1
|
Xie S, Jiang L, Song W, Zheng J, Liu Y, Chen S, Yan X. Skeletal muscle feature of different populations in large yellow croaker ( Larimichthys crocea): from an epigenetic point of view. Front Mol Biosci 2024; 11:1403861. [PMID: 39015478 PMCID: PMC11249746 DOI: 10.3389/fmolb.2024.1403861] [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: 03/20/2024] [Accepted: 06/04/2024] [Indexed: 07/18/2024] Open
Abstract
Fish skeletal muscle is composed of well-defined fiber types. In order to identify potential candidate genes affecting muscle growth and development under epigenetic regulation. Bisulfite sequencing was utilized to analyze and compare the muscle DNA methylation profiles of Larimichthys crocea inhabiting different environments. The results revealed that DNA methylation in L. crocea was predominantly CG methylation, with 2,396 differentially methylated regions (DMRs) identified through comparisons among different populations. The largest difference in methylation was observed between the ZhouShan and JinMen wild populations, suggesting that L. crocea may have undergone selection and domestication. Additionally, GO and KEGG enrichment analysis of differentially methylated genes (DMGs) revealed 626 enriched GO functional categories, including various muscle-related genes such as myh10, myf5, myf6, ndufv1, klhl31, map3k4, syn2b, sostdc1a, bag4, and hsp90ab. However, significant enrichment in KEGG pathways was observed only in the JinMen and XiangShan populations of L. crocea. Therefore, this study provides a theoretical foundation for a better understanding of the epigenetic regulation of skeletal muscle growth and development in L. crocea under different environmental conditions.
Collapse
Affiliation(s)
- Shangwei Xie
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
- Nanji Archipelago National Marine Nature Reserve Administration, Wenzhou, Zhejiang Province, China
| | - Lihua Jiang
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Weihua Song
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Jialang Zheng
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Yifan Liu
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Shun Chen
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Xiaojun Yan
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| |
Collapse
|
2
|
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
|
3
|
Zhang W, Zhang L, Feng Y, Lin D, Yang Z, Zhang Z, Ma Y. Genome-wide profiling of DNA methylome and transcriptome reveals epigenetic regulation of Urechis unicinctus response to sulfide stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172238. [PMID: 38582121 DOI: 10.1016/j.scitotenv.2024.172238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
Sulfide is a well-known environmental pollutant that can have detrimental effects on most organisms. However, few metazoans living in sulfide-rich environments have developed mechanisms to tolerate and adapt to sulfide stress. Epigenetic mechanisms, including DNA methylation, have been shown to play a vital role in environmental stress adaptation. Nevertheless, the precise function of DNA methylation in biological sulfide adaptation remains unclear. Urechis unicinctus, a benthic organism inhabiting sulfide-rich intertidal environments, is an ideal model organism for studying adaptation to sulfide environments. In this study, we conducted a comprehensive analysis of the DNA methylome and transcriptome of U. unicinctus after exposure to 50 μM sulfide. The results revealed dynamic changes in the DNA methylation (5-methylcytosine) landscape in response to sulfide stress, with U. unicinctus exhibiting elevated DNA methylation levels following stress exposure. Integrating differentially expressed genes (DEGs) and differentially methylated regions (DMRs), we identified a crucial role of gene body methylation in predicting gene expression. Furthermore, using a DNA methyltransferase inhibitor, we validated the involvement of DNA methylation in the sulfide stress response and the gene regulatory network influenced by DNA methylation. The results indicated that by modulating DNA methylation levels during sulfide stress, the expression of glutathione S-transferase, glutamyl aminopeptidase, and cytochrome c oxidase could be up-regulated, thereby facilitating the metabolism and detoxification of exogenous sulfides. Moreover, DNA methylation was found to regulate and enhance the oxidative phosphorylation pathway, including NADH dehydrogenase, isocitrate dehydrogenase, and ATP synthase. Additionally, DNA methylation influenced the regulation of Cytochrome P450 and macrophage migration inhibitory factor, both of which are closely associated with oxidative stress and stress resistance. Our findings not only emphasize the role of DNA methylation in sulfide adaptation but also provide novel insights into the potential mechanisms through which marine organisms adapt to environmental changes.
Collapse
Affiliation(s)
- Wenqing Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Long Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Yuxin Feng
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Dawei Lin
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Zhi Yang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Zhifeng Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China; Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Yubin Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| |
Collapse
|
4
|
Shi Y, Zhu Z, Chen Q, Chen X. DNA methylation regulates B cell activation via repressing Pax5 expression in teleost. Front Immunol 2024; 15:1363426. [PMID: 38404580 PMCID: PMC10884147 DOI: 10.3389/fimmu.2024.1363426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 01/25/2024] [Indexed: 02/27/2024] Open
Abstract
In mammals, the transcription factor Pax5 is a key regulator of B cell development and maturation and specifically expressed in naive/mature B cells but repressed upon B cell activation. Despite the long-standing proposal that Pax5 repression is essential for proper B cell activation, the underlying mechanisms remain largely elusive. In this study, we used a teleost model to elucidate the mechanisms governing Pax5 repression during B cell activation. Treatment with lipopolysaccharide (LPS) and chitosan oligosaccharide (COS) significantly enhanced the antibody secreting ability and phagocytic capacity of IgM+ B cells in large yellow croaker (Larimichthys crocea), coinciding with upregulated expression of activation-related genes, such as Bcl6, Blimp1, and sIgM, and downregulated expression of Pax5. Intriguingly, two CpG islands were identified within the promoter region of Pax5. Both CpG islands exhibited hypomethylation in naive/mature B cells, while CpG island1 was specifically transited into hypermethylation upon B cell activation. Furthermore, treatment with DNA methylation inhibitor 5-aza-2'-deoxycytidine (AZA) prevented the hypermethylation of CpG island1, and concomitantly impaired the downregulation of Pax5 and activation of B cells. Finally, through in vitro methylation experiments, we demonstrated that DNA methylation exerts an inhibitory effect on promoter activities of Pax5. Taken together, our findings unveil a novel mechanism underlying Pax5 repression during B cell activation, thus promoting the understanding of B cell activation process.
Collapse
Affiliation(s)
- Yuan Shi
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhuo Zhu
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiuxuan Chen
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinhua Chen
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Fuzhou Institute of Oceanography, Fuzhou, China
| |
Collapse
|
5
|
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
|
6
|
Lin YL, Zhu ZX, Ai CH, Xiong YY, De Liu T, Lin HR, Xia JH. Transcriptome and DNA Methylation Responses in the Liver of Yellowfin Seabream Under Starvation Stress. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:150-160. [PMID: 36445545 DOI: 10.1007/s10126-022-10188-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/23/2022] [Indexed: 06/16/2023]
Abstract
Fish suffer from starvation due to environmental risks such as extreme weather in the wild and due to insufficient feedings in farms. Nutrient problems from short-term or long-term starvation conditions can result in stress-related health problems for fish. Yellowfin seabream (Acanthopagrus latus) is an important marine economic fish in China. Understanding the molecular responses to starvation stress is vital for propagation and culturing yellowfin seabream. In this study, the transcriptome and genome-wide DNA methylation levels in the livers of yellowfin seabream under 14-days starvation stress were analyzed. One hundred sixty differentially expressed genes (DEGs) by RNA-Seq analysis and 737 differentially methylated-related genes by whole genome bisulfite sequencing analysis were identified. GO and KEGG pathway enrichment analysis found that energy metabolism-related pathways such as glucose metabolism and lipid metabolism were in response to starvation. Using bisulfite sequencing PCR, we confirmed the presence of CpG methylation differences within the regulatory region of a DEG ppargc1a in response to 14-days starvation stress. This study revealed the molecular responses of livers in response to starvation stress at the transcriptomic and whole genome DNA methylation levels in yellowfin seabream.
Collapse
Affiliation(s)
- Yi Long Lin
- College of Life Sciences, State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zong Xian Zhu
- College of Life Sciences, State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Chun Hui Ai
- College of Life Sciences, State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ying Ying Xiong
- College of Life Sciences, State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Tong De Liu
- College of Life Sciences, State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hao Ran Lin
- College of Life Sciences, State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jun Hong Xia
- College of Life Sciences, State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, People's Republic of China.
| |
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
|
He L, Shi X, Zeng X, Zhou F, Lan T, Chen M, Han K. Characterization of the glucocorticoid receptor of large yellow croaker (Larimichthys crocea) and its expression in response to salinity and immune stressors. Comp Biochem Physiol A Mol Integr Physiol 2021; 265:111124. [PMID: 34863943 DOI: 10.1016/j.cbpa.2021.111124] [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: 08/31/2021] [Revised: 11/26/2021] [Accepted: 11/28/2021] [Indexed: 10/19/2022]
Abstract
Glucocorticoids are steroidal hormones critical to stress responses in vertebrates. To gain further insight into the role of the glucocorticoid receptor (GR) in acute stress responses in teleost fish, the relevant cDNA of large yellow croaker (Larimichthys crocea; LcGR) was cloned using the rapid amplification of cDNA ends (RACE) technique. Multiple alignment of the amino acids (aa) of LcGR and the GR of other teleosts indicated LcGR contained four commonly conserved domains and lacked the 9-aa insert seen in GR1. Phylogenetic analysis of the amino acid sequence revealed that LcGR grouped most closely with the GR2 of other teleosts and can therefore be considered a GR2 subtype. In healthy L. crocea, Lcgr mRNA was found to be expressed at high levels in the gill, brain, and muscle tissue, expressed at intermediate levels in heart and stomach tissue, and expressed at low levels in the kidney, intestine, head kidney, liver, and spleen tissue. The response of L. crocea to acute low-salinity stress was tested, with a significant increase in plasma cortisol concentration after 3 h, peaking after 6 h, and gradually returning to base levels. Regarding changes of Lcgr expression in different body tissues under the stress, there was up-regulation of the Lcgr transcript in the brain, liver, and gill tissues, but not in muscle tissue. Responses to pathogen mimics were also tested. Injection with lipopolysaccharide resulted in Lcgr expression, with an increase-decrease-increase trend in the head kidney. In contrast, a down-regulation of Lcgr expression in the head kidney was observed throughout the experimental period upon injection of polyinosinic:polycytidylic acid, revealing different roles of Lcgr for different types of pathogens. The results offer novel insights about the effects of different stressors on GR gene expression in L. crocea, and can facilitate further investigations into stress responses in other mariculture fish species.
Collapse
Affiliation(s)
- Liangyin He
- College of Life Science, Ningde Normal University, Ningde 352100, China; Engineering Research Center of Mindong Aquatic Product Deep-Processing, Ningde Normal University, Ningde 352100, China.
| | - Xiaoli Shi
- College of Life Science, Ningde Normal University, Ningde 352100, China; Engineering Research Center of Mindong Aquatic Product Deep-Processing, Ningde Normal University, Ningde 352100, China
| | - Xianyuan Zeng
- College of Life Science, Ningde Normal University, Ningde 352100, China; Engineering Research Center of Mindong Aquatic Product Deep-Processing, Ningde Normal University, Ningde 352100, China
| | - Fengfang Zhou
- College of Life Science, Ningde Normal University, Ningde 352100, China
| | - Tianzheng Lan
- College of Life Science, Ningde Normal University, Ningde 352100, China
| | - Maosen Chen
- College of Life Science, Ningde Normal University, Ningde 352100, China
| | - Kunhuang Han
- College of Life Science, Ningde Normal University, Ningde 352100, China; Engineering Research Center of Mindong Aquatic Product Deep-Processing, Ningde Normal University, Ningde 352100, China.
| |
Collapse
|
9
|
Differences in DNA methylation between slow and fast muscle in Takifugu rubripes. Gene 2021; 801:145853. [PMID: 34274464 DOI: 10.1016/j.gene.2021.145853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/22/2021] [Accepted: 07/13/2021] [Indexed: 12/20/2022]
Abstract
Fish skeletal muscle is comprised of fast muscle (FM) and slow muscle (SM), which constitutes 60% of total the body mass. Fish skeletal muscle can affect fish swimming activity, which is important for aquaculture due to its growth-potentiating effects. DNA methylation can influence gene expression level. We previously identified multiple differentially expressed genes (DEGs) between FM and SM in Takifugu rubripes. However, it is unknown if the expression levels of these DEGs are influenced by DNA methylation. In the present study, we used DNA methylation sequencing to study the DNA methylation profiles of FM and SM in T. rubripes. SM had higher overall methylation levels than FM. A total of 8479 differentially methylated genes (DMGs) and 3407 DMGs containing differentially methylated regions (DMRs) in the promoter regions between FM and SM were identified. After enrichment analysis, we found functionally relevant DMGs between FM and SM, including Kapca, Plcd3a, Plcd1, Pi3k, Tsp4b and Pgfrb in the hedgehog signaling pathway and phosphatidylinositol (PI)-related pathways. Due to the different methylation levels of these genes between FM and SM, the expression levels of Kapca, Plcd3a, Plcd1, Pi3k, and Tsp4b were higher in FM and Pgfrb was higher in SM. There were differences in the hedgehog signaling pathway and PI-related pathways between FM and SM. In SM, the cytokine-cytokine receptor interaction promoted focal adhesion, while ECM-receptor interactions promoted focal adhesion in FM. These results provide information regarding the difference between FM and SM in T. rubripes.
Collapse
|
10
|
Perpiñán S. Wh-Movement, Islands, and Resumption in L1 and L2 Spanish: Is (Un)Grammaticality the Relevant Property? Front Psychol 2020; 11:395. [PMID: 32265773 PMCID: PMC7108788 DOI: 10.3389/fpsyg.2020.00395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 02/20/2020] [Indexed: 11/15/2022] Open
Abstract
This study reflects on the meaning of the results of a self-paced grammaticality judgment task that tested island configurations (with gaps and resumptive pronouns) in L1 and L2 speakers of Spanish. Results indicated that resumptive pronouns do not rescue extractions from islands, as traditionally assumed in grammatical theory, and propose that islands are essentially an interpretative or processing matter, and not only a grammatical one, as in Kluender (1998). This study further challenges the L2 studies that proposed that L2 learners are fundamentally different from native speakers because they usually fail to reject island configurations, and shows that L2 learners are sensitive to the same processing and interpretative mechanisms that native speakers employ to parse island configurations. Generally speaking, this study proposes that apparent purely syntactic restrictions such as extractions from islands might not depend on their grammatical formation, but on other relevant factors such as plausibility, embedding, and processability, which together with grammatical well-formedness configure a more holistic and useful notion of linguistic acceptability.
Collapse
Affiliation(s)
- Sílvia Perpiñán
- Department of Applied Linguistics, Universitat Internacional de Catalunya, Barcelona, Spain
| |
Collapse
|
11
|
Fan X, Hou T, Sun T, Zhu L, Zhang S, Tang K, Wang Z. Starvation stress affects the maternal development and larval fitness in zebrafish (Danio rerio). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 695:133897. [PMID: 31425978 DOI: 10.1016/j.scitotenv.2019.133897] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/15/2019] [Accepted: 08/11/2019] [Indexed: 06/10/2023]
Abstract
The starvation is a common and severe stress for animal survival and development. In aquatic environment, many fish suffer starvation stress in different extent because of the natural migration or feed limitation. When subjected to starved conditions, organisms will employ various adaptive physiological, biochemical, and behavioral changes to regulate metabolism and maintain homeostasis. In the present study, adult female zebrafish were deprived of feed for 1 to 3 weeks to detect the starved effects on adults and larvae. The results showed that biological indexes, RNA/DNA ratios, and nutritional indexes significantly decreased in the female fish after starvation. The number of mature follicles reduced while the average spawning diameter of oocytes increased. For the larvae, the maternal starvation stress distinctly delayed embryonic hatching, decreased larval body length, disrupted larval swimming ability, and reduced survival rate at early-life stages. Furthermore, we found that DNA methylation might conduce to the downregulated mRNA expression of anti-Müllerian hormone and cytochrome P450 aromatase in retarded ovaries under starved conditions. Significant effects on autophagic transcription were shown in maternal ovary and larvae responded to starvation stress. Taken together, our study systematically revealed the reproductive impairments of starvation stress and would facilitate the investigation of environmental stress in teleost fish.
Collapse
Affiliation(s)
- Xiaoteng Fan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tingting Hou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tianzi Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Long Zhu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuai Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kui Tang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| |
Collapse
|
12
|
Xiu Y, Shao C, Zhu Y, Li Y, Gan T, Xu W, Piferrer F, Chen S. Differences in DNA Methylation Between Disease-Resistant and Disease-Susceptible Chinese Tongue Sole ( Cynoglossus semilaevis) Families. Front Genet 2019; 10:847. [PMID: 31572451 PMCID: PMC6753864 DOI: 10.3389/fgene.2019.00847] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 08/14/2019] [Indexed: 12/12/2022] Open
Abstract
DNA methylation, the most widely studied and most well-understood epigenetic modification, has been reported to play crucial roles in diverse processes. Although it has been found that DNA methylation can modulate the expression of immune-related genes in teleosts, a systemic analysis of epigenetic regulation on teleost immunity has rarely been performed. In this research, we employed whole-genome bisulfite sequencing to investigate the genome-wide DNA methylation profiles in select disease-resistant Cynoglossus semilaevis (DR-CS, family 14L006) and disease-susceptible C. semilaevis (DS-CS, family 14L104) against Vibrio harveyi infection. The results showed that following selective breeding, DR-CS had higher DNA methylation levels and different DNA methylation patterns, with 3,311 differentially methylated regions and 6,456 differentially methylated genes. Combining these data with the corresponding transcriptome data, we identified several immune-related genes that exhibited differential expression levels that were modulated by DNA methylation. Specifically, DNA methylation of tumor necrosis factor–like and lipopolysaccharide-binding protein-like was significantly correlated with their expression and significantly contributed to the disease resistance of the selected C. semilaevis family. In conclusion, we suggest that artificial selection for disease resistance in Chinese tongue sole causes changes in DNA methylation levels in important immune-related genes and that these epigenetic changes are potentially involved in multiple immune responses in Chinese tongue sole.
Collapse
Affiliation(s)
- Yunji Xiu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; 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.,School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; 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
| | - Ying Zhu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; 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
| | - Yangzhen Li
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; 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
| | - Tian Gan
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; 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
| | - Wenteng Xu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; 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
| | - Francesc Piferrer
- Institut de Ciències del Mar (ICM), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Songlin Chen
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; 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
| |
Collapse
|