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

Nature Methods
Bo XiaChengqi Yi

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.

References

Jun 5, 2003·Biochemistry·Dong WangStephen J Lippard
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Apr 15, 2011·Nature·Kristine WilliamsKristian Helin
Apr 16, 2011·Bioinformatics·Felix Krueger, Simon R Andrews
Jul 2, 2011·Angewandte Chemie·Toni PfaffenederThomas Carell
Jun 12, 2012·Cell·Shu XiaoSheng Zhong
Feb 26, 2013·Cell·Cornelia G SpruijtMichiel Vermeulen
Aug 13, 2013·Trends in Biochemical Sciences·Chun-Xiao Song, Chuan He
Oct 1, 2013·Cell·Chloe M Rivera, Bing Ren
Apr 24, 2014·Nature Chemistry·Michael J BoothShankar Balasubramanian
Nov 21, 2014·Nature Chemistry·Martin BachmanShankar Balasubramanian

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Citations

Mar 29, 2016·Trends in Cancer·Maria GuillamotIannis Aifantis
Mar 5, 2016·Cell Chemical Biology·Kai ChenChuan He
Aug 2, 2016·Nature Reviews. Genetics·Heng ZhuJiang Qian
Mar 30, 2017·Chemical Society Reviews·Yuqi ChenXiang Zhou
May 31, 2017·Nature Reviews. Genetics·Xiaoji Wu, Yi Zhang
Dec 19, 2015·Angewandte Chemie·Biswajit SamantaClaudia Höbartner
Jul 26, 2017·Journal of the American Chemical Society·Fengchao LiChuanzheng Zhou
Aug 3, 2018·Chemical Record : an Official Publication of the Chemical Society of Japan ... [et Al.]·Takuma SueokaAkimitsu Okamoto
Dec 24, 2018·Journal of Separation Science·James AsensoDao-Quan Tang
Dec 18, 2019·Essays in Biochemistry·Ksenia SkvortsovaPhillippa Taberlay
Aug 26, 2016·Angewandte Chemie·Meng SuThomas Carell
May 23, 2020·Protein & Cell·Lin-Yong ZhaoChengqi Yi
Apr 30, 2017·Experimental & Molecular Medicine·Jungeun AnMyunggon Ko
Jun 19, 2019·Nature Chemistry·Zheng J LiuShankar Balasubramanian
Jan 31, 2016·Science China. Life Sciences·Jinying PengChengqi Yi
Feb 28, 2019·Chembiochem : a European Journal of Chemical Biology·Hu ZengChengqi Yi
Jul 1, 2017·Chemical Science·Chaoxing LiuXiang Zhou
Jul 16, 2019·DNA Repair·Yingqian Zhang, Chuanzheng Zhou
Jul 14, 2021·Nature Communications·Bo HeChengqi Yi

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Methods Mentioned

BETA
deamination
PCR
pull-down
ChIP-seq
dot blot
TAB-Seq

Software Mentioned

Homer
Click Chemistry Tools
CET
bismark
fC

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