title: Modulation of DNA binding protein affinity directly affects target site demethylation.
abstract: It has recently been shown that in Xenopus, DNA demethylation at promoter regions may involve protein-DNA interactions, based on the specificity of the demethylated sites. Utilizing a stable episomal system in human cells, we recently mapped the sites and dissected the steps of demethylation at oriP sites bound by EBNA1 protein. Although it is clear that protein binding is required for demethylation of the oriP sites, it is uncertain whether this is a unique feature of the replication origin or whether it is a general phenomenon for all DNA sequences to which sequence-specific proteins are bound. In the present study, we utilize the well-defined Escherichia coli lac repressor/operator system in human cells to determine whether protein binding to methylated DNA, in a region that is neither a replication origin nor a promoter, can also lead to demethylation of the binding sites. We found that demethylation specified by protein binding is not unique to the replication origin or to the promoter. We also found that transcriptional activity does not influence demethylation of the lac operator. Isopropyl-beta-D-thiogalactopyranoside (IPTG), an inhibitor of the lac repressor, can prevent demethylation of the lac operator DNA sites and can modulate demethylation of the lac operator by affecting the binding affinity of the lac repressor. Using this system, a titration of protein binding can be done. This titration permits one to infer that protein binding site occupancy is the determinant of demethylation at DNA sites and permits a determination of how this process progresses over time.
authors.affiliation: Department of Urology and Department of Biochemistry and Molecular Biology, University of Southern California, Norris Cancer Center, Los Angeles, California 90033, USA.
authors.forename: I G
authors.initials: IG
authors.lastname: Lin
authors.forename: T J
authors.initials: TJ
authors.lastname: Tomzynski
authors.forename: Q
authors.initials: Q
authors.lastname: Ou
authors.forename: C L
authors.initials: CL
authors.lastname: Hsieh
mesh_terms: D001426:Bacterial Proteins; D002460:Cell Line; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004926:Escherichia coli; D029968:Escherichia coli Proteins; D005786:Gene Expression Regulation; D006801:Humans; D007544:Isopropyl Thiogalactoside / Q000494:pharmacology; D007763:Lac Operon; D056968:Lac Repressors; D008156:Luciferases / Q000235:genetics; D010957:Plasmids; D011485:Protein Binding; D018741:Replication Origin / Q000235:genetics; D012097:Repressor Proteins; D014162:Transfection
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D056968:Lac Repressors; C539064:LacI protein, E coli; D012097:Repressor Proteins; D007544:Isopropyl Thiogalactoside; D008156:Luciferases