Similar to DNA methylation, DNA hydroxymethylation is an epigenetic mechanism that modifies the 5 position of cytosine by adding a hydroxymethyl group to DNA. Although this mechanism is not entirely understood, DNA hydroxymethylation is thought to be implicated in numerous important biological processes including differentiation, and is capable of impacting gene expression.
The epigenetic modification 5-hydroxymethylcytosine (5-hmC) is considered an intermediate step in the process of active demethylation of 5-methylcytosine (5-mC), caused by the oxidation of 5-mC as a result of the TET (ten eleven translocation) family of enzymes, TET1, TET2, and TET3 (see figure 1). Since around 2009, 5-hmC has been considered the “6th base,” following 5-mC, the “5th base” and interest in this epigenetic process has recently grown. Initial research showed that the distribution of 5-hmC is tissue-dependent in human tissues and that the level of 5-hmC varied in cancer cells. Studies suggest that it plays a role in stem cell pluripotency and cancer development.
Because one of the most popular methods for assessing the methylation status of cytosines known as bisulfite sequencing cannot distinguish between 5-mC and 5-hmC, various other techniques have been developed. Getting a wholesome view of methylation status by analyzing DNA methylation and DNA hydroxymethylation allows researchers to gain a proper and accurate assessment of the entire sample without misrepresentation of amount of methylation.