Effects of salinity stress on methylation of the liver genome and complement gene in large yellow croaker (Larimichthys crocea)

Integrative whole-genome methylation and transcriptome analysis reveals epigenetic modulation of glucose metabolism by dietary berberine in blunt snout bream (Megalobrama amblycephala)

The present research was designed to explore the epigenetic mechanism by which dietary berberine (BBR) affects glucose metabolism in fish. Blunt snout bream (Megalobrama amblycephala) is susceptible to disturbances in glucose metabolism when subjected to prolonged high-carbohydrate diets. This study aimed to elucidate whether BBR can enhance glucose regulation in M. amblycephala via modulating DNA methylation levels. Fish (average weight of 20.36 ± 1.44 g) were administered a normal-carbohydrate diet (NC, 30 % carbohydrate), a high-carbohydrate diet (HC, 43 % carbohydrate), or a high-carbohydrate diet supplemented with 50 mg/kg berberine (HB) for 10 weeks. Subsequently, global DNA methylation level, whole-genome bisulfite sequencing (WGBS), RNA-seq, bisulfite sequencing PCR, and real-time quantitative PCR were employed to analyze the DNA methylation patterns and transcription results of the liver genome. The findings indicated that high carbohydrate diets induced glucose metabolism disorders in M. amblycephala, whereas BBR mitigated these metabolic disturbances by reducing methylation levels. WGBS results revealed that CG-type cytosine methylation predominated, and that DNA methylation mainly occurred in promoter, intron, and exon regions. Furthermore, analyses demonstrated a negative correlation between DNA methylation around the transcriptional start site and gene expression levels for 47 genes. Functional enrichment analysis revealed that these genes were associated with 60 KEGG pathways, including 12 genes implicated in the amelioration of insulin resistance, reduction of gluconeogenesis, and maintenance of glucose homeostasis. Consequently, we generated a comprehensive catalog of liver DNA methylation in M. amblycephala, which provides a foundational framework for future investigations into the epigenetic regulation of glucose metabolism by BBR.

Epigenetic regulation of physiological resilience to ammonia nitrogen stress in the Pacific whiteleg shrimp Penaeus vannamei: Evidence from genome-wide DNA methylation dynamics

Although DNA methylation has emerged as an essential epigenetic mechanism modulating organismal responses to abiotic stresses, its involvement in the physiological resilience of marine invertebrates like shrimp to ammonia nitrogen toxicity remains enigmatic. Here, we performed the first comprehensive dissection of genome-wide DNA methylation dynamics in the Pacific whiteleg shrimp Penaeus vannamei exposed to ammonia nitrogen, based on whole-genome bisulfite sequencing and transcriptome analyses. In the genome of P. vannamei, three DNA methyltransferases (DNMT1, DNMT2 and DNMT3a), one DNA demethylase (TET2) and four methyl-CpG binding proteins (MBD2, MBD4, Kaiso, and UHRF1) were present. About 1.68-1.87 % of cytosine nucleotides were methylated, and higher percentages of cytosines in the CpG context (5.23 %-6.34 %) was methylated compared with the CHG and CHH contexts. Methylated cytosines were mostly enriched in the coding DNA sequence, and methylation peaks occurred near the transcription end sites. Following ammonia exposure, 4203 differentially expressed genes (DEGs) and 1100 differentially methylated genes (DMGs) were identified. The DMGs accounted for 4.4 % of the total gene reservoir in P. vannamei genome, and 212 shared genes were found between the DEGs and DMGs. Genes exhibiting significant methylation and expression changes were enriched in various pathways including the FoxO signaling pathway, autophagy and endocytosis. Among them was a group of genes related to energy metabolism, antioxidation response and detoxification metabolism, highlighting involvement of DNA methylation in fine-tuning these crucial physiological processes. These findings provide new insights into the regulatory roles of DNA methylation in the physiological resilience of marine invertebrates to aquatic stressors.

Environmental influence on single methylation variation sites (SMVs) in the large yellow croaker (Larimichthys crocea): identification and correlation analysis

BACKGROUND

Larimichthys crocea is an important aquaculture species along the southeastern coast of China, with diverse environment and farming practices since artificial breeding, these different aquatic habitats are subject to significant variations in environmental factors that may involve modulation of gene expression through epigenetic mechanisms to enable species to survive and reproduce.

METHODS AND RESULTS

This study aimed to identify methylation variation sites (SMVs) in different sequence contexts (CG, CHG, and CHH) within populations of L. crocea in different habitats. All SMV sites were subjected to linear regression with environmental factors to identify candidate genes involved environmental stress. The results indicate a significant correlation between SMV sites and various environmental factors. For the wild populations in Jinmen and Zhanjiang, the primary environmental pressures for adapting are temperature and salinity. In contrast, for the domesticated populations in Zhoushan and farmed population in Xiangshan, the main environmental pressures are nitrate and dissolved oxygen. Furthermore, genes related to temperature adaptation in different aquatic environments were identified, including nr3c2, igf1, hsp70, trpm3, and fgf1. The gene rasa3 was found to be associated with pH adaptation, while genes such as atp6ap1lb, slc15a4, and gpr39 were linked to salinity, ammonia nitrogen, and dissolved oxygen. Research on the association between single methylation variation sites (SMVs) and environmental factors in aquatic organisms is scarce.

CONCLUSIONS

These results suggest that selection pressures can influence a significant proportion of methylation sites in this species, indirectly implying that epigenetic variation is not solely attributed to patterns of genetic variation, but is also closely linked to environmental differences. These results highlight the complex interactions between epigenetic regulation and environmental influences. Hence, this study provides preliminary evidence for a new perspective on the role of methylation patterns in L. crocea in environmental adaptation.

The survival, gene expression, and DNA methylation of Paralichthys olivaceus impacted by the decay of green tide and bacterial infection in both laboratory and field simulation experiments

The recurring appearance of Ulva prolifera green tides has become a pressing environmental issue, especially for marine transportation, tourism, and aquaculture in the stage of decomposition. An abundance of decaying U. prolifera leads to water acidification, hypoxia and pathogenic microorganism proliferation, threatening marine germplasm resources, particularly benthic organisms with weak escape ability. Epigenetic modification is considered to be one of the molecular mechanisms involved in the plastic adaptive response to environmental changes. However, few studies concerning the specific impact of decaying green tide on benthic animals at the epigenetic level. In this study, decomposing algal effluents of U. prolifera, sediments containing uncorrupted U. prolifera, pathogenic microorganism were considered as impact factors, to reveal the effect of decaying U. prolifera on marine economic benthic species, Paralichthys olivaceus, using both field and laboratory simulation experiments. Field simulation experiment showed higher mortality rates and serious histopathological damage than the laboratory simulation experiment. And both the decaying U. prolifera and the sediment containing U. prolifera were harmful to P. olivaceus. Genome-wide DNA methylation and transcription correlation analyses showed that the response of P. olivaceus to green tide stress and bacterial infection was mainly mediated by immune signaling pathways such as PI3K-Akt signaling pathway. DNA methylation regulates the expression of immune-related genes involved in the PI3K-Akt signaling pathway, which enables P. olivaceus to adapt to the adverse environmental stresses by resisting apoptosis. In summary, this research analyzed the potential role of P. olivaceus in decaying U. prolifera, which is of great significance for understanding the impact of decaying green tide on marine commercial fish and also provides some theoretical guidance for the proliferation and release of fish seedlings.

Immune and regulative characterization of complement-related gene cfhl5 in response to Vibrio harveyi challenge in Cynoglossus semilaevis

Complement factor H-related protein (CFHR) plays an important role in regulating complement activation and defensive responses. The function of CFHR2 (complement factor H related 2), a member of the CFHR family, in fish remains unclear. Here, we report the genetic relationship, expression characteristics and regulatory mechanism of cfhl5 (complement factor H like 5) gene, which encodes CFHR2 in Chinese tongue sole. We observed that the cfhl5 gene was widely expressed in several tissues, such as brain, heart and immune organs, and was most abundantly expressed in liver. After injection with Vibrio harveyi, the expression of cfhl5 was up-regulated significantly in liver, spleen and kidney at 12 or 24 hours post infection (hpi), suggesting an involvement of this gene in the acute immune response. Knockdown of cfhl5 in liver cells significantly up-regulated the expression of the pro-inflammatory cytokines tnf-α (tumor necrosis factor-alpha) and il1β (interleukin-1beta), the immunomodulatory factor il10 (interleukin-10) and the lectin complement pathway gene masp1 (MBL-associated serine protease 1), and down-regulated the expression of complement components c3 (complement 3) and cfi (complement factor I). In our previous work, we found that cfhl5 gene was significantly higher methylated and lower expressed in the resistant family compared with the susceptible family. Therefore, we used dual-luciferase reporter system to determine the effect of DNA methylation on this gene and found that DNA methylation could inhibit the promoter activity to reduce its expression. These results demonstrated that the expression of cfhl5 is regulated by DNA methylation, and this gene might play an important role in the immune response by regulating the expression of cytokines and complement components genes in Chinese tongue sole.

Environmental epigenetics: Exploring phenotypic plasticity and transgenerational adaptation in fish

Epigenetics plays a vital role in the interaction between living organisms and their environment by regulating biological functions and phenotypic plasticity. Considering that most aquaculture activities take place in open or natural habitats that are vulnerable to environmental changes. Promising findings from recent research conducted on various aquaculture species have provided preliminary evidence suggesting a link between epigenetic mechanisms and economically valuable characteristics. Environmental stressors, including climate changes (thermal stress, hypoxia, and water salinity), anthropogenic impacts such as (pesticides, crude oil pollution, nutritional impacts, and heavy metal) and abiotic factors (infectious diseases), can directly trigger epigenetic modifications in fish. While experiments have confirmed that many epigenetic alterations caused by environmental factors have plastic responses, some can be permanently integrated into the genome through genetic integration and promoting rapid transgenerational adaptation in fish. These environmental factors might cause irregular DNA methylation patterns in genes related to many biological events leading to organs dysfunction by inducing alterations in genes related to oxidative stress or apoptosis. Moreover, these environmental issues alter DNA/histone methylation leading to decreased reproductive competence. This review emphasizes the importance of understanding the effects of environmentally relevant issues on the epigenetic regulation of phenotypic variations in fish. The goal is to expand our knowledge of how epigenetics can either facilitate or hinder species' adaptation to these adverse conditions. Furthermore, this review outlines the areas that warrant further investigation in understanding epigenetic reactions to various environmental issues.

Dietary arginine regulates the growth performance, antioxidant capacity, and immune response in Culter alburnus

Culter alburnus is sensitive to stressors. Arginine is a precursor of nitric oxide, which can effectively relieve the level of oxidative stress and improve the antioxidant and immune capacity of fish. The effect of different arginine levels on topmouth culter (Culter alburnus) fry development performance, liver antioxidant capacity, and immune parameters were investigated in this study. Five diets (1.96%, ARG1, control group; 2.28%, ARG2; 2.52%, ARG3; 2.81%, ARG4; 3.09%, ARG5) were used to feed fry (initial weight 0.31 ± 0.01 g) for 8 weeks. The data showed that the final weight (FW), weight gain rate (WGR), and specific growth rate (SGR) of the ARG3 and ARG4 groups were significantly improved, while the feed conversion ratio (FCR) reduced significantly. Compared with the ARG1 group, all groups remarkably reduced the crude ash content of the whole body. The activity of hepatic superoxide dismutase (SOD) and the content of hepatic glutathione (GSH) were significantly increased in the ARG3 and ARG4 groups, while the malondialdehyde (MDA) content was significantly decreased. Compared with the ARG1 group, arginine levels in ARG2, ARG3, and ARG4 groups up-regulated the expression levels of Nrf2, down-regulated the gene expression level of Keap1 in the liver. And the expression of Nrf2/Keap1 pathway downstream genes Mn-SOD and CAT was up-regulated in ARG2 and ARG3 groups. Furthermore, the expression levels of MyD88 and IL-1β were down-regulated, and the anti-inflammatory gene TGF-β expression levels were up-regulated in the ARG2, ARG3, and ARG4 groups. Additionally, compared to the ARG1 group, there was a significant increase in the relative expression levels of the C3 and C4 genes in the ARG4 group. In conclusion, 2.28-2.81% dietary arginine levels improved the growth performance, promoted antioxidant capacity, and enhance immune response. The optimal level of arginine was determined by the quadratic regression analysis of SGR and FCR to be 2.55% of diet (5.43% of dietary protein) and 2.53% of diet (5.38% of dietary protein), accordingly.

Genome-wide identification, evolution of DNA methyltransferases and their expression under salinity stress in Larimichthys crocea

DNA methyltransferases (Dnmts) are responsible for DNA methylation which influences patterns of gene expression and plays a crucial role in response to environmental changes. In this study, 7 LcDnmt genes were identified in the genome of large yellow croaker (Larimichthys crocea). The comprehensive analysis was conducted on gene structure, protein and location site of LcDnmts. LcDnmt proteins belonged to three groups (Dnmt1, Dnmt2, and Dnmt3) according to their conserved domains and phylogenetic analysis. Although Dnmt3 can be further divided into three sub groups (Dnmt3a, Dnmt3b, and Dnmt3l), there is no Dnmnt3l member in the large yellow croaker. Phylogenetic analysis revealed that the Dnmt family was highly conserved in teleosts. Expression patterns derived from the RNA-seq, qRT-PCR and Western blot analysis revealed that 2 LcDnmt genes (LcDnmt1 and LcDnmt3a2) significantly regulated under salinity stress in the liver, which was found to be dominantly expressed in the intestine and brain, respectively. These two genes may play an important role in the salinity stress of large yellow croaker and represent candidates for future functional analysis. Our results revealed the conservation of Dnmts during evolution and indicated a potential role of Dnmts in epigenetic regulation of response to salinity stress.

Identification of key overlapping DEGs and molecular pathways under multiple stressors in the liver of Nile tilapia (Oreochromis niloticus)

The identification of key genes and molecular pathways that are involved in the response to stressors is crucial for controlling stress in fish and sustainable aquaculture. Environmental stressors can induce stress responses in aquatic animals, resulting in compromised immune function, inhibited growth, and increased mortality rates. mRNA-seq analysis provides a powerful tool to identify key genes and pathways associated with stress response. In the present study, mRNA-seq analysis was employed to identify key overlapping differentially expressed genes (DEGs) and molecular pathways under salinity, nitrite, copper, and pH stress in the liver of Nile tilapia (Oreochromis niloticus). The pathways associated with the immune response, oxygen transport, homeostasis, and oxidative stress were enriched across all stressors. The top KEGG pathways were complement and coagulation cascades, PPAR signaling pathway, and cardiac muscle contraction. The top GO enrichment terms were oxidoreductase activity, aerobic respiration, endopeptidase inhibitor activity, endopeptidase regulator activity, heme binding, and iron ion binding. The complement genes (C3, C4, C5, factor B, and factor H), alpha-2-macroglobulin (A2M), hemoglobin subunit epsilon (HBE), hemoglobin subunit alpha (HBA), coagulation factor genes (XI and X) and the cytochrome c oxidase (COX) gene family (cox1, cox2, cox3, cytochrome P450) were identified as key shared genes across multiple stressors. The discovery of these genes and molecular pathways provided a better understanding of the molecular mechanism underlying the stress response in Nile tilapia. The results of the present study can facilitate the development of stress management strategies in Nile tilapia.

Genome-wide DNA methylation mediates the resistance to vibriosis in Cynoglossus semilaevis

Chinese tongue sole (Cynoglossus semilaevis) is an economically important marine fish in China. However, vibriosis has caused huge mortality and economic losses in its culturing industry. To reveal the effect of DNA methylation on the resistance to vibriosis in tongue sole, we conducted RNA sequencing and whole genome bisulfite sequencing (WGBS), and compared the gene expressions and DNA methylation patterns between the resistant and susceptible families. We identified a total of 741 significantly differentially expressed genes (DEGs) in kidney and 17460 differentially methylated genes (DMGs), which were both enriched in immune-related pathways, such as "cAMP signaling pathway" and "NOD-like receptor signaling pathway". Through the correlation analysis of DEGs and DMGs, we identified two important immune pathways, including "complement and coagulation cascades", and "cytokine-cytokine receptor interaction", which played important roles in regulating the inflammation level and immune homeostasis. For example, the expression of proinflammatory cytokine il17c was down-regulated under the regulation of DNA methylation; in addition, the expression of protease-activated receptor 3 (par3) was up-regulated, which could induce the up-expressionof il8. These results demonstrated that the regulation of DNA methylation on the genes involved in immune responses might contribute to the resistance to vibriosis in tongue sole, and provided a basis for the control of diseases in fish aquaculture.

The role of salinity on genome-wide DNA methylation dynamics in European sea bass gills

Epigenetic modifications, like DNA methylation, generate phenotypic diversity in fish and ultimately lead to adaptive evolutionary processes. Euryhaline marine species that migrate between salinity-contrasted habitats have received little attention regarding the role of salinity on whole-genome DNA methylation. Investigation of salinity-induced DNA methylation in fish will help to better understand the potential role of this process in salinity acclimation. Using whole-genome bisulfite sequencing, we compared DNA methylation patterns in European sea bass (Dicentrarchus labrax) juveniles in seawater and after freshwater transfer. We targeted the gill as a crucial organ involved in plastic responses to environmental changes. To investigate the function of DNA methylation in gills, we performed RNAseq and assessed DNA methylome-transcriptome correlations. We showed a negative correlation between gene expression levels and DNA methylation levels in promoters, first introns and first exons. A significant effect of salinity on DNA methylation dynamics with an overall DNA hypomethylation in freshwater-transferred fish compared to seawater controls was demonstrated. This suggests a role of DNA methylation changes in salinity acclimation. Genes involved in key functions as metabolism, ion transport and transepithelial permeability (junctional complexes) were differentially methylated and expressed between salinity conditions. Expression of genes involved in mitochondrial metabolism (tricarboxylic acid cycle) was increased, whereas the expression of DNA methyltransferases 3a was repressed. This study reveals novel links between DNA methylation, mainly in promoters and first exons/introns, and gene expression patterns following salinity change.