A nucleobase analogue that is cytosine in which the hydrogen at position 5 is replaced by a hydroxymethyl group.

Chemical properties

Chemical formula Net charge Average mass
C5H7N3O2 0 141.12800

Recommended notation

Name 5-hydroxymethylcytosine
Abbreviation 5hmC
Symbol h
Complement guanine:5-hydroxymethylcytosine
Symbol 2


4-amino-5-(hydroxymethyl)pyrimidin-2(1H)-one Nc1nc(=O)[nH]cc1CO
  • 4-amino-5-(hydroxymethyl)-2(1h)-pyrimidinone
  • 5-hydroxymethylcytosine

Mapping techniques

Method Method detail Resolution Enrichment or limitation References
(GLIB/CMS)-seq chemical conversion and immunoprecipitation low
Aba-seq restriction endonuclease high
BS-seq chemical conversion single-base
DMAB-seq DNMT1 conversion single-base CpG contexts only
HELP assay restriction endonuclease low microarray probes
HMST-seq restriction endonuclease low
MBD-seq affinity-based low
MRE-seq affinity-based low
Maxam–Gilbert sequencing single-base
MeDIP-seq affinity-based low
Methyl-MAPS affinity-based low
Methyl-seq restriction endonuclease low
MethylCap-seq affinity-based low salt gradient stratification
MspJI recognition restriction endonuclease low specific fragments
PBAT chemical conversion single-base
Pvu-seal-seq enzyme-mediated chemical tagging single-base
RRBS chemical conversion single-base methylation-insensitive restriction digestion
RRHP restriction endonuclease single-base restriction digestion
SMRT direct detection single-base target sequences
SMRT-BS chemical conversion single-base target sequences
TAB-seq chemical conversion single-base
TAmC-seq chemical tagging high
Tn5mC-seq chemical conversion single-base
hMeDIP-seq affinity-based low
nanopore direct detection single-base target sequences
sulfur/selenium tagging chemical tagging high
tungsten-oxidation chemical conversion single-base
β-GT–based tagging chemical tagging high


Origin Function Functional detail Organisms References
natural demethylation intermediate and epigenetic mark
  • Homo sapiens
  • Mus musculus