AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation

Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Nature Chemical Biology (Impact Factor: 13.22). 07/2012; 8(9):751-8. DOI: 10.1038/nchembio.1042
Source: PubMed

ABSTRACT Activation-induced deaminase (AID)/APOBEC-family cytosine deaminases, known to function in diverse cellular processes from antibody diversification to mRNA editing, have also been implicated in DNA demethylation, a major process for transcriptional activation. Although oxidation-dependent pathways for demethylation have been described, pathways involving deamination of either 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC) have emerged as alternatives. Here we address the biochemical plausibility of deamination-coupled demethylation. We found that purified AID/APOBECs have substantially reduced activity on 5mC relative to cytosine, their canonical substrate, and no detectable deamination of 5hmC. This finding was explained by the reactivity of a series of modified substrates, where steric bulk was increasingly detrimental to deamination. Further, upon AID/APOBEC overexpression, the deamination product of 5hmC was undetectable in genomic DNA, whereas oxidation intermediates remained detectable. Our results indicate that the steric requirements for cytosine deamination are one intrinsic barrier to the proposed function of deaminases in DNA demethylation.

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Available from: Huijue Jia, Aug 17, 2015
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    • "In fact, oxidation of 5mC to 5hmC by TET1 has been shown to promote DNA demethylation in the adult brain (Guo et al, 2011b). This study suggests the involvement of the AID/APOBEC family of cytidine deaminases in 5hmC demethylation, but more recent studies suggest that these deaminases favor unmodified cytosine (Nabel et al, 2012). Nevertheless , knockdown of endogenous TET1 in the dentate gyrus of the hippocampus can reverse the demethylation observed in the promoter region of Bdnf and Fgf1 (Guo et al, 2011a) in animals that receive synchronous electroconvulsive therapy (Ma et al, 2009). "
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    • "Hence, even though it seems likely that 5hmC and TET proteins have an important role during fetal germ cell development, Tet1 is dispensable in the development of normal murine germ cells. Our results tend to suggest an active demethylation pathway initiated by the deaminase APOBEC1 and not TETs, as CIS cells expressed APOBEC1 and the downstream BER components MBD4, APEX1 and PARP1, where the latter indeed have been demonstrated to be involved in active DNA demethylation in murine PGCs (Morgan et al, 2004; Hajkova et al, 2010; Popp et al, 2010; Hashimoto et al, 2012; Nabel et al, 2012). However, contradictory results regarding the level of expression of APOBEC1 in murine PGCs have been reported (Hajkova et al, 2010; Kagiwada et al, 2013). "
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