title: Pyrene-based quantitative detection of the 5-formylcytosine loci symmetry in the CpG duplex content during TET-dependent demethylation.
abstract: Methylcytosine (5mC) is mostly symmetrically distributed in CpG sites. Ten-eleven-translocation (TET) proteins are the key enzymes involved in active DNA demethylation through stepwise oxidation of 5mC. However, oxidation pathways of TET enzymes in the symmetrically methylated CpG context are still elusive. Employing the unique fluorescence properties of pyrene group, we designed and synthesized a sensitive fluorescence-based probe not only to target 5-formylcytosine (5fC) sites, but also to distinguish symmetric from asymmetric 5fC sites in the double stranded DNA context during TET-dependent 5mC oxidation process. Using this novel probe, we revealed dominant levels of symmetric 5fC among total 5fC sites during in vitro TET-dependent 5mC oxidation and novel mechanistic insights into the TET-dependent 5mC oxidation in the mCpG context.
authors.affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 (USA).
authors.forename: Liang
authors.initials: L
authors.lastname: Xu
authors.forename: Ying-Chu
authors.initials: YC
authors.lastname: Chen
authors.forename: Jenny
authors.initials: J
authors.lastname: Chong
authors.forename: Andrea
authors.initials: A
authors.lastname: Fin
authors.forename: Lisa S
authors.initials: LS
authors.lastname: McCoy
authors.forename: Jun
authors.initials: J
authors.lastname: Xu
authors.forename: Chao
authors.initials: C
authors.lastname: Zhang
authors.forename: Dong
authors.initials: D
authors.lastname: Wang
mesh_terms: D018899:CpG Islands; D003596:Cytosine / Q000031:analogs & derivatives* / Q000032:analysis; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000378:metabolism; D005456:Fluorescent Dyes / Q000032:analysis* / Q000138:chemical synthesis; D010084:Oxidation-Reduction; D011721:Pyrenes / Q000032:analysis* / Q000138:chemical synthesis; D015398:Signal Transduction; D013050:Spectrometry, Fluorescence
chemical_list: C560973:5-formylcytosine; D004268:DNA-Binding Proteins; D005456:Fluorescent Dyes; D011721:Pyrenes; D003596:Cytosine; D004247:DNA; C030984:pyrene
keywords: 5-formylcytosine; DNA demethylation; TET oxidation; pyrene fluorescence