DNA methylation on N6-adenine in mammalian embryonic stem cells

Abstract

It has been widely accepted that 5-methylcytosine is the only form of DNA methylation in mammalian genomes. Here we identify N6-methyladenine as another form of DNA modification in mouse embryonic stem cells. Alkbh1 encodes a demethylase for N6-methyladenine. An increase of N6-methyladenine levels in Alkbh1-deficient cells leads to transcriptional silencing. N6-methyladenine deposition is inversely correlated with the evolutionary age of LINE-1 transposons; its deposition is strongly enriched at young (<1.5 million years old) but not old (>6 million years old) L1 elements. The deposition of N6-methyladenine correlates with epigenetic silencing of such LINE-1 transposons, together with their neighbouring enhancers and genes, thereby resisting the gene activation signals during embryonic stem cell differentiation. As young full-length LINE-1 transposons are strongly enriched on the X chromosome, genes located on the X chromosome are also silenced. Thus, N6-methyladenine developed a new role in epigenetic silencing in mammalian evolution distinct from its role in gene activation in other organisms. Our results demonstrate that N6-methyladenine constitutes a crucial component of the epigenetic regulation repertoire in mammalian genomes.

Widespread adenine N6-methylation of active genes in fungi

“…1a). In Dikarya, we observed 6mA levels broadly similar to those previously reported in model eukaryotic genomes [1][2][3][4] , ranging from 0.048% (Leucosporidiella creatinivora; Pucciniomycotina) to 0.21% (Protomyces lactucaedebilis; Taphrinomycotina). In contrast, we found high levels of 6mA in some early-diverging fungi, where up to 2.8% (Hesseltinella vesiculosa; Mucoromycotina) of all adenines were methylated (Fig.…”

“…However, genomic 6mA has recently been demonstrated to play crucial roles in both gene and transposon regulation, where it either (i) suppresses expression of transposable elements in animals during development [2][3][4] or (ii) is associated with promoters of actively expressed genes and is involved in nucleosome positioning in algae 1 . These studies demonstrate that while 6mA is present in eukaryotes, it may serve distinct genomic functions across diverse phylogenetic groups.…”

“…Despite slight variations of MAC characteristics (Fig. 2c), all earlydiverging fungi displayed strong avoidance of 6mA deposition at one ApT-containing trinucleotide, TAT (and its reverse complement, ATA), ) maximum-likelihood phylogeny constructed including 285 single-copy genes from all lineages sequenced in this study and four references in which 6mA has been analyzed previously [1][2][3][4] . Node ages indicate date of divergence, from ref.…”

A new twist on epigenetics

“…Within the year, Xiao's group and another led by John Gurdon of the Gurdon Institute in Cambridge, UK, showed that 6 mA can be found at exceedingly low levels in a variety of vertebrate species including mouse and human 13,14 . When Xiao's group looked at the distribution of the mark in mouse embryonic stem cells, the team found the strongest peaks on the X chromosome.…”

“…Here, the mark seemed to be involved in silencing gene expression. The researchers also identified an enzyme that seems to be a 6 mA eraser 14 .…”