Abstract
DNA methylation is a crucial, abundant mechanism of gene regulation in vertebrates. It is less prevalent in many other metazoan organisms and completely absent in some key model species, such as Drosophila melanogaster and Caenorhabditis elegans. We report here a comprehensive study of the presence and absence of DNA methyltransferases (DNMTs) in 138 Ecdysozoa, covering Arthropoda, Nematoda, Priapulida, Onychophora, and Tardigrada. Three of these phyla have not been investigated for the presence of DNA methylation before. We observe that the loss of individual DNMTs independently occurred multiple times across ecdysozoan phyla. We computationally predict the presence of DNA methylation based on CpG rates in coding sequences using an implementation of Gaussian Mixture Modeling, MethMod. Integrating both analysis we predict two previously unknown losses of DNA methylation in Ecdysozoa, one within Chelicerata (Mesostigmata) and one in Tardigrada. In the early-branching Ecdysozoa Priapulus caudatus, we predict the presence of a full set of DNMTs and the presence of DNA methylation. We are therefore showing a very diverse and independent evolution of DNA methylation in different ecdysozoan phyla spanning a phylogenetic range of more than 700 million years.
Highlights
DNA methylation is prominent in vertebrates, where it is considered a fundamental part of epigenetic programming (Lyko 2018)
We investigated the presence of DNA methyltransferases (DNMTs) in 138 species using a carefully designed homology search strategy aiming at minimizing false negatives
6 species are from Ecdysozoa groups outside of Nematoda or Arthropoda
Summary
DNA methylation is prominent in vertebrates, where it is considered a fundamental part of epigenetic programming (Lyko 2018). Several non-vertebrate model organisms, such as Drosophila melanogaster, Caenorhabditis elegans and Saccharomyces cerevisiae (Zemach et al 2010; Raddatz et al 2013) lack DNA methylation. It was discovered early-on, that some insects must have a DNA methylation mechanism. Several studies have investigated the heterogenous distribution of DNA methylation in insects (Field et al 2004; Bewick et al 2017; Provataris et al 2018) and other arthropods (de Mendoza et al 2019b; Gatzmann et al 2018). The highest levels are found in Romanomermis culicivorax and low amounts in Trichinella spiralis, Trichuris muris and Plectus
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