5-Methylcytosine !

5-Methylcytosine is cytosine with an extra methyl group; it is the main epigenetic mark on DNA and usually switches genes off.

Updated 2026-11-01

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Key facts

It is found mostly in CpG dinucleotides; CpG islands in active promoters are unmethylated.
Methylated promoter → silenced gene (binding of MBD proteins and histone deacetylases).
Its spontaneous deamination gives thymine (not uracil), a C→T change that is hard to spot: CpGs are mutation 'hot spots'.
TET enzymes oxidise it to 5-hydroxymethylcytosine and open the way to demethylation.

Cytosine with a methyl group (–CH₃) on carbon 5 of the pyrimidine ring.
The methyl sits in the major groove: it does not change pairing with guanine, but it does change which proteins bind.
In DNA it is made after replication: DNMT transfers the methyl from S-adenosylmethionine.

Promoter hypermethylation (MLH1, BRCA1, MGMT) silences tumour-suppressor genes in cancer.
The hypomethylating drugs azacitidine and decitabine lower 5-methylcytosine and reactivate genes in myelodysplastic syndromes.
Methylation of the FMR1 promoter explains gene silencing in fragile X.

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Which enzyme makes 5-methylcytosine, and what is the methyl donor?

DNA methyltransferases (DNMT), using S-adenosylmethionine.

Why are CpG dinucleotides mutation hot spots?

5-Methylcytosine deaminates to thymine, a normal DNA base that repair struggles to recognise: a C→T transition remains.

What does promoter methylation usually do?

It silences the gene, because it attracts proteins that compact chromatin and blocks activator binding.

Molecules are shown in their neutral form, as the databases deposit them; in the cell the acids and phosphates are ionised.

Educational information, not medical advice. For any symptom, see a health professional.

Sources: 5-Methylcytosine (CID 65040) (PubChem, NCBI, 2026) · Public domain; What is epigenetics?: MedlinePlus Genetics (MedlinePlus, US National Library of Medicine, 2026); Epigenetic regulation of gene expression (Reactome, 2026); Textbook of Biochemistry for Medical Students, 6th ed. (Jaypee Brothers Medical Publishers (Vasudevan DM, Sreekumari S, Vaidyanathan K), 2011).

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