Developing a DNA Methylation Profile For Early Zebrafish Embryos

 DNA methylation is an epigenetic marker that is thought to be involved in silencing gene expression.  Interestingly, it has been observed that the zebrafish embryo genome undergoes extensive demethylation and subsequent remethylation before zygotic transcription begins.  Moreover, this drastic change in the DNA methylation state is critical for the survival of the embryo.  However, it is unclear exactly which regions of DNA are targeted for methylation as the embryo approaches zygotic transcription.  It is hypothesized that transposable elements and genes for gametogenesis are among the potential methylation targets.  The targeting mechanism is not understood; however, small, noncoding RNAs are thought to play a role.  Regardless, a precise characterization of the methylation dynamics in early zebrafish embryos could provide valuable insight into the factors underlying embryonic development.

Here, bisulfite conversion is used in combination with Illumina sequencing to develop a methylation profile for the zebrafish embryo as it progresses through various stages of development.  Bisulfite treatment of unmethylated DNA converts cytosine nucleotides to uracil.  However, methylated cytosine residues are unaffected by this reaction.  Hence, a chronological methylation profile can be established by extracting DNA from embryos in various stages of development and comparing the high throughput sequencing results.  This experiment will provide valuable information regarding the targets of DNA methylation in the zebrafish embryo.