DNA demethylation

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Abstract
Cytosine 5′ methylation of CpG dinucleotides within and around genes exerts a major influence on transcription in many plants and animals (1–3). DNA methylation can be causal for transcriptional silencing (4–5) and targets the machinery necessary to assemble specialized chromatin enriched in deacetylated histones (6–8). Once established in somatic cells, CpG methylation patterns within the genome are very stable and provide an attractive mechanism for segregating a large fraction of stably repressed chromatin (9–11). In contrast, DNA methylation is remarkably dynamic during early mammalian development and in certain tumor cells (12, 13). Alterations in the methylation status of the entire genome (14, 15), individual chromosomes (16), and specific genes (17–20) are essential for normal development (21, 22) and can promote tumorigenesis (23, 24). Understanding how these important transitions might be regulated requires the biochemical definition of the enzymatic processes that both methylate and demethylate the genome. Two mammalian DNA methyltransferases have been functionally defined (25, 26) from a family of related proteins (26, 27). Dnmt1 is essential for inactivation of the X chromosome and genomic imprinting in the mammalian embryo (21). This large enzyme (1,620 amino acids) is targeted to replication foci consistent with the rapid remethylation of DNA in somatic cells (28–30). Like the prokaryotic cytosine-5 methyltransferases with which it shares homology, the enzyme makes use of the Michael addition mechanism to carry out the reaction by first increasing the reactivity of the C-5 position of cytosine (31–33). An enzyme cysteinyl thiolate forms a covalent linkage with C-6 of cytosine, and the carboxyl group of an invariant glutamyl residue protonates the N-3 position to create a cytosine 4, 5 enamine. This reactive moiety attacks the sulfonium linked methyl group …