DNA Methylation on N6-Adenine in C. elegans

Abstract

Summary In mammalian cells, DNA methylation on the 5th position of cytosine (5mC) plays an important role as an epigenetic mark. However, DNA methylation was considered to be absent in C. elegans because of the lack of detectable 5mC as well as homologs of the cytosine DNA methyltransferases. Here, using multiple approaches, we demonstrate the presence of adenine N6-methylation (6mA) in C. elegans DNA. We further demonstrate that this modification increases trans-generationally in a paradigm of epigenetic inheritance. Importantly, we identify a DNA demethylase, NMAD-1, and a potential DNA methyltransferase, DAMT-1, which regulate 6mA levels and crosstalk between methylation of histone H3K4me2 and 6mA, and control the epigenetic inheritance of phenotypes associated with the loss of the H3K4me2 demethylase spr-5. Together, these data identify a DNA modification in C. elegans and raise the exciting possibility that 6mA may be a carrier of heritable epigenetic information in eukaryotes.

Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification

“…3); hence, it might functionally back up the absent METTL3/METTL14 dyad and operate on ssRNA. This is also consistent with the single‐strand biased motifs identified for C. elegans damt‐1 53. Therefore, at least in some organisms, the METTL4 representative could be predominantly an RNA MTase.…”

“…Because a large fraction of genes are actively transcribed during germ‐line development, these marks might need to be reset to restore the ground state during meiosis and zygote development. Consistent with this, buildup of m 6 A and H3K4me2 levels is correlated with infertility that emerges after several generations 53. The asymmetric DNA motifs of m 6 A in C. elegans are reminiscent of mRNA motifs of methylation catalyzed by enzymes of the related METTL3/METTL14 clades 126.…”

“…Knockdown of the H3K9me binding protein eap‐1 121, which reduces H3K4me2 levels in spr‐5 mutant worms, also reduced levels of m 6 A in spr‐5 mutant worms. This indicates a tight link between H3K4me2 and m 6 A marks in C. elegans 53. Given that across eukaryotes H3K4me2 is acquired during active transcription 125, here too m 6 A might show a link to active transcription.…”

“…Surprisingly, m 6 A was also identified in C. elegans in which no type of DNA methylation had previously been observed 53. In wild‐type worms, m 6 A levels are variable (0.01–0.4% of adenines) but consistently elevated in certain mutant backgrounds (see below).…”

“…3). Recent work in the nematode Caenorhabditis elegans suggests that it is likely to be a DNA MTase 53. The remaining eukaryotic subclades of the Ime4‐like/MT‐A70 clade show even more sporadic phyletic patterns, distantly related microbial eukaryotes being united close together in the phylogenetic tree (Fig.…”