Recent Results

Gamete to Embryo DNA Methylation Reprogramming in Zebrafish –

During early zebrafish development, the DNA methylation patterns of the two parental genomes are harmonized such that genes important for early development lack DNA methylation, while the rest of the genome (including genes involved in terminal differentiation “Late Development”) becomes highly methylated. Prior to our recent results, it was unknown how these “Early Development” genes underwent DNA methylation reprogramming. However, one thing was clear – the maternal genome was reprogrammed to become identical to the paternal genome, and the paternal genomic DNA methylation patterns were maintained. (Potok et al. Cell. 2013).


To explain how the Early Development genes became demethylation on the maternal genome, we hypothesized that a ‘Placeholder’ chromatin feature was inherited from sperm and established on the maternal genome to facilitate DNA demethylation by blocking DNA methyltransferases (DNMTs).


During my postdoctoral training in Dr. Brad Cairns laboratory, I tested this hypothesis, and was successful in identifying the ‘Placeholder’ nucleosome. Our publication (Murphy et al. Cell 2018) describes the many genomics studies that we used to identify ‘Placeholder’ candidates, and also details the gain- and loss- of function approaches we used to test ‘Placeholder’ nucleosome’s capacity for regulating DNA methylation reprogramming.



Here I summarize our main conclusions:

DNA methylation reprogramming during zebrafish cleavage phase relies on both establishment and antagonism of Placeholder nucleosomes to enable proper transcriptional activation. Placeholder is established at regions gradually undergoing maternal DNA demethylation, and antagonized at regions undergoing default acquisition of DNA methylation. This mechanism ensures that both housekeeping and many developmental genes acquire Placeholder, and lack DNA methylation. Concurrent with zygotic transcriptional activation, the histone mark H3K4me3 is acquired at activated housekeeping genes, and bivalent marks are established at ‘poised’ developmental genes. Developmental genes expressed much later in development lack Placeholder, and are DNA methylated.