Evolutionary conservation and divergence of embryonic DNA methylome remodelling in fishes
Methylation of cytosines is the most abundant DNA modification in vertebrates that plays crucial roles in cellular differentiation and identity. Therefore, after fertilization, DNA methylation patterns inherited from parental gametes are remodelled into a state compatible with embryogenesis. In mammals, this is achieved through global erasure and re-establishment of DNA methylation patterns. However, in non-mammalian vertebrates like zebrafish, no global erasure has been observed. To investigate the evolutionary conservation of DNA methylation remodelling in anamniotes, we generated base resolution DNA methylome datasets of developing lamprey, medaka and zebrafish-medaka hybrid embryos. In contrast to previous reports, we show that medaka display comparable DNA methylome dynamics to zebrafish with high gametic DNA methylation levels (Sperm: ~90%; Egg: ~75%), and adoption of a paternal-like methylome during early embryogenesis. Similar DNA methylation reprogramming events were also observed during lamprey embryogenesis, however those occurred at a much larger scale (~30% of the genome) and involved transitions in partially methylated DNA (PMD) states. Lastly, we found remarkable evolutionary conservation of DNA methylation remodelling patterns in zebrafish-medaka hybrids, indicative of compatible DNA methylation maintenance machinery in divergent teleost species. Overall, these results suggest strong evolutionary conservation of DNA methylation remodelling pathways in vertebrates, which is distinct from the global DNA methylome erasure seen in mammals.