N3methylcytosine

N3-methylcytosine, or 3-methylcytosine (m3C), is a methylated form of cytosine in which a methyl group is attached to the nitrogen at position 3 of the cytosine ring. It occurs in two distinct contexts: as a DNA lesion formed by exposure to alkylating agents, and as a natural RNA modification found in various RNA species, notably transfer RNA and ribosomal RNA.

In DNA, N3-methylcytosine arises from alkylating compounds such as methyl nitrosourea or methyl methanesulfonate. The modification disrupts normal base pairing because the N3 position participates in hydrogen bonding, which can block replication and transcription and contribute to cytotoxicity and mutagenesis. It is considered a form of DNA damage rather than a canonical epigenetic mark. Repair is typically carried out by the AlkB family of oxidative demethylases, which remove the methyl group and restore normal cytosine, though additional repair pathways such as base excision repair can also participate depending on context.

In RNA, m3C is a genuine post-transcriptional modification detected in tRNA and rRNA, and occasionally in mRNA. It occurs at specific cytosine residues and can influence RNA structure and decoding accuracy by altering base pairing and local geometry. The biological roles of RNA m3C are an area of active study, with implications for translation efficiency and RNA stability. Writers (methyltransferases) install m3C, while cellular demethylases can remove it, reflecting reversible regulation in some systems. Detection typically relies on mass spectrometry or specialized sequencing methods.