Extensive DNA methylome rearrangement during early lamprey embryogenesis

Abstract

DNA methylation (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, teleosts, for example, exhibit localized maternal-to-paternal 5mC remodeling. Here, we studied 5mC dynamics during the embryonic development of sea lamprey, a jawless vertebrate which occupies a critical phylogenetic position as the sister group of the jawed vertebrates. We employed 5mC quantification in lamprey embryos and 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. We further demonstrate that sequences eliminated during programmed genome rearrangement (PGR), 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.

The contribution of epigenetic variation to evolution in crows

“…Furthermore, as our primary interest is on DNA methylation divergence between taxa, integrating two metrics of taxonomic divergence (i.e., parental comparisons in two experiments and hybrid index in another) will identify sites verifiably corresponding to taxonomic divergence. While financial constraints may cause our study to miss small-effect DNA methylation loci due to sample size limitations, our sample size within each experiment matches those in other WGBS [72][73][74][75][76] and RRBS [77][78][79][80][81] studies. Our multiexperimentally validated approach offers a novel framework to assess both inter-experimental batch effects and repeatability in a conservative framework, and our preferred approach in contrast to an approach which maximizes DMP discovery at the cost of false positives.…”