5-Methylcytosine is a modified cytosine with a methyl group attached to carbon 5 of its ring. In DNA, it retains the usual pairing relationship with guanine, so DNA methylation can change the chemical information on a sequence without changing its ordinary C/G base-pair identity.
A chemical difference makes the mark experimentally readable. In conventional bisulfite sequencing, treatment converts unmethylated cytosine to a form read as thymine after amplification, while 5-Methylcytosine is relatively protected. Comparing the resulting sequences reveals methylation at individual positions. The method introduced by M. Frommer and colleagues in 1992 turned a modification invisible in a simple four-letter DNA string into a positional readout.[ref]
A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands by M. Frommer and others. 1992, abstract: bisulfite conversion and strand-level sequencing
A methylation measurement must still be interpreted in its genomic and cellular context; the mark does not mean universal shutdown of transcription. New to topics? Read the docs here!