Cytosine is the most commonly altered base, with methylation being the most common addition. In vertebrates, this modified based, called 5-methylcytosine (5mC), is found primarily in the CpG context—on cytosines followed by guanines. Recent research has revealed that this base can be further modified into a number of variants, including 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), though these modifications are generally rare. Researchers are still hunting for the functions of such DNA bases, but evidence points to their roles in gene regulation and DNA integrity, affecting learning and memory.

DNA modification Found in which species/type of organism Found in what genomic context/cell type Frequency in human or mouse genome Molecular roles
5-methylcytosine (5mC) Ubiquitous,
some exceptions
Primarily CG but also found in other contexts, ubiquitous 2 percent
to 4 percent of C
Represses gene expression
5-hydroxymethylcytosine (5hmC) Vertebrates, some fungi, protozoans Primarily CG, enriched in brain and other differentiated tissues 0.1 percent
to 0.8 percent of C
Intermediate for demethylation, other roles debated
5-formylcytosine (5fC) Vertebrates, some fungi, protozoans Primarily CG, enriched in mouse embryonic stem cells <0.002 percent of C Intermediate for demethylation, other roles debated
5-carboxylcytosine (5caC) Vertebrates, some fungi, protozoans Primarily CG, enriched in mouse embryonic stem cells <0.0003 percent of C Intermediate for demethylation, other roles debated

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