Location: Genomics and Bioinformatics ResearchTitle: Global and gene specific DNA methylation changes during zebrafish development) Author
Submitted to: Comparative Biochemistry and Physiology
Publication Type: Peer reviewed journal
Publication Acceptance Date: 7/17/2013
Publication Date: 5/9/2013
Publication URL: http://handle.nal.usda.gov/10113/61098
Citation: Fang, X., Corrales, J., Thornton, C., Scheffler, B.E., Willett, K.L. 2013. Global and gene specific DNA methylation changes during zebrafish development. Comparative Biochemistry and Physiology. Part B. 166:99-108. DOI.org/10.1016/j.cbpb.2013.07.007. Interpretive Summary: DNA methylation is an important contributor to gene expression levels in many organisms and different environmental conditions, developmental stages and even genetic background can influence the degree and location of the site where the DNA is methylated. DNA methylation is a process where DNA is modified by the addition or subtraction of a methyl group and typically at locations where there are the two base pairs CG. Often there is a high inverse correlation of between the degree of DNA methylation in the promoter and gene expression. If a promoter is highly methylated then gene expression is often repressed. This correlation does not always exist when the methylation occurs in the gene body. In this research, zebrafish was used a model fish species, because its genome has been sequenced, to study DNA methylation in fish. Methylation and gene expression patterns were studied for five genes. CG sites in the promoter and/or gene body were examined for methylation at early embryonic stages and adult livers. The results show that DNA methylation patterns were gene specific for the five genes. The results also show that at late embryogenesis that there is an overall significant decrease in the percentage of methylation. Overall the results show an unexpected additional wave of methylation (demethylation) during embryogenesis for one of the genes and that methylation, and thus epigenetic modification, appear to play a role during zebrafish embryogenesis which need to be considered in future studies on fish development.
Technical Abstract: DNA methylation is dynamic through the life of an organism. In this study, we measured the global and gene specific DNA methylation changes in zebrafish at different developmental stages. We found that the methylation percentage of cytosines was 11.75 ± 0.96% in 3.3 hour post fertilization (hpf) zebrafish embryos. The methylation level decreased significantly to 5.20 ± 0.13% in 96 hpf zebrafish larvae and then increased significantly to 9.09 ± 1.55% in female adult livers. This indicates a wave of DNA demethylation is occurring during late embryogenesis or early larval development in zebrafish. The decreased expression of DNMT1 and increased expression of GNMT in the later stage of embryogenesis (96 hpf) may be the related to the relative hypomethylation at this stage. However, the global demethylation at this time-point was only reflected in one of the five genes CpG region investigated (c-Myca). The timing of formation of the DNA methylation patterns was gene specific. The de novo methylation of Ras-association domain family member 1 (RASSF1), telomerase reverse transcriptase (TERT), c-Jun and c-Myca occurred rapidly during early embryogenesis. However, in the vasa promoter, the methylation pattern was established at later stages of development. Therefore, as the role of epigenetic modification is studied throughout development, it will be important to consider changes at a gene specific and CpG island specific basis. Further studies are needed to investigate which DNA regions in zebrafish larvae are responsible for the overall apparent demethylation and their related biological significance.