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. 2012 May 18;336(6083):934-7.
doi: 10.1126/science.1220671. Epub 2012 Apr 26.

Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution

Michael J Booth  1 , Miguel R Branco, Gabriella Ficz, David Oxley, Felix Krueger, Wolf Reik, Shankar Balasubramanian
Affiliations

Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution

Michael J Booth et al. Science. .

Abstract

5-Methylcytosine can be converted to 5-hydroxymethylcytosine (5hmC) in mammalian DNA by the ten-eleven translocation (TET) enzymes. We introduce oxidative bisulfite sequencing (oxBS-Seq), the first method for quantitative mapping of 5hmC in genomic DNA at single-nucleotide resolution. Selective chemical oxidation of 5hmC to 5-formylcytosine (5fC) enables bisulfite conversion of 5fC to uracil. We demonstrate the utility of oxBS-Seq to map and quantify 5hmC at CpG islands (CGIs) in mouse embryonic stem (ES) cells and identify 800 5hmC-containing CGIs that have on average 3.3% hydroxymethylation. High levels of 5hmC were found in CGIs associated with transcriptional regulators and in long interspersed nuclear elements, suggesting that these regions might undergo epigenetic reprogramming in ES cells. Our results open new questions on 5hmC dynamics and sequence-specific targeting by TETs.

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