The genetic background and temperature together influence the DNA methylation of genes related to sexual development in the European sea bass

Abstract

The temperature influences on sex determination are mediated by alterations on DNA methylation patterns that correlate with expression changes and ultimately the sexual phenotype. In the European sea bass, a fish with a polygenic sex determination system with temperature influences, these alterations occur in the promoter of gonadal aromatase (cyp19a1a). However, it remains unknown whether changes in DNA methylation occur in other genes related to sexual development, as well as the contribution of the genetic component of the system to the epigenetic response to temperature and to the sex-specific patterns. Here, we produced full-sib families by crossing 4 sires with 1 dam, which were reared at low or high temperature during the thermosensitive period (TSP). The methylation levels in the regulatory regions of 7 genes related to sexual development were measured in two hundred fish from the offspring using a custom-designed targeted bisulfite sequencing approach. There were male-bias in the sex ratios of the offspring according to sire and early developmental temperature. The DNA methylation levels of cyp19a1a were higher in males and in fish reared at high temperature, while in dmrt1 the opposite pattern was evident; both genes showing also sire-specific responses. We showed that there is a critical methylation threshold only below which an inverse correlation of DNA methylation with gene expression is present. Furthermore, we present indication of father-to-daughter transmission of the methylation state in the CpGs of several genes, the methylation levels of which were stable between sires and their offspring reared at low temperature. Importantly, we identified genes most responsive to temperature and used this panel of CpGs for Principal Component Analysis (PCA). By this process, we were able to predict sex for the first time with high success. These results reveal a complex epigenetic layer, influenced at the same time by the genetic background and the early developmental environment, which contributes to the sexual phenotypic outcome