Local chromatin microenvironment determines DNMT activity: from DNA methyltransferase to DNA demethylase or DNA dehydroxymethylase

Abstract

Insights on active DNA demethylation disproved the original assumption that DNA methylation is a stable epigenetic modification. Interestingly, mammalian DNA methyltransferases 3A and 3B (DNMT-3A and -3B) have also been reported to induce active DNA demethylation, in addition to their well-known function in catalyzing methylation. In situations of extremely low levels of S-adenosyl methionine (SAM), DNMT-3A and -3B might demethylate C-5 methyl cytosine (5mC) via deamination to thymine, which is subsequently replaced by an unmodified cytosine through the base excision repair (BER) pathway. Alternatively, 5mC when converted to 5- hydroxymethylcytosine (5hmC) by TET enzymes, might be further modified to an unmodified cytosine by DNMT-3A and -3B under oxidized redox conditions, although exact pathways are yet to be elucidated. Interestingly, even direct conversion of 5mC to cytosine might be catalyzed by DNMTs. Here, we summarize the evidence on the DNA dehydroxymethylase and demethylase activity of DNMT-3A and -3B. Although physiological relevance needs to be demonstrated, the current indications on the 5mC- and 5hmC-modifying activities of de novo DNA C-5 methyltransferases shed a new light on these enzymes. Despite the extreme circumstances required for such unexpected reactions to occur, we here put forward that the chromatin microenvironment can be locally exposed to extreme conditions, and hypothesize that such waves of extremes allow enzymes to act in differential ways.

Keywords: 5caC, 5-carboxylcytosine; 5fC, 5-formylcytosine; 5hmC, 5 hydroxymethylcytosine; 5mC, 5-methylcytosine; AID, activation-induced cytidine deaminase; APOBEC, apolipoprotein B mRNA editing enzyme catalytic polypeptide-like; BER, base excision and repair; C, cytosine; CGI, CpG islands; DNA dehydroxymethylation; DNA demethylation; DNMT, DNA methyltransferase; DNMTs; GADD45, growth arrest and DNA-damage-inducible protein 45; RARE, retinoic acid response element; S-adenosyl methionine (SAM); SAM, S-adenosyl methionine; TDG, thymine DNA glycosylase; TET, ten-eleven translocation.; chromatin microenvironment; oxidizing redox state.

Figure 1.

Involvement of DNMTs in the active DNA methylation process. In the presence of SAM, DNMT-3A and -3B transfer a methyl group to the C5 of the activated cytosine to form 5mC (1). Whereas in the absence of SAM, DNMT1 (DNMT3s have not been analyzed) can couple a formaldehyde to the activated C to form 5hmC directly (2). When 5mC is formed, DNMT-mediated active DNA demethylation can, depending on the environment, proceed via 3 different pathways: Independently of the DNMTs, TET enzymes can directly convert 5mC to 5hmC (3). When SAM levels are low or completely depleted, DNMT-3A and -3B can contribute to the active DNA demethylation process. In the case of low SAM levels, DNMT-3A and -3B catalyze the deamination of 5mC to T (4). T is in turn replaced by an unmodified C via the BER pathway (5). In the case of absence of SAM combined with high levels of CA²⁺ and an oxidized redox environment, DNMT-3A and -3B can convert 5mC to an unmodified C (6). Also the conversion of 5hmC to an unmethylated C might be catalyzed by DNMT-3A and -3B. This reaction can take place when SAM depletion is combined with an oxidizing redox environment (7).