title: Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming.
abstract: TET proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC are excised by mammalian DNA glycosylase TDG, implicating 5mC oxidation in DNA demethylation. Here, we show that the genomic locations of 5fC can be determined by coupling chemical reduction with biotin tagging. Genome-wide mapping of 5fC in mouse embryonic stem cells (mESCs) reveals that 5fC preferentially occurs at poised enhancers among other gene regulatory elements. Application to Tdg null mESCs further suggests that 5fC production coordinates with p300 in remodeling epigenetic states of enhancers. This process, which is not influenced by 5hmC, appears to be associated with further oxidation of 5hmC and commitment to demethylation through 5fC. Finally, we resolved 5fC at base resolution by hydroxylamine-based protection from bisulfite-mediated deamination, thereby confirming sites of 5fC accumulation. Our results reveal roles of active 5mC/5hmC oxidation and TDG-mediated demethylation in epigenetic tuning at regulatory elements.
authors.affiliation: Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.
authors.forename: Chun-Xiao
authors.initials: CX
authors.lastname: Song
authors.forename: Keith E
authors.initials: KE
authors.lastname: Szulwach
authors.forename: Qing
authors.initials: Q
authors.lastname: Dai
authors.forename: Ye
authors.initials: Y
authors.lastname: Fu
authors.forename: Shi-Qing
authors.initials: SQ
authors.lastname: Mao
authors.forename: Li
authors.initials: L
authors.lastname: Lin
authors.forename: Craig
authors.initials: C
authors.lastname: Street
authors.forename: Yujing
authors.initials: Y
authors.lastname: Li
authors.forename: Mickael
authors.initials: M
authors.lastname: Poidevin
authors.forename: Hao
authors.initials: H
authors.lastname: Wu
authors.forename: Juan
authors.initials: J
authors.lastname: Gao
authors.forename: Peng
authors.initials: P
authors.lastname: Liu
authors.forename: Lin
authors.initials: L
authors.lastname: Li
authors.forename: Guo-Liang
authors.initials: GL
authors.lastname: Xu
authors.forename: Peng
authors.initials: P
authors.lastname: Jin
authors.forename: Chuan
authors.initials: C
authors.lastname: He
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism; D000818:Animals; D003596:Cytosine / Q000031:analogs & derivatives* / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000378:metabolism*; D044127:Epigenesis, Genetic; D005821:Genetic Techniques; D055106:Genome-Wide Association Study; D051379:Mice; D050436:Regulatory Elements, Transcriptional; D050880:p300-CBP Transcription Factors / Q000378:metabolism
chemical_list: C560973:5-formylcytosine; D044503:5-Methylcytosine; D003596:Cytosine; D050880:p300-CBP Transcription Factors