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Fish Nutrition Program and Epigenetic Regulation
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Fish Nutrition Program and Epigenetic Regulation

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 August 2025 | Viewed by 2420

Special Issue Editor

Dr. Linghong Miao

E-Mail Website
Guest Editor
1. Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
2. Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
Interests: feed nutrients; fish nutritional physiology; stress and welfare; molecular biology; epigenetic regulation

Special Issue Information

Dear Colleagues,

Fish nutrition programs play a crucial role in the growth, development, and overall health of fish populations in aquaculture. Epigenetic regulation, on the other hand, involves changes in gene expression that do not involve alterations to the DNA sequence itself but are instead influenced by environmental factors such as nutrition. A well-designed fish nutrition program ensures that fish receive all the essential nutrients required for optimal growth and health. Nutrients such as amino acids, fatty acids, vitamins, and minerals are vital for various physiological processes, including epigenetic regulation. For example, certain nutrients act as cofactors or substrates for enzymes involved in epigenetic modifications, such as DNA methylation and histone acetylation. These nutritional factors provided through fish diets can influence epigenetic mechanisms, affecting gene expression patterns and, consequently, fish phenotype. For instance, certain nutrients may modulate DNA methylation patterns or histone modifications, thereby altering the expression of genes related to growth, immunity, reproduction, and stress response in fish. Furthermore, epigenetic programming during early life stages is particularly sensitive to environmental cues, including nutrition. Early nutrition can have long-lasting effects on the epigenome of fish, influencing their growth trajectory, disease resistance, and reproductive performance later in life. Therefore, optimizing early life nutrition through tailored feeding programs can promote desirable epigenetic modifications and improve overall fish performance. Nutritional strategies aimed at enhancing immune function and stress tolerance can modulate epigenetic pathways involved in immune gene expression and stress response signaling. In summary, fish nutrition programs can exert profound effects on epigenetic regulation, shaping gene expression patterns and phenotypic traits in farmed fish.

The objective of this Topic is to present the most recent advancements in understanding the intricate interplay between fish nutrition and epigenetics. We welcome original research, reviews, and perspective articles describing in vivo, in vitro, and in silico studies. We look forward to receiving your contributions.

Please join us in creating a diverse collection of articles for a variety of topics. We look forward to receiving contributions.

Dr. Linghong Miao
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • nutrients
  • nutritional strategies
  • molecule regulation
  • growth
  • immunity
  • reproduction
  • stress response
  • epigenetic modifications

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Published Papers (2 papers)

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Research

17 pages, 9850 KiB  
Article
m6A Methylation Mediated Autophagy and Nucleotide-Binding Oligomerization Domain-like Receptors Signaling Pathway Provides New Insight into the Mitigation of Oxidative Damage by Mulberry Leaf Polysaccharides
by Wenqiang Jiang, Yan Lin, Linjie Qian, Siyue Lu, Zhengyan Gu, Xianping Ge and Linghong Miao
Int. J. Mol. Sci. 2025, 26(9), 4345; https://doi.org/10.3390/ijms26094345 - 2 May 2025
Viewed by 292
Abstract
m6A methylation modification is an important genetic modification involved in biological processes such as sexual maturation, antibacterial, and antiviral in aquatic animals. However, few studies have been conducted in aquatic animals on the relationship between m6A methylation modification and [...] Read more.
m6A methylation modification is an important genetic modification involved in biological processes such as sexual maturation, antibacterial, and antiviral in aquatic animals. However, few studies have been conducted in aquatic animals on the relationship between m6A methylation modification and autophagy-inflammation induced by lipid metabolism disorders. In the present study, a high-fat (HF) group and HF-MLP group (1 g mulberry leaf polysaccharides (MLPs)/1 kg HF diet) were set up. The mid-hind intestines of Megalobrama amblycephala juveniles from the two groups were collected for MeRIP-seq and RNA-seq after an 8-week feeding trial. The m6A peaks in the HF and HF-MLP groups were mainly enriched in the 3′ Untranslated Region (3′UTR), Stop codon, and coding sequence (CDS) region. Compared with the HF group, the m6A peaks in the HF-MLP group were shifted toward the 5′UTR region. ‘RRACH’ was the common m6A methylation motif in the HF and HF-MLP groups. Methyltransferase mettl14 and wtap expression in the intestines of the HF-MLP group were significantly higher compared with the HF group (p < 0.05). A total of 21 differentially expressed genes(DEGs) with different peaks were screened by the combined MeRIP-seq and RNA-seq analysis. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis enriched BCL2 interacting protein 3 (bnip3) to autophagy–animal and mitophagy–animal signaling pathways, etc., and nucleotide-binding domain leucine-rich repeat protein 1 (nlrp1) was enriched to the Nucleotide-binding oligomerization domain (NOD)-like receptor signaling pathway. Combined MeRIP-seq and RNA-seq analysis indicated that the expression pattern of bnip3 was hyper-up and that of nlrp1 was hyper-down. Gene Set Enrichment Analysis (GSEA) analysis confirmed that the intestinal genes of HF-MLP group positively regulate lysosomal and autophagy–animal signaling pathways. In the present study, we demonstrated that m6A methylation modification plays a role in regulating autophagy-inflammatory responses induced by HF diets by MLPs, and further explored the molecular mechanisms by which MLPs work from the epigenetic perspective. Full article
(This article belongs to the Special Issue Fish Nutrition Program and Epigenetic Regulation)
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15 pages, 1632 KiB  
Article
Transcriptomic and Epigenomic Responses to Cortisol-Mediated Stress in Rainbow Trout (Oncorhynchus mykiss) Skeletal Muscle
by Daniela Aravena-Canales, Valentina Valenzuela-Muñoz, Cristian Gallardo-Escarate, Alfredo Molina and Juan Antonio Valdés
Int. J. Mol. Sci. 2024, 25(14), 7586; https://doi.org/10.3390/ijms25147586 - 10 Jul 2024
Cited by 2 | Viewed by 1589
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Fish Nutrition Program and Epigenetic Regulation)
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