Common responses of fish embryos to metals: an integrated analysis of transcriptomes and methylomes in zebrafish embryos under the stress of copper ions or silver nanoparticles

Recently, the responses of embryos to Cu2+ or AgNP stresses have been investigated, but few studies have been performed on the common responses of embryos to both Cu2+ and AgNPs, the same kind of stressor metal. In this study, a large number of commonly down-regulated and up-regulated differentially expressed genes (DEGs) were revealed in both Cu2+- and AgNP-stressed embryos. The down-regulated DEGs were enriched in myosin complex and muscle structure development, ion transport and metal ion binding, transmission of nerve impulses, etc., and the up-regulated DEGs were enriched in heart development, iron ion binding, etc. Based on the whole-genome bisulfite sequencing (WGBS) in both Cu2+- and AgNP-stressed embryos, a total of 57 and 64 differentially methylated genes (DMGs) were identified in Cu2+ embryos and AgNP embryos, with 15 and 12 of them being common ion-relevant genes, respectively. The correlation of the gene transcriptional expression and the methylated status of some common DMGs were further verified. The integrated analysis of transcriptomes and methylomes in zebrafish embryos stressed with Cu2+ or AgNPs revealed for the first time their common transcriptional and methylomic responses to the same kind of stressor metals, and revealed that ion-relevant genes were mostly differentially expressed and methylated genes in both Cu2+- and AgNP-stressed embryos.