DNA demethylation

DNA demethylation is a process of removal of methyl group from nucleotide in DNA. DNA demethylation could be passive and active. Passive process takes place in the absence of methylation of newly synthesised DNA strands by DNMT1 during several replication rounds (for example, upon 5-Azacytidine treatment). Active DNA demethylation occurs via active dismiss of methyl group.

Examples of active DNA demethylation

All the cases of DNA demethylation could be divided on global (genome wide) and specific (when just specific sequences are demethylated). The genome wide DNA demethylation occurs:

1. In mammals:
   1. In male pronucleus of zygote immediately after fertilization;
   2. Possibly in the primordial germ cells (PGCs) of 11.5-12.5 day old embryos;
2. Possibly in amphibia - during midblastula transition

Examples of specific DNA demethylation:

1. Gene imprinting during plant reproduction;
2. Electroconvulsive stimulation-induced demethylation of neurotrophic factor genes in dentate gyrus neurons in the mouse brain ^[1][2]

Possible mechanisms of active DNA demethylation

There are several proposed hypothetical mechanisms of active DNA demethylation:

A Direct removal of 5-methylcytosine

1. Direct removal of methyl group. This process has quite low thermodynamic probability.
2. Removal of methylated bases (either by direct removal of methylcytosine, or through cytosine deamination followed by removal of thymine from thymine/guanosine mismatch), followed by insertion of unmethylated one using base excision repair machinery (BER).
3. Removal of entire DNA patch and following filling it with new nucleotides by nucleotide excision repair (NER).

B Removal of 5-methylcytosine via further modified cytosine bases

Oxidation of the methyl group generates 5-Hydroxymethylcytosine. Several mechanisms have been proposed to mediate demethylation of 5-hydroxymethylcytosines.^[3][4] This base can be either deaminated by AID/Apobec enzymes to give 5-Hydroxymethyluracil^[2]. Alternatively, TET enzymes can further oxidize 5-hydroxymethylcytosine to 5-Formylcytosine and 5-Carboxylcytosine.^{[5][6] [7]}

1. Both the deamination and the oxidation products have been shown to be repaired by TDG, a glycosylase which is involved in base excision repair.^{[6][8] [9]} A base excision mediated demethylation mechanism would yield double strand breaks if it occurs on large scale in CpG islands.
2. The carboxyl and formyl groups of 5-Formylcytosine and 5-Carboxylcytosine could be enzymatically removed without excision of the base. ^[5][4][3][7] Precedent for similar reactions is found in biosynthetic pathways.

Reference

1. ^ Ma, DK; Jang, MH, Guo, JU, Kitabatake, Y, Chang, ML, Pow-Anpongkul, N, Flavell, RA, Lu, B, Ming, GL, Song, H (2009-02-20). "Neuronal activity-induced Gadd45b promotes epigenetic DNA demethylation and adult neurogenesis.". Science 323 (5917): 1074–7. doi:10.1126/science.1166859. PMC 2726986. PMID 19119186. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2726986. 
2. ^ ^{a b} Guo, JU; Su, Y, Zhong, C, Ming, GL, Song, H (2011-04-29). "Hydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA Demethylation in the Adult Brain". Cell 145 (3): 423–34. doi:10.1016/j.cell.2011.03.022. PMC 3088758. PMID 21496894. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3088758. 
3. ^ ^{a b} Wu, SC; Zhang, Y (2010 Sep). "Active DNA demethylation: many roads lead to Rome". Nature reviews. Molecular cell biology 11 (9): 607–20. doi:10.1038/nrm2950. PMID 20683471. 
4. ^ ^{a b} Globisch, Daniel; Münzel, Martin, Müller, Markus, Michalakis, Stylianos, Wagner, Mirko, Koch, Susanne, Brückl, Tobias, Biel, Martin, Carell, Thomas (23 December 2010). "Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates". PLoS ONE 5 (12): e15367. doi:10.1371/journal.pone.0015367. PMC 3009720. PMID 21203455. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3009720. 
5. ^ ^{a b} Pfaffeneder, Toni; Hackner, Benjamin, Truss, Matthias, Münzel, Martin, Müller, Markus, Deiml, Christian A., Hagemeier, Christian, Carell, Thomas (30 June 2011). "The Discovery of 5-Formylcytosine in Embryonic Stem Cell DNA". Angew. Chem., Int. Ed. 50: 7008–7012. doi:10.1002/anie.201103899. PMID 21721093. 
6. ^ ^{a b} He, YF; Li, BZ, Li, Z, Liu, P, Wang, Y, Tang, Q, Ding, J, Jia, Y, Chen, Z, Li, L, Sun, Y, Li X, Dai, Q, Song, CX, Zhang, K, He, C, Xu, GL (4 August 2011). "Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA". Science 333 (6047): 1303–1307. 
7. ^ ^{a b} Ito, S; Li, S, Dai, Q, Wu, SC, Collins, SB, Swenberg, JA, He, C, Zhang, Y (21 July 2011). "Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine". Science 333 (6047): 1300–1303. 
8. ^ Maiti, A; Drohat, AC (23 August 2011). "Thymine DNA Glycosylase Can Rapidly Excise 5-Formylcytosine and 5-Carboxylcytosine". J. Biol. Chem. 286 (41): 35334–8. 
9. ^ Cannon, SV; Cummings, GW, Teebor, GW (1988). "5-Hydroxymethylcytosine DNA Glycosylase Activity in Mammalian Tissue". Biochem. Biophys. Res. Commun. 151: 1173–1179.