Nutriepigenomic effects of plant protein-based aquafeeds on zebrafish intestine

Epigenetic mechanisms, including histone modifications, DNA methylation, noncoding RNA and chromatin structure rearrangements, can produce heritable changes in gene expression without changing the underlying DNA sequence itself (Bird, 2007). Epigenetic changes can be modulated by environmental factors including nutrition and dietary changes (Guerrero-Bosagna and Skinner, 2014). Over the past decade, there has been a large increase in the use of plant-based proteins in aquafeeds. With this transition from “blue” marine to “green” vegetarian diets, fish could be exposed to phytochemicals/phytoestrogens that are known to induce epigenetic modifications in vertebrates. However, the effect of plant ingredients on the epigenome of fishes is barely understood. Therefore, this study had the aim to investigate nutriepigenomic effects of plant protein-based aquafeeds on fish intestine using zebrafish as a model. Diets containing 30% of typical plant proteins that are frequently used in salmon feeds in aquaculture, i.e. wheat, soy or pea, were evaluated in comparison with a control diet comprising only of marine proteins. Feeding trials were conducted for 6 weeks and the zebrafish were fed a daily ratio of 2.5% of their bodyweight. A genome-wide analysis of DNA methylation patterns was performed by reduced representation bisulfite sequencing (RRBS) to examine global epigenetic alterations in the mid intestine of the fish. For RRBS, DNA from 4 replicate samples per dietary group were digested with MspI followed by library preparation and bisulfite conversion, and subsequently sequenced on the NextSeq 500 (Illumina) at a 20x CpG coverage. Bisulfite-specific DNA mapping to the zebrafish genome and differential methylation calling were carried out using BAT. Changes in DNA methylation patterns correlated with diet were identified by large-scale integrated region-based enrichment analysis. The findings from this study indicated that plant ingredients could induce epigenetic modifications in the intestine of fish. Histological analysis also revealed some moderate diet-specific changes in the intestinal mucosa. This knowledge will be extended to a commercially important species for the aquaculture industry by testing selected methylated loci from the zebrafish model on on-growing Atlantic salmon fed with the same plant ingredients used in the present study. References Bird, A. (2007). "Perceptions of epigenetics." Nature 447(7143): 396-398. Guerrero-Bosagna, C. M. and M. K. Skinner (2014). "Environmental epigenetics and phytoestrogen/phytochemical exposures." J. Steroid Biochem. Mol. Biol. 139: 270-276. Acknowledgements: This work was supported by the Norwegian Research Council through a post-doctoral fellowship to A.K.S.D. and a research grant to C.K.F. (NFR 267944 and 254822, respectively).