DNA methylation and demethylation in mammals

Abstract

Cell type-specific DNA methylation patterns are established during mammalian development and maintained in adult somatic cells. Understanding how these patterns of 5-methylcytosine are established and maintained requires the elucidation of mechanisms for both DNA methylation and demethylation. The enzymes involved in the de novo methylation of DNA and the maintenance of the resulting methylation patterns have been fairly well characterized. However, important remaining challenges are to understand how DNA methylation systems function in vivo and in the context of chromatin. In addition, the enzymes and mechanisms for demethylation remain to be elucidated. There is still no consensus as to how active enzymatic demethylation is achieved in mammalian cells, but recent studies implicate base excision repair for genome-wide DNA demethylation in germ cells and early embryos.

Figures

FIGURE 1.

Overview of mechanisms involved in DNA methylation and demethylation in mammals. A, DNMTs catalyze the covalent addition of a methyl group to C-5 of cytosine. B, most of the cytosine methylation occurs within CpG dinucleotides, and a distinction can be made between two DNMT activities: de novo and maintenance methylation. Methylation patterns are established during early development by de novo methyltransferases DNMT3A and DNMT3B and maintained through somatic cell divisions by maintenance methyltransferase DNMT1, which acts preferentially on the hemimethylated CpG sites generated by DNA replication. DNA demethylation can be achieved either passively, by the failure of maintenance methylation after DNA replication, or actively, by replication-independent processes. The enzymes responsible for active demethylation have not been conclusively identified in mammals.

FIGURE 2.

Schematic structure of human DNMTs and DNMT3-like protein. Conserved methyltransferase motifs in the catalytic domain are indicated in Roman numerals. NLS, nuclear localization signal; RFT, replication foci-targeting domain; BAH, bromo-adjacent homology domain; PWWP, a domain containing a conserved proline-tryptophan-tryptophan-proline motif; PHD, a cysteine-rich region containing an atypical plant homeodomain; aa, amino acids. DNMT3L lacks the critical methyltransferase motifs and is catalytically inactive.

FIGURE 3.

Models for DNA demethylation mechanisms involving BER. In plants, the 5mC base can be directly removed by the DME/ROS1 family of 5mC DNA glycosylases, resulting in an abasic site that is repaired by the BER process. In mammals, no efficient 5mC glycosylases have been conclusively identified, and an alternative pathway initiated by deamination of 5mC has been proposed. Candidate deaminases include AID and APOBEC1, which convert 5mC to thymine. The resulting thymine could be repaired by BER initiated by a T-G mismatch glycosylase such as MBD4 or TDG. Recently, it has been shown that mouse and human TET family proteins can catalyze conversion of 5mC to 5hmC, a new modified base found in mammalian DNA. It is tempting to speculate that 5hmC could be repaired by a BER process, although, so far, no 5hmC DNA glycosylases have been identified.