Intragenomic Decarboxylation of 5‐Carboxy‐2′‐deoxycytidine

Abstract

Cellular DNA is composed of four canonical nucleosides (dA, dC, dG and T), which form two Watson-Crick base pairs. In addition, 5-methylcytosine (mdC) may be present. The methylation of dC to mdC is known to regulate transcriptional activity. Next to these five nucleosides, the genome, particularly of stem cells, contains three additional dC derivatives, which are formed by stepwise oxidation of the methyl group of mdC with the help of Tet enzymes. These are 5-hydroxymethyl-dC (hmdC), 5-formyl-dC (fdC), and 5carboxy-dC (cadC). It is believed that fdC and cadC are converted back into dC, which establishes an epigenetic control cycle that starts with methylation of dC to mdC, followed by oxidation and removal of fdC and cadC. While fdC was shown to undergo intragenomic deformylation to give dC directly, a similar decarboxylation of cadC was postulated but not yet observed on the genomic level. By using metabolic labelling, we show here that cadC decarboxylates in several cell types, which confirms that both fdC and cadC are nucleosides that are directly converted back to dC within the genome by CÀC bond cleavage.

Bisulfite-free and single-nucleotide resolution sequencing of DNA epigenetic modification of 5-hydroxymethylcytosine using engineered deaminase

“…5 The resulting 5fC and 5caC undergo base excision repair or direct deformylation or decarboxylation to restore unmodied cytosines. [5][6][7][8][9] The discovery of 5hmC in mammalian genomes is a landmark in epigenomics study. 10 Similar to 5mC in DNA, 5hmC is also viewed as a vital epigenetic marker that could modulate gene expression.…”

“…5 The resulting 5fC and 5caC undergo base excision repair or direct deformylation or decarboxylation to restore unmodified cytosines. 5–9…”

Recent Advances in Deciphering the Mechanisms and Biological Functions of DNA Demethylation

“…[ 52 ] Subsequently, both our group and the Carell group provided further evidence for the direct decarboxylation of 5caC in mammalian genomes. [ 28,53 ] We employed a metabolic labeling assay using 2'‐fluorinated 5caC nucleoside (F‐5caC) and 2'‐fluorinated 5caC nucleoside triphosphate (F‐5caCTP) as tracing reagents (Figure 4A). [ 28,53 ] Similar to the direct deformylation of 5fC, the direct decarboxylation of 5caC was also observed to be a rapid process that occurs in various mammalian cell lines.…”

5-methylcytosine turnover: Mechanisms and therapeutic implications in cancer

“…In addition, oxidized forms of 5 mC are poor substrates for methylation maintenance by DNMT1 and as such lead to a lower fidelity in 5mc patterns after DNA replication. Finally, TDG-independent removal of 5 fC and 5caC has been suggested to occur through direct deformylation or decarboxylation in cells but the involved enzymes still need to be discovered ( Iwan et al, 2018 ; Kamińska et al, 2021 ).…”