AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation

Christopher S. Nabel, Huijue Jia, Yu Ye, Li Shen, Hana L. Goldschmidt, James Stivers, Yi Zhang, Rahul M. Kohli

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)751-758
Number of pages8
JournalNature Chemical Biology
Volume8
Issue number9
DOIs
StatePublished - Sep 2012

Fingerprint

Deamination
Cytosine
DNA
5-Methylcytosine
Cytosine Deaminase
Transcriptional Activation
APOBEC Deaminases
AICDA (activation-induced cytidine deaminase)
Messenger RNA
Antibodies
5-hydroxymethylcytosine

ASJC Scopus subject areas

  • Cell Biology
  • Molecular Biology

Cite this

Nabel, C. S., Jia, H., Ye, Y., Shen, L., Goldschmidt, H. L., Stivers, J., ... Kohli, R. M. (2012). AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation. Nature Chemical Biology, 8(9), 751-758. https://doi.org/10.1038/nchembio.1042

AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation. / Nabel, Christopher S.; Jia, Huijue; Ye, Yu; Shen, Li; Goldschmidt, Hana L.; Stivers, James; Zhang, Yi; Kohli, Rahul M.

In: Nature Chemical Biology, Vol. 8, No. 9, 09.2012, p. 751-758.

Research output: Contribution to journalArticle

Nabel, CS, Jia, H, Ye, Y, Shen, L, Goldschmidt, HL, Stivers, J, Zhang, Y & Kohli, RM 2012, 'AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation', Nature Chemical Biology, vol. 8, no. 9, pp. 751-758. https://doi.org/10.1038/nchembio.1042
Nabel, Christopher S. ; Jia, Huijue ; Ye, Yu ; Shen, Li ; Goldschmidt, Hana L. ; Stivers, James ; Zhang, Yi ; Kohli, Rahul M. / AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation. In: Nature Chemical Biology. 2012 ; Vol. 8, No. 9. pp. 751-758.
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