In mammals, early embryogenesis is characterized by two waves of global DNA methylation reprogramming. The first wave encompasses the erasure of DNA methylation inherited from highly differentiated gametes after fertilization while the second wave takes place in primordial germ cells (PGCs) shortly after implantation. Genome-wide DNA demethylation might play a role in the acquisition of totipotency, is necessary for the erasure of genomic imprinting and X chromosome reactivation in PGCs, and likely imposes a barrier for the inheritance of epimutations. Anamniote vertebrates (such as fish or frogs) lack the post-fertilization wave of global DNA methylation reprogramming.
However, it still remains elusive whether the acquisition of PGC fate in anamniotes requires extensive DNA demethylation similar to mammals. Here we performed base-resolution DNA methylome and transcriptome profiling of PGCs during the first 36 hours of zebrafish embryogenesis. Notably, this developmental window coincides with the period when germline reprogramming is observed in mammals. We revealed that zebrafish embryos do not undergo genome-wide DNA demethylation in early PGCs, largely retaining embryonic DNA methylation pattern, which, in turn, is inherited from sperm. Furthermore, we identified DNA methylation changes located in the vicinity of cell adhesion, polarity and migration-regulating genes, which could participate in governing PGCs to the prospective gonad. Germline-specific genes, although being exclusively expressed in PGCs, do not harbour any PGC-specific DNA methylation differences. Besides known PGC markers, we identified an additional group of putative germline regulators in zebrafish, which exhibited evolutionary conservation of their expression patterns in both mice and humans.
Overall, our data provide strong evidence for the retention of paternal epigenetic memory in zebrafish PGCs thereby implying that anamniotes and mammals employ distinct strategies in terms of germline epigenome remodelling. Moreover, the observed lack of methylome remodelling in zebrafish makes it a potentially useful model organism for transgenerational epigenetic inheritance studies.