title: Formation of stress-specific p53 binding patterns is influenced by chromatin but not by modulation of p53 binding affinity to response elements.
abstract: The p53 protein is crucial for adapting programs of gene expression in response to stress. Recently, we revealed that this occurs partly through the formation of stress-specific p53 binding patterns. However, the mechanisms that generate these binding patterns remain largely unknown. It is not established whether the selective binding of p53 is achieved through modulation of its binding affinity to certain response elements (REs) or via a chromatin-dependent mechanism. To shed light on this issue, we used a microsphere assay for protein-DNA binding to measure p53 binding patterns on naked DNA. In parallel, we measured p53 binding patterns within chromatin using chromatin immunoprecipitation and DNase I coupled to ligation-mediated polymerase chain reaction footprinting. Through this experimental approach, we revealed that UVB and Nutlin-3 doses, which lead to different cellular outcomes, induce similar p53 binding patterns on naked DNA. Conversely, the same treatments lead to stress-specific p53 binding patterns on chromatin. We show further that altering chromatin remodeling using an histone acetyltransferase inhibitor reduces p53 binding to REs. Altogether, our results reveal that the formation of p53 binding patterns is not due to the modulation of sequence-specific p53 binding affinity. Rather, we propose that chromatin and chromatin remodeling are required in this process.
authors.affiliation: Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Millau
authors.forename: Omari J
authors.initials: OJ
authors.lastname: Bandele
authors.forename: Josiann
authors.initials: J
authors.lastname: Perron
authors.forename: Nathalie
authors.initials: N
authors.lastname: Bastien
authors.forename: Eric F
authors.initials: EF
authors.lastname: Bouchard
authors.forename: Luc
authors.initials: L
authors.lastname: Gaudreau
authors.forename: Douglas A
authors.initials: DA
authors.lastname: Bell
authors.forename: Régen
authors.initials: R
authors.lastname: Drouin
mesh_terms: D001665:Binding Sites; D002478:Cells, Cultured; D002843:Chromatin / Q000378:metabolism*; D050759:Cyclin-Dependent Kinase Inhibitor p21 / Q000235:genetics / Q000378:metabolism; D004247:DNA / Q000378:metabolism; D004791:Enzyme Inhibitors / Q000494:pharmacology; D051548:Histone Acetyltransferases / Q000037:antagonists & inhibitors; D006801:Humans; D007093:Imidazoles / Q000494:pharmacology; D010879:Piperazines / Q000494:pharmacology; D011485:Protein Binding; D012333:RNA, Messenger / Q000378:metabolism; D020218:Response Elements; D013312:Stress, Physiological; D013729:Terpenes / Q000494:pharmacology; D016159:Tumor Suppressor Protein p53 / Q000378:metabolism*; D014466:Ultraviolet Rays
chemical_list: D002843:Chromatin; D050759:Cyclin-Dependent Kinase Inhibitor p21; D004791:Enzyme Inhibitors; D007093:Imidazoles; D010879:Piperazines; D012333:RNA, Messenger; D013729:Terpenes; D016159:Tumor Suppressor Protein p53; C482205:nutlin 3; D004247:DNA; D051548:Histone Acetyltransferases; C054597:garcinol