whole-genome bisulfite sequencing of zebrafish liver from control and leucine-stimulated zebrafish

Early nutritional programming affects a series of metabolism, growth and development in mammals. mTOR signaling pathway is the center of protein regulation, and it has been suggested that mTOR signaling pathway can be activated by branched chain amino acids (such as leucine) in mammals, but it is rarely reported in fish. DNA methylation is an epigenetic modification that plays a critical role in individual development, genetic imprinting, embryogenesis and diseased occurrence. However, little is known regarding activation mechanism of mTOR signaling pathway at the epigenetic level, such as via DNA methylation. In this research, zebrafish (Danio rerio) was used as experimental fish to study the effects of early leucine stimulation on TOR signaling pathway during larvae and adult stage, three days post hatching (dph) zebrafish larvaes were raised in 1.0% leucine from 3 to 13 dph during the critical developmental stages early in life and compared to a control group, then the larvaes in leucine treatment group were reared in normal water for 70 days from 13 to 83 dph. It showed that a growth performance was improved and the phosphorylation of S6k and S6 was significantly enhanced, significantly higher mRNA levels for whole fish (13 dph) and liver (83 dph) genes involved in protein synthesis and glycolipid metabolism were found in zebrafish in leucine treatment group. Furthermore, we also compared the DNA methylation profiles of liver tissues (83 dph) between control and leucine-stimulated zebrafish, we found that the genome-wide methylation levels of CHG and CHH methylation types in the leucine treatment group were significantly increased, four DMGs were found to be involved in mTOR signaling pathway, which were analyzed by quantitative PCR. These results described that the mechanism of regulating protein synthesis and glycolipid metabolism were mediated by mTOR signaling pathway. It provided a theoretical basis on mTOR signaling pathway induced by early nutrition programming in fish. In addition, this study also revealed the global DNA methylation pattern of zebrafish liver between normal and leucine-stimulated conditions. It will contribute to further understanding of the molecular mechanism behind mTOR signaling pathway mediated by amino acid.