Evolution of epigenetic regulation in Coleoptera

Epigenetic modifications provide a genetic basis for one and the same insect species operating in different niches and thereby showing different morphology. DNA methylation and histone posttranslational modifications are representatives of epigenetic regulation systems, both with fundamental importance for embryonic and postembryonic development. Besides both being evolutionary old mechanisms, with their major components being highly conserved, large differences can be found in the methylation marks of vertebrates and invertebrates. Insects show remarkable evolutionary flexibility in epigenetic regulation. This is particularly demonstrable in beetles (Coleoptera), where some species show CpG methylation while others lost it and accordingly partly or even completely lost genes encoding DNA methyltransferases (DNMT1 and DNMT3). Histone modifications and DNA methylation to some extent interact in order to shape the chromatin landscape. Observing the independent loss of DNMTs and DNA methylation in Ecdysozoa raises questions about the role of DNA methylation in epigenetic regulation and its integration into the system. We want to understand how tightly the DNA methylation system was coupled to the histone modification system before the repetitive losses, and which conditions drive or allow those losses. With the combined power of bioinformatics, sequencing technologies such as Enzymatic-Methyl (EM)-Seq, Cut&Tag, and RNA-Seq, and functional validation we are addressing this question, thereby aiming to identify epigenetic factors potentially linking those systems in a multi-layered -omics approach. Furthermore, we want to understand the functional role of de novo and maintenance DNA methylation, using RNAi, thereby potentially elucidating alternative functions of DNA methyltransferases. Our project addressing the surprising evolutionary flexibility in epigenetic regulation will contribute the basic knowledge of the evolution of epigenetic regulation systems even more generally, beyond insects.