Evolutionary analysis indicates that DNA alkylation damage is a byproduct of cytosine DNA methyltransferase activity

Methylation at the 5 position of cytosine in DNA (5meC), is a key epigenetic mark in eukaryotes. Once introduced, 5meC can be maintained through DNA replication due to the activity of “maintenance” DNA methyltransferases.. Despite their ancient origin, DNA methylation pathways differ widely across metazoans, such that 5meC is either confined to transcribed genes or lost altogether in several lineages. Here we use comparative epigenomics to investigate the evolution of DNA methylation. Although the model nematode C. elegans has lost DNA methylation, more basal nematodes retain cytosine DNA methylation, targeted to repeat loci. Unexpectedly, we find that DNA methylation coevolves with the DNA alkylation repair enzyme ALKB2 across eukaryotes. We further show that DNA methyltransferases introduce the toxic lesion 3meC into DNA both in vitro and in vivo. Alkylation damage is thus intrinsically associated with DNA methyltransferase activity, and this may promote the loss of DNA methylation in many species.