title: A Chemical Probe Targets DNA 5-Formylcytosine Sites and Inhibits TDG Excision, Polymerases Bypass, and Gene Expression.
abstract: Dynamic regulation and faithful maintenance of proper DNA methylation patterns are essential for many cellular functions. 5-Formylcytosine (5fC), a newly discovered oxidized form of methylcytosine (mC) is involved in active DNA demethylation process. The latest progresses suggest exciting novel functional roles of this residue. Chemical tools are desired to further elucidate the functional roles of 5fC and to modulate dynamics of DNA demethylation and downstream biological processes. Here we designed and constructed a chemical probe, consisting of an aldehyde targeting group and an intercalation group. This molecule can selectively react with 5fC and subsequently inhibit base excision by thymine DNA glycosylase (TDG) and cause significant pausing for both DNA and RNA polymerase elongation. Further investigation using a GFP reporter system in living cells revealed that the ligand modification in 5fC sites at 5'-UTR of the GFP gene greatly inhibited the GFP expression level. These results altogether confirmed our successful design and established a new approach for generating functional ligands that target the formylcytosine sites and modulate 5fC-related biological processes.
authors.affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, 92093, United States.
authors.forename: Liang
authors.initials: L
authors.lastname: Xu
authors.affiliation: Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States.
authors.forename: Ying-Chu
authors.initials: YC
authors.lastname: Chen
authors.affiliation: Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania 15213, United States ; University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, Pennsylvania 15213, United States.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Nakajima
authors.affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, 92093, United States.
authors.forename: Jenny
authors.initials: J
authors.lastname: Chong
authors.affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, 92093, United States.
authors.forename: Lanfeng
authors.initials: L
authors.lastname: Wang
authors.affiliation: Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania 15213, United States ; University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, Pennsylvania 15213, United States.
authors.forename: Li
authors.initials: L
authors.lastname: Lan
authors.affiliation: Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States.
authors.forename: Chao
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, 92093, United States.
authors.forename: Dong
authors.initials: D
authors.lastname: Wang