Bisulfite sequencing is widely used to profile epigenetic DNA marks at single-base resolution, but it cannot distinguish between 5-methylcytosine (5-mC), a common repressive modification, and the oxidative product 5-hydroxymethylcytosine (5-hmC) because both are protected from bisulfite conversion to uracil. But 5-hmC may be an informative mark in its own right. Booth et al. report a way to oxidize 5-hmC to an intermediate form that is susceptible to bisulfite conversion. When a batch of DNA is split and subjected to both bisulfite and oxidative bisulfite sequencing, the positions and relative levels of both 5-mC and 5-hmC can be determined. Oxidation, which is specific to 5-hmC, converted 95% of residues in synthetic DNA with a low false-positive rate. The authors profiled 5-mC and 5-hmC at single-base resolution in mouse embryonic stem cells.
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Sequencing 5-hydroxymethylcytosine. Nat Methods 9, 533 (2012). https://doi.org/10.1038/nmeth.2057
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DOI: https://doi.org/10.1038/nmeth.2057
