DNA demethylation

DNA demethylation is the process of removal of a methyl group from nucleotides in DNA. DNA demethylation could be passive or active. The 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 direct removal of a methyl group independently of DNA replication.

Examples DNA Demethylation

All the cases of DNA demethylation can be divided as global (genome wide) or locus-specific (when just specific sequences are demethylated). The genome-wide DNA demethylation occurs:

  1. In mammals:
    1. In the male pronucleus of zygote immediately after fertilization;
    2. In mouse primordial germ cells (PGCs) between E8.5-11.5 day old embryos;[1]
  2. Possibly in amphibia - during midblastula transition.

Examples of specific DNA demethylation:

  1. Genomic imprinting during plant reproduction;
  2. Electroconvulsive stimulation-induced demethylation of neurotrophic factor genes in dentate gyrus neurons in the mouse brain.[2][3]

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.[4][5] This base can be either deaminated by AID/Apobec enzymes to give 5-Hydroxymethyluracil.[3] Alternatively, TET enzymes can further oxidize 5-hydroxymethylcytosine to 5-Formylcytosine and 5-Carboxylcytosine.[6][7][8]

  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.[7][9][10] 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.[4][5][6][8] Precedent for similar reactions is found in biosynthetic pathways.

DNA hydroxymethylation

DNA hydroxymethylation has been proposed to act as a specific epigenetic mark opposing DNA methylation, rather than a passive intermediate in the de-methylation pathway. DNA hydroxymethylation in vivo is sometimes associated with labile nucleosomes, which are more easy to disassemble and to out-compete by transcription factors during cell development [11]

See also


References

  1. ↑ Hackett, JA; Sengupta, R; Zylicz, JJ; Murakami, K; Lee, C; Down, T; Surani, MA (2012-12-06). "Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine.". Science 339 (6118): 448–52. doi:10.1126/science.1229277. PMID 23223451.
  2. ↑ 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.
  3. 1 2 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.
  4. 1 2 Wu, SC; Zhang, Y (Sep 2010). "Active DNA demethylation: many roads lead to Rome". Nature reviews. Molecular cell biology 11 (9): 607–20. doi:10.1038/nrm2950. PMID 20683471.
  5. 1 2 Globisch, Daniel; Münzel, Martin; Müller, Markus; Michalakis, Stylianos; Wagner, Mirko; Koch, Susanne; Brückl, Tobias; Biel, Martin; Carell, Thomas (23 December 2010). Croft, Anna Kristina, ed. "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.
  6. 1 2 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 (31): 7008–7012. doi:10.1002/anie.201103899. PMID 21721093.
  7. 1 2 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. doi:10.1126/science.1210944. PMC 3462231. PMID 21817016.
  8. 1 2 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. doi:10.1126/science.1210597. PMC 3495246. PMID 21778364.
  9. ↑ 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. doi:10.1074/jbc.C111.284620. PMC 3195571. PMID 21862836.
  10. ↑ Cannon, SV; Cummings, GW; Teebor, GW (1988). "5-Hydroxymethylcytosine DNA Glycosylase Activity in Mammalian Tissue". Biochem. Biophys. Res. Commun. 151 (3): 1173–1179. doi:10.1016/S0006-291X(88)80489-3. PMID 3355548.
  11. ↑ Teif, Vladimir; Beshnova, Daria A.; Vainshtein, Yevhen; Marth, Caroline; Mallm, Jan-Philipp; Höfer, Thomas; Rippe, Karsten (8 May 2014). "Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development". Genome Research 24 (8): 1285–1295. doi:10.1101/gr.164418.113. PMID 24812327.

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