Nucleic acid modifications with epigenetic significance - PubMed (original) (raw)

Review

Nucleic acid modifications with epigenetic significance

Ye Fu et al. Curr Opin Chem Biol. 2012 Dec.

Abstract

Epigenetic modifications influence gene expression without alterations to the underlying nucleic acid sequence. In addition to the well-known 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC) have recently been discovered in genomic DNA, which all result from iterative oxidation of 5mC by the TET (Ten-Eleven-Translocate) family of enzymes. Recent studies have proposed the roles of these oxidized cytosines in mediating active demethylation of 5mC. Through affinity-based genome-wide sequencing and oxidation-assisted base-resolution sequencing methods, 5hmC is found to be dynamically regulated during development, and is enriched mainly in distal regulatory elements in human and mouse embryonic cells. Among RNA modifications, N(6)-methyladenosine (m(6)A) is a widespread yet poorly studied base modification in mRNA and non-coding RNA. The recent discovery that m(6)A in RNA is the major substrate of the fat mass and obesity associated (FTO) protein draws attention to the potential regulatory functions of reversible RNA methylations, which can be dynamic, and could be important in many fundamental cellular functions.

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Figures

Figure 1

(a) Dynamic regulation of 5mC, 5hmC, 5fC, and 5caC in DNA. DNMT3A and DNMT3B are responsible for de novo methylation to establish new methylation pattern, while 5mC is maintained during replication by DNMT1-catalyzed methylation of the newly synthesized DNA strand. TET enzymes can catalyze the oxidation of 5mC to 5hmC, 5fC, and 5caC in Fe(II) and α-ketoglutarate(α-KG)-dependent manner. 5fC and 5caC are recognized by DNA glycosylase TDG and converted to cytosine through base excision repair (BER) in an active demthylation. 5hmC may be deaminated by APOBC3 or AID to form 5hmU, which could undergo base excision by TDG and BER in order to restore the unmodified cytosine. (b) Proposed mechanism of oxidation of 5mC to 5hmC, 5fC, and 5caC by iron(II)/α-ketoglutarate (α-KG)-dependent Tet proteins. Dioxygen is activated by the iron(II) center to generate an peroxide intermediate that also covalently activates the α-KG cofactor. This intermediate further fragments to form an iron(IV)-oxo species which oxidizes the C-H bond of the substrate.

Figure 2

(a) Methylation and demethylation of m6A in RNA. Methylation of internal adenosines in RNA is catalyzed by a yet to be fully identified methyltransferase complex. FTO catalyzes the oxidative demethylation of m6A in poly(A)-RNA with hydroxymethyladenosine (hm6A) as a proposed intermediate. (b) FTO is an iron(II)/α-KG-dependent dioxygenase, which activates dioxygen using the iron(II) center and the α-KG cofactor. Subsequent oxidation of the N-methyl group yields hm6A as a potential intermediate, which further releases one molecule of formaldehyde to afford the unmethylated adenosine.

Figure 3

(a) Single-base resolution sequencing of 5hmC. In TAB-Seq, 5hmC is first protected with glucose. After oxidation of 5mC to 5caC, only glucose-protected 5hmC is resistant to bisulfite deamination, and will be sequenced as C, while original C and 5mC will be sequenced as T. (b) In oxBS-Seq, DNA is either treated with bisulfite or first oxidized with NaRuO4, and then treated with bisulfite. Without oxidation, 5hmC is resistant to deamination. Once 5hmC is oxidized to 5fC it is prone to deamination. The site and abundance can be obtained by comparing the sequencing difference between these two treatments. (c) Schematic distribution of 5hmC. 5hmC is highest in distal-regulatory elements including p300-binding sites, predicted enhancers, CTCF-binding sites, and DNase I hypersensitive sites compared to other regions such as gene bodies. Results suggest active demethylation at gene regulatory elements.

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Nucleic acid modifications with epigenetic significance - PubMed (original) (raw)