Environmental influences on DNA methylation in the European sea bass (Dicentrarchus labrax)

Abstract

The environmental information an organism receives during early development is integrated through epigenetic mechanisms, such as DNA methylation. The gene expression or the ability to respond to environmental factors experienced later in life may be altered by this process. We have focused our studies on two types of environmental factors that confer changes in DNA methylation: temperature and farming conditions. First, we studied temperature effects on DNA methylation of the aromatase promoter, the enzyme that converts androgens into estrogens and is essential for ovarian development, in 1-year old sea bass. We showed that males had higher DNA methylation levels than females and that high temperature led to increased DNA methylation levels in females, leading a portion of them to differentiate into males. Next, we applied eight different temperature treatments on sea bass larvae and used the Methylation Sensitive Amplified Polymorphism (MSAP) technique to detect global changes in DNA methylation. We found statistically significant differences in global DNA methylation between all groups of fish. Furthermore, moving to the singlenucleotide level employing using next generation sequencing technologies, specifically Reduced Representative Bisulfite Sequencing (RRBS), we examined the genome-wide DNA methylation in 3-year-old fish treated with natural or high temperature during the thermosensitive period. We used two tissues: muscle and testis, and we found ~12000 differentially methylated CpGs (DMCs) in muscle and ~3000 DMCs in testis, the majority of which were located in close proximity to genes and their regulatory elements. Concerning the effect of farming conditions on DNA methylation, we compared wild with farmed sea bass at the single-nucleotide level using RRBS. We detected DMCs in both testis and muscle, most of which could be functionally important, since they are localized near genes. Genes involved in reproduction, such as sox9, sox3 and lhr, contain DMCs, therefore their expression is probably differentially regulated. Here, we have investigated genome-wide DNA methylation alterations influenced by the environmental conditions, moving from a low resolution level informative for global differences to the single nucleotide resolution level for important genes. We suggest that the environment during early development results in long lasting changes on DNA methylation of genes, including genes related to reproduction