonal stimuli, mechanoadaptive processes follow. Specifically, exercise provides the mechanical stimulus necessary to offset adaptive bone resorption or promote adaptive bone formation. The collective effects of both decreased bone resorption and increased bone formation optimize bone strength during youth and preserve it later in life. These theoretical constructs provide physiologic foundations for promoting exercise throughout life.
Collapse
Affiliation(s)
- Julie M. Hughes
- Military Performance Division, United States Army Research Institute of Environmental Medicine, Natick, MA, United States
| | - Katelyn I. Guerriere
- Military Performance Division, United States Army Research Institute of Environmental Medicine, Natick, MA, United States
| | - Kristin L. Popp
- Military Performance Division, United States Army Research Institute of Environmental Medicine, Natick, MA, United States
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, United States
| | - Colleen M. Castellani
- Military Performance Division, United States Army Research Institute of Environmental Medicine, Natick, MA, United States
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, United States
| | - Stefan M. Pasiakos
- Military Performance Division, United States Army Research Institute of Environmental Medicine, Natick, MA, United States
| |
Collapse
|
5
|
Mehta TK, Man A, Ciezarek A, Ranson K, Penman D, Di-Palma F, Haerty W. Chromatin accessibility in gill tissue identifies candidate genes and loci associated with aquaculture relevant traits in tilapia. Genomics 2023; 115:110633. [PMID: 37121445 DOI: 10.1016/j.ygeno.2023.110633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/02/2023]
Abstract
The Nile tilapia (Oreochromis niloticus) accounts for ∼9% of global freshwater finfish production however, extreme cold weather and decreasing freshwater resources has created the need to develop resilient strains. By determining the genetic bases of aquaculture relevant traits, we can genotype and breed desirable traits into farmed strains. We generated ATAC-seq and gene expression data from O. niloticus gill tissues, and through the integration of SNPs from 27 tilapia species, identified 1168 highly expressed genes (4% of all Nile tilapia genes) with highly accessible promoter regions with functional variation at transcription factor binding sites (TFBSs). Regulatory variation at these TFBSs is likely driving gene expression differences associated with tilapia gill adaptations, and differentially segregate in freshwater and euryhaline tilapia species. The generation of novel integrative data revealed candidate genes e.g., prolactin receptor 1 and claudin-h, genetic relationships, and loci associated with aquaculture relevant traits like salinity and osmotic stress acclimation.
Collapse
Affiliation(s)
| | | | | | - Keith Ranson
- Institute of Aquaculture, University of Stirling, Scotland, UK
| | - David Penman
- Institute of Aquaculture, University of Stirling, Scotland, UK
| | - Federica Di-Palma
- School of Biological Sciences, University of East Anglia, Norwich, UK; Genome British Columbia, Vancouver, Canada
| | - Wilfried Haerty
- Earlham Institute (EI), Norwich, UK; School of Biological Sciences, University of East Anglia, Norwich, UK
| |
Collapse
|
6
|
Li L, He S, Lin MH, Zhang YP, Kuhl H, Liang XF. Whole-genome resequencing and bisulfite sequencing provide new insights into the feeding habit domestication in mandarin fish ( Siniperca chuatsi). Front Genet 2023; 13:1088081. [PMID: 36712873 PMCID: PMC9878154 DOI: 10.3389/fgene.2022.1088081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/28/2022] [Indexed: 01/14/2023] Open
Abstract
Mandarin fish (Siniperca chuatsi) is one of the most economically important fish in China. However, it has the peculiar feeding habit that it feeds solely on live prey fish since first-feeding, while refuses dead prey fish or artificial diets. After the specific training procedure, partial individuals could accept dead prey fish and artificial diets. The genetic basis of individual difference in artificial diet feeding habit is still unknown. In the present study, the resequencing was performed between 10 individuals which could be domesticated to accept artificial diets and 10 individuals which could not. Through the selective sweep analysis based on heterozygosity (Hp) and population differentiation coefficient (Fst), 57 candidate windows were identified as the putative selected regions for feeding habit domestication of mandarin fish, involved in 149 genes. These genes were related to memory, vision and olfaction function, which could be potential targets of molecular marker assistant breeding of artificial diet feeding trait. Beside of the DNA sequence, we also explored the potential role of DNA methylation in feeding habit domestication in mandarin fish. Whole-genome bisulfite sequencing was performed between the individuals which could be domesticated to accept artificial diets and those could not. 5,976 differentially methylated regions were identified, referring to 3,522 genes, such as the genes involved in cAMP signaling pathway. The DNA methylation changes of these genes might contribute to the adaption of artificial diets in mandarin fish. In conclusion, the putative selected regions and the differentially methylated regions were identified in the whole genome, providing new insights into the feeding habit domestication from live prey fish to artificial diets in mandarin fish. And the involved genes were identified as the candidate genes for molecular breeding of artificial diet utilization in mandarin fish.
Collapse
Affiliation(s)
- Ling Li
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Shan He
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Ming-Hui Lin
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Yan-Peng Zhang
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Heiner Kuhl
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany,*Correspondence: Xu-Fang Liang, ; Heiner Kuhl,
| | - Xu-Fang Liang
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China,*Correspondence: Xu-Fang Liang, ; Heiner Kuhl,
| |
Collapse
|
7
|
Liu Z, Zhou T, Gao D. Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture. Front Genet 2022; 13:994471. [PMID: 36406125 PMCID: PMC9666392 DOI: 10.3389/fgene.2022.994471] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/20/2022] [Indexed: 11/25/2022] Open
Abstract
Major progress has been made with genomic and genetic studies in aquaculture in the last decade. However, research on epigenetic regulation of aquaculture traits is still at an early stage. It is apparent that most, if not all, aquaculture traits are regulated at both genetic and epigenetic levels. This paper reviews recent progress in understanding of genetic and epigenetic regulation of important aquaculture traits such as growth, reproduction, disease resistance, and stress responses. Although it is challenging to make generalized statements, DNA methylation is mostly correlated with down-regulation of gene expression, especially when at promoters and enhancers. As such, methylation of growth factors and their receptors is negatively correlated with growth; hypomethylation of genes important for stress tolerance is correlated with increased stress tolerance; hypomethylation of genes important for male or female sex differentiation leads to sex differentiation into males or females, respectively. It is apparent that environmental regulation of aquaculture traits is mediated at the level of epigenetic regulation, and such environment-induced epigenetic changes appeared to be intergenerationally inherited, but evidences for transgenerational inheritance are still limited.
Collapse
Affiliation(s)
- Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States,*Correspondence: Zhanjiang Liu,
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Dongya Gao
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States
| |
Collapse
|
8
|
Wang N, Yang Q, Wang J, Shi R, Li M, Gao J, Xu W, Yang Y, Chen Y, Chen S. Integration of Transcriptome and Methylome Highlights the Roles of Cell Cycle and Hippo Signaling Pathway in Flatfish Sexual Size Dimorphism. Front Cell Dev Biol 2021; 9:743722. [PMID: 34926443 PMCID: PMC8675331 DOI: 10.3389/fcell.2021.743722] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/29/2021] [Indexed: 01/14/2023] Open
Abstract
Sexual size dimorphism (SSD) is the difference in segments or body size between sexes prevalent in various species. Understanding the genetic architecture of SSD has remained a significant challenge owing to the complexity of growth mechanisms and the sexual influences among species. The Chinese tongue sole (Cynoglossus semilaevis), which exhibits a female-biased SSD and sex reversal from female to pseudomale, is an ideal model for exploring SSD mechanism at the molecular level. The present study aimed to integrate transcriptome and methylome analysis to unravel the genetic and epigenetic changes in female, male, and pseudomale C. semilaevis. The somatotropic and reproductive tissues (brain, liver, gonad, and muscle) transcriptomes were characterized by RNA-seq technology. Transcriptomic analysis unravelled numerous differentially expressed genes (DEGs) involved in cell growth and death-related pathways. The gonad and muscle methylomes were further employed for screening differentially methylated genes (DMGs). Relatively higher DNA methylation levels were observed in the male and pseudomale individuals. In detail, hypermethylation of the chromosome W was pronounced in the pseudomale group than in the female group. Furthermore, weighted gene co-expression network analysis showed that turquoise and brown modules positively and negatively correlated with the female-biased SSD, respectively. A combined analysis of the module genes and DMGs revealed the female-biased mRNA transcripts and hypomethylated levels in the upstream and downstream regions across the cell cycle-related genes. Moreover, the male and pseudomale-biased gene expression in the hippo signaling pathway were positively correlated with their hypermethylation levels in the gene body. These findings implied that the activation of the cell cycle and the inhibition of the hippo signaling pathway were implicated in C. semilaevis female-biased SSD. In addition, the dynamic expression pattern of the epigenetic regulatory factors, including dnmt1, dnmt3a, dnmt3b, and uhrf1, among the different sexes correspond with their distinct DNA methylation levels. Herein, we provide valuable clues for understanding female-biased SSD in C. semilaevis.
Collapse
Affiliation(s)
- Na Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
| | - Qian Yang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Jialin Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Rui Shi
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Ming Li
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jin Gao
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Wenteng Xu
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
| | - Yingming Yang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
| | - Yadong Chen
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
| | - Songlin Chen
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, China
| |
Collapse
|
9
|
Si Y, He F, Wen H, Li S, He H. Effects of low salinity on epigenetic changes of growth hormone and growth hormone receptor in half smooth tongue sole (Cynoglossus semilaevis). REPRODUCTION AND BREEDING 2021. [DOI: 10.1016/j.repbre.2021.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
|
10
|
Su H, Ma D, Shang H, Fan J, Zhu H. DNA methylation of the prkaca gene involved in osmoregulation in tilapia hybrids (Oreochromis mossambicus × Oreochromis hornorum). Gene 2020; 752:144791. [PMID: 32439378 DOI: 10.1016/j.gene.2020.144791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 05/10/2020] [Accepted: 05/15/2020] [Indexed: 01/16/2023]
Abstract
Prkaca consists of the catalytic subunit alpha protein kinase A (PKA), which is involved in many cellular processes. In this study, the cDNA and genomic sequences of prkaca in tilapia hybrids (Oreochromis mossambicus × Oreochromis hornorum) were cloned and analysed. The results showed the prkaca gene consists of 11 exons and 10 introns, and its protein contains 351 amino acid residues and is clustered with Oreochromis niloticus, Maylandia zebra and Haplochromis burtoni first in a phylogenetic tree. Amino acid alignment indicates that prkaca shares the highest identity (100%) to Oreochromis niloticus, Maylandia zebra and Haplochromis burtoni. Two CpG islands of prkaca were found by MethPrimer software, and 32 CG sites were found in the proximal promoter. The methylation level of prkaca in the hybrids (0.31%) was significantly lower than that of their parents (0.94% and 3.43%) in kidney tissue (P < 0.05). The gene expression levels and DNA methylation levels of prkaca in muscle and kidney tissues of the tilapia hybrids were detected by quantitative real-time PCR and bisulfite sequencing PCR and showed a negative correlation under saline-alkali stress. The results of this research demonstrated that DNA methylation levels and prkaca mRNA expression levels were inversely correlated under saline-alkali stress, implying that heterosis is likely accompanied by DNA methylation alterations. This research provides new clues for further investigations of DNA methylation and heterosis in hybrid fish.
Collapse
Affiliation(s)
- Huanhuan Su
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Dongmei Ma
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Huiwen Shang
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Jiajia Fan
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Huaping Zhu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
| |
Collapse
|
11
|
Liu H, Lamm MS, Rutherford K, Black MA, Godwin JR, Gemmell NJ. Large-scale transcriptome sequencing reveals novel expression patterns for key sex-related genes in a sex-changing fish. Biol Sex Differ 2015; 6:26. [PMID: 26613014 PMCID: PMC4660848 DOI: 10.1186/s13293-015-0044-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/09/2015] [Indexed: 12/25/2022] Open
Abstract
Background Teleost fishes exhibit remarkably diverse and plastic sexual developmental patterns. One of the most astonishing is the rapid socially controlled female-to-male (protogynous) sex change observed in bluehead wrasses (Thalassoma bifasciatum). Such functional sex change is widespread in marine fishes, including species of commercial importance, yet its underlying molecular basis remains poorly explored. Methods RNA sequencing was performed to characterize the transcriptomic profiles and identify genes exhibiting sex-biased expression in the brain (forebrain and midbrain) and gonads of bluehead wrasses. Functional annotation and enrichment analysis were carried out for the sex-biased genes in the gonad to detect global differences in gene products and genetic pathways between males and females. Results Here we report the first transcriptomic analysis for a protogynous fish. Expression comparison between males and females reveals a large set of genes with sex-biased expression in the gonad, but relatively few such sex-biased genes in the brain. Functional annotation and enrichment analysis suggested that ovaries are mainly enriched for metabolic processes and testes for signal transduction, particularly receptors of neurotransmitters and steroid hormones. When compared to other species, many genes previously implicated in male sex determination and differentiation pathways showed conservation in their gonadal expression patterns in bluehead wrasses. However, some critical female-pathway genes (e.g., rspo1 and wnt4b) exhibited unanticipated expression patterns. In the brain, gene expression patterns suggest that local neurosteroid production and signaling likely contribute to the sex differences observed. Conclusions Expression patterns of key sex-related genes suggest that sex-changing fish predominantly use an evolutionarily conserved genetic toolkit, but that subtle variability in the standard sex-determination regulatory network likely contributes to sexual plasticity in these fish. This study not only provides the first molecular data on a system ideally suited to explore the molecular basis of sexual plasticity and tissue re-engineering, but also sheds some light on the evolution of diverse sex determination and differentiation systems. Electronic supplementary material The online version of this article (doi:10.1186/s13293-015-0044-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hui Liu
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Melissa S Lamm
- Department of Biological Sciences, North Carolina State University, Raleigh, NC USA ; W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC USA
| | - Kim Rutherford
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - John R Godwin
- Department of Biological Sciences, North Carolina State University, Raleigh, NC USA ; W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC USA
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| |
Collapse
|
12
|
Si Y, Ding Y, He F, Wen H, Li J, Zhao J, Huang Z. DNA methylation level of cyp19a1a and Foxl2 gene related to their expression patterns and reproduction traits during ovary development stages of Japanese flounder (Paralichthys olivaceus). Gene 2015; 575:321-30. [PMID: 26343797 DOI: 10.1016/j.gene.2015.09.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 01/14/2023]
Abstract
Foxl2 and cyp19a1a genes are crucial for the ovarian development, and Foxl2 could play a direct regulatory role on cyp19a1a transcription. In this study, we aimed to study DNA methylation status and mRNA expression patterns of Foxl2 and cyp19a1a genes during ovarian development of female Japanese flounder. The relative expression level of cyp19a1a and Foxl2 gene during the gonadal development stages was measured by quantitative PCR. Moreover, DNA methylation status in the promoter and coding regions of the two genes was detected by bisulfite sequencing. The estradiol-17β (E2) was measured by radioimmunoassay. The results showed low expression levels of cyp19a1a and Foxl2 genes in stages II and V, while the highest expression levels were detected in stage IV. The variation trend of the methylation level of all CpG sites in promoter and exon 1 of cyp19a1a gene and three CpG rich regions in coding region of Foxl2 gene was negatively associated with their expression levels during the ovarian development. In addition, two CpG sites in promoter and seven CpG sites in exon 1 of cyp19a1a were on the putative transcription factors binding sequence. Further studies showed that the forkhead domain, which is important for Foxl2 binding to cyp19a1a was located in the F1 and F2 region. These results provide a powerful theoretical basis for the regulatory mechanism on Foxl2 regulating cyp19a1a and promoting gonadal differentiation towards the female pathway, and further reveal that Foxl2 and cyp19a1a play a vital role in the female Japanese flounder gonad development.
Collapse
Affiliation(s)
- Yufeng Si
- The Key Laboratory of Mariculture,Ministry of Education,Ocean University of China,Qingdao 266003,China; Fisheries College,Ocean University of China,Qingdao 266003,China
| | - Yuxia Ding
- The Key Laboratory of Mariculture,Ministry of Education,Ocean University of China,Qingdao 266003,China; Fisheries College,Ocean University of China,Qingdao 266003,China
| | - Feng He
- The Key Laboratory of Mariculture,Ministry of Education,Ocean University of China,Qingdao 266003,China; Fisheries College,Ocean University of China,Qingdao 266003,China.
| | - Haishen Wen
- The Key Laboratory of Mariculture,Ministry of Education,Ocean University of China,Qingdao 266003,China; Fisheries College,Ocean University of China,Qingdao 266003,China
| | - Jifang Li
- The Key Laboratory of Mariculture,Ministry of Education,Ocean University of China,Qingdao 266003,China; Fisheries College,Ocean University of China,Qingdao 266003,China
| | - Junli Zhao
- The Key Laboratory of Mariculture,Ministry of Education,Ocean University of China,Qingdao 266003,China; Fisheries College,Ocean University of China,Qingdao 266003,China
| | - Zhengju Huang
- The Key Laboratory of Mariculture,Ministry of Education,Ocean University of China,Qingdao 266003,China; Fisheries College,Ocean University of China,Qingdao 266003,China
| |
Collapse
|
13
|
Zhao JL, Si YF, He F, Wen HS, Li JF, Ren YY, Zhao ML, Huang ZJ, Chen SL. Polymorphisms and DNA methylation level in the CpG site of the GHR1 gene associated with mRNA expression, growth traits and hormone level of half-smooth tongue sole (Cynoglossus semilaevis). FISH PHYSIOLOGY AND BIOCHEMISTRY 2015; 41:853-865. [PMID: 25893903 DOI: 10.1007/s10695-015-0052-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 04/07/2015] [Indexed: 06/04/2023]
Abstract
The objectives of the present study were to estimate the GHR1 gene mutations and methylation status of CpGs, and whether those mutations and methylation were involved in the regulation of GHR1 gene expression, hormone level and growth traits in half-smooth tongue sole (Cynoglossus semilaevis). Identification of single-nucleotide polymorphisms was performed on 43 male fish. Through polymerase chain reaction-single-strand conformation polymorphism and sequencing, two SNPs were found. SNP1 [c.G1357A (p.Val376Ile)] creating one CpG site located in exon 8 was named L1 locus, and SNP2 (c.G1479A) located in exon 9 was named L2 locus. Individuals were divided into three genotypes, AA, AG and GG according to L1 locus (GG genotype had one more CpG site because of the mutation), and into two genotypes, AA- and GG-based on L2 locus. The results showed that only L1 locus was significantly associated with body weight (P < 0.01), gonad weight (P ≤ 0.05), triiodothyronine (T3) level (P ≤ 0.05) and mRNA expression (P < 0.01). At L1 locus, newly created CpG site in GG genotype was highly methylated (93.3 %), while there was no difference of methylation level in the other two CpG sites among three genotypes. AA genotype and AG genotype having higher T3 level were significantly different (P ≤ 0.05) from GG genotype. There were significant differences among body weights of AA, AG and GG genotypes (P < 0.01). Gonad weights of AA genotype and AG genotype were significantly lower than GG genotype. The GHR1 mRNA expression of GG genotype was significantly lower than AA and AG genotypes (P < 0.01). These implied that mutations and methylation status of GHR1 gene might influence the hormone level, growth traits and gene expression in male half-smooth tongue sole and the L1 locus could be regarded as a potential candidate genetic and epigenetic marker in half-smooth tongue sole selection.
Collapse
Affiliation(s)
- J L Zhao
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Bjelobaba I, Janjic MM, Kucka M, Stojilkovic SS. Cell Type-Specific Sexual Dimorphism in Rat Pituitary Gene Expression During Maturation. Biol Reprod 2015; 93:21. [PMID: 26063874 DOI: 10.1095/biolreprod.115.129320] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 06/03/2015] [Indexed: 12/24/2022] Open
Abstract
The most obvious functional differences between mammalian males and females are related to the control of reproductive physiology and include patterns of GnRH and gonadotropin release, the timing of puberty, sexual and social behavior, and the regulation of food intake and body weight. Using the rat as the best-studied mammalian model for maturation, we examined the expression of major anterior pituitary genes in five secretory cell types of developing males and females. Corticotrophs show comparable Pomc profiles in both sexes, with the highest expression occurring during the infantile period. Somatotrophs and lactotrophs also exhibit no difference in Gh1 and Prl profiles during embryonic to juvenile age but show the amplification of Prl expression in females and Gh1 expression in males during peripubertal and postpubertal ages. Gonadotrophs exhibit highly synchronized Lhb, Fshb, Cga, and Gnrhr expression in both sexes, but the peak of expression occurs during the infantile period in females and at the end of the juvenile period in males. Thyrotrophs also show different developmental Tshb profiles, which are synchronized with the expression of gonadotroph genes in males but not in females. These results indicate the lack of influence of sex on Pomc expression and the presence of two patterns of sexual dimorphism in the expression of other pituitary genes: a time shift in the peak expression during postnatal development, most likely reflecting the perinatal sex-specific brain differentiation, and modulation of the amplitude of expression during late development, which is secondary to the establishment of the hypothalamic-pituitary-gonadal and -thyroid axes.
Collapse
Affiliation(s)
- Ivana Bjelobaba
- Section on Cellular Signaling, Program in Developmental Neuroscience, The Eunice Kennedy Shiver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Marija M Janjic
- Section on Cellular Signaling, Program in Developmental Neuroscience, The Eunice Kennedy Shiver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Marek Kucka
- Section on Cellular Signaling, Program in Developmental Neuroscience, The Eunice Kennedy Shiver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Stanko S Stojilkovic
- Section on Cellular Signaling, Program in Developmental Neuroscience, The Eunice Kennedy Shiver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|