Multiomics reveal associations between CpG methylation, histone modifications and transcription in a species that has lost DNMT3, the Colorado potato beetle

Abstract Insects display exceptional phenotypic plasticity, which can be mediated by epigenetic modifications, including CpG methylation and histone modifications. In vertebrates, both are interlinked and CpG methylation is associated with gene repression. However, little is known about these regulatory systems in invertebrates, where CpG methylation is mainly restricted to gene bodies of transcriptionally active genes. A widely conserved mechanism involves the co-transcriptional deposition of H3K36 trimethylation and the targeted methylation of unmethylated CpGs by the de novo DNA methyltransferase DNMT3. However, DNMT3 has been lost multiple times in invertebrate lineages raising the question of how the links between CpG methylation, histone modifications and gene expression are affected by its loss. Here, we report the epigenetic landscape of Leptinotarsa decemlineata, a beetle species that has lost DNMT3 but retained CpG methylation. We combine RNA-seq, enzymatic methyl-seq and CUT&Tag to study CpG methylation and patterns of H3K36me3 and H3K27ac histone modifications on a genome-wide scale. Despite the loss of DNMT3, H3K36me3 mirrors CpG methylation patterns. Together, they give rise to signature profiles for expressed and non-expressed genes. H3K27ac patterns, which show no association with CpG methylation, have a prominent peak at the transcription start site that is predictive of expressed genes. Our study provides new insights into the evolutionary flexibility of epigenetic modification systems that urge caution when generalizing across species. Research highlights Despite lacking DNMT3, EM-seq revealed CpG methylation in the Colorado potato beetle. CUT&Tag showed an association of H3K36me3 and H3K27ac with transcription, while only H3K36me3 aligns with CpG methylation, demonstrating epigenetic flexibility.