5-Hydroxymethyl-2′-deoxycytidine (5hmC), known as “the sixth base of DNA”, is produced by the Tet family Fe(II)-dependent oxygenases, which catalyze the oxidation of 5-Methyl-2′-deoxycytidine (5mC) to 5hmC. The conversion of 5mC into 5hmC is assumed to be the first step in a pathway leading towards DNA demethylation. The functional role of 5hmC in mammalian genomes is still unclear but it is known that 5hmC is critical for brain development and loss of 5hmC levels has been associated with leukemia and melanoma[2,3,4].
Oxidative bisulfite sequencing (oxBS-seq) and Tet-assisted bisulfite sequencing (TAB-Seq) are currently used for whole genome mapping of 5hmC at single base resolution. Both techniques are expensive and require special facilities with experienced personnel. Shahal et al. however, recently reported a high throughput method for simple direct optical detection of 5hmC content in genomic DNA making use of Click Chemistry with DBCO-CY5 (Figure 1).
Jena Bioscience offer a selection of epigenetic tools:
- Carboxy Cytidine (caC):
- 5-Carboxy-2′-deoxycytidine (N-1067)
- Click Chemistry Reagents
- Formyl Cytidine (fC):
- 5-Formyl-2′-deoxycytidine (N-1069)
- Hydroxymethyl Cytidines (5hmC):
- Methyl Cytidines (mC):
- Münzel et al. (2011) 5-Hydroxymethylcytosin, die sechste Base des Genoms. Angew. Chem. 123:6588.
- Tahiliani et al. (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324 (5929):930.
- Lian et al. (2012) Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma. Cell 150 (6):1135.
- Ko et al. (2010) Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 468 (7325):839.
- Booth et al. (2013) Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine. Nat. Protoc. 8 (10):1841.
- Booth et al. (2012) Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 336 (6083):934.
- Shahal et al. (2014) Spectroscopic quantification of 5-Hydroxymethylcytosine in genomic DNA. Anal. Chem. 86:8231.
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