Active DNA demethylation: many roads lead to Rome

Abstract

In mammals and plants, DNA methylation refers to the addition of a methyl group to the fifth carbon of base C. Active DNA demethylation involves the enzymatic replacement of 5-methylcytosine (5meC) with C. Global DNA demethylation has only been seen during early development in the zygotic paternal pronuclei and in primordial germ cells. However, imprinted genes are protected from demethylation in the zygote. Loci-specific active DNA demethylation has been seen in somatic cells such as post-mitotic neurons and is important for the expression of neurogenesis genes. Recent studies have also indicated that nuclear hormone target promoters experience periodic methylation and demethylation that correlates with nuclear receptor binding and target gene expression. In plants, biochemical and genetic evidence support the notion that DNA demethylation is achieved through base excision repair (BER) initiated by the Demeter (Dme) family of 5meC glycosylases. It is unlikely that mammals use a similar mechanism as the mammalian glycosylases T DNA glycosylase (TDG) and methyl-CpG-binding domain protein 4 (MBD4) possess weak excision activity against 5meC compared to T. In contrast to the direct excision of 5meC, meC may first be deaminated to generate T and the resulting mismatch can initiate BER. Studies in zebrafish embryos have supported such a cooperative model, whereby deamination of 5meC can be carried out by activation-induced deaminase (AID), and T•G mismatch is repaired by MBD4. The ten-eleven translocation (TET) family of proteins can hydroxylate 5meC to generate 5-hydroxymethylcytosine (5hmC), a modification that is present in embryonic stem (ES) cells and Purkinje neurons. The functional consequences and fate of 5hmC are unclear. However, TET1 plays a crucial role in ES cell identity as knockdown of TET1 results in defects in ES cell self-renewal and maintenance. Recent studies have established a role for the elongator complex in zygotic paternal pronuclei demethylation as knockdown of the elongator components elongator complex protein 1 (ELP1), ELP3 and ELP4 impairs paternal genome demethylation. Although direct biochemical evidence is currently lacking, the radical SAM domain of ELP3 seems to be involved in the demethylation process. Because promoter methylation of tumour suppressor genes has been implicated in cancer, understanding the mechanisms of DNA demethylation will facilitate the development of novel therapies. In addition, identification of the DNA demethylases also has implications in somatic cell reprogramming as promoter demethylation of pluripotent genes is crucial for this process.