Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a

Current evidence indicates that methylation of cytosine in mammalian DNA is restricted to both strands of the symmetrical sequence CpG, although there have been sporadic reports that sequences other than CpG may also be methy lated. We have used a dual-labeling nearest neighbor technique and bisulphi te genomic sequencing methods to investigate the nearest neighbors of 5-met hylcytosine residues in mammalian DNA. We find that embryonic stem cells, b ut not somatic tissues, have significant cytosine-5 methylation at CpA and, to a lesser extent, at CpT. As the expression of the de novo methyltransfe rase Dnmt3a correlates well with the presence of non-CpG methylation, we as ked whether Dnmt3a might be responsible for this modification. Analysis of genomic methylation in transgenic Drosophila expressing Dnmt3a reveals that Dnmt3a is predominantly a CpG methylase but also is able to induce methyla tion at CpA and at CpT.