5-hydroxymethylcytosine

5-Hydroxymethylcytosine

Names
IUPAC name 6-Amino-5-(hydroxymethyl)-1H-pyrimidin-2-one
Identifiers
CAS Number	1123-95-1 N
3D model (Jmol)	Interactive image Interactive image
ChEBI	CHEBI:76792 N
ChemSpider	63916 Y
PubChem CID	70751
InChI InChI=1S/C5H7N3O2/c6-4-3(2-9)1-7-5(10)8-4/h1,9H,2H2,(H3,6,7,8,10) Y Key: RYVNIFSIEDRLSJ-UHFFFAOYSA-N Y InChI=1/C5H7N3O2/c6-4-3(2-9)1-7-5(10)8-4/h1,9H,2H2,(H3,6,7,8,10) Key: RYVNIFSIEDRLSJ-UHFFFAOYAT
SMILES C1=NC(=O)NC(=C1CO)N O=C1/N=C\C(=C(\N)N1)CO
Properties
Chemical formula	C5H7N3O2
Molar mass	141.13 g/mol
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
N  (what is YN ?)
Infobox references

5-Hydroxymethylcytosine is a DNA pyrimidine nitrogen base derived from cytosine. It is potentially important in epigenetics, because the hydroxymethyl group on the cytosine can possibly switch a gene on and off. It was first seen in bacteriophages in 1952. However, in 2009 it was found to be abundant in human and mouse brains, as well as in embryonic stem cells. In mammals, it can be generated by oxidation of 5-methylcytosine, a reaction mediated by the Tet family of enzymes. Its molecular formula is C₅H₇N₃O₂.

Every mammalian cell seems to contain 5-Hydroxymethylcytosine, but the levels vary significantly depending on the cell type. The highest levels are found in neuronal cells of the central nervous system. The amount of hydroxymethylcytosine increases with age, as shown in mouse hippocampus and cerebellum.

The exact function of this nitrogen base is still not fully elucidated, but it is thought that it may regulate gene expression or prompt DNA demethylation. This hypothesis is supported by the fact that artificial DNA that contains 5-hydroxymethylcytosines (5hmC) can be converted into unmodified cytosines once introduced into mammalian cells. Moreover, 5hmC is highly enriched in primordial germ cells, where it apparently plays a role in global DNA demethylation. Additionally, 5-Formylcytosine, an oxidation product of 5-Hydroxymethylcytosine and possible intermediate of an oxidative demethylation pathway was detected in DNA from embryonic stem cells, although no significant amounts of these putative demethylation intermediates could be detected in mouse tissue. 5-Hydroxymethylcytosine may be especially important in the central nervous system, as it is found in very high levels there. Reduction in the 5-Hydroxymethylcytosine levels have been found associated with impaired self-renewal in embryonic stem cells. 5-Hydroxymethylcytosine is also associated with labile, unstable nucleosomes which are frequently repositioned during cell differentiation.