Pyrene-Based Quantitative Detection of the 5-Formylcytosine Loci Symmetry in the CpG Duplex Content during TET-Dependent Demethylation†
Dr. Liang Xu
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 (USA)
Search for more papers by this authorYing-Chu Chen
Department of Chemistry, University of Southern California, Los Angeles, CA 90089 (USA)
Search for more papers by this authorJenny Chong
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 (USA)
Search for more papers by this authorDr. Andrea Fin
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093 (USA)
Search for more papers by this authorDr. Lisa S. McCoy
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093 (USA)
Search for more papers by this authorDr. Jun Xu
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 (USA)
Search for more papers by this authorProf. Dr. Chao Zhang
Department of Chemistry, University of Southern California, Los Angeles, CA 90089 (USA)
Search for more papers by this authorCorresponding Author
Prof. Dr. Dong Wang
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 (USA)
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 (USA)Search for more papers by this authorDr. Liang Xu
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 (USA)
Search for more papers by this authorYing-Chu Chen
Department of Chemistry, University of Southern California, Los Angeles, CA 90089 (USA)
Search for more papers by this authorJenny Chong
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 (USA)
Search for more papers by this authorDr. Andrea Fin
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093 (USA)
Search for more papers by this authorDr. Lisa S. McCoy
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093 (USA)
Search for more papers by this authorDr. Jun Xu
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 (USA)
Search for more papers by this authorProf. Dr. Chao Zhang
Department of Chemistry, University of Southern California, Los Angeles, CA 90089 (USA)
Search for more papers by this authorCorresponding Author
Prof. Dr. Dong Wang
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 (USA)
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 (USA)Search for more papers by this authorD.W. acknowledges the NIH (GM102362), Kimmel Scholar Award from the Sidney Kimmel Foundation for Cancer Research, and start-up funds from Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD for support. C.Z. acknowledges the American Cancer Society (IRG-5800754) and the University of Southern California for funding support. We appreciate Dr. Yongxuan Su and Dr. Tetsuya Kawamura (UCSD) for great help in HPLC and mass spec experiments. We appreciate Prof. Yitzhak Tor’s insightful comments for this manuscript.
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.
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