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Katirtzoglou A, Hansen SB, Sveier H, Martin MD, Brealey JC, Limborg MT. Genomic context determines the effect of DNA methylation on gene expression in the gut epithelium of Atlantic salmon ( Salmo salar). Epigenetics 2024; 19:2392049. [PMID: 39151124 PMCID: PMC11332636 DOI: 10.1080/15592294.2024.2392049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 07/23/2024] [Accepted: 08/06/2024] [Indexed: 08/18/2024] Open
Abstract
The canonical view of DNA methylation, a pivotal epigenetic regulation mechanism in eukaryotes, dictates its role as a suppressor of gene activity, particularly within promoter regions. However, this view is being challenged as it is becoming increasingly evident that the connection between DNA methylation and gene expression varies depending on the genomic location and is therefore more complex than initially thought. We examined DNA methylation levels in the gut epithelium of Atlantic salmon (Salmo salar) using whole-genome bisulfite sequencing, which we correlated with gene expression data from RNA sequencing of the same gut tissue sample (RNA-seq). Assuming epigenetic signals might be pronounced between distinctive phenotypes, we compared large and small fish, finding 22 significant associations between 22 differentially methylated regions and 21 genes. We did not detect significant methylation differences between large and small fish. However, we observed a consistent signal of methylation levels around the transcription start sites (TSS), being negatively correlated with the expression levels of those genes. We found both negative and positive associations of methylation levels with gene expression further upstream or downstream of the TSS, revealing a more unpredictable pattern. The 21 genes showing significant methylation-expression correlations were involved in biological processes related to salmon health, such as growth and immune responses. Deciphering how DNA methylation affects the expression of such genes holds great potential for future applications. For instance, our results suggest the importance of genomic context in targeting epigenetic modifications to improve the welfare of aquaculture species like Atlantic salmon.
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Affiliation(s)
- Aikaterini Katirtzoglou
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren B. Hansen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael D. Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jaelle C. Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Terrestrial Biodiversity, Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Morten T. Limborg
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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2
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Freij K, Cleveland B, Biga P. Remodeling of the epigenetic landscape in rainbow trout, Oncorhynchus mykiss, offspring in response to maternal choline intake. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101348. [PMID: 39515277 DOI: 10.1016/j.cbd.2024.101348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 10/25/2024] [Accepted: 10/26/2024] [Indexed: 11/16/2024]
Abstract
This project focused on evaluating the effects of maternal dietary choline intake on global DNA methylation profiles and related transcriptional changes in rainbow trout offspring. Three experimental diets were formulated to test different levels of choline intake: (a) 2065 ppm choline (Low Choline, 0 % supplementation), (b) 5657 ppm choline (Medium Choline, 0.6 % supplementation), and (c) 9248 ppm choline (High Choline, 1.2 % choline supplementation). Six rainbow trout families were fed experimental diets beginning 18 months post-hatch until spawning; their offspring were fed a commercial diet. Reduced representation bisulfite sequencing (RRBS) was utilized to measure genome-wide methylation in offspring immediately after hatching. When comparing to the Medium Choline offspring, differential DNA methylation occurred more in the Low Choline offspring than High Choline, especially in genic features like promoters. The differentially methylated CpGs (q ≤ 0.01) were identified evenly between CpG islands and shores in the genome, mostly found in the introns of genes. Genes such as fabp2 and leap2B associated with protein binding, fatty acid binding, DNA binding, and response to bacteria were differentially methylated and detected as differentially regulated genes by previous RNA-seq analysis. Although these findings indicate that levels of dietary choline available in broodstock diets alter offspring DNA methylation;, most differentially expressed genes were not associated with differential DNA methylation, suggesting additional mechanisms playing a role in regulating gene expression in response to maternal choline intake.
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Affiliation(s)
- Khalid Freij
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA. https://twitter.com/@FreijKhalid
| | - Beth Cleveland
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service (ARS-USDA), Kearneysville, WV 25430, USA
| | - Peggy Biga
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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3
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Metzger DCH, Earhart ML, Schulte PM. Genomic and Epigenomic Influences on Resilience across Scales: Lessons from the Responses of Fish to Environmental Stressors. Integr Comp Biol 2024; 64:853-866. [PMID: 38632046 PMCID: PMC11445785 DOI: 10.1093/icb/icae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 04/08/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024] Open
Abstract
Understanding the factors that influence the resilience of biological systems to environmental change is a pressing concern in the face of increasing human impacts on ecosystems and the organisms that inhabit them. However, most considerations of biological resilience have focused at the community and ecosystem levels, whereas here we discuss how including consideration of processes occurring at lower levels of biological organization may provide insights into factors that influence resilience at higher levels. Specifically, we explore how processes at the genomic and epigenomic levels may cascade up to influence resilience at higher levels. We ask how the concepts of "resistance," or the capacity of a system to minimize change in response to a disturbance, and "recovery," or the ability of a system to return to its original state following a disturbance and avoid tipping points and resulting regime shifts, map to these lower levels of biological organization. Overall, we suggest that substantial changes at these lower levels may be required to support resilience at higher levels, using selected examples of genomic and epigenomic responses of fish to climate-change-related stressors such as high temperature and hypoxia at the levels of the genome, epigenome, and organism.
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Affiliation(s)
- David C H Metzger
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Madison L Earhart
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Patricia M Schulte
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Clinton M, Wyness AJ, Martin SAM, Brierley AS, Ferrier DEK. Association of microbial community structure with gill disease in marine-stage farmed Atlantic salmon (Salmo salar); a yearlong study. BMC Vet Res 2024; 20:340. [PMID: 39090695 PMCID: PMC11293161 DOI: 10.1186/s12917-024-04125-5] [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: 02/12/2024] [Accepted: 06/10/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Understanding the relationship between resident microbiota and disease in cultured fish represents an important and emerging area of study. Marine gill disorders in particular are considered an important challenge to Atlantic salmon (Salmo salar) aquaculture, however relatively little is known regarding the role resident gill microbiota might play in providing protection from or potentiating different gill diseases. Here, 16S rRNA sequencing was used to examine the gill microbiome alongside fish health screening in farmed Atlantic salmon. Results were used to explore the relationship between microbial communities and gill disease. RESULTS Microbial community restructuring was observed throughout the sampling period and linked to varied drivers of change, including environmental conditions and severity of gill pathology. Taxa with significantly greater relative abundance on healthier gills included isolates within genus Shewanella, and taxa within family Procabacteriaceae. In contrast, altered abundance of Candidatus Branchiomonas and Rubritalea spp. were associated with damaged gills. Interestingly, more general changes in community richness and diversity were not associated with altered gill health, and thus not apparently deleterious to fish. Gross and histological gill scoring demonstrated seasonal shifts in gill pathology, with increased severity of gill damage in autumn. Specific infectious causes that contributed to observed pathology within the population included the gill disorder amoebic gill disease (AGD), however due to the uncontrolled nature of this study and likely mixed contribution of various causes of gill disease to observed pathology results do not strongly support an association between the microbial community and specific infectious or non-infectious drivers of gill pathology. CONCLUSIONS Results suggest that the microbial community of farmed Atlantic salmon gills undergo continual restructuring in the marine environment, with mixed influences upon this change including environmental, host, and pathogenic factors. A significant association of specific taxa with different gill health states suggests these taxa might make meaningful indicators of gill health. Further research with more frequent sampling and deliberate manipulation of gills would provide important advancement of knowledge in this area. Overall, although much is still to be learnt regarding what constitutes a healthy or maladapted gill microbial community, the results of this study provide clear advancement of the field, providing new insight into the microbial community structure of gills during an annual production cycle of marine-stage farmed Atlantic salmon.
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Affiliation(s)
- Morag Clinton
- Scottish Oceans Institute, University of St Andrews, St Andrews, UK.
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK, USA.
- Sitka Sound Science Center, Alaska, Sitka, USA.
| | - Adam J Wyness
- Scottish Oceans Institute, University of St Andrews, St Andrews, UK
- Scottish Association for Marine Science, Oban, UK
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, University of Aberdeen, Aberdeen, UK
| | | | - David E K Ferrier
- Scottish Oceans Institute, University of St Andrews, St Andrews, UK.
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Aravena-Canales D, Valenzuela-Muñoz V, Gallardo-Escarate C, Molina A, Valdés JA. Transcriptomic and Epigenomic Responses to Cortisol-Mediated Stress in Rainbow Trout ( Oncorhynchus mykiss) Skeletal Muscle. Int J Mol Sci 2024; 25:7586. [PMID: 39062828 PMCID: PMC11276852 DOI: 10.3390/ijms25147586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/05/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
The production and release of cortisol during stress responses are key regulators of growth in teleosts. Understanding the molecular responses to cortisol is crucial for the sustainable farming of rainbow trout (Oncorhynchus mykiss) and other salmonid species. While several studies have explored the genomic and non-genomic impacts of cortisol on fish growth and skeletal muscle development, the long-term effects driven by epigenetic mechanisms, such as cortisol-induced DNA methylation, remain unexplored. In this study, we analyzed the transcriptome and genome-wide DNA methylation in the skeletal muscle of rainbow trout seven days after cortisol administration. We identified 550 differentially expressed genes (DEGs) by RNA-seq and 9059 differentially methylated genes (DMGs) via whole-genome bisulfite sequencing (WGBS) analysis. KEGG enrichment analysis showed that cortisol modulates the differential expression of genes associated with nucleotide metabolism, ECM-receptor interaction, and the regulation of actin cytoskeleton pathways. Similarly, cortisol induced the differential methylation of genes associated with focal adhesion, adrenergic signaling in cardiomyocytes, and Wnt signaling. Through integrative analyses, we determined that 126 genes showed a negative correlation between up-regulated expression and down-regulated methylation. KEGG enrichment analysis of these genes indicated participation in ECM-receptor interaction, regulation of actin cytoskeleton, and focal adhesion. Using RT-qPCR, we confirmed the differential expression of lamb3, itga6, limk2, itgb4, capn2, and thbs1. This study revealed for the first time the molecular responses of skeletal muscle to cortisol at the transcriptomic and whole-genome DNA methylation levels in rainbow trout.
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Affiliation(s)
- Daniela Aravena-Canales
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370035, Chile; (D.A.-C.); (A.M.)
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile; (V.V.-M.); (C.G.-E.)
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile; (V.V.-M.); (C.G.-E.)
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Naturaleza, Universidad San Sebastián, Concepción 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Cristian Gallardo-Escarate
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile; (V.V.-M.); (C.G.-E.)
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Alfredo Molina
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370035, Chile; (D.A.-C.); (A.M.)
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile; (V.V.-M.); (C.G.-E.)
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andres Bello, Quintay 2340000, Chile
| | - Juan Antonio Valdés
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370035, Chile; (D.A.-C.); (A.M.)
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile; (V.V.-M.); (C.G.-E.)
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andres Bello, Quintay 2340000, Chile
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Lorgen-Ritchie M, Chalmers L, Clarkson M, Taylor JF, MacKenzie S, Migaud H, Martin SAM. Impact of freshwater rearing history on Atlantic salmon gill response to viral stimulation post seawater transfer. FISH & SHELLFISH IMMUNOLOGY 2024; 150:109653. [PMID: 38801843 DOI: 10.1016/j.fsi.2024.109653] [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: 01/18/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Land-based recirculating aquaculture systems (RAS) have risen in prevalence in recent years for Atlantic salmon production, enabling intensive production which allows increased growth and environmental control, but also having the potential for reducing water use and eutrophication. The Atlantic salmon has an anadromous life history with juvenile stages in freshwater (FW) and on-growing in seawater (SW), enabled by a transformational process known as smoltification. The timing of smoltification and transfer of smolts from FW to SW is critical under commercial production with high mortalities during this period. The impact of FW rearing system on immune function following seawater transfer (SWT) is not well understood. In this study parr were raised in either RAS or a traditional open-LOCH system until smolting and then transferred to a common marine environment. Two-weeks post-SWT fish were immune stimulated with a viral mimic (poly I:C) for 24 h to assess the ability to mount an antiviral immune response, assessed by whole transcriptome analysis of gill tissue, an important immune organ in fish. We show that unstimulated smolts reared in the LOCH had higher immune gene expression than those reared in RAS as determined by functional analysis. However, following stimulation, smolts reared in the RAS mounted a greater magnitude of response with a suite of immune genes displaying higher fold induction of transcription compared to LOCH reared smolts. We suggest RAS smolts have a lower steady state immune-associated transcriptome likely due to an unvarying environment, in terms of environmental factors and lack of exposure to pathogens, which shows a compensatory mechanism following stimulation allowing immune 'catch-up' with those reared in the LOCH. Alternatively, the RAS fish are experiencing an excessive response to the immune stimulation.
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Affiliation(s)
- Marlene Lorgen-Ritchie
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Lynn Chalmers
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Michael Clarkson
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - John F Taylor
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Simon MacKenzie
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Herve Migaud
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK.
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Ren X, Zhao J, Hu J. Non-concordant epigenetic and transcriptional responses to acute thermal stress in western mosquitofish (Gambusia affinis). Mol Ecol 2024:e17332. [PMID: 38529738 DOI: 10.1111/mec.17332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 03/27/2024]
Abstract
Climate change is intensifying the frequency and severity of extreme temperatures. Understanding the molecular mechanisms underlying the ability to cope with acute thermal stress is key for predicting species' responses to extreme temperature events. While many studies have focused on the individual roles of gene expression, post-transcriptional processes and epigenetic modifications in response to acute thermal stress, the relative contribution of these molecular mechanisms remains unclear. The wide range of thermal limits of western mosquitofish (Gambusia affinis) provides an opportunity to explore this interplay. Here, we quantified changes in gene expression, alternative splicing, DNA methylation and microRNA (miRNA) expression in muscle tissue dissected from mosquitofish immediately after reaching high (CTmax) or low thermal limit (CTmin). Although the numbers of genes showing expression and splicing changes in response to acute temperature stress were small, we found a possibly larger and non-redundant role of splicing compared to gene expression, with more genes being differentially spliced (DSGs) than differentially expressed (DEGs), and little overlap between DSGs and DEGs. We also identified a small proportion of CpGs showing significant methylation change (i.e. differentially methylated cytosines, DMCs) in fish at thermal limits; however, there was no overlap between DEGs and genes annotated with DMCs in both CTmax and CTmin experiments. The weak interplay between epigenetic modifications and gene expression was further supported by our discoveries of no differentially expressed miRNAs. These findings provide novel insights into the relative role of different molecular mechanisms underlying immediate responses to extreme temperatures and demonstrate non-concordant responses of epigenetic and transcriptional mechanisms to acute temperature stress.
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Affiliation(s)
- Xingyue Ren
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, P. R. China
| | - Junjie Zhao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, P. R. China
| | - Juntao Hu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, P. R. China
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Franke A, Beemelmanns A, Miest JJ. Are fish immunocompetent enough to face climate change? Biol Lett 2024; 20:20230346. [PMID: 38378140 PMCID: PMC10878809 DOI: 10.1098/rsbl.2023.0346] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 01/26/2024] [Indexed: 02/22/2024] Open
Abstract
Ongoing climate change has already been associated with increased disease outbreaks in wild and farmed fish. Here, we evaluate the current knowledge of climate change-related ecoimmunology in teleosts with a focus on temperature, hypoxia, salinity and acidification before exploring interactive effects of multiple stressors. Our literature review reveals that acute and chronic changes in temperature and dissolved oxygen can compromise fish immunity which can lead to increased disease susceptibility. Moreover, temperature and hypoxia have already been shown to enhance the infectivity of certain pathogens/parasites and to accelerate disease progression. Too few studies exist that have focussed on acidification, but direct immune effects seem to be limited while salinity studies have led to contrasting results. Likewise, multi-stressor experiments essential for unravelling the interactions of simultaneously changing environmental factors are still scarce. This ultimately impedes our ability to estimate to what extent climate change will hamper fish immunity. Our review about epigenetic regulation mechanisms highlights the acclimation potential of the fish immune response to changing environments. However, due to the limited number of epigenetic studies, overarching conclusions cannot be drawn. Finally, we provide an outlook on how to better estimate the effects of realistic climate change scenarios in future immune studies in fish.
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Affiliation(s)
- Andrea Franke
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 26129 Oldenburg, Germany
- Alfred-Wegener-Institute, Helmholtz-Centre for Polar and Marine Research (AWI), 27570 Bremerhaven, Germany
| | - Anne Beemelmanns
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V0A6 Québec, Canada
| | - Joanna J. Miest
- School of Psychology and Life Sciences, Canterbury, Kent CT1 1QU, UK
- School of Science, University of Greenwich, Chatham Maritime, Kent ME4 4TB, UK
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Liu A, Zeng F, Wang L, Zhen H, Xia X, Pei H, Dong C, Zhang Y, Ding J. High temperature influences DNA methylation and transcriptional profiles in sea urchins (Strongylocentrotus intermedius). BMC Genomics 2023; 24:491. [PMID: 37641027 PMCID: PMC10464075 DOI: 10.1186/s12864-023-09616-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND DNA methylation plays an important role in life processes by affecting gene expression, but it is still unclear how DNA methylation is controlled and how it regulates gene transcription under high temperature stress conditions in Strongylocentrotus intermedius. The potential link between DNA methylation variation and gene expression changes in response to heat stress in S. intermedius was investigated by MethylRAD-seq and RNA-seq analysis. We screened DNA methylation driver genes in order to comprehensively elucidate the regulatory mechanism of its high temperature adaptation at the DNA/RNA level. RESULTS The results revealed that high temperature stress significantly affected not only the DNA methylation and transcriptome levels of S. intermedius (P < 0.05), but also growth. MethylRAD-seq analysis revealed 12,129 CG differential methylation sites and 966 CWG differential methylation sites, and identified a total of 189 differentially CG methylated genes and 148 differentially CWG methylated genes. Based on KEGG enrichment analysis, differentially expressed genes (DEGs) are mostly enriched in energy and cell division, immune, and neurological damage pathways. Further RNA-seq analysis identified a total of 1968 DEGs, of which 813 genes were upregulated and 1155 genes were downregulated. Based on the joint MethylRAD-seq and RNA-seq analysis, metabolic processes such as glycosaminoglycan degradation, oxidative phosphorylation, apoptosis, glutathione metabolism, thermogenesis, and lysosomes are regulated by DNA methylation. CONCLUSIONS High temperature affected the DNA methylation and expression levels of genes such as MOAP-1, GGT1 and RDH8, which in turn affects the metabolism of HPSE, Cox, glutathione, and retinol, thereby suppressing the immune, energy metabolism, and antioxidant functions of the organism and finally manifesting as stunted growth. In summary, the observations in the present study improve our understanding of the molecular mechanism of the response to high temperature stress in sea urchin.
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Affiliation(s)
- Anzheng Liu
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Fanshuang Zeng
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Luo Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China.
| | - Hao Zhen
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Xinglong Xia
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Honglin Pei
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Changkun Dong
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Yanmin Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
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Pham K, Ho L, D'Incal CP, De Cock A, Berghe WV, Goethals P. Epigenetic analytical approaches in ecotoxicological aquatic research. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 330:121737. [PMID: 37121302 DOI: 10.1016/j.envpol.2023.121737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/15/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
Environmental epigenetics has become a key research focus in global climate change studies and environmental pollutant investigations impacting aquatic ecosystems. Specifically, triggered by environmental stress conditions, intergenerational DNA methylation changes contribute to biological adaptive responses and survival of organisms to increase their tolerance towards these conditions. To critically review epigenetic analytical approaches in ecotoxicological aquatic research, we evaluated 78 publications reported over the past five years (2016-2021) that applied these methods to investigate the responses of aquatic organisms to environmental changes and pollution. The results show that DNA methylation appears to be the most robust epigenetic regulatory mark studied in aquatic animals. As such, multiple DNA methylation analysis methods have been developed in aquatic organisms, including enzyme restriction digestion-based and methyl-specific immunoprecipitation methods, and bisulfite (in)dependent sequencing strategies. In contrast, only a handful of aquatic studies, i.e. about 15%, have been focusing on histone variants and post-translational modifications due to the lack of species-specific affinity based immunological reagents, such as specific antibodies for chromatin immunoprecipitation applications. Similarly, ncRNA regulation remains as the least popular method used in the field of environmental epigenetics. Insights into the opportunities and challenges of the DNA methylation and histone variant analysis methods as well as decreasing costs of next generation sequencing approaches suggest that large-scale epigenetic environmental studies in model and non-model organisms will soon become available in the near future. Moreover, antibody-dependent and independent methods, such as mass spectrometry-based methods, can be used as an alternative epigenetic approach to characterize global changes of chromatin histone modifications in future aquatic research. Finally, a systematic guide for DNA methylation and histone variant methods is offered for ecotoxicological aquatic researchers to select the most relevant epigenetic analytical approach in their research.
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Affiliation(s)
- Kim Pham
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium.
| | - Long Ho
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium
| | - Claudio Peter D'Incal
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Andrée De Cock
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium
| | - Wim Vanden Berghe
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Peter Goethals
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium
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Al-Ashhab A, Alexander-Shani R, Avrahami Y, Ehrlich R, Strem RI, Meshner S, Shental N, Sharon G. Sparus aurata and Lates calcarifer skin microbiota under healthy and diseased conditions in UV and non-UV treated water. Anim Microbiome 2022; 4:42. [PMID: 35729615 PMCID: PMC9210813 DOI: 10.1186/s42523-022-00191-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/10/2022] [Indexed: 11/15/2022] Open
Abstract
Background The welfare of farmed fish is influenced by numerous environmental and management factors. Fish skin is an important site for immunity and a major route by which infections are acquired. The objective of this study was to characterize bacterial composition variability on skin of healthy, diseased, and recovered Gilthead Seabream (Sparus aurata) and Barramundi (Lates calcarifer). S. aurata, which are highly sensitive to gram-negative bacteria, were challenged with Vibrio harveyi. In addition, and to provide a wider range of infections, both fish species (S. aurata and L. calcarifer) were infected with gram-positive Streptococcus iniae, to compare the response of the highly sensitive L. calcarifer to that of the more resistant S. aurata. All experiments also compared microbial communities found on skin of fish reared in UV (a general practice used in aquaculture) and non-UV treated water tanks. Results Skin swab samples were taken from different areas of the fish (lateral lines, abdomen and gills) prior to controlled infection, and 24, 48 and 72 h, 5 days, one week and one-month post-infection. Fish skin microbial communities were determined using Illumina iSeq100 16S rDNA for bacterial sequencing. The results showed that naturally present bacterial composition is similar on all sampled fish skin sites prior to infection, but the controlled infections (T1 24 h post infection) altered the bacterial communities found on fish skin. Moreover, when the naturally occurring skin microbiota did not quickly recover, fish mortality was common following T1 (24 h post infection). We further confirmed the differences in bacterial communities found on skin and in the water of fish reared in non-UV and UV treated water under healthy and diseased conditions. Conclusions Our experimental findings shed light on the fish skin microbiota in relation to fish survival (in diseased and healthy conditions). The results can be harnessed to provide management tools for commercial fish farmers; predicting and preventing fish diseases can increase fish health, welfare, and enhance commercial fish yields. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00191-y.
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12
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Mukiibi R, Peñaloza C, Gutierrez A, Yáñez JM, Houston RD, Robledo D. The impact of Piscirickettsia salmonis infection on genome-wide DNA methylation profile in Atlantic Salmon. Genomics 2022; 114:110503. [PMID: 36244592 DOI: 10.1016/j.ygeno.2022.110503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 10/01/2022] [Accepted: 10/12/2022] [Indexed: 11/04/2022]
Abstract
Salmon rickettsial septicaemia (SRS), caused by the bacteria Piscirickettsia salmonis (P. salmonis), is responsible for significant mortality in farmed Atlantic salmon in Chile. Currently there are no effective treatments or preventive measures for this disease, although genetic selection or genome engineering to increase salmon resistance to SRS are promising strategies. The accuracy and efficiency of these strategies are usually influenced by the available biological background knowledge of the disease. The aim of this study was to investigate DNA methylation changes in response to P. salmonis infection in the head kidney and liver tissue of Atlantic salmon, and the interaction between gene expression and DNA methylation in the same tissues. The head kidney and liver methylomes of 66 juvenile salmon were profiled using reduced representation bisulphite sequencing (RRBS), and compared between P. salmonis infected animals (3 and 9 days post infection) and uninfected controls, and between SRS resistant and susceptible fish. Methylation was correlated with matching RNA-Seq data from the same animals, revealing that methylation in the first exon leads to an important repression of gene expression. Head kidney methylation showed a clear response to the infection, associated with immunological processes such as actin cytoskeleton regulation, phagocytosis, endocytosis and pathogen associated pattern receptor signaling. Our results contribute to the growing understanding of the role of methylation in regulation of gene expression and response to infectious diseases and could inform the incorporation of epigenetic markers into genomic selection for disease resistant and the design of diagnostic epigenetic markers to better manage fish health in salmon aquaculture.
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Affiliation(s)
- Robert Mukiibi
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK
| | - Alejandro Gutierrez
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK; Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago, Chile
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK.
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, The University of Edinburgh, Edinburgh, UK.
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13
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Klykken C, Boissonnot L, Reed AK, Whatmore P, Attramadal K, Olsen RE. Gene expression patterns in Atlantic salmon (Salmo salar) with severe nephrocalcinosis. JOURNAL OF FISH DISEASES 2022; 45:1645-1658. [PMID: 35862221 PMCID: PMC9796406 DOI: 10.1111/jfd.13687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 05/24/2023]
Abstract
Nephrocalcinosis is a common disorder in farmed Atlantic salmon, but the consequences for the fish physiology are not well understood. We performed a transcriptome study in kidneys of Atlantic salmon (Salmo salar) smolts without and with severe chronic nephrocalcinosis (NC). The study revealed that numerous genes are differentially expressed in fish with NC compared with healthy salmon. The most evident changes in gene expression patterns in the NC group were a massive downregulation of metabolism and energy production, upregulation of signalling pathways important for tissue repair and function maintenance and upregulation of inflammatory responses. Overall, the extensive tissue damage and the gene regulation responses that affect salmon with severe nephrocalcinosis are highly likely to have dramatic consequences on fish survival.
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Affiliation(s)
- Christine Klykken
- Aqua Kompetanse ASFlatangerNorway
- Department of Biology, Faculty of Science and TechnologyNorwegian University of Science and TechnologyTrondheimNorway
| | | | | | - Paul Whatmore
- eResearch DepartmentQueensland Univesity of TechnologyBrisbaneQLDAustralia
| | - Kari Attramadal
- Department of Biotechnology and Food ScienceFaculty of Science and TechnologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Rolf Erik Olsen
- Department of Biology, Faculty of Science and TechnologyNorwegian University of Science and TechnologyTrondheimNorway
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14
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Bani L, Orioli V, Giacchini R, Parenti P, Dondina O, Prokić M, Faggio C, Campli G. Can antioxidant responses be induced by habitat fragmentation process? OIKOS 2022. [DOI: 10.1111/oik.09292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luciano Bani
- Dept of Earth and Environmental Sciences, Univ. of Milano‐Bicocca Milan Italy
- World Biodiversity Association onlus c/o NAT LAB Forte Inglese Portoferraio (Livorno) Italy
| | - Valerio Orioli
- Dept of Earth and Environmental Sciences, Univ. of Milano‐Bicocca Milan Italy
| | - Roberto Giacchini
- Dept of Earth and Environmental Sciences, Univ. of Milano‐Bicocca Milan Italy
| | - Paolo Parenti
- Dept of Earth and Environmental Sciences, Univ. of Milano‐Bicocca Milan Italy
| | - Olivia Dondina
- Dept of Earth and Environmental Sciences, Univ. of Milano‐Bicocca Milan Italy
| | - Marko Prokić
- Dept of Physiology, Inst. for Biological Research ‘Siniša Stanković', National Inst. of Republic of Serbia, Univ. of Belgrade Belgrade Serbia
| | - Caterina Faggio
- Dept of Chemical, Biological, Pharmaceutical and Environmental Sciences, Univ. of Messina Messina Messina Italy
| | - Giulia Campli
- Dept of Ecology and Evolution, Swiss Inst. of Bioinformatics, Univ. of Lausanne Biophore Lausanne Switzerland
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15
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Chan SKN, Suresh S, Munday P, Ravasi T, Bernal MA, Schunter C. The alternative splicing landscape of a coral reef fish during a marine heatwave. Ecol Evol 2022; 12:e8738. [PMID: 35342554 PMCID: PMC8933327 DOI: 10.1002/ece3.8738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 11/09/2022] Open
Abstract
Alternative splicing is a molecular mechanism that enables a single gene to encode multiple transcripts and proteins by post-transcriptional modification of pre-RNA molecules. Changes in the splicing scheme of genes can lead to modifications of the transcriptome and the proteome. This mechanism can enable organisms to respond to environmental fluctuations. In this study, we investigated patterns of alternative splicing in the liver of the coral reef fish Acanthochromis polyacanthus in response to the 2016 marine heatwave on the Great Barrier Reef. The differentially spliced (DS; n = 40) genes during the onset of the heatwave (i.e., 29.49°C or +1°C from average) were related to essential cellular functions such as the MAPK signaling system, Ca(2+) binding, and homeostasis. With the persistence of the heatwave for a period of one month (February to March), 21 DS genes were detected, suggesting that acute warming during the onset of the heatwave is more influential on alternative splicing than the continued exposure to elevated temperatures. After the heatwave, the water temperature cooled to ~24.96°C, and fish showed differential splicing of genes related to cyto-protection and post-damage recovery (n = 26). Two-thirds of the DS genes detected across the heatwave were also differentially expressed, revealing that the two molecular mechanisms act together in A. polyacanthus to cope with the acute thermal change. This study exemplifies how splicing patterns of a coral reef fish can be modified by marine heatwaves. Alternative splicing could therefore be a potential mechanism to adjust cellular physiological states under thermal stress and aid coral reef fishes in their response to more frequent acute thermal fluctuations in upcoming decades.
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Affiliation(s)
- Stanley Kin Nok Chan
- Swire Institute of Marine ScienceSchool of Biological SciencesThe University of Hong KongHong Kong SARChina
| | - Sneha Suresh
- Swire Institute of Marine ScienceSchool of Biological SciencesThe University of Hong KongHong Kong SARChina
| | - Phillip Munday
- Australian Research Council Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
| | - Timothy Ravasi
- Australian Research Council Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
- Marine Climate Change UnitOkinawa Institute of Science and Technology Graduate UniversityOnna‐sonJapan
| | - Moisés A. Bernal
- Department of Biological SciencesCollege of Science and MathematicsAuburn UniversityAuburnAlabamaUSA
| | - Celia Schunter
- Swire Institute of Marine ScienceSchool of Biological SciencesThe University of Hong KongHong Kong SARChina
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16
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Guo H, Dixon B. Understanding acute stress-mediated immunity in teleost fish. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2021; 2:100010. [DOI: 10.1016/j.fsirep.2021.100010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/19/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022] Open
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17
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Uren Webster TM, Consuegra S, Garcia de Leaniz C. Early life stress causes persistent impacts on the microbiome of Atlantic salmon. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2021; 40:100888. [PMID: 34365156 PMCID: PMC8600188 DOI: 10.1016/j.cbd.2021.100888] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/27/2021] [Accepted: 07/27/2021] [Indexed: 01/06/2023]
Abstract
Farmed fish are commonly exposed to stress in intensive aquaculture systems, often leading to immune impairment and increased susceptibility to disease. As microbial communities associated with the gut and skin are vital to host health and disease resilience, disruption of microbiome integrity could contribute to the adverse consequences of stress exposure. Little is known about how stress affects the fish microbiome, especially during sensitive early life stages when initial colonisation and proliferation of host-associated microbial communities take place. Therefore, we compared the effects of two aquaculture-relevant early-life stressors on the gut and skin microbiome of Atlantic salmon fry (four months post hatching) using 16S rRNA amplicon sequencing. Acute cold stress applied during late embryogenesis had a pronounced, lasting effect on the structure of the skin microbiome, as well as a less consistent effect on the gut microbiome. Follow-up targeted qPCR assays suggested that this is likely due to disruption of the egg shell microbial communities at the initial stages of microbiome colonisation, with persistent effects on community structure. In contrast, chronic post hatching stress altered the structure of the gut microbiome, but not that of the skin. Both types of stress promoted similar Gammaproteobacteria ASVs, particularly within the genera Acinetobacter and Aeromonas, which include several important opportunistic fish pathogens. Our results demonstrate the sensitivity of the salmon microbiome to environmental stressors during early life, with potential associated health impacts on the host. We also identified common signatures of stress in the salmon microbiome, which may represent useful microbial stress biomarkers.
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18
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Mikryakov DV, Pronina GI, Suvorova TA, Sokolova AS, Mikryakov VR, Petrushin AB. Some Indicators of Nonspecific Immunity of Various Breeding Groups of Carp in Different Periods of the Annual Cycle. BIOL BULL+ 2021. [DOI: 10.1134/s1062359021040105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
A comparative study of some parameters of nonspecific immunity in the Angelinskii rubella-resistant variant of the scaly and mirror groups of carp in the prespawning and late feeding periods was carried out. The level of the antimicrobial properties of the C-reactive protein, nonspecific immune complexes in the blood serum, and phagocytic activity of neutrophils were studied. The study showed interbreed and inter-seasonal differences in some indicators. It is concluded that the higher level of bacteriostatic activity of blood serum in the rubella-resistant variant, compared with other groups of carp, provides a low percentage of immunodeficient individuals and resistance to pathogens of infectious diseases.
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19
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Cádiz MI, López ME, Díaz-Domínguez D, Cáceres G, Marin-Nahuelpi R, Gomez-Uchida D, Canales-Aguirre CB, Orozco-terWengel P, Yáñez JM. Detection of selection signatures in the genome of a farmed population of anadromous rainbow trout (Oncorhynchus mykiss). Genomics 2021; 113:3395-3404. [PMID: 34339816 DOI: 10.1016/j.ygeno.2021.07.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 07/06/2021] [Accepted: 07/28/2021] [Indexed: 11/26/2022]
Abstract
Domestication processes and artificial selection are likely to leave signatures that can be detected at a molecular level in farmed rainbow trout (Oncorhynchus mykiss). These signatures of selection are genomic regions that contain functional genetic variants conferring a higher fitness to their bearers. We genotyped 749 rainbow trout from a commercial population using a rainbow trout Axiom 57 K SNP array panel and identified putative genomic regions under selection using the pcadapt, Composite Likelihood Ratio (CLR) and Integrated Haplotype Score (iHS) methods. After applying quality-control pipelines and statistical analyses, we detected 12, 96 and 16 SNPs putatively under selection, associated with 96, 781 and 115 candidate genes, respectively. Several of these candidate genes were associated with growth, early development, reproduction, behavior and immune system traits. In addition, some of the SNPs were found in interesting regions located in autosomal inversions on Omy05 and Omy20. These findings could represent a genome-wide map of selection signatures in farmed rainbow trout and could be important in explaining domestication and selection for genetic traits of commercial interest.
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Affiliation(s)
- María I Cádiz
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago 8820808, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - María E López
- Department of Aquatic Resources, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| | | | - Giovanna Cáceres
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago 8820808, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile
| | - Rodrigo Marin-Nahuelpi
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - Daniel Gomez-Uchida
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - Cristian B Canales-Aguirre
- Centro i~Mar, Universidad de Los Lagos, Camino Chinquihue 6 km, Puerto Montt, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | | | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile.
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20
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Krasnov A, Burgerhout E, Johnsen H, Tveiten H, Bakke AF, Lund H, Afanasyev S, Rebl A, Johansen LH. Development of Atlantic Salmon (Salmo salar L.) Under Hypoxic Conditions Induced Sustained Changes in Expression of Immune Genes and Reduced Resistance to Moritella viscosa. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.722218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Atlantic salmon is characterized with high sensitivity to low dissolved oxygen (DO) levels. Hypoxia can affect diverse biological processes with consequences that can be manifested immediately or with delay. Effects of hypoxia on the immune system and the resistance to a bacterial pathogen were investigated. Two groups were reared at, respectively, normal (NO, 80–100%) and low (LO, 60%) levels of DO over 10 months after which both groups were reared at NO. Smoltification was initiated after 13 months by a winter signal for 6 weeks, followed by constant light for 6 weeks. Samples were collected at the start and end of the constant light period. Expression of 92 immune and stress genes was analyzed in the gill, head kidney, and spleen using a Biomark HD. Most of differentially expressed genes showed higher levels in LO fish compared to NO fish; many immune genes were downregulated during smoltification and these changes were stronger in NO fish. A notable exception was pro-inflammatory genes upregulated in gill of NO fish. Further, salmon were challenged with Moritella viscosa, the causative agent of winter ulcer. Mortality was registered from 5 days post infection (dpi) to the end of trial at 36 dpi. Survival was consistently higher in NO than LO fish, reaching a maximum difference of 18% at 21–23 dpi that reduced to 10% at the end. Analyses with a genome-wide microarray at 36 dpi showed strong responses to the pathogen in gill and spleen. Notable features were the stimulation of eicosanoid metabolism, suggesting an important role of lipid mediators of inflammation, and the downregulation of chemokines. Many immune effectors were activated, including multiple lectins and acute phase proteins, enzymes producing free radicals, and matrix metalloproteinases. The transcriptomic changes induced with a bacterial challenge were similar in NO and LO. After the challenge, interferons a and g and panel of genes of innate antiviral immunity showed higher expression in LO, especially in the gill. The results from the present study suggest that chronic hypoxia in early life stimulated immune genes and attenuated their downregulation associated with smoltification. However, these changes did not improve protection against a bacterial pathogen of major concern in salmon aquaculture.
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21
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Léger JAD, Athanasio CG, Zhera A, Chauhan MF, Simmons DBD. Hypoxic responses in Oncorhynchus mykiss involve angiogenesis, lipid, and lactate metabolism, which may be triggered by the cortisol stress response and epigenetic methylation. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100860. [PMID: 34126312 DOI: 10.1016/j.cbd.2021.100860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 05/14/2021] [Accepted: 06/01/2021] [Indexed: 10/21/2022]
Abstract
The incidence of hypoxia in water bodies is increasing more rapidly than aquatic life can adapt. This study aimed to determine the effects of hypoxia on fish physiology, as well as protein expression through proteomics. To do this, 40 rainbow trout were divided into normoxic control (11.5 mg/L dissolved oxygen) and hypoxic treatment (5 mg/L dissolved oxygen) tanks for a period of 7 days. Fish were then anesthetized and blood was sampled. Fish were then euthanized and heart and liver samples were taken. Blood glucose, cortisol and lipid, body and liver mass, fork length, hematocrit and, blood cell counts and global heart methylation were measured. Red blood cell counts were significantly lower, while hematocrit and mean corpuscular volume were significantly higher in the hypoxic treatment. Global DNA methylation was significantly decreased in hypoxic heart tissue. Plasma cortisol and 18:1 monoacylglyerol increased, while 15:0-18:1 phosphatidylethanolamine, and 18:1 lysophosphatidylethanolamine decreased in plasma of rainbow trout under hypoxic conditions. Plasma proteomics revealed 70 significantly altered proteins (p < 0.05) in the hypoxia treatment (Data are available via ProteomeXchange with identifier PXD026589). Many of these molecular changes appear to be related to the observed increase in red blood cell volume and epigenetic modifications, as well as to angiogenesis, lipid, and glucose metabolism. This study highlights a range of cellular and molecular responses in the blood and plasma of freshwater fish that may be phenotypic adaptions to hypoxia, and that could aid in diagnosing the health status of wild fish populations using several, potential, discovered biomarkers.
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Affiliation(s)
- Jessica A D Léger
- University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, ON L1G 0C5, Canada.
| | - Camila G Athanasio
- University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, ON L1G 0C5, Canada
| | - Aaleen Zhera
- University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, ON L1G 0C5, Canada.
| | - Mohammed Faiz Chauhan
- University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, ON L1G 0C5, Canada.
| | - Denina B D Simmons
- University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, ON L1G 0C5, Canada.
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22
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Proteomic analysis of pikeperch seminal plasma provides novel insight into the testicular development of domesticated fish stocks. Animal 2021; 15:100279. [PMID: 34126386 DOI: 10.1016/j.animal.2021.100279] [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: 02/24/2021] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 11/22/2022] Open
Abstract
Control of the reproduction of domesticated stocks is considered a prerequisite for aquaculture development of pikeperch. However, knowledge about the physiology of the captive pikeperch male reproductive system and the biology of semen is very limited, especially regarding protein characteristics. The aims of our study were to characterize pikeperch sperm quantity and quality parameters and to analyze changes in the proteome of the same males spawned for the first and second times. Moreover, attempts were made to generate the first proteomic library of seminal plasma proteins. Semen collected during the first spawning season was characterized by lower sperm concentration and volume than for the second season. Using mass spectrometry-based label-free quantitative proteomics, we identified 850 proteins in the seminal plasma of pikeperch from both spawning seasons, and 65 seminal proteins were found to be differentially abundant between the first and second spawning seasons. The majority of differentially abundant proteins were involved in stress and immune responses, developmental processes, cofactor metabolic processes, proteolysis, cellular oxidant detoxification and organization of the extracellular matrix (ECM). In addition, several proteins unique to pikeperch seminal plasma were identified, including antifreeze proteins, hibernation-specific plasma proteins, lectins and vitellogenin. In summary, our results indicate that males that spawned for the first time were characterized by incompletely mature gonads and the expression of proteins associated with the early phase of spermatogenesis and ECM organization. On the other hand, males that spawned for the second time exhibited advanced gonadal maturation and expression of proteins related to the late stage of spermatogenesis and sperm maturation, including regulation of reactive oxygen species generation, bicarbonate production, sperm elongation and separation. The identification of a large number of seminal plasma proteins provides a valuable resource for understanding the functions of seminal plasma and the molecular mechanisms involved in testicular development and maturation in domesticated fish, which is a prerequisite for better control of reproduction in captivity.
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23
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Voisin AS, Suarez Ulloa V, Stockwell P, Chatterjee A, Silvestre F. Genome-wide DNA methylation of the liver reveals delayed effects of early-life exposure to 17-α-ethinylestradiol in the self-fertilizing mangrove rivulus. Epigenetics 2021; 17:473-497. [PMID: 33892617 DOI: 10.1080/15592294.2021.1921337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Organisms exposed to endocrine disruptors in early life can show altered phenotype later in adulthood. Although the mechanisms underlying these long-term effects remain poorly understood, an increasing body of evidence points towards the potential role of epigenetic processes. In the present study, we exposed hatchlings of an isogenic lineage of the self-fertilizing fish mangrove rivulus for 28 days to 4 and 120 ng/L of 17-α-ethinylestradiol. After a recovery period of 140 days, reduced representation bisulphite sequencing (RRBS) was performed on the liver in order to assess the hepatic genome-wide methylation landscape. Across all treatment comparisons, a total of 146 differentially methylated fragments (DMFs) were reported, mostly for the group exposed to 4 ng/L, suggesting a non-monotonic effect of EE2 exposure. Gene ontology analysis revealed networks involved in lipid metabolism, cellular processes, connective tissue function, molecular transport and inflammation. The highest effect was reported for nipped-B-like protein B (NIPBL) promoter region after exposure to 4 ng/L EE2 (+ 21.9%), suggesting that NIPBL could be an important regulator for long-term effects of EE2. Our results also suggest a significant role of DNA methylation in intergenic regions and potentially in transposable elements. These results support the ability of early exposure to endocrine disruptors of inducing epigenetic alterations during adulthood, providing plausible mechanistic explanations for long-term phenotypic alteration. Additionally, this work demonstrates the usefulness of isogenic lineages of the self-fertilizing mangrove rivulus to better understand the biological significance of long-term alterations of DNA methylation by diminishing the confounding factor of genetic variability.
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Affiliation(s)
- Anne-Sophie Voisin
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, Namur, Belgium
| | - Victoria Suarez Ulloa
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, Namur, Belgium
| | - Peter Stockwell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Frédéric Silvestre
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, Namur, Belgium
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24
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Merz MP, Turner JD. Is early life adversity a trigger towards inflammageing? Exp Gerontol 2021; 150:111377. [PMID: 33905877 DOI: 10.1016/j.exger.2021.111377] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023]
Abstract
There are many 'faces' of early life adversity (ELA), such as childhood trauma, institutionalisation, abuse or exposure to environmental toxins. These have been implicated in the onset and severity of a wide range of chronic non-communicable diseases later in life. The later-life disease risk has a well-established immunological component. This raises the question as to whether accelerated immune-ageing mechanistically links early-life adversity to the lifelong health trajectory resulting in either 'poor' or 'healthy' ageing. Here we examine observational and mechanistic studies of ELA and inflammageing, highlighting common and distinct features in these two life stages. Many biological processes appear in common including reduction in telomere length, increased immunosenescence, metabolic distortions and chronic (viral) infections. We propose that ELA shapes the developing immune, endocrine and nervous system in a non-reversible way, creating a distinct phenotype with accelerated immunosenescence and systemic inflammation. We conclude that ELA might act as an accelerator for inflammageing and age-related diseases. Furthermore, we now have the tools and cohorts to be able to dissect the interaction between ELA and later life phenotype. This should, in the near future, allow us to identify the ecological and mechanistic processes that are involved in 'healthy' or accelerated immune-ageing.
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Affiliation(s)
- Myriam P Merz
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, 2 avenue de Université, L-4365 Esch-sur-Alzette, Luxembourg
| | - Jonathan D Turner
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg.
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25
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Krick MV, Desmarais E, Samaras A, Guéret E, Dimitroglou A, Pavlidis M, Tsigenopoulos C, Guinand B. Family-effects in the epigenomic response of red blood cells to a challenge test in the European sea bass (Dicentrarchus labrax, L.). BMC Genomics 2021; 22:111. [PMID: 33563212 PMCID: PMC7871408 DOI: 10.1186/s12864-021-07420-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/31/2021] [Indexed: 12/13/2022] Open
Abstract
Abstract Background In fish, minimally invasive blood sampling is widely used to monitor physiological stress with blood plasma biomarkers. As fish blood cells are nucleated, they might be a source a potential new markers derived from ‘omics technologies. We modified the epiGBS (epiGenotyping By Sequencing) technique to explore changes in genome-wide cytosine methylation in the red blood cells (RBCs) of challenged European sea bass (Dicentrarchus labrax), a species widely studied in both natural and farmed environments. Results We retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% (unique best hits). Minor changes in RBC methylome appeared to manifest after the challenge test and a family-effect was detected. Only fifty-seven differentially methylated cytosines (DMCs) close to 51 distinct genes distributed on 17 of 24 linkage groups (LGs) were detected between RBCs of pre- and post-challenge individuals. Thirty-seven of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences. While further investigation remains necessary, few DMC-related genes associated to the Brain Derived Neurotrophic Factor, a protein that favors stress adaptation and fear memory, appear relevant to integrate a centrally produced stress response in RBCs. Conclusion Our modified epiGBS protocol was powerful to analyze patterns of cytosine methylation in RBCs of D. labrax and to evaluate the impact of a challenge using minimally invasive blood samples. This study is the first approximation to identify epigenetic biomarkers of exposure to stress in fish. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07420-9.
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Affiliation(s)
- Madoka Vera Krick
- UMR UM CNRS IRD EPHE ISEM- Institut des Sciences de l'Evolution de Montpellier, Montpellier, France
| | - Erick Desmarais
- UMR UM CNRS IRD EPHE ISEM- Institut des Sciences de l'Evolution de Montpellier, Montpellier, France
| | | | - Elise Guéret
- UMR UM CNRS IRD EPHE ISEM- Institut des Sciences de l'Evolution de Montpellier, Montpellier, France.,Univ. Montpellier, CNRS, INSERM, Montpellier, France.,Montpellier GenomiX, France Génomique, Montpellier, France
| | | | - Michalis Pavlidis
- Department of Biology, University of Crete, 70013, Heraklion, Greece
| | - Costas Tsigenopoulos
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), 715 00, Heraklion, Greece
| | - Bruno Guinand
- UMR UM CNRS IRD EPHE ISEM- Institut des Sciences de l'Evolution de Montpellier, Montpellier, France.
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Djordjevic B, Morales-Lange B, McLean Press C, Olson J, Lagos L, Mercado L, Øverland M. Comparison of Circulating Markers and Mucosal Immune Parameters from Skin and Distal Intestine of Atlantic Salmon in Two Models of Acute Stress. Int J Mol Sci 2021; 22:ijms22031028. [PMID: 33494146 PMCID: PMC7864346 DOI: 10.3390/ijms22031028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 01/13/2023] Open
Abstract
Ensuring salmon health and welfare is crucial to maximize production in recirculation aquaculture systems. Healthy and robust mucosal surfaces of the skin and intestine are essential to achieve this goal because they are the first immunological defenses and are constantly exposed to multistressor conditions, such as infectious diseases, suboptimal nutrition, and environmental and handling stress. In this work, Atlantic salmon, split from a single cohort, were subjected to acute hypoxia stress or 15-min crowding stress and observed over a 24-h recovery period. Samples were collected from fish at 0, 1, 3, 6, 12 and 24 h post-stress to analyze plasma-circulating markers of endocrine function (cortisol), oxidative stress (glutathione peroxidase) and immune function (interleukin 10 (IL-10), annexin A1). In addition, mucosal barrier function parameters were measured in the skin mucus (Muc-like protein and lysozyme) and distal intestine (simple folds, goblet cell size and goblet cell area). The results showed that both acute stress models induced increases of circulating cortisol in plasma (1 h post-stress), which then returned to baseline values (initial control) at 24 h post-stress. Moreover, the hypoxia stress was mostly related to increased oxidative stress and IL-10 production, whereas the crowding stress was associated with a higher production of Muc-like protein and lysozyme in the skin mucus. Interestingly, in the distal intestine, smaller goblet cells were detected immediately and one hour after post-hypoxia stress, which could be related to rapid release of the cellular content to protect this organ. Finally, the correlation of different markers in the hypoxic stress model showed that the circulating levels of cortisol and IL-10 were directly proportional, while the availability of Muc-like proteins was inversely proportional to the size of the goblet cells. On the other hand, in the crowding stress model, a proportional relationship was established between plasma cortisol levels and skin mucus lysozyme. Our results suggest key differences in energy partitioning between the two acute stress models and support the need for further investigation into the interplay of multistressor conditions and strategies to modulate immunological aspects of mucosal surfaces.
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Affiliation(s)
- Brankica Djordjevic
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway; (L.L.); (M.Ø.)
- Correspondence: (B.D.); (B.M-L.)
| | - Byron Morales-Lange
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway; (L.L.); (M.Ø.)
- Correspondence: (B.D.); (B.M-L.)
| | - Charles McLean Press
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1430 Ås, Norway;
| | - Jake Olson
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA;
| | - Leidy Lagos
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway; (L.L.); (M.Ø.)
| | - Luis Mercado
- Grupo de Marcadores Inmunológicos en Organismos Acuáticos, Pontificia Universidad Católica de Valparaíso, 2950 Valparaíso, Chile;
| | - Margareth Øverland
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway; (L.L.); (M.Ø.)
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Moraleda-Prados J, Caballero-Huertas M, Valdivieso A, Joly S, Ji J, Roher N, Ribas L. Epigenetic differences in the innate response after immune stimulation during zebrafish sex differentiation. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 114:103848. [PMID: 32888969 DOI: 10.1016/j.dci.2020.103848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Infections are able to trigger epigenetic modifications; however, epigenetic-mediating infections in the immune system in fish is currently unavailable. Within this purpose, zebrafish were immune-stimulated with three lipopolysaccharides (LPS) during sex differentiation. Methylation patterns of three immune genes were studied by a candidate gene approach together with gene expression analysis, and in adulthood, sex ratios were determined. It was shown that the entrance of LPS was through the gills and accumulated in the pronephros. Significant hypomethylation levels of CASP9 and a significant CpG site for IL1β after Pseudomonas aeruginosa LPS exposure were found. No methylation difference was observed for TNFα. Gene expression and correlation data differed among studied genes. Sex ratios showed a feminization in dose and LPS strain-dependent manner. Here, it is provided epigenetic regulatory mechanisms derived by innate response and the first evidence of possible epigenetic interactions between the immune and reproductive systems.
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Affiliation(s)
- J Moraleda-Prados
- Institut de Ciències del Mar, Spanish National Research Council (CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - M Caballero-Huertas
- Institut de Ciències del Mar, Spanish National Research Council (CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain; Institute of Aquatic Ecology (IEA), Department of Environmental Sciences. Faculty of Sciences, University of Girona (UdG), Campus Montilivi, 17003 Girona, Spain
| | - A Valdivieso
- Institut de Ciències del Mar, Spanish National Research Council (CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - S Joly
- Institut de Ciències del Mar, Spanish National Research Council (CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - J Ji
- Institut de Biotecnologia i Biomedicina (IBB) and Dep. de Biologia Cel·lular, Fisiologia Animal i Immunologia, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain; Department of Marine Science and Engineering, Nanjing Normal University, Nanjing, China
| | - N Roher
- Institut de Biotecnologia i Biomedicina (IBB) and Dep. de Biologia Cel·lular, Fisiologia Animal i Immunologia, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
| | - L Ribas
- Institut de Ciències del Mar, Spanish National Research Council (CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain.
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Nilsson E, Sadler-Riggleman I, Beck D, Skinner MK. Differential DNA methylation in somatic and sperm cells of hatchery vs wild (natural-origin) steelhead trout populations. ENVIRONMENTAL EPIGENETICS 2021; 7:dvab002. [PMID: 34040807 PMCID: PMC8132314 DOI: 10.1093/eep/dvab002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/09/2021] [Accepted: 03/01/2021] [Indexed: 05/06/2023]
Abstract
Environmental factors such as nutrition, stress, and toxicants can influence epigenetic programming and phenotypes of a wide variety of species from plants to humans. The current study was designed to investigate the impacts of hatchery spawning and rearing on steelhead trout (Oncorhynchus mykiss) vs the wild fish on a molecular level. Additionally, epigenetic differences between feeding practices that allow slow growth (2 years) and fast growth (1 year) hatchery trout were investigated. The sperm and red blood cells (RBC) from adult male slow growth/maturation hatchery steelhead, fast growth/maturation hatchery steelhead, and wild (natural-origin) steelhead were collected for DNA preparation to investigate potential alterations in differential DNA methylation regions (DMRs) and genetic mutations, involving copy number variations (CNVs). The sperm and RBC DNA both had a large number of DMRs when comparing the hatchery vs wild steelhead trout populations. The DMRs were cell type specific with negligible overlap. Slow growth/maturation compared to fast growth/maturation steelhead also had a larger number of DMRs in the RBC samples. A number of the DMRs had associated genes that were correlated to various biological processes and pathologies. Observations demonstrate a major epigenetic programming difference between the hatchery and wild natural-origin fish populations, but negligible genetic differences. Therefore, hatchery conditions and growth/maturation rate can alter the epigenetic developmental programming of the steelhead trout. Interestingly, epigenetic alterations in the sperm allow for potential epigenetic transgenerational inheritance of phenotypic variation to future generations. The impacts of hatchery exposures are not only important to consider on the fish exposed, but also on future generations and evolutionary trajectory of fish in the river populations.
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Affiliation(s)
- Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Ingrid Sadler-Riggleman
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
- Correspondence address. Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA. Tel: +1-509-335-1524; E-mail:
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Roh H, Kim A, Kim N, Lee Y, Kim DH. Multi-Omics Analysis Provides Novel Insight into Immuno-Physiological Pathways and Development of Thermal Resistance in Rainbow Trout Exposed to Acute Thermal Stress. Int J Mol Sci 2020; 21:E9198. [PMID: 33276666 PMCID: PMC7731343 DOI: 10.3390/ijms21239198] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/16/2022] Open
Abstract
In recent years, poikilothermic animals such as fish have increasingly been exposed to stressful high-temperature environments due to global warming. However, systemic changes in fish under thermal stress are not fully understood yet at both the transcriptome and proteome level. Therefore, the objective of this study was to investigate the immuno-physiological responses of fish under extreme thermal stress through integrated multi-omics analysis. Trout were exposed to acute thermal stress by raising water temperature from 15 to 25 °C within 30 min. Head-kidney and plasma samples were collected and used for RNA sequencing and two-dimensional gel electrophoresis. Gene enrichment analysis was performed: differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were identified to interpret the multi-omics results and identify the relevant biological processes through pathway analysis. Thousands of DEGs and 49 DEPs were identified in fish exposed to thermal stress. Most of these genes and proteins were highly linked to DNA replication, protein processing in the endoplasmic reticulum, cell signaling and structure, glycolysis activation, complement-associated hemolysis, processing of released free hemoglobin, and thrombosis and hypertension/vasoconstriction. Notably, we found that immune disorders mediated by the complement system may trigger hemolysis in thermally stressed fish, which could have serious consequences such as ferroptosis and thrombosis. However, antagonistic activities that decrease cell-free hemoglobin, heme, and iron might be involved in alleviating the side effects of thermally induced immuno-physiological disorders. These factors may represent the major thermal resistance traits that allow fish to overcome extreme thermal stress. Our findings, based on integration of multi-omics data from transcriptomics and proteomics analyses, provide novel insight into the pathogenesis of acute thermal stress and temperature-linked epizootics.
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Affiliation(s)
- HyeongJin Roh
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan 48513, Korea; (H.R.); (N.K.); (Y.L.)
| | - Ahran Kim
- Pathology Research Division, National Institute of Fisheries Science, Busan 46083, Korea;
| | - Nameun Kim
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan 48513, Korea; (H.R.); (N.K.); (Y.L.)
| | - Yoonhang Lee
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan 48513, Korea; (H.R.); (N.K.); (Y.L.)
| | - Do-Hyung Kim
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan 48513, Korea; (H.R.); (N.K.); (Y.L.)
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30
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Schwartz TS. The Promises and the Challenges of Integrating Multi-Omics and Systems Biology in Comparative Stress Biology. Integr Comp Biol 2020; 60:89-97. [PMID: 32386307 DOI: 10.1093/icb/icaa026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Comparative stress biology is inherently a systems biology approach with the goal of integrating the molecular, cellular, and physiological responses with fitness outcomes. In this way, the systems biology approach is expected to provide a holistic understanding of how different stressors result in different fitness outcomes, and how different individuals (or populations or species) respond to stressors differently. In this perceptive article, I focus on the use of multiple types of -omics data in stress biology. Targeting students and those researchers who are considering integrating -omics approaches in their comparative stress biology studies, I discuss the promise of the integration of these measures for furthering our holistic understanding of how organisms respond to different stressors. I also discuss the logistical and conceptual challenges encountered when working with -omics data and the current hurdles to fully utilize these data in studies of stress biology in non-model organisms.
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Affiliation(s)
- Tonia S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
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31
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Konstantinidis I, Sætrom P, Mjelle R, Nedoluzhko AV, Robledo D, Fernandes JMO. Major gene expression changes and epigenetic remodelling in Nile tilapia muscle after just one generation of domestication. Epigenetics 2020; 15:1052-1067. [PMID: 32264748 PMCID: PMC7116051 DOI: 10.1080/15592294.2020.1748914] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/23/2020] [Accepted: 03/25/2020] [Indexed: 12/29/2022] Open
Abstract
The historically recent domestication of fishes has been essential to meet the protein demands of a growing human population. Selection for traits of interest during domestication is a complex process whose epigenetic basis is poorly understood. Cytosine hydroxymethylation is increasingly recognized as an important DNA modification involved in epigenetic regulation. In the present study, we investigated if hydroxymethylation plays a role in fish domestication and demonstrated for the first time at a genome-wide level and single nucleotide resolution that the muscle hydroxymethylome changes after a single generation of Nile tilapia (Oreochromis niloticus, Linnaeus) domestication. The overall decrease in hydroxymethylcytosine levels was accompanied by the downregulation of 2015 genes in fish reared in captivity compared to their wild progenitors. In contrast, several myogenic and metabolic genes that can affect growth potential were upregulated. There were 126 differentially hydroxymethylated cytosines between groups, which were not due to genetic variation; they were associated with genes involved in immune-, growth- and neuronal-related pathways. Taken together, our data unveil a new role for DNA hydroxymethylation in epigenetic regulation of fish domestication with impact in aquaculture and implications in artificial selection, environmental adaptation and genome evolution.
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Affiliation(s)
| | - Pål Sætrom
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Computer Science, Norwegian University of Science and Technology, Trondheim, Norway
- Bioinformatics Core facility-BioCore, Norwegian University of Science and Technology, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Robin Mjelle
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
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Kelly T, Johnsen H, Burgerhout E, Tveiten H, Thesslund T, Andersen Ø, Robinson N. Low Oxygen Stress During Early Development Influences Regulation of Hypoxia-Response Genes in Farmed Atlantic Salmon ( Salmo salar). G3 (BETHESDA, MD.) 2020; 10:3179-3188. [PMID: 32636218 PMCID: PMC7466997 DOI: 10.1534/g3.120.401459] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022]
Abstract
Survival and growth of developing salmonids are negatively affected by low oxygen levels within gravel nests in natural streams, and hypoxic stress is often experienced by farmed Atlantic salmon (Salmo salar) within hatcheries. Exposure to hypoxia during early development may have long-lasting effects by altering epigenetic marks and gene expression in oxygen regulatory pathways. Here, we examine the transcriptomic response to low dissolved oxygen (DO) in post-hatch salmon reared continuously in 30%, 60% or 100% DO from fertilization until start of feeding. RNA sequencing revealed multiple differentially expressed genes, including oxygen transporting hemoglobin embryonic α subunit (hbae) and EGLN3 family hypoxia-inducible factor 3 (egln3) which regulates the stability of hypoxia inducible factor 1α (HIF-1α). Both hbae and egln3 displayed expression levels inversely correlated to oxygen concentration, and DNA methylation patterns within the egln3 promoter were negatively associated with the transcript levels. These results suggest that epigenetic processes are influenced by low oxygen levels during early development in Atlantic salmon to upregulate hypoxia-response genes.
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Affiliation(s)
- Tara Kelly
- Sustainable Aquaculture Laboratory- Temperate and Tropical (SALTT), School of BioSciences, The University of Melbourne, Parkville 3010, Australia
| | | | | | | | | | - Øivind Andersen
- Nofima, N-9291 Tromsø, Norway
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (NMBU), N-1433, Ås, Norway
| | - Nicholas Robinson
- Nofima, N-9291 Tromsø, Norway
- Sustainable Aquaculture Laboratory- Temperate and Tropical (SALTT), School of BioSciences, The University of Melbourne, Parkville 3010, Australia
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Li J, Su X, Dai L, Chen N, Fang C, Dong Z, Fu J, Yu Y, Wang W, Zhang H, Wang H, Ji Y, Liu Y, Cheng L, Shi G, Zhang S, Yang Y, Deng H. Temporal DNA methylation pattern and targeted therapy in colitis-associated cancer. Carcinogenesis 2020; 41:235-244. [PMID: 31802101 DOI: 10.1093/carcin/bgz199] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/19/2019] [Accepted: 12/04/2019] [Indexed: 02/05/2023] Open
Abstract
DNA methylation plays a crucial role in the pathogenesis of various diseases, including colorectal cancer (CRC). However, the global and temporal DNA methylation pattern during initiation and progression of colitis-associated cancer (CAC) are still unknown, including the potential therapeutic strategy of targeting methylation for CAC. In the present study, the global DNA methylation pattern was determined at different time points during CAC using DNA methylation sequencing, followed by the Starburst plot integrating alterations and potential functional prediction analysis. After demonstrating the regulatory role of DNA methyltransferases (DNMTs) on the expression of hub-genes in CRC cells, DNMT inhibitors were administered to treat CAC mice. Our results indicated that 811 genes were hypermethylated at different time points during initiation and progression of CAC. Genes that were downregulated and hypermethylated during CAC, including hub-genes BAD and inositol polyphosphate phosphatase-like 1 (INPPL1), were involved in MAPK signaling pathways, kit receptor signaling pathways, apoptosis and EGF/EGFR signaling pathways. Upregulated DNMTs (DNMT1, DNMT3A and DNMT3B) mediated downregulation and hypermethylation of BAD and INPPL1 in CAC and CRC cells. Low doses of DNMT inhibitors (decitabine (DAC) and azacitidine (AZA)) exerted efficient antitumor effects in CAC, accompanied with upregulation of BAD and INPPL1 expression, and apoptosis induction. In summary, the present study demonstrates the temporal DNA methylation pattern during CAC and provides a novel therapeutic strategy for treating this disease.
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Affiliation(s)
- Junshu Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Xiaolan Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Lei Dai
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Na Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Chao Fang
- Department of Gastrointestinal Surgery, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Zhexu Dong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Jiamei Fu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Yan Yu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Wenshuang Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Hantao Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Huiling Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Yanhong Ji
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Yi Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Lin Cheng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Gang Shi
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Shuang Zhang
- Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Yang Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
| | - Hongxin Deng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, P. R. China
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34
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Uren Webster TM, Rodriguez-Barreto D, Consuegra S, Garcia de Leaniz C. Cortisol-Related Signatures of Stress in the Fish Microbiome. Front Microbiol 2020; 11:1621. [PMID: 32765459 PMCID: PMC7381252 DOI: 10.3389/fmicb.2020.01621] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/22/2020] [Indexed: 12/11/2022] Open
Abstract
Exposure to environmental stressors can compromise fish health and fitness. Little is known about how stress-induced microbiome disruption may contribute to these adverse health effects, including how cortisol influences fish microbial communities. We exposed juvenile Atlantic salmon to a mild confinement stressor for two weeks. We then measured cortisol in the plasma, skin-mucus, and feces, and characterized the skin and fecal microbiome. Fecal and skin cortisol concentrations increased in fish exposed to confinement stress, and were positively correlated with plasma cortisol. Elevated fecal cortisol was associated with pronounced changes in the diversity and structure of the fecal microbiome. In particular, we identified a marked decline in the lactic acid bacteria Carnobacterium sp. and an increase in the abundance of operational taxonomic units within the classes Clostridia and Gammaproteobacteria. In contrast, cortisol concentrations in skin-mucus were lower than in the feces, and were not related to any detectable changes in the skin microbiome. Our results demonstrate that stressor-induced cortisol production is associated with disruption of the gut microbiome, which may, in turn, contribute to the adverse effects of stress on fish health. They also highlight the value of using non-invasive fecal samples to monitor stress, including simultaneous determination of cortisol and stress-responsive bacteria.
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Affiliation(s)
- Tamsyn M. Uren Webster
- Centre for Sustainable Aquatic Research, College of Science, Swansea University, Swansea, United Kingdom
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35
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Bai L, Zhang S, Deng Y, Song C, Kang G, Dong Y, Wang Y, Gao F, Huang H. Comparative genomics analysis of Acinetobacter haemolyticus isolates from sputum samples of respiratory patients. Genomics 2020; 112:2784-2793. [PMID: 32209379 DOI: 10.1016/j.ygeno.2020.03.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/27/2020] [Accepted: 03/20/2020] [Indexed: 12/25/2022]
Abstract
Acinetobacter haemolyticus (A. haemolyticus) is a significant Acinetobacter pathogen, and the resistance of A. haemolyticus continues to rise due to abuse of antibiotics and the frequent gene exchange between bacteria in hospital. In this study, we performed complete genome sequencing of two A. haemolyticus strains TJR01 and TJS01 to improve our understanding of pathogenic and resistance of A. haemolyticus. Both TJR01 and TJS01 contain one chromosome and two plasmids. Compared to TJS01, more virulence factors (VFs) associated pathogenicity and resistant genes were predicted in TJR01 due to T4SS and integron associated with combination and transport. Antimicrobial susceptibility results were consistent with sequencing. We suppose TJS01 was a susceptive strain and TJR01 was an acquired multidrug resistance strain due to plasmid-mediated horizontal gene transfer. We hope these findings may be helpful for clinical treatment of A. haemolyticus infection and reduce the risk of potential outbreak infection.
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Affiliation(s)
- Liang Bai
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - ShaoCun Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Yong Deng
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | | | - GuangBo Kang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | | | - Yue Wang
- Institute of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Feng Gao
- Department of Physics, School of Science, Frontier Science Center of Synthetic Biology (MOE), Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China.
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
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36
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Hu J, Askary AM, Thurman TJ, Spiller DA, Palmer TM, Pringle RM, Barrett RDH. The Epigenetic Signature of Colonizing New Environments in Anolis Lizards. Mol Biol Evol 2020; 36:2165-2170. [PMID: 31147693 DOI: 10.1093/molbev/msz133] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Founder populations often show rapid divergence from source populations after colonizing new environments. Epigenetic modifications can mediate phenotypic responses to environmental change and may be an important mechanism promoting rapid differentiation in founder populations. Whereas many long-term studies have explored the extent to which divergence between source and founder populations is genetically heritable versus plastic, the role of epigenetic processes during colonization remains unclear. To investigate epigenetic modifications in founding populations, we experimentally colonized eight small Caribbean islands with brown anole lizards (Anolis sagrei) from a common source population. We then quantitatively measured genome-wide DNA methylation in liver tissue using reduced representation bisulfite sequencing of individuals transplanted onto islands with high- versus low-habitat quality. We found that lizard sex and habitat quality explained a significant proportion of epigenetic variation. Differentially methylated cytosines mapped to genes that encode proteins with functions likely to be relevant to habitat change (e.g., signal transduction, immune response, circadian rhythm). This study provides experimental evidence of a relationship between epigenetic responses and the earliest stages of colonization of novel environments in nature and suggests that habitat quality influences the nature of these epigenetic modifications.
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Affiliation(s)
- Juntao Hu
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Arash M Askary
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Timothy J Thurman
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada.,Smithsonian Tropical Research Institute, Panamá, República de Panamá
| | - Dave A Spiller
- Section of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA
| | - Todd M Palmer
- Mpala Research Centre, Nanyuki, Kenya.,Department of Biology, University of Florida, Gainesville, FL
| | - Robert M Pringle
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ
| | - Rowan D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
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37
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Wogan GOU, Yuan ML, Mahler DL, Wang IJ. Genome-wide epigenetic isolation by environment in a widespread Anolis lizard. Mol Ecol 2019; 29:40-55. [PMID: 31710739 DOI: 10.1111/mec.15301] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 10/26/2019] [Accepted: 11/08/2019] [Indexed: 12/12/2022]
Abstract
Epigenetic changes can provide a pathway for organisms to respond to local environmental conditions by influencing gene expression. However, we still know little about the spatial distribution of epigenetic variation in natural systems, how it relates to the distribution of genetic variation and the environmental structure of the landscape, and the processes that generate and maintain it. Studies examining spatial patterns of genetic and epigenetic variation can provide valuable insights into how ecological and population processes contribute to epigenetic divergence across heterogeneous landscapes. Here, we perform a comparative analysis of spatial genetic and epigenetic variation based on 8,459 single nucleotide polymorphisms (SNPs) and 8,580 single methylation variants (SMVs) from eight populations of the Puerto Rican crested anole, Anolis cristatellus, an abundant lizard in the adaptive radiations of anoles on the Greater Antilles that occupies a diverse range of habitats. Using generalized dissimilarity modelling and multiple matrix regression, we found that genome-wide epigenetic differentiation is strongly correlated with environmental divergence, even after controlling for the underlying genetic structure. We also detected significant associations between key environmental variables and 96 SMVs, including 42 located in promoter regions or gene bodies. Our results suggest an environmental basis for population-level epigenetic differentiation in this system and contribute to better understanding how environmental gradients structure epigenetic variation in nature.
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Affiliation(s)
- Guinevere O U Wogan
- Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley, CA, USA
| | - Michael L Yuan
- Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley, CA, USA
| | - D Luke Mahler
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley, CA, USA
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38
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Rodriguez‐Barreto D, Rey O, Uren‐Webster TM, Castaldo G, Consuegra S, Garcia de Leaniz C. Transcriptomic response to aquaculture intensification in Nile tilapia. Evol Appl 2019; 12:1757-1771. [PMID: 31548855 PMCID: PMC6752142 DOI: 10.1111/eva.12830] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 12/21/2022] Open
Abstract
To meet future global demand for fish protein, more fish will need to be farmed using fewer resources, and this will require the selection of nonaggressive individuals that perform well at high densities. Yet, the genetic changes underlying loss of aggression and adaptation to crowding during aquaculture intensification are largely unknown. We examined the transcriptomic response to aggression and crowding in Nile tilapia, one of the oldest and most widespread farmed fish, whose social structure shifts from social hierarchies to shoaling with increasing density. A mirror test was used to quantify aggression and skin darkening (a proxy for stress) of fish reared at low and high densities, and gene expression in the hypothalamus was analysed among the most and least aggressive fish at each density. Fish reared at high density were darker, had larger brains, were less active and less aggressive than those reared at low density and had differentially expressed genes consistent with a reactive stress-coping style and activation of the hypothalamus-pituitary-interrenal (HPI) axis. Differences in gene expression among aggressive fish were accounted for by density and the interaction between density and aggression levels, whereas for nonaggressive fish differences in gene expression were associated with individual variation in skin brightness and social stress. Thus, the response to crowding in Nile tilapia is context dependent and involves different neuroendocrine pathways, depending on social status. Knowledge of genes associated with the response to crowding may pave the way for more efficient fish domestication, based on the selection of nonaggressive individuals with increasing tolerance to chronic stress necessary for aquaculture intensification.
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Affiliation(s)
| | - Olivier Rey
- Centre for Sustainable Aquatic Research (CSAR), College of ScienceSwansea UniversitySwanseaUK
- Université de Perpignan Via DomitiaPerpignanFrance
| | - Tamsyn M. Uren‐Webster
- Centre for Sustainable Aquatic Research (CSAR), College of ScienceSwansea UniversitySwanseaUK
| | - Giovanni Castaldo
- Centre for Sustainable Aquatic Research (CSAR), College of ScienceSwansea UniversitySwanseaUK
- Systemic Physiological and Ecotoxicological Research, Department of BiologyUniversity of AntwerpAntwerpBelgium
| | - Sonia Consuegra
- Centre for Sustainable Aquatic Research (CSAR), College of ScienceSwansea UniversitySwanseaUK
| | - Carlos Garcia de Leaniz
- Centre for Sustainable Aquatic Research (CSAR), College of ScienceSwansea UniversitySwanseaUK
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39
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Rider CF, Carlsten C. Air pollution and DNA methylation: effects of exposure in humans. Clin Epigenetics 2019; 11:131. [PMID: 31481107 PMCID: PMC6724236 DOI: 10.1186/s13148-019-0713-2] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/22/2019] [Indexed: 12/11/2022] Open
Abstract
Air pollution exposure is estimated to contribute to approximately seven million early deaths every year worldwide and more than 3% of disability-adjusted life years lost. Air pollution has numerous harmful effects on health and contributes to the development and morbidity of cardiovascular disease, metabolic disorders, and a number of lung pathologies, including asthma and chronic obstructive pulmonary disease (COPD). Emerging data indicate that air pollution exposure modulates the epigenetic mark, DNA methylation (DNAm), and that these changes might in turn influence inflammation, disease development, and exacerbation risk. Several traffic-related air pollution (TRAP) components, including particulate matter (PM), black carbon (BC), ozone (O3), nitrogen oxides (NOx), and polyaromatic hydrocarbons (PAHs), have been associated with changes in DNAm; typically lowering DNAm after exposure. Effects of air pollution on DNAm have been observed across the human lifespan, but it is not yet clear whether early life developmental sensitivity or the accumulation of exposures have the most significant effects on health. Air pollution exposure-associated DNAm patterns are often correlated with long-term negative respiratory health outcomes, including the development of lung diseases, a focus in this review. Recently, interventions such as exercise and B vitamins have been proposed to reduce the impact of air pollution on DNAm and health. Ultimately, improved knowledge of how exposure-induced change in DNAm impacts health, both acutely and chronically, may enable preventative and remedial strategies to reduce morbidity in polluted environments.
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Affiliation(s)
- Christopher F Rider
- Respiratory Medicine, Faculty of Medicine, Chan-Yeung Centre for Occupational and Environmental Respiratory Disease (COERD), University of British Columbia, Vancouver, British Columbia, Canada. .,Diamond Health Care Centre 7252, 2775 Laurel Street, Vancouver, BC, V5Z 1 M9, Canada.
| | - Chris Carlsten
- Respiratory Medicine, Faculty of Medicine, Chan-Yeung Centre for Occupational and Environmental Respiratory Disease (COERD), University of British Columbia, Vancouver, British Columbia, Canada.,Diamond Health Care Centre 7252, 2775 Laurel Street, Vancouver, BC, V5Z 1 M9, Canada.,Institute for Heart and Lung Health, University of British Columbia, Vancouver, British Columbia, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
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40
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Masud N, Ellison A, Cable J. A neglected fish stressor: mechanical disturbance during transportation impacts susceptibility to disease in a globally important ornamental fish. DISEASES OF AQUATIC ORGANISMS 2019; 134:25-32. [PMID: 32132270 DOI: 10.3354/dao03362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The transport of fish in aquaculture and the ornamental trade exposes fish to multiple stressors that can cause mass mortalities and economic loss. Previous research on fish transport has largely focussed on chemical stress related to deterioration in water quality. However, mechanical disturbance during routine fish transport is unpredictable and is a neglected potential stressor when studying fish welfare. Stress-induced immunosuppression caused by mechanical disturbance can increase the chances of contracting infections and can significantly increase infection burden. Here, using a model host-parasite system (guppy Poecilia reticulata and the monogenean ectoparasite Gyrodactylus turnbulli) and a new method of bagging fish (Breathing Bags™), which reduces mechanical disturbance during fish transport, we investigated how parasite infections contracted after simulated transport impact infection trajectories on a globally important ornamental freshwater species. Guppies exposed to mechanical transport disturbance suffered significantly higher parasite burden compared to fish that did not experience transport disturbance. Unfortunately, there was no significant reduction in parasite burden of fish transported in the Breathing Bags™ compared to standard polythene carrier bags. Thus, transport-induced mechanical disturbance, hitherto neglected as a stressor, can be detrimental to disease resistance and highlights the need for specific management procedures to reduce the impact of infectious diseases following routine fish transport.
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Affiliation(s)
- N Masud
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
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