Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods

Abstract

Cytosine methylation is an ancient epigenetic modification yet its function and extent within genomes is highly variable across eukaryotes. In mammals, methylation controls transposable elements and regulates the promoters of genes. In insects, DNA methylation is generally restricted to a small subset of transcribed genes, with both intergenic regions and transposable elements (TEs) depleted of methylation. The evolutionary origin and the function of these methylation patterns are poorly understood. Here we characterise the evolution of DNA methylation across the arthropod phylum. While the common ancestor of the arthropods had low levels of TE methylation and did not methylate promoters, both of these functions have evolved independently in centipedes and mealybugs. In contrast, methylation of the exons of a subset of transcribed genes is ancestral and widely conserved across the phylum, but has been lost in specific lineages. Remarkably the same set of genes are likely to be methylated in all species that retained exon-enriched methylation. We show that these genes have characteristic patterns of expression correlating to broad transcription initiation sites and well-positioned nucleosomes, providing new insights into potential mechanisms driving methylation patterns over hundreds of millions of years.Author SummaryAnimals develop from a single cell to form a complex organism with many specialised cells. Almost all of the fantastic variety of cells must have the same sequence of DNA, and yet they have distinct identities that are preserved even when they divide. This remarkable process is achieved by turning different sets of genes on or off in different types of cell using molecular mechanisms known as “epigenetic gene regulation”.Surprisingly, though all animals need epigenetic gene regulation, there is a huge diversity in the mechanisms that they use. Characterising and explaining this diversity is crucial in understanding the functions of epigenetic pathways, many of which have key roles in human disease. We studied how one particular type of epigenetic regulation, known as DNA methylation, has evolved within arthropods. Arthropods are an extraordinarily diverse group of animals ranging from horseshoe crabs to fruit flies. We discovered that the levels of DNA methylation and where it is found within the genome changes rapidly throughout arthropod evolution. Nevertheless, there are some features of DNA methylation that seem to be the same across most arthropods-in particular we found that there is a tendency for a similar set of genes to acquire methylation of DNA in most arthropods, and that this is conserved over 350 million years. We discovered that these genes have distinct features that might explain how methylation gets targeted. Our work provides important new insights into the evolution of DNA methylation and gives some new hints to its essential functions.

DNA methylation in cockroaches is essential in early embryo development and reduces gene expression noise

“…vitripennis (Wang et al 2013). Moreover, CG methylation in B. germanica tends to concentrate towards the 3' region of the gene, in line with general DNA methylation trends in insects (Bewick et al 2017;Lewis et al 2020). In holometabolan species, DNA methylation appears to be biased towards the exons close to the 5' region of the gene (Bonasio et al 2012;Hunt et al 2013;Wang et al 2013;Glastad et al 2016), while in hemimetabolans it presents higher levels towards the 3' region of the gene coding part (Glastad et al 2016;Bewick et al 2019).…”

“…In general, our findings in embryos are similar to those observed by Bewick et al (2019) in B. germanica adults, using whole-genome bisulfite sequencing data. These authors found similar general levels of CG methylation, with the highest being observed in intragenic regions rather than intergenic regions, and which tended to concentrate towards the 3' UTR (Bewick et al 2019;Lewis et al 2020).…”

Adaptive evolution in DNMT2 supports its role in the dipteran immune response

“…Where it has been studied, for example in Drosophila melanogaster, loss of function of DNMT2 is not associated with any severe developmental issues or lethality (Goll, et al 2006). Additionally, DNMT2-only insects like fruit flies and other holometabolous insects exhibit very low to no CpG methylation across their genome, in line with DNMT2's lack of DNA MTase activity (Lewis, et al 2020). Recent studies suggest that DNMT2 is a part of the cellular stress response that also acts against external stressors like pathogen challenges.…”

“…Consistent with DNMT2's role as a bona fide RNA MTase, evidence of genome-wide CpG methylation is nearly absent in these insects, leaving the biological role of this MTase unclear (Takayama, et al 2014;Lewis, et al 2020). Past studies investigating the biological function of DNMT2 suggest that it functions as a predominantly cytoplasmic protein during cellular stress, which can lead to increased longevity and greater host survival under stress conditions (Lin, et al 2005;.…”

“…Homologs of DNMT2 are present in the vast majority of animal, fungal and plant species. Notably, DNMT2 is the only known DNMT present in dipteran insects like Drosophila melanogaster, Aedes aegypti, Aedes albopictus, Culex quinquefasciatus and Anopheles gambiae (Lewis, et al 2020). By extension, it is conceivable that all members of Drosophila and Culicidae families are DNMT2-only organisms.…”