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Figure 1. Dynamic cycle of DNA cytosine methylation-demethylation of the vertebrate genomes. (A) Methylation at the 5-position of C, in particular those at CpG dyads, on the vertebrate genomes is accomplished by the three DNMTs. Different pathways of demethylation of mC on the vertebrate DNAs are also depicted. (B) First, mC can be oxidized to hmC by TETs or oxidative stress. (C) Both mC and hmC are then converted to C through enzymatic deamination followed by the BER DNA repair pathway. (D) Sometimes hmC can be oxidized to fC and caC by TETs and then converted to C by BER. (E) In addition, mC has been suggested to be removable directly through NER. (F) The in vitro demethylation studies suggest that DNMT3A and DNMT3B could act as DNA dehydroxymethylases to directly convert hmC to C under oxidative stress. (G) Furthermore, all three DNMTs could act as DNA demethylases to directly convert mC to C in the presence of calcium ions under nonreducing conditions. For details and references, see text. BER: Base-excision repair; C: Cytosine; caC: carboxyl C; DNMT: DNA methyltransferase; fC: formyl C; hmC: 5-hydroxymethylcytosine; mC: 5-methylcytosine; NER: Nucleotide excision repair.
(Figure omitted. See article PDF.)
Figure 2. Possible roles of DNA methyltransferase in active DNA demethylation and dehydroxymethylation during early development. A model of the possible involvement of DNMTs in active demethylation of the vertebrate genomes during early development is presented. Immediately following sperm entry into the egg, a calcium wave triggers the oocyte activation and might also switch the DNMTs to function as Ca ++ -dependent demethylases. To reset the DNA methylation patterns, TET3-dependent conversion of mC to hmC, as shown by immunofluorescence staining, becomes marked on the paternal genome in the male PN after the early PN3 stage of the zygote. Later, the hmC and mC on the paternal as well as maternal genomes are massively diluted through passive DNA demethylation during early cleavage divisions. Significantly, a small prereplicative mC loss in both PN could be detected, by immunofluorescence staining and/or bisulfite sequencing, as early as at the PN2 stage of the zygote. This argues that active DNA demethylation occurs regionally on the two genomes. It is proposed that DNMTs, in particular DNMT3A, participate in the active DNA demethylation of both...