After discovering that DNA methylation plays a key role in silencing hundreds of viral insertions in the protist Amoebidium, we began to question whether this was a rare exception or a widespread but overlooked phenomenon across eukaryotes. To explore this, we sought to expand our observations to a broader range of lineages. The challenge, however, lies in identifying species that have retained functional 5mC machinery, as the loss of DNA methylation is surprisingly common across the eukaryotic tree.
We focused on three species from distinct eukaryotic supergroups: Acanthamoeba castellanii (Amoebozoa), Naegleria gruberi (Heterolobosea), and Cyanophora paradoxa (Glaucophyta). In all three, we found that 5mC acts as a repressive mark, primarily targeting transposable elements and transcriptionally silent genes. As we extended our analysis to additional lineages, we repeatedly observed that viral insertions tend to localise within methylated, transcriptionally repressed regions of the genome. This pattern supports a broader model in which epigenetic silencing contributes to the genomic containment of potentially harmful, horizontally acquired DNA. This has been published in MBE:
Focusing on Acanthamoeba, we collaborated with John Archibald’s group at Dalhousie University. By comparing two high-quality, chromosome-scale assemblies (Neff and C3 strains), we observed extensive macrosynteny between the genomes, yet found that strain-specific regions were consistently enriched for giant virus insertions. These insertions derived from nuclear-replicating viruses, so we hypothesize they are the kind most likely to integrate accidentally into the host genome. This work can be found in BMC Biology:
