Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale.
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.
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.|Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
Bo
http://orcid.org/0000-0003-0929-7253
B
Xia
Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA.|Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois, USA.
Dali
D
Han
Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA.|Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois, USA.
Xingyu
X
Lu
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.|Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
Zhaozhu
Z
Sun
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.|Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
Ankun
A
Zhou
Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
Qiangzong
Q
Yin
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.|Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
Hu
H
Zeng
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.|Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
Menghao
M
Liu
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.|Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
Xiang
X
Jiang
Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
Wei
W
Xie
Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA.|Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois, USA.|Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.|Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
Chuan
C
He
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.|Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.|Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.|Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
Chengqi
C
Yi
D044503:5-Methylcytosine / Q000737:chemistry / Q000031:analogs & derivatives; D000818:Animals; D002460:Cell Line; D018899:CpG Islands; D003596:Cytosine / Q000031:analogs & derivatives* / Q000737:chemistry; D019175:DNA Methylation; D017931:DNA Primers / Q000737:chemistry; D057890:Epigenomics; D005786:Gene Expression Regulation; D016678:Genome; D051379:Mice; D008822:Mice, Transgenic; D009841:Oligonucleotides / Q000235:genetics; D010100:Oxygen / Q000737:chemistry; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*; D013234:Stem Cells / Q000166:cytology; D013447:Sulfites / Q000737:chemistry
C560974:5-carboxylcytosine; C560973:5-formylcytosine; D017931:DNA Primers; D009841:Oligonucleotides; D013447:Sulfites; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine; C042345:hydrogen sulfite; D010100:Oxygen