Project Details
Projekt
Evolution of epigenetic regulation in beetles (Coleoptera)
Subject Area
Evolution, Anthropology
Bioinformatics and Theoretical Biology
Bioinformatics and Theoretical Biology
Term
since 2022
Project identifier
Deutsche Forschungsgemeinschaft (DFG) - Project number 503349225
Epigenetic processes affect the relationship between genotype and phenotype via regulation of gene expression. They are supposed to be key for evolutionary innovations. Insects show a remarkable evolutionary flexibility in epigenetic regulation. Our project makes use of the diversity across the Coleoptera to gain a deeper understanding of the evolution of epigenetic regulation systems. Beetles are particularly suited for studying potential mutual dependencies and alternative functions of DNA CpG methylation and histone modification, because some species show CpG methylation, while others have lost it. Accordingly, genes encoding DNA methyltransferases (Dnmt1 and Dnmt3) have been partially or completely lost in some beetle species. In Phase I of GEvol, we successfully established EM-seq and CUT&Tag as novel techniques for studying DNA methylation and histone modifications, respectively, and applied these techniques to nine beetle species. For example, the Colorado potato beetle lost Dnmt3, but in contrast to the red flour beetle retained relatively high levels of CpG methylation, with H3K36me3 mirroring the CpG methylation patterns. Our results urge caution when generalizing across species and suggest evolutionary fluidity of epigenetic regulatory systems. We studied Dnmt genes and genes that connect DNA methylation and histone modifications, both form a comparative-bioinformatics perspective and functionally using RNAi-mediated knock-down in several beetle species. In Phase II, we will fully leverage the expertise and data obtained in Phase I to continue and focus our comparative approach across beetle species, aiming at a deeper understanding of the evolution of epigenetic regulation systems. We will study connections and evolutionary transitions between the co-existing epigenetic regulation systems and now also include CpG methylation in different tissues to understand the maintenance of methylation in the absence of DNMT3. We will include further candidate genes for functional studies using RNAi of potential connectors between CpG methylation and histone modifications. Moreover, we will combine our obtained data with the targeted inclusion of further histone marks to study the regulation of expression of duplicated genes as a key process where epigenetic mechanisms are supposed to be crucial. Finally, together with other GEvol project, we aim at generating and testing hypotheses about evolutionary pressures that lead to transitions in epigenetic regulation, and its consequences.
DFG Programme
Priority Programmes
