N (6)-Hydroxymethyladenine: a hydroxylation derivative of N(6)-methyladenine in genomic DNA of mammals

In addition to DNA cytosine methylation (5-methyl-2′-deoxycytidine, m(5)dC), DNA adenine methylation (N(6)-methyl-2′-deoxyadenosine, m(6)dA) is another DNA modification that has been discovered in eukaryotes. Recent studies demonstrated that the content and distribution of m(6)dA in genomic DNA of vertebrates and mammals exhibit dynamic regulation, indicating m(6)dA may function as a potential epigenetic mark in DNA of eukaryotes besides m(5)dC. Whether m(6)dA undergoes the further oxidation in a similar way to m(5)dC remains elusive. Here, we reported the existence of a new DNA modification, N(6)-hydroxymethyl-2′-deoxyadenosine (hm(6)dA), in genomic DNA of mammalian cells and tissues. We found that hm(6)dA can be formed from the hydroxylation of m(6)dA by the Fe(2+)- and 2-oxoglutarate-dependent ALKBH1 protein in genomic DNA of mammals. In addition, the content of hm(6)dA exhibited significant increase in lung carcinoma tissues. The increased expression of ALKBH1 in lung carcinoma tissues may contribute to the increase of hm(6)dA in DNA. Taken together, our study reported the existence and formation of hm(6)dA in genomic DNA of mammals.