scholarly journals DNA Methylation Dynamics in Atlantic Salmon (Salmo salar) Challenged With High Temperature and Moderate Hypoxia

2021 ◽  
Vol 7 ◽  
Author(s):  
Anne Beemelmanns ◽  
Laia Ribas ◽  
Dafni Anastasiadi ◽  
Javier Moraleda-Prados ◽  
Fábio S. Zanuzzo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
High Temperature ◽  
Atlantic Salmon ◽  
Salmo Salar ◽  
Environmental Changes ◽  
Regulatory Elements ◽  
Cpg Methylation ◽  
Epigenetic Mechanism ◽  
Moderate Hypoxia ◽  
Hypoxia Exposure

The marine environment is predicted to become warmer and more hypoxic, and these conditions may become a challenge for marine fish species. Phenotypically plastic responses facilitating acclimatization to changing environments can be mediated by DNA methylation through the modulation of gene expression. To investigate whether temperature and hypoxia exposure induce DNA methylation changes, we challenged post-smolt Atlantic salmon (Salmo salar) to increasing temperatures (12 → 20°C, 1°C week–1) under normoxia or moderate hypoxia (∼70% air saturation) and compared responses in the liver after 3 days or 4 weeks at 20°C. DNA methylation was studied in six genes related to temperature stress (cirbp, serpinh1), oxidative stress (prdx6, ucp2), apoptosis (jund), and metabolism (pdk3). Here, we report that exposure to high temperature, alone or combined with hypoxia, affected the methylation of CpG sites within different genomic regulatory elements around the transcription start of these temperature/hypoxia biomarker genes. Yet, we uncovered distinct CpG methylation profiles for each treatment group, indicating that each environmental condition may induce different epigenetic signatures. These CpG methylation responses were strongly dependent on the duration of stress exposure, and we found reversible, but also persistent, CpG methylation changes after 4 weeks of exposure to 20°C. Further, several of these changes in CpG methylation correlated with transcriptional changes, and thus, can be considered as regulatory epigenetic marks (epimarkers). Our study provides insights into the dynamic associations between CpG methylation and transcript expression in Atlantic salmon, and suggests that this epigenetic mechanism may mediate physiological acclimation to short-term and long-term environmental changes.

scholarly journals Dietary Fish Oil Alters DNA Methylation of Genes Involved in Polyunsaturated Fatty Acid Biosynthesis in Muscle and Liver of Atlantic Salmon ( Salmo salar )

Lipids ◽  
2019 ◽  
Vol 54 (11-12) ◽  
pp. 725-739 ◽  
Author(s):  
Nicola A. Irvine ◽  
Bente Ruyter ◽  
Tone‐Kari Østbye ◽  
Anna K. Sonesson ◽  
Karen A. Lillycrop ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Fatty Acid ◽  
Atlantic Salmon ◽  
Fish Oil ◽  
Salmo Salar ◽  
Polyunsaturated Fatty Acid ◽  
Fatty Acid Biosynthesis ◽  
Acid Biosynthesis ◽  
Atlantic Salmon Salmo Salar ◽  
Dietary Fish

A temporal perspective on population structure and gene flow in Atlantic salmon (Salmo salar) in Newfoundland, Canada

2010 ◽  
Vol 67 (2) ◽  
pp. 225-242 ◽  
Author(s):  
Friso P. Palstra ◽  
Daniel E. Ruzzante
Keyword(s):  
Population Dynamics ◽  
Population Structure ◽  
Gene Flow ◽  
Atlantic Salmon ◽  
Salmo Salar ◽  
Environmental Changes ◽  
Population Connectivity ◽  
Temporal Perspective ◽  
Atlantic Salmon Salmo Salar ◽  
Contemporary Gene Flow

Studying population structure and gene flow patterns on temporal scales facilitates an evaluation of the consequences of demographic, physical, and environmental changes on the stability and persistence of populations. Here, we examine temporal genetic variation within and among Atlantic salmon ( Salmo salar ) rivers in Newfoundland and Labrador, Canada, using samples collected over a period of six decades (1951–2004). Our objective was to evaluate temporal changes in population connectivity associated with the closure of a commercial marine fishery. Despite demographic instability, we find that population structure remained temporally stable over more than 50 years. However, age structure can affect results when not taken into consideration, particularly in populations of large effective size where genetic drift is not strong. Where weak signals of genetic differentiation did not complicate analyses, contemporary migration was often asymmetric, yet low, suggesting patterns of intermittent gene flow. Nevertheless, we find some links between changes in population dynamics and contemporary gene flow. These findings may therefore imply that management decisions impacting the contemporary population dynamics of individual Atlantic salmon rivers can also affect the genetic stability of this species as a whole.

scholarly journals The impact of Piscirickettsia Salmonis infection on genome-wide DNA methylation profile in Atlantic Salmon

2021 ◽  
Author(s):  
Robert Mukiibi ◽  
Carolina Peñaloza ◽  
Alejandro Gutierrez ◽  
José M. Yáñez ◽  
Ross D. Houston ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Atlantic Salmon ◽  
Negative Correlation ◽  
Regulation Of Gene Expression ◽  
Head Kidney ◽  
Epigenetic Mechanism ◽  
Piscirickettsia Salmonis ◽  
The Impact

Salmon rickettsial septicaemia (SRS), caused by the intracellular bacteria Piscirickettsia Salmonis, generates significant mortalities to farmed Atlantic salmon, particularly in Chile. Due to its economic importance, a wealth of research has focussed on the biological mechanisms underlying pathogenicity of P. salmonis, the host response, and genetic variation in host resistance. DNA methylation is a fundamental epigenetic mechanism that influences almost every biological process via the regulation of gene expression and plays a key role in the response of an organism to stimuli. In the current study, the role of head kidney and liver DNA methylation in the response to P. salmonis infection was investigated in a commercial Atlantic salmon population. A total of 66 salmon were profiled using reduced representation bisulphite sequencing (RRBS), with head kidney and liver methylomes compared between infected animals (3 and 9 days post infection) and uninfected controls. These included groups of salmon with divergent (high or low) breeding values for resistance to P. salmonis infection, to examine the influence of genetic resistance. Head kidney and liver showed organ-specific global methylation patterns, but with similar distribution of methylation across gene features. Integration of methylation with RNA-Seq data revealed that methylation levels predominantly showed a negative correlation with gene expression, although positive correlations were also observed. Methylation within the first exon showed the strongest negative correlation with gene expression. A total of 911 and 813 differentially methylated CpG sites were identified between infected and control samples in the head kidney at 3 and 9 days respectively, whereas only 30 and 44 sites were differentially methylated in the liver. Differential methylation in the head kidney was associated with immunological processes such as actin cytoskeleton regulation, phagocytosis, endocytosis and pathogen associated pattern receptor signaling. We also identified 113 and 48 differentially methylated sites between resistant and susceptible fish in the head kidney and liver respectively. Our results contribute to the growing understanding of the role of methylation in regulation of gene expression and response to infectious diseases, and in particular reveal key immunological functions regulated by methylation in Atlantic salmon in response to P. salmonis.

Analysis of DNA Methylation and Transcription During Granulopoiesis Reveals Timed Methylation Changes in Low CpG Areas That Correlate with Changed Transcriptional Activity.

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 2334-2334
Author(s):  
Rönnerblad Michelle ◽  
Olofsson Tor ◽  
Iyadh Douagi ◽  
Sören Lehmann ◽  
Karl Ekwall ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Conflicts Of Interest ◽  
Cell Types ◽  
Cpg Methylation ◽  
Epigenetic Mechanism ◽  
450K Array ◽  
Chi Square ◽  
Heterochromatin Formation ◽  
Chi Square Test

Abstract Abstract 2334 Accumulating evidence demonstrates that epigenetic changes, including DNA methylation play a central role in differentiation, providing cellular memory and stabilizing lineage choice in hematopoiesis1–3. DNA methylation is an important epigenetic mechanism involved in transcriptional regulation, heterochromatin formation and the normal development of many organisms. In this study we investigated the DNA methylome and transcriptome of human cells in four separate differentiation stages in granulopoiesis, ranging from the multipotent Common Myeloid progenitor (CMP) to terminally differentiated bone marrow neutrophils (PMN). To this end we employed HumanMethylation 450 BeadChip (450K array) from Illumina with extensive genomic coverage and mRNA expression arrays (Illumina). Temporally distinct methylation changes during granulopoiesis Differential methylation between two cell stages was defined as an average difference in β value of at least 0.17 (p ≤ 0.05). We detected 12132 DMSs during granulopoiesis. Of these the majority showed decreased methylation during granulopoeisis (10771 CpGs) and a smaller set gained methylation (1658 CpGs). Strikingly, increases in methylation predominantly occur between CMP and GMP, the two least mature cell types. Some CpGs also show increased methylation in the GMP-PMC transition, while very few CpG sites increase at the final stage of differentiation from PMC to PMN. Although reduction of methylation occurs at all stages of granulopoiesis, the greatest change is between GMP and PMC. It is striking that the DNA methylation patterns preferentially change at points of lineage restriction, and that the greatest change occurs upon loss of oligopotency between GMP and PMC. DMSs within CGIs were greatly underrepresented (p<0.001 with chi-square test), while DMSs were overrepresented in shelves (p<0.001) and open sea (p<0.001). Thus, methylation appears to be more dynamic outside of CGIs during granulocytic development. For all regions the variation within enhancers was greater than outside of enhancers indicating greater methylation changes in enhancers compared to non-enhancers. In addition, CpGs in enhancer regions are significantly enriched in the list of DMSs (p<0.001, chi-square test) further supporting the observation that enhancer regions display dynamic DNA methylation changes during granulopoiesis. Changes in gene expression correlate with DNA methylation changes There was a significant overlap between genes showing decreased methylation and genes with increased expression as well as for the reverse comparison between genes with increased methylation and decreased expression. Thus, support a general anticorrelation between DNA methylation and gene expression. Azurophilic granule proteins showed increased expression peaking in PMC and a rapid decrease toward PMN. CpG methylation levels for those genes decreased concomitantly with the peak in expression. We report cell population specific changes of DNA methylation levels. The main reduction of CpG methylation coincides with the loss of oligopotency at the transition from GMP-PMC. This suggests a role of DNA methylation in regulating cell plasticity and lineage choice. Disclosures: No relevant conflicts of interest to declare.

scholarly journals A framework for understanding Atlantic salmon (Salmo salar) life history

1998 ◽  
Vol 55 (S1) ◽  
pp. 48-58 ◽  
Author(s):  
Elizabeth A Marschall ◽  
Thomas P Quinn ◽  
Derek A Roff ◽  
Jeffrey A Hutchings ◽  
Neil B Metcalfe ◽  
...  
Keyword(s):  
Life History ◽  
Atlantic Salmon ◽  
Salmo Salar ◽  
Life History Traits ◽  
Environmental Changes ◽  
Individual Life ◽  
Atlantic Salmon Salmo Salar ◽  
Large Size ◽  
The Family ◽  
Long Time

We took a hierarchical approach to understanding Atlantic salmon (Salmo salar) life history patterns by first comparing salmonids to other teleosts, next comparing Atlantic salmon to other salmonids, and finally, mapping correlations among individual life history traits within Atlantic salmon. The combination of anadromy, large eggs, nest construction and egg burial by females, and large size at maturity differentiates salmonids from most other teleosts. Within the family Salmonidae, there is considerable variation in all traits but Atlantic salmon are generally in the middle of the range. Within Atlantic salmon, we were able to map correlations among individual life history traits, but we found that we still lacked an understanding comprehensive and quantitative enough to allow us to predict how the entire life history should respond to environmental changes. Thus, we proposed several general courses of action: (i) use models to synthesize complex patterns and relationships, (ii) collect long time series of data in individual systems, and (iii) design experiments to assess phenotypic plasticity and how environmental influences differ from genetic effects and constraints.

scholarly journals Hypoxia during incubation does not affect aerobic performance or haematology of Atlantic salmon (Salmo salar) when re-exposed in later life

2019 ◽  
Vol 7 (1) ◽  
Author(s):  
Andrew T Wood ◽  
Sarah J Andrewartha ◽  
Nicholas G Elliott ◽  
Peter B Frappell ◽  
Timothy D Clark
Keyword(s):  
Atlantic Salmon ◽  
Metabolic Rate ◽  
Salmo Salar ◽  
Later Life ◽  
Hypoxia Tolerance ◽  
Aerobic Performance ◽  
Hypoxia Exposure ◽  
Short And Long Term ◽  
Fish Performance

Abstract Hypoxia in aquatic ecosystems is becoming increasingly prevalent, potentially reducing fish performance and survival by limiting the oxygen available for aerobic activities. Hypoxia is a challenge for conserving and managing fish populations and demands a better understanding of the short- and long-term impacts of hypoxic environments on fish performance. Fish acclimate to hypoxia via a variety of short- and long-term physiological modifications in an attempt to maintain aerobic performance. In particular, hypoxia exposure during early development may result in enduring cardio-respiratory modifications that affect future hypoxia acclimation capacity, yet this possibility remains poorly investigated. We incubated Atlantic salmon (Salmo salar) in normoxia (~100% dissolved oxygen [DO, as percent air saturation]), moderate hypoxia (~63% DO) or cyclical hypoxia (100–25% DO daily) from fertilization until 113 days post-fertilization prior to rearing all groups in normoxia for a further 8 months. At ~11 months of age, subsets of each group were acclimated to hypoxia (50% DO) for up to 44 days prior to haematology, aerobic metabolic rate and hypoxia tolerance measurements. Hypoxia exposure during incubation (fertilization to 113 days post-fertilization) did not affect the haematology, aerobic performance or hypoxia tolerance of juvenile salmon in later life. Juveniles acclimated to hypoxia increased maximum aerobic metabolic rate and aerobic scope by ~23 and ~52%, respectively, when measured at 50% DO but not at 100% DO. Hypoxia-incubated juveniles also increased haematocrit and haemoglobin concentration but did not affect acute hypoxia tolerance (critical oxygen level and DO at LOE). Thus, while Atlantic salmon possess a considerable capacity to physiologically acclimate to hypoxia by improving aerobic performance in low oxygen conditions, we found no evidence that this capacity is influenced by early-life hypoxia exposure.

The impacts of increasing temperature and moderate hypoxia on the production characteristics, cardiac morphology and haematology of Atlantic Salmon (Salmo salar)

Aquaculture ◽  
2020 ◽  
Vol 519 ◽  
pp. 734874 ◽  
Author(s):  
Anthony K. Gamperl ◽  
Olufemi O. Ajiboye ◽  
Fábio S. Zanuzzo ◽  
Rebeccah M. Sandrelli ◽  
Ellen de Fátima C. Peroni ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Salmo Salar ◽  
Moderate Hypoxia ◽  
Cardiac Morphology ◽  
Atlantic Salmon Salmo Salar ◽  
Increasing Temperature ◽  
Production Characteristics
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