The best-known epigenetic mechanism that imposes a roadblock to nuclear reprogramming is DNA methylation. Reprogramming by nuclear transfer, by cell fusion and by induced pluripotency is associated with a global reversal of DNA methylation so that somatic nuclei closely resemble those of ES cells [9,24,40–42]. DNA demethylation of repressed genes is required for gene reactivation during reprogramming [9,43,44] and the failure of this has been correlated with poor development of cloned embryos [45]. Derivation of mouse ES cells by nuclear transfer is more efficient when the donor nuclei lack DNA methyltransferase 1 (Dnmt1), an enzyme needed for DNA methylation [46] and the transient inhibition of Dnmt1 has also been found to help the transition from partially to fully reprogrammed iPS cells (Table 1) [25,44]. Therefore, DNA demethylation is a key step during nuclear reprogramming, although it is not clear how much of it results from active DNA demethylation versus passive loss through cell divisions. Eggs and oocytes seem to induce DNA demethylation more efficiently than does transcription factor-based reprogramming [24]. The mechanisms of active DNA demethylation are currently being unravelled and include hydroxylation of methylated cytosines by Tet enzymes and/or deamination by AID/APOBECs followed by DNA repair [9,47,48].
