One-carbon metabolism nutrients impact the interplay between DNA methylation and gene expression in liver, enhancing protein synthesis in Atlantic Salmon

Abstract Supplementation of one-carbon (1C) metabolism micronutrients, which include B-vitamins and methionine, is essential for the healthy growth and development of Atlantic salmon ( Salmo salar ). However, the recent shift towards non-fish meal diets in salmon aquaculture has led to the need for reassessments of recommended micronutrient levels. Despite the importance of 1C metabolism in growth performance and various cellular regulations, the molecular mechanisms affected by these dietary alterations are less understood. To investigate the molecular effect of 1C nutrients, we analysed gene expression and DNA methylation using two types of omics data: RNA sequencing (RNA-seq) and reduced-representation bisulfite sequencing (RRBS). We collected liver samples at the end of a feeding trial that lasted 220 days through the smoltification stage, where fish were fed three different levels of four key 1C nutrients: methionine, vitamin B6, B9, and B12. Our results indicate that the dosage of 1C nutrients significantly impacts genetic and epigenetic regulations in the liver of Atlantic salmon, particularly in biological pathways related to protein synthesis. The interplay between DNA methylation and gene expression in these pathways may play an important role in the mechanisms underlying growth performance affected by 1C metabolism. Author Summary Atlantic salmon rely on one-carbon (1C) metabolism micronutrients like B-vitamins and methionine, which they acquire through their diets. Small pelagic fish are the primary source in the wild, but finding sustainable alternatives such as plants, insects, and algae is challenging as salmon aquaculture expands. Adjusting nutrient levels when changing base ingredients further complicates the task. Understanding the molecular mechanisms affected by these micronutrients is crucial for aquaculture sustainability. In this study, we investigated the molecular effects of 1C metabolism micronutrients on Atlantic salmon. Liver samples from salmon fed varying levels of key 1C nutrients over a 220-day trial were analysed using RNA sequencing (RNA-seq) and reduced-representation bisulfite sequencing (RRBS) to assess gene expression and DNA methylation, respectively. Our results revealed significant impacts of 1C nutrient dosage on genetic and epigenetic regulations in the salmon liver, particularly in protein synthesis pathways. The interplay between DNA methylation and gene expression in these pathways influences growth performance under 1C metabolism. Uncovering molecular changes resulting from dietary alterations provides valuable insights to optimize nutritional requirements in salmon aquaculture, supporting sustainable production and welfare of this important species.