Extensive DNA methylome rearrangement during early lamprey embryogenesis

DNA methylation (5-methylcytosine, 5mC) is a repressive gene regulatory mark widespread in vertebrate genomes, yet the developmental dynamics in which 5mC patterns are established vary across species. While mammals undergo two rounds of global 5mC erasure, the zebrafish genome exhibits localized maternal-to-paternal 5mC remodeling, in which the sperm epigenome is inherited in the early embryo. To date, it is unclear how evolutionarily conserved such 5mC remodeling strategies are, and what their biological function is. Here, we studied 5mC dynamics during the embryonic development of sea lamprey (Petromyzon marinus), a jawless vertebrate which occupies a critical phylogenetic position as the sister group of the jawed vertebrates. We employed base-resolution 5mC quantification in the lamprey germline, embryonic and somatic tissues, and discovered large-scale maternal-to-paternal epigenome remodeling that affects >30% of the embryonic genome and is predominantly associated with partially methylated domains (PMDs). We further demonstrate that sequences eliminated during programmed genome rearrangement (PGR), a hallmark of lamprey embryogenesis, are hypermethylated in sperm prior to the onset of PGR. Our study thus unveils important insights into the evolutionary origins of vertebrate 5mC reprogramming, and how this process might participate in diverse developmental strategies.