Abstract
Active DNA demethylation in mammals involves oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). However, genome-wide detection of 5fC at single-base resolution remains challenging. Here we present fC-CET, a bisulfite-free method for whole-genome analysis of 5fC based on selective chemical labeling of 5fC and subsequent C-to-T transition during PCR. Base-resolution 5fC maps showed limited overlap with 5hmC, with 5fC-marked regions more active than 5hmC-marked ones.
Publication types
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
MeSH terms
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5-Methylcytosine / chemistry
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Animals
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Cell Line
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CpG Islands
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Cytosine / analogs & derivatives*
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Cytosine / chemistry
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DNA Methylation*
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DNA Primers / chemistry
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Epigenomics
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Gene Expression Regulation
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Genome
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Mice
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Mice, Transgenic
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Oligonucleotides / genetics
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Oxygen / chemistry
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Polymerase Chain Reaction
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Sequence Analysis, DNA / methods*
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Stem Cells / cytology
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Sulfites / chemistry
Substances
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5-carboxylcytosine
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5-formylcytosine
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DNA Primers
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Oligonucleotides
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Sulfites
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5-hydroxymethylcytosine
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5-Methylcytosine
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Cytosine
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hydrogen sulfite
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Oxygen