Transgenerational actions of fish feed and the effect on epigenetic regulation of gene transcription

The availability of marine raw materials used for feed in the aquaculture industry is declining due to increased feed production. Today, up to 90% of the marine raw materials used in fish feed are replaced by plant-based ingredients. This may have negative consequences for growth and quality of the fish if the changes in nutrient composition is not corrected. Plant-based feeds include naturally lower levels of B-vitamins and certain amino acids, than the feeds based on marine ingredients. More specifically, vitamin B6, vitamin B12, folate and the amino acids methionine are required for fundamental biochemical processes involved in the utilization of the energy from the main nutrients and building substances for growth. In addition, methionine, vitamin B6, vitamin B12 and folate are key nutrients for methylation reactions (1-C). They are important for proper regulation of gene transcription through epigenetic regulation. A process central for epigenetic regulation of gene transcription is DNA methylation whereby methyl groups are donated to the cytosines on top of the DNA sequence. DNA methylation regulates the accessibility for gene transcription. Epigenetic regulation of DNA can be inherited from the mother and father to the next generation, and it has been shown to be sensitive to environmental factors like nutrition and stress. So far no studies have explored if fish feed affects the epigenetic regulation of DNA. The hypothesis in this project was that the level of 1-C nutrients in the diet influence gene expression patterns through DNA methylation. We have designed plant-based diets with either high or low levels of 1-C nutrients and fed zebrafish (a model organism) and Atlantic salmon (Cooperation with EU project ARRAINA). The results from the zebrafish experiment shows that the diet with a low content of 1-C nutrients affects growth, blood health, survival and fertility in the first generation. This fish was crossed to produce 2nd, 3rd and 4th generations. RNA sequencing showed that 307 genes were differentially expressed between the feeding groups for embryo F1 generation, while 239 genes were differentially expressed in liver dissected from mature F1 males. In addition, the amount of lipid in the liver of F1 fish significantly increased by B-vitamin deficiency given to the first generation (F0). Preliminary results from the DNA methylation studies shows that there are both areas in the DNA and single nucleotide having different methylation status between the feed groups in F1. That means that the feed given to F0 can affect the phenotype, gene expression patterns and DNA methylation in the F1 generation.

Abstract: The aquaculture industry has, during the last decade, replaced the feed ingredients from fish meal and fish oil with plant based alternatives. Negative effects on growth performance and flesh quality are observed, but how the fish feed compositi on affect the epigenetic regulation of gene transcription during the different life stages and across generations remains an important and unexplored field. Epigenetics encompasses changes in gene expression profiles without alterations in the genomic DNA sequence. These changes arise from the inherited epigenetic regulation of the gene, but are also sensitive to environmental factors like nutrition. This project will answer how feed enriched with methyl donors regulates gene expression patterns by DNA me thylation, directly and across generations in fish. Zebrafish will be used as a model prior to studies on Atlantic salmon. To date there are no studies on nutritional epigenetic regulation in fish, and through this project we establish advanced epigenetic procedures for transgenerationl fish studies.