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Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale.

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.

SUBMITTER: Xia B 

PROVIDER: S-EPMC4626315 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature

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Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale.

Xia Bo B   Han Dali D   Lu Xingyu X   Sun Zhaozhu Z   Zhou Ankun A   Yin Qiangzong Q   Zeng Hu H   Liu Menghao M   Jiang Xiang X   Xie Wei W   He Chuan C   Yi Chengqi C  

Nature methods 20150907 11

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  ...[more]

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