DNA Demethylation in Zebrafish Involves the Coupling of a Deaminase, a Glycosylase, and Gadd45

By Kunal Rai, Ian J. Huggins, Smitha R. James, A. Karpf, David A Jones, B. Cairns. Cell, 2008

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SUMMARY Evidence for active DNA demethylation in vertebrates is accumulating, but the mechanisms and enzymes remain unclear. Using zebrafish embryos we provide evidence for 5-methylcytosine (5-meC) removal in vivo via the coupling of a 5-meC deaminase (AID, which converts 5-meC to thymine) and a G:T mismatch-specific thymine glycosylase (Mbd4). The injection of methylated DNA into embryos induced a potent DNA demethylation activity, which was attenuated by depletion of AID or the non enzymatic factor Gadd45. Remarkably, overexpression of the deaminase/glycosylase pair AID/Mbd4 in vivo caused demethylation of the bulk genome and injected methylated DNA fragments, likely involving a G:T intermediate. Furthermore, AID or Mbd4 knockdown caused the remethylation of a set of common genes. Finally, Gadd45 promoted demethylation and enhanced functional interactions between deaminase/glycosylase pairs. Our results provide evidence for a coupled mechanism of 5-meC demethylation, whereby AID deaminates 5-meC, followed by thymine base excision by Mbd4, promoted by Gadd45.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/78368196ac208e0173f111d6ca2e55f79bf3410c

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Citations in the corpus

Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain (2011, neutral): “Notably, APOBEC1 and APOBEC2 have both been implicated in active DNA demethylation in vertebrates (Morgan et al., 2004; Rai et al., 2008).”
DNA methylation: superior or subordinate in the epigenetic hierarchy? (2011, background): “Jeong et al.82 reported that both DNMT3A and DNMT3B are strongly anchored to nucleosomes, whereas DNMT1 interacts primarily with linker DNA.”
Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine (2011, background): “Furthermore, it was reported that the protein GADD45A promotes demethylation of CpG-methylated DNA (29), perhaps in conjunction with excision repair activities (23, 30).”
Linking DNA methylation and histone modification: patterns and paradigms (2009, background): “Several studies now suggest that active DNA demethylation might be accomplished through a process of DNA repai”
Epigenetic regulation of neurogenesis in the adult mammalian brain (2011, background): “…including DNA excision repair-based mechanisms involving the Growth arrest and DNA damage-inducible protein 45 (Gadd45) family of proteins (Morgan et al., 2004; Rai et al., 2008; Gehring et al., 2009; Ma et al., 2009c) and Radial SAM mechanisms involving the elongator complex (Okada et al., 2010).”
Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. (2010, background): “Interestingly, Gadd45a-deficient mice develop a lupus-like syndrome (Salvador et al. 2002).”
Nuclear Receptor-Induced Chromosomal Proximity and DNA Breaks Underlie Specific Translocations in Cancer (2009, positive): “Recently, Gadd45, which is a well-known irradiation-induced protein, was shown to play an important role in mediating AID actions by forming a functional complex with AID ( Rai et al., 2008 ).”
Induced pluripotency: history, mechanisms, and applications. (2010, background): “Consistent with this finding, Aid, together with Gadd45 and Mbd4, has been shown to elicit DNA demethylation in zebrafish (Rai et al. 2008).”
DNA Methylation and Its Basic Function (2013, background): “Overexpression of AID/APOBEC promotes DNA demethylation in zebrafish (Rai et al, 2008), whereas knockdown or knockout inhibits the DNA demethylation of various genes necessary for cellular reprogramming and development (Bhutani et al, 2010; Muramatsu et al, 2000; Popp et al, 2010).”
DNA Demethylation Dynamics (2011, background): “…et al., 2011; Ficz et al., 2011; Guo et al., 2011; He et al., 2011; Ito et al., 2011; Koh et al., 2011; Pastor et al., 2011; Popp et al., 2010; Rai et al., 2008; Song et al., 2011; Williams et al., 2011;Wu et al., 2011a, 2011b; Xu et al., 2011) have identified key players in this process,…”
Reversing DNA Methylation: Mechanisms, Genomics, and Biological Functions (2014, positive): “While some evidence suggests that Gadd45 may induce active DNA demethylation in Xenopus laevis embryos andmammalian cells (Ma et al., 2009; Rai et al., 2008; Schmitz et al., 2009), conflicting results were also reported (Jin et al.”