In mammals and plants, DNA methylation refers to the addition of a methyl group to the fifth carbon of base C. Active DNA demethylation involves the enzymatic replacement of 5-methylcytosine (5meC) with C.
Global DNA demethylation has only been seen during early development in the zygotic paternal pronuclei and in primordial germ cells. However, imprinted genes are protected from demethylation in the zygote.
Loci-specific active DNA demethylation has been seen in somatic cells such as post-mitotic neurons and is important for the expression of neurogenesis genes. Recent studies have also indicated that nuclear hormone target promoters experience periodic methylation and demethylation that correlates with nuclear receptor binding and target gene expression.
In plants, biochemical and genetic evidence support the notion that DNA demethylation is achieved through base excision repair (BER) initiated by the Demeter (Dme) family of 5meC glycosylases. It is unlikely that mammals use a similar mechanism as the mammalian glycosylases T DNA glycosylase (TDG) and methyl-CpG-binding domain protein 4 (MBD4) possess weak excision activity against 5meC compared to T.
In contrast to the direct excision of 5meC, meC may first be deaminated to generate T and the resulting mismatch can initiate BER. Studies in zebrafish embryos have supported such a cooperative model, whereby deamination of 5meC can be carried out by activation-induced deaminase (AID), and T•G mismatch is repaired by MBD4.
The ten-eleven translocation (TET) family of proteins can hydroxylate 5meC to generate 5-hydroxymethylcytosine (5hmC), a modification that is present in embryonic stem (ES) cells and Purkinje neurons. The functional consequences and fate of 5hmC are unclear. However, TET1 plays a crucial role in ES cell identity as knockdown of TET1 results in defects in ES cell self-renewal and maintenance.
Recent studies have established a role for the elongator complex in zygotic paternal pronuclei demethylation as knockdown of the elongator components elongator complex protein 1 (ELP1), ELP3 and ELP4 impairs paternal genome demethylation. Although direct biochemical evidence is currently lacking, the radical SAM domain of ELP3 seems to be involved in the demethylation process.
Because promoter methylation of tumour suppressor genes has been implicated in cancer, understanding the mechanisms of DNA demethylation will facilitate the development of novel therapies. In addition, identification of the DNA demethylases also has implications in somatic cell reprogramming as promoter demethylation of pluripotent genes is crucial for this process.
DNA methylation is one of the best-characterized epigenetic modifications and has been implicated in numerous biological processes, including transposable element silencing, genomic imprinting and X chromosome inactivation. Compared with other epigenetic modifications, DNA methylation is thought to be relatively stable. Despite its role in long-term silencing, DNA methylation is more dynamic than originally thought as active DNA demethylation has been observed during specific stages of development. In the past decade, many enzymes have been proposed to carry out active DNA demethylation and growing evidence suggests that, depending on the context, this process may be achieved by multiple mechanisms. Insight into how DNA methylation is dynamically regulated will broaden our understanding of epigenetic regulation and have great implications in somatic cell reprogramming and regenerative medicine.
Subscribe to Journal
Get full journal access for 1 year
only $21.58 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Jaenisch, R. & Bird, A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nature Genet. 33, 245–254 (2003).
Jenuwein, T. & Allis, C. D. Translating the histone code. Science 293, 1074–1080 (2001).
Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007).
Esteller, M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nature Rev. Genet. 8, 286–298 (2007).
Feinberg, A. P. & Tycko, B. The history of cancer epigenetics. Nature Rev. Cancer 4, 143–153 (2004).
Pogribny, I. P. & Beland, F. A. DNA hypomethylation in the origin and pathogenesis of human diseases. Cell. Mol. Life Sci. 66, 2249–2261 (2009).
Santos-Reboucas, C. B. & Pimentel, M. M. Implication of abnormal epigenetic patterns for human diseases. Eur. J. Hum. Genet. 15, 10–17 (2007).
Law, J. A. & Jacobsen, S. E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Rev. Genet. 11, 204–220 (2010).
Goll, M. G. & Bestor, T. H. Eukaryotic cytosine methyltransferases. Annu. Rev. Biochem. 74, 481–514 (2005).
Okano, M., Xie, S. & Li, E. Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases. Nature Genet. 19, 219–220 (1998).
Okano, M., Bell, D. W., Haber, D. A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257 (1999).
Bestor, T. H. & Ingram, V. M. Two DNA methyltransferases from murine erythroleukemia cells: purification, sequence specificity, and mode of interaction with DNA. Proc. Natl Acad. Sci. USA 80, 5559–5563 (1983).
Bestor, T., Laudano, A., Mattaliano, R. & Ingram, V. Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases. J. Mol. Biol. 203, 971–983 (1988).
Hermann, A., Goyal, R. & Jeltsch, A. The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites. J. Biol. Chem. 279, 48350–48359 (2004).
Li, E., Bestor, T. H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992).
Ooi, S. K. & Bestor, T. H. The colorful history of active DNA demethylation. Cell 133, 1145–1148 (2008).
Mayer, W., Niveleau, A., Walter, J., Fundele, R. & Haaf, T. Demethylation of the zygotic paternal genome. Nature 403, 501–502 (2000).
Oswald, J. et al. Active demethylation of the paternal genome in the mouse zygote. Curr. Biol. 10, 475–478 (2000). References 17 and 18 report the first observation of genome-wide active DNA demethylation in the paternal pronucleus based on 5meC immunostaining in developing zygotes. Reference 18 also provides bisulphite sequencing evidence for active demethylation.
Ajduk, A., Yamauchi, Y. & Ward, M. A. Sperm chromatin remodeling after intracytoplasmic sperm injection differs from that of in vitro fertilization. Biol. Reprod. 75, 442–51 (2006).
Aoki, E. & Schultz, R. M. DNA replication in the 1-cell mouse embryo: stimulatory effect of histone acetylation. Zygote 7, 165–172 (1999).
Bouniol-Baly, C., Nguyen, E., Besombes, D. & Debey, P. Dynamic organization of DNA replication in one-cell mouse embryos: relationship to transcriptional activation. Exp. Cell Res. 236, 201–211 (1997).
Ferreira, J. & Carmo-Fonseca, M. Genome replication in early mouse embryos follows a defined temporal and spatial order. J. Cell Sci. 110, 889–897 (1997).
Howlett, S. K. & Bolton, V. N. Sequence and regulation of morphological and molecular events during the first cell cycle of mouse embryogenesis. J. Embryol. Exp. Morphol. 87, 175–206 (1985).
Luthardt, F. W. & Donahue, R. P. Pronuclear DNA synthesis in mouse eggs. An autoradiographic study. Exp. Cell Res. 82, 143–151 (1973).
Yamauchi, Y., Ward, M. A. & Ward, W. S. Asynchronous DNA replication and origin licensing in the mouse one-cell embryo. J. Cell. Biochem. 107, 214–223 (2009).
Kishigami, S. et al. Epigenetic abnormalities of the mouse paternal zygotic genome associated with microinsemination of round spermatids. Dev. Biol. 289, 195–205 (2006).
Dean, W. et al. Conservation of methylation reprogramming in mammalian development: aberrant reprogramming in cloned embryos. Proc. Natl Acad. Sci. USA 98, 13734–13738 (2001).
Fulka, H., Mrazek, M., Tepla, O. & Fulka, J. Jr. DNA methylation pattern in human zygotes and developing embryos. Reproduction 128, 703–708 (2004).
Beaujean, N. et al. Non-conservation of mammalian preimplantation methylation dynamics. Curr. Biol. 14, R266–R267 (2004).
Beaujean, N. et al. The effect of interspecific oocytes on demethylation of sperm DNA. Proc. Natl Acad. Sci. USA 101, 7636–7640 (2004).
Santos, F., Hendrich, B., Reik, W. & Dean, W. Dynamic reprogramming of DNA methylation in the early mouse embryo. Dev. Biol. 241, 172–182 (2002).
Barton, S. C. et al. Genome-wide methylation patterns in normal and uniparental early mouse embryos. Hum. Mol. Genet. 10, 2983–2987 (2001).
Olek, A. & Walter, J. The pre-implantation ontogeny of the H19 methylation imprint. Nature Genet. 17, 275–276 (1997).
Lane, N. et al. Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse. Genesis 35, 88–93 (2003).
Rougier, N. et al. Chromosome methylation patterns during mammalian preimplantation development. Genes Dev. 12, 2108–2113 (1998).
Dean, W., Santos, F. & Reik, W. Epigenetic reprogramming in early mammalian development and following somatic nuclear transfer. Semin. Cell Dev. Biol. 14, 93–100 (2003).
Aoki, F., Worrad, D. M. & Schultz, R. M. Regulation of transcriptional activity during the first and second cell cycles in the preimplantation mouse embryo. Dev. Biol. 181, 296–307 (1997).
Monk, M., Boubelik, M. & Lehnert, S. Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development 99, 371–382 (1987).
Howlett, S. K. & Reik, W. Methylation levels of maternal and paternal genomes during preimplantation development. Development 113, 119–127 (1991).
Carlson, L. L., Page, A. W. & Bestor, T. H. Properties and localization of DNA methyltransferase in preimplantation mouse embryos: implications for genomic imprinting. Genes Dev. 6, 2536–2541 (1992).
Hirasawa, R. et al. Maternal and zygotic Dnmt1 are necessary and sufficient for the maintenance of DNA methylation imprints during preimplantation development. Genes Dev. 22, 1607–1616 (2008).
Li, X. et al. A maternal-zygotic effect gene, Zfp57, maintains both maternal and paternal imprints. Dev. Cell 15, 547–557 (2008).
Ohinata, Y. et al. A signaling principle for the specification of the germ cell lineage in mice. Cell 137, 571–584 (2009).
Saitou, M. Germ cell specification in mice. Curr. Opin. Genet. Dev. 19, 386–395 (2009).
Hajkova, P. et al. Epigenetic reprogramming in mouse primordial germ cells. Mech. Dev. 117, 15–23 (2002). The authors report rapid loss of DNA methylation in PGCs during their migration through the genital ridge.
Lee, J. et al. Erasing genomic imprinting memory in mouse clone embryos produced from day 11.5 primordial germ cells. Development 129, 1807–1817 (2002).
Yamazaki, Y. et al. Reprogramming of primordial germ cells begins before migration into the genital ridge, making these cells inadequate donors for reproductive cloning. Proc. Natl Acad. Sci. USA 100, 12207–12212 (2003).
Bruniquel, D. & Schwartz, R. H. Selective, stable demethylation of the interleukin-2 gene enhances transcription by an active process. Nature Immunol. 4, 235–240 (2003).
Martinowich, K. et al. DNA methylation-related chromatin remodeling in activity-dependent BDNF gene regulation. Science 302, 890–893 (2003).
Kangaspeska, S. et al. Transient cyclical methylation of promoter DNA. Nature 452, 112–115 (2008).
Metivier, R. et al. Cyclical DNA methylation of a transcriptionally active promoter. Nature 452, 45–50 (2008). References 50 and 51 report that transcriptional cycling on activation by oestrogens coincides with periodic rounds of promoter methylation and demethylation of pS2 . The demethylation process correlates with the recruitment of certain repair proteins.
Kim, M. S. et al. DNA demethylation in hormone-induced transcriptional derepression. Nature 461, 1007–1012 (2009).
Gjerset, R. A. & Martin, D. W. Jr. Presence of a DNA demethylating activity in the nucleus of murine erythroleukemic cells. J. Biol. Chem. 257, 8581–8583 (1982).
Weiss, A., Keshet, I., Razin, A. & Cedar, H. DNA demethylation in vitro: involvement of RNA. Cell 86, 709–718 (1996).
Swisher, J. F., Rand, E., Cedar, H. & Marie Pyle, A. Analysis of putative RNase sensitivity and protease insensitivity of demethylation activity in extracts from rat myoblasts. Nucleic Acids Res. 26, 5573–5580 (1998).
Bhattacharya, S. K., Ramchandani, S., Cervoni, N. & Szyf, M. A mammalian protein with specific demethylase activity for mCpG DNA. Nature 397, 579–583 (1999).
Ng, H. H. et al. MBD2 is a transcriptional repressor belonging to the MeCP1 histone deacetylase complex. Nature Genet. 23, 58–61 (1999).
Hendrich, B. & Bird, A. Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol. Cell. Biol. 18, 6538–6547 (1998).
Hendrich, B., Guy, J., Ramsahoye, B., Wilson, V. A. & Bird, A. Closely related proteins MBD2 and MBD3 play distinctive but interacting roles in mouse development. Genes Dev. 15, 710–723 (2001).
Klose, R. J., Kallin, E. M. & Zhang, Y. JmjC-domain-containing proteins and histone demethylation. Nature Rev. Genet. 7, 715–727 (2006).
Klose, R. J. & Zhang, Y. Regulation of histone methylation by demethylimination and demethylation. Nature Rev. Mol. Cell Biol. 8, 307–318 (2007).
Smiley, J. A., Kundracik, M., Landfried, D. A., Barnes, V. R. Sr & Axhemi, A. A. Genes of the thymidine salvage pathway: thymine-7-hydroxylase from a Rhodotorula glutinis cDNA library and iso-orotate decarboxylase from Neurospora crassa. Biochim. Biophys. Acta 1723, 256–264 (2005).
Lepesheva, G. I. & Waterman, M. R. Sterol 14α-demethylase cytochrome P450 (CYP51), a P450 in all biological kingdoms. Biochim. Biophys. Acta 1770, 467–477 (2007).
Sancar, A., Lindsey-Boltz, L. A., Unsal-Kacmaz, K. & Linn., S. Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu. Rev. Biochem. 73, 39–85 (2004).
Zhu, J. K. Active DNA demethylation mediated by DNA glycosylases. Annu. Rev. Genet. 43, 143–166 (2009).
Choi, Y. et al. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110, 33–42 (2002).
Gong, Z. et al. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111, 803–814 (2002).
Agius, F., Kapoor, A. & Zhu, J. K. Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc. Natl Acad. Sci. USA 103, 11796–11801 (2006).
Gehring, M. et al. DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 124, 495–506 (2006).
Morales-Ruiz, T. et al. DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases. Proc. Natl Acad. Sci. USA 103, 6853–6858 (2006). Together with references 68, shows that ROS1 possesses 5meC glycosylase activity, and together with reference 69, shows that DME is also an active 5meC glycosylase.
Penterman, J. et al. DNA demethylation in the Arabidopsis genome. Proc. Natl Acad. Sci. USA 104, 6752–6757 (2007).
Gehring, M., Bubb, K. L. & Henikoff, S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324, 1447–1451 (2009).
Ortega-Galisteo, A. P., Morales-Ruiz, T., Ariza, R. R. & Roldan-Arjona, T. Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks. Plant Mol. Biol. 67, 671–681 (2008).
Jost, J. P. Nuclear extracts of chicken embryos promote an active demethylation of DNA by excision repair of 5-methyldeoxycytidine. Proc. Natl Acad. Sci. USA 90, 4684–4688 (1993).
Jost, J. P., Siegmann, M., Sun, L. & Leung, R. Mechanisms of DNA demethylation in chicken embryos. Purification and properties of a 5-methylcytosine-DNA glycosylase. J. Biol. Chem. 270, 9734–9739 (1995).
Fremont, M. et al. Demethylation of DNA by purified chick embryo 5-methylcytosine-DNA glycosylase requires both protein and RNA. Nucleic Acids Res. 25, 2375–2380 (1997).
Jost, J. P. et al. A chicken embryo protein related to the mammalian DEAD box protein p68 is tightly associated with the highly purified protein–RNA complex of 5-MeC-DNA glycosylase. Nucleic Acids Res. 27, 3245–3252 (1999).
Zhu, B. et al. 5-methylcytosine-DNA glycosylase activity is present in a cloned G/T mismatch DNA glycosylase associated with the chicken embryo DNA demethylation complex. Proc. Natl Acad. Sci. USA 97, 5135–5139 (2000).
Bennett, M. T. et al. Specificity of human thymine DNA glycosylase depends on N-glycosidic bond stability. J. Am. Chem. Soc. 128, 12510–12519 (2006).
Boland, M. J. & Christman, J. K. Characterization of Dnmt3b:thymine-DNA glycosylase interaction and stimulation of thymine glycosylase-mediated repair by DNA methyltransferase(s) and RNA. J. Mol. Biol. 379, 492–504 (2008).
Li, Y. Q., Zhou, P. Z., Zheng, X. D., Walsh, C. P. & Xu, G. L. Association of Dnmt3a and thymine DNA glycosylase links DNA methylation with base-excision repair. Nucleic Acids Res. 35, 390–400 (2007).
Zhu, B. et al. 5-Methylcytosine DNA glycosylase activity is also present in the human MBD4 (G/T mismatch glycosylase) and in a related avian sequence. Nucleic Acids Res. 28, 4157–4165 (2000).
Santos, F. & Dean, W. Epigenetic reprogramming during early development in mammals. Reproduction 127, 643–651 (2004).
Millar, C. B. et al. Enhanced CpG mutability and tumorigenesis in MBD4-deficient mice. Science 297, 403–405 (2002).
Hendrich, B., Hardeland, U., Ng, H. H., Jiricny, J. & Bird, A. The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature 401, 301–304 (1999).
Conticello, S. G. The AID/APOBEC family of nucleic acid mutators. Genome Biol. 9, 229 (2008).
Navaratnam, N. et al. The p27 catalytic subunit of the apolipoprotein B mRNA editing enzyme is a cytidine deaminase. J. Biol. Chem. 268, 20709–20712 (1993).
Teng, B., Burant, C. F. & Davidson, N. O. Molecular cloning of an apolipoprotein B messenger RNA editing protein. Science 260, 1816–1819 (1993).
Muramatsu, M. et al. Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell 102, 553–563 (2000).
Revy, P. et al. Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the Hyper-IgM syndrome (HIGM2). Cell 102, 565–575 (2000).
Morgan, H. D., Dean, W., Coker, H. A., Reik, W. & Petersen-Mahrt, S. K. Activation-induced cytidine deaminase deaminates 5-methylcytosine in DNA and is expressed in pluripotent tissues: implications for epigenetic reprogramming. J. Biol. Chem. 279, 52353–52360 (2004).
Popp, C. et al. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 463, 1101–1105 (2010). By using high-throughput bisulphite sequencing, the authors show that knockout of AID results in reduced DNA demethylation in PGCs.
Rai, K. et al. DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and GADD45. Cell 135, 1201–1212 (2008). Using zebrafish embryos, the authors show that an injected methylated substrate can be demethylated through the cooperative action of a deaminase (AID), a T glycosylase (MBD4) and GADD45A.
Hirano, K. et al. Targeted disruption of the mouse apobec-1 gene abolishes apolipoprotein B mRNA editing and eliminates apolipoprotein B48. J. Biol. Chem. 271, 9887–9890 (1996).
Morrison, J. R. et al. Apolipoprotein B RNA editing enzyme-deficient mice are viable despite alterations in lipoprotein metabolism. Proc. Natl Acad. Sci. USA 93, 7154–7159 (1996).
Bandaru, B., Wyszynski, M. & Bhagwat, A. S. HpaII methyltransferase is mutagenic in Escherichia coli. J. Bacteriol. 177, 2950–2952 (1995).
Shen, J. C., Rideout, W. M. 3rd & Jones, P. A. High frequency mutagenesis by a DNA methyltransferase. Cell 71, 1073–1080 (1992).
Zingg, J. M., Shen, J. C., Yang, A. S., Rapoport, H. & Jones, P. A. Methylation inhibitors can increase the rate of cytosine deamination by (cytosine-5)-DNA methyltransferase. Nucleic Acids Res. 24, 3267–3275 (1996).
Wyszynski, M., Gabbara, S. & Bhagwat, A. S. Cytosine deaminations catalyzed by DNA cytosine methyltransferases are unlikely to be the major cause of mutational hot spots at sites of cytosine methylation in Escherichia coli. Proc. Natl Acad. Sci. USA 91, 1574–1578 (1994).
Yebra, M. J. & Bhagwat, A. S. A cytosine methyltransferase converts 5-methylcytosine in DNA to thymine. Biochemistry 34, 14752–14757 (1995).
Chen, D. et al. T:G mismatch-specific thymine-DNA glycosylase potentiates transcription of estrogen-regulated genes through direct interaction with estrogen receptor α. J. Biol. Chem. 278, 38586–38592 (2003).
Jost, J. P., Thiry, S. & Siegmann, M. Estradiol receptor potentiates, in vitro, the activity of 5-methylcytosine DNA glycosylase. FEBS Lett. 527, 63–66 (2002).
Barreto, G. et al. Gadd45a promotes epigenetic gene activation by repair-mediated DNA demethylation. Nature 445, 671–675 (2007).
Zhan, Q. Gadd45a, a p53- and BRCA1-regulated stress protein, in cellular response to DNA damage. Mutat. Res. 569, 133–143 (2005).
Smith, M. L. et al. Interaction of the p53-regulated protein Gadd45 with proliferating cell nuclear antigen. Science 266, 1376–1380 (1994).
Smith, M. L. et al. Antisense GADD45 expression results in decreased DNA repair and sensitizes cells to UV-irradiation or cisplatin. Oncogene 13, 2255–2263 (1996).
Schmitz, K. M. et al. TAF12 recruits Gadd45a and the nucleotide excision repair complex to the promoter of rRNA genes leading to active DNA demethylation. Mol. Cell 33, 344–353 (2009).
Jin, S. G., Guo, C. & Pfeifer, G. P. GADD45A does not promote DNA demethylation. PLoS Genet. 4, e1000013 (2008).
Engel, N. et al. Conserved DNA methylation in Gadd45a−/− mice. Epigenetics 4, 98–9 (2009).
Ma, D. K. et al. Neuronal activity-induced Gadd45b promotes epigenetic DNA demethylation and adult neurogenesis. Science 323, 1074–1077 (2009).
Okada, Y., Yamagata, K., Hong, K., Wakayama, T. & Zhang, Y. A role for the elongator complex in zygotic paternal genome demethylation. Nature 463, 554–558 (2010). Using single-cell live imaging coupled with siRNA knockdown approaches, this paper reports the identification of the elongator complex as one of the factors required for zygotic paternal pronuclei demethylation.
Falnes, P. O., Johansen, R. F. & Seeberg, E. AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli. Nature 419, 178–182 (2002).
Trewick, S. C., Henshaw, T. F., Hausinger, R. P., Lindahl, T. & Sedgwick, B. Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage. Nature 419, 174–178 (2002).
Tsukada, Y. et al. Histone demethylation by a family of JmjC domain-containing proteins. Nature 439, 811–816 (2006).
Warn-Cramer, B. J., Macrander, L. A. & Abbott, M. T. Markedly different ascorbate dependencies of the sequential α-ketoglutarate dioxygenase reactions catalyzed by an essentially homogeneous thymine 7-hydroxylase from Rhodotorula glutinis. J. Biol. Chem. 258, 10551–10557 (1983).
Cliffe, L. J. et al. JBP1 and JBP2 are two distinct thymidine hydroxylases involved in J biosynthesis in genomic DNA of African trypanosomes. Nucleic Acids Res. 37, 1452–1462 (2009).
Yu, Z. et al. The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase. Nucleic Acids Res. 35, 2107–2115 (2007).
Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930–935 (2009). Shows that 5hmC is present in ES cells, and identifies TET1 as the enzyme responsible for generating 5hmC from 5meC.
Ito, S. et al. Role of Tet proteins in 5mC to 5hmC conversion, ES cell self-renewal, and ICM specification. Nature 18 Jul 2010 (doi:10.1038/nature0 9303). Shows that all three members of the TET family are capable of converting 5meC to 5hmC. In addition, knockdown of TET1 in ES cells and two-cell embryos reveals that TET1 is important for ES cell identity and ICM specification.
Lorsbach, R. B. et al. TET1, a member of a novel protein family, is fused to MLL in acute myeloid leukemia containing the t(10;11)(q22;q23). Leukemia 17, 637–641 (2003).
Ono, R. et al. LCX, leukemia-associated protein with a CXXC domain, is fused to MLL in acute myeloid leukemia with trilineage dysplasia having t(10;11)(q22;q23). Cancer Res. 62, 4075–4080 (2002).
Penn, N. W., Suwalski, R., O'Riley, C., Bojanowski, K. & Yura, R. The presence of 5-hydroxymethylcytosine in animal deoxyribonucleic acid. Biochem. J. 126, 781–790 (1972).
Kothari, R. M. & Shankar, V. 5-Methylcytosine content in the vertebrate deoxyribonucleic acids: species specificity. J. Mol. Evol. 7, 325–329 (1976).
Kriaucionis, S. & Heintz, N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324, 929–930 (2009). Shows that 5hmC is present in Purkinje neurons.
Jin, S. G., Kadam, S. & Pfeifer, G. P. Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res. 38, e125 (2010).
Valinluck, V. et al. Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). Nucleic Acids Res. 32, 4100–4108 (2004).
Valinluck, V. & Sowers, L. C. Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1. Cancer Res. 67, 946–950 (2007).
Cannon, S. V., Cummings, A. & Teebor, G. W. 5-Hydroxymethylcytosine DNA glycosylase activity in mammalian tissue. Biochem. Biophys. Res. Commun. 151, 1173–1179 (1988).
Boorstein, R. J. et al. Definitive identification of mammalian 5-hydroxymethyluracil DNA N-glycosylase activity as SMUG1. J. Biol. Chem. 276, 41991–41997 (2001).
Privat, E. & Sowers, L. C. Photochemical deamination and demethylation of 5-methylcytosine. Chem. Res. Toxicol. 9, 745–750 (1996).
Alegria, A. H. Hydroxymethylation of pyrimidine mononucleotides with formaldehyde. Biochim. Biophys. Acta 149, 317–324 (1967).
Liutkeviciute, Z., Lukinavicius, G., Masevicius, V., Daujotyte, D. & Klimasauskas, S. Cytosine-5-methyltransferases add aldehydes to DNA. Nature Chem. Biol. 5, 400–402 (2009).
Abdel-Wahab, O. et al. Genetic characterization of TET1, TET2, and TET3 alterations in myeloid malignancies. Blood 114, 144–147 (2009).
Delhommeau, F. et al. Mutation in TET2 in myeloid cancers. N. Engl. J. Med. 360, 2289–2301 (2009).
Jankowska, A. M. et al. Loss of heterozygosity 4q24 and TET2 mutations associated with myelodysplastic/myeloproliferative neoplasms. Blood 113, 6403–6410 (2009).
Kosmider, O. et al. TET2 mutation is an independent favorable prognostic factor in myelodysplastic syndromes (MDSs). Blood 114, 3285–3291 (2009).
Langemeijer, S. M. et al. Acquired mutations in TET2 are common in myelodysplastic syndromes. Nature Genet. 41, 838–842 (2009).
Mohamedali, A. M. et al. Novel TET2 mutations associated with UPD4q24 in myelodysplastic syndrome. J. Clin. Oncol. 27, 4002–4006 (2009).
Saint-Martin, C. et al. Analysis of the ten-eleven translocation 2 (TET2) gene in familial myeloproliferative neoplasms. Blood 114, 1628–1632 (2009).
Tefferi, A. et al. Detection of mutant TET2 in myeloid malignancies other than myeloproliferative neoplasms: CMML, MDS, MDS/MPN and AML. Leukemia 23, 1343–1345 (2009).
Nolte, F. & Hofmann, W. K. Myelodysplastic syndromes: molecular pathogenesis and genomic changes. Ann. Hematol. 87, 777–795 (2008).
Daskalakis, M. et al. Demethylation of a hypermethylated P15/INK4B gene in patients with myelodysplastic syndrome by 5-Aza-2′-deoxycytidine (decitabine) treatment. Blood 100, 2957–64 (2002).
Silverman, L. R. et al. Randomized controlled trial of azacitidine in patients with the myelodysplastic syndrome: a study of the cancer and leukemia group B. J. Clin. Oncol. 20, 2429–2440 (2002).
Allen, M. D. et al. Solution structure of the nonmethyl-CpG-binding CXXC domain of the leukaemia-associated MLL histone methyltransferase. EMBO J. 25, 4503–4512 (2006).
Hawkes, N. A. et al. Purification and characterization of the human elongator complex. J. Biol. Chem. 277, 3047–3052 (2002).
Kim, J. H., Lane, W. S. & Reinberg, D. Human elongator facilitates RNA polymerase II transcription through chromatin. Proc. Natl Acad. Sci. USA 99, 1241–1246 (2002).
Greenwood, C., Selth, L. A., Dirac-Svejstrup, A. B. & Svejstrup, J. Q. An iron-sulfur cluster domain in Elp3 important for the structural integrity of elongator. J. Biol. Chem. 284, 141–149 (2009).
Li, Q. et al. The elongator complex interacts with PCNA and modulates transcriptional silencing and sensitivity to DNA damage agents. PLoS Genet. 5, e1000684 (2009).
Paraskevopoulou, C., Fairhurst, S. A., Lowe, D. J., Brick, P. & Onesti, S. The elongator subunit Elp3 contains a Fe4S4 cluster and binds S-adenosylmethionine. Mol. Microbiol. 59, 795–806 (2006).
Cokus, S. J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 (2008).
Li, M. et al. Sensitive digital quantification of DNA methylation in clinical samples. Nature Biotechnol. 27, 858–863 (2009).
Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T. & Henikoff, S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genet. 39, 61–69 (2007).
Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 (2008). Together with reference 150, provides single-nucleotide resolution maps of DNA methylation patterns in the A. thaliana genome.
Flusberg, B. A. et al. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nature Methods 7, 461–465 (2010).
Jones, P. A. & Baylin, S. B. The fundamental role of epigenetic events in cancer. Nature Rev. Genet. 3, 415–428 (2002).
Gal-Yam, E. N., Saito, Y., Egger, G. & Jones, P. A. Cancer epigenetics: modifications, screening, and therapy. Annu. Rev. Med. 59, 267–280 (2008).
Karberg, S. Switching on epigenetic therapy. Cell 139, 1029–1031 (2009).
Torres-Padilla, M. E., Bannister, A. J., Hurd, P. J., Kouzarides, T. & Zernicka-Goetz, M. Dynamic distribution of the replacement histone variant H3.3 in the mouse oocyte and preimplantation embryos. Int. J. Dev. Biol. 50, 455–461 (2006).
van der Heijden, G. W. et al. Asymmetry in histone H3 variants and lysine methylation between paternal and maternal chromatin of the early mouse zygote. Mech. Dev. 122, 1008–1022 (2005).
Arney, K. L., Bao, S., Bannister, A. J., Kouzarides, T. & Surani, M. A. Histone methylation defines epigenetic asymmetry in the mouse zygote. Int. J. Dev. Biol. 46, 317–320 (2002).
Cowell, I. G. et al. Heterochromatin, HP1 and methylation at lysine 9 of histone H3 in animals. Chromosoma 111, 22–36 (2002).
Liu, H., Kim, J. M. & Aoki, F. Regulation of histone H3 lysine 9 methylation in oocytes and early pre-implantation embryos. Development 131, 2269–2280 (2004).
Santos, F., Peters, A. H., Otte, A. P., Reik, W. & Dean, W. Dynamic chromatin modifications characterise the first cell cycle in mouse embryos. Dev. Biol. 280, 225–236 (2005).
Erhardt, S. et al. Consequences of the depletion of zygotic and embryonic enhancer of zeste 2 during preimplantation mouse development. Development 130, 4235–4248 (2003).
Nakamura, T. et al. PGC7/Stella protects against DNA demethylation in early embryogenesis. Nature Cell Biol. 9, 64–71 (2007).
Payer, B. et al. Stella is a maternal effect gene required for normal early development in mice. Curr. Biol. 13, 2110–2117 (2003).
Takahashi, K. et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861–872 (2007).
Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006).
Gidekel, S. & Bergman, Y. A unique developmental pattern of Oct-3/4 DNA methylation is controlled by a cis-demodification element. J. Biol. Chem. 277, 34521–34530 (2002).
Hattori, N. et al. Epigenetic regulation of Nanog gene in embryonic stem and trophoblast stem cells. Genes Cells 12, 387–396 (2007).
Hattori, N. et al. Epigenetic control of mouse Oct-4 gene expression in embryonic stem cells and trophoblast stem cells. J. Biol. Chem. 279, 17063–17069 (2004).
Li, J. Y. et al. Synergistic function of DNA methyltransferases Dnmt3a and Dnmt3b in the methylation of Oct4 and Nanog. Mol. Cell Biol. 27, 8748–8759 (2007).
Mikkelsen, T. S. et al. Dissecting direct reprogramming through integrative genomic analysis. Nature 454, 49–55 (2008).
Han, D. W. et al. Pluripotential reprogramming of the somatic genome in hybrid cells occurs with the first cell cycle. Stem Cells 26, 445–454 (2008).
Tada, M., Takahama, Y., Abe, K., Nakatsuji, N. & Tada, T. Nuclear reprogramming of somatic cells by in vitro hybridization with ES cells. Curr. Biol. 11, 1553–1558 (2001).
Hanna, J. et al. Direct cell reprogramming is a stochastic process amenable to acceleration. Nature 462, 595–601 (2009).
Bhutani, N. et al. Reprogramming towards pluripotency requires AID-dependent DNA demethylation. Nature 463, 1042–1047 (2010). Interspecies heterokaryon experiments reveal that AID is required for demethylation of the OCT4 and nanog promoters during reprogramming.
We thank S. J. Booker for discussions regarding the radical SAM mechanism, and K. Hong and A. D'Alessio for critical comments on the manuscript. We apologize to colleagues whose work cannot be cited owing to space constraints. Work in the Zhang laboratory is supported by the National Institutes of Health (GM68804) and the Howard Hughes Medical Institute, of which Y.Z. is an investigator.
The authors declare no competing financial interests.
- Imprinted gene
A gene that is expressed in a parent-of-origin-specific manner.
- Inactive X chromosome
The copy of X chromosome that is silenced in female chromosomes in order to equalize the expression of genes located in the X chromosome in males and females.
- DNA methyltransferase
An enzyme that catalyses the addition of a methyl group to C or A.
- Hemi-methylated DNA
Duplex DNA in which only one of the two strands is methylated.
- Zona pellucida
The glycoprotein coat that surrounds the oocytes and the early embryos of mammals.
- Polar body
The structure that is extruded from the oocyte during meiosis and contains one haploid set of chromosomes.
The production of a diploid offspring from two sets of haploid maternal gametes and no paternal contribution.
Parthenogenesis in which the embryo contains only maternal chromosomes owing to the failure of the sperm to fuse with the egg nucleus.
- Digynic triploid
An embryo that contains two maternal genomes and one paternal genome.
- Bisulphite sequencing
A technique in which the treatment of DNA with bisulphite, which converts C to U but does not modify meC, is used to determine the DNA methylation pattern.
An embryonic stage that is characterized by the formation of the first definitive lineages.
- Primordial germ cell
One of a population of embryonic cells from which germ cells are formed.
- RNA editing
The post-transcriptional modification of RNA primary sequence by the insertion and/or deletion of specific bases, or the chemical modification of adenosine to inosine or cytidine to uridine.
- Somatic hypermutation
The mutation of the immunoglobulin variable region in mature B cells during an immune response. It results in affinity maturation of the antibody response. Like class switch recombination, it requires activation-induced cytidine deaminase.
- Class switch recombination
A mechanism that changes the class or isotype of antibody produced by an activated B cell. This does not change the affinity towards an antigen, but instead allows for interaction with different effector molecules.
(Jumonji C). An evolutionarily conserved motif. Proteins containing this domain are predicted to be protein hydroxylases or histone demethylases.
- Base J-binding protein
A protein that binds to base J (β-D-glucosylhydroxymethyl-U), a modified T produced by hydroxylation and glucosylation of the methyl group of T.
- Elongator complex
A protein complex originally identified in budding yeast to be associated with the elongating and hyperphosphorylated RNA polymerase II. It has also been implicated in tRNA modification, exocytosis and neuronal maturation.
- SAM domain
A protein domain containing an Fe–S cluster that uses S-adenosylmethionine (SAM) to catalyse various radical reactions.
About this article
Cite this article
Wu, S., Zhang, Y. Active DNA demethylation: many roads lead to Rome. Nat Rev Mol Cell Biol 11, 607–620 (2010). https://doi.org/10.1038/nrm2950
Epigenetic silencing of TET1 mediated hydroxymethylation of base excision repair pathway during lung carcinogenesis
Environmental Pollution (2021)
Journal of Chemical Theory and Computation (2021)
Genome-wide investigation of the dynamic changes of epigenome modifications after global DNA methylation editing
Nucleic Acids Research (2021)
Transcriptomic and epigenomics atlas of myotubes reveals insight into the circadian control of metabolism and development
Characterization of deoxyribonucleic methylation and transcript abundance of sex-related genes during tempera ture-dependent sex determination in Mauremys reevesii†
Biology of Reproduction (2020)