Identification of universal and cell-type specific p53 DNA binding

• Published in: BMC cell biology 2020-02, Vol.21 (1), p.5-12, Article 5
• Main Authors: Hafner, Antonina, Kublo, Lyubov, Tsabar, Michael, Lahav, Galit, Stewart-Ornstein, Jacob
• Format: Article
• Language: English
• Subjects: Binding Sites; Biochemistry; Cancer; Cancer therapies; Cell cycle; Cell Line, Tumor; ChIP-seq; Chromatin; Chromatin - metabolism; Chromatin Immunoprecipitation Sequencing; Datasets; Deoxyribonucleic acid; DNA; DNA binding; DNA damage; DNA repair; Gene expression; Genes; Genetic research; Genome; Genomes; Genomics; Health aspects; Humans; Ionizing radiation; Mesenchyme; Organ Specificity - genetics; p53; p53 Protein; Protein Binding - radiation effects; Radiation (Physics); Radiation, Ionizing; RNA-Seq; Stem cells; Transcription factors; Tumor cell lines; Tumor proteins; Tumor suppressor genes; Tumor Suppressor Protein p53 - genetics; Tumor Suppressor Protein p53 - metabolism; Tumors
• ISSN: 2661-8850; 2661-8850; 1471-2121
• DOI: 10.1186/s12860-020-00251-8

The tumor suppressor p53 is a major regulator of the DNA damage response and has been suggested to selectively bind and activate cell-type specific gene expression programs. However recent studies and meta-analyses of genomic data propose largely uniform, and condition independent p53 binding and thus question the selective and cell-type dependent function of p53. To systematically assess the cell-type specificity of p53, we measured its association with DNA in 12 p53 wild-type cancer cell lines, from a range of epithelial linages, in response to ionizing radiation. We found that the majority of bound sites were occupied across all cell lines, however we also identified a subset of binding sites that were specific to one or a few cell lines. Unlike the shared p53-bound genome, which was not dependent on chromatin accessibility, the association of p53 with these atypical binding sites was well explained by chromatin accessibility and could be modulated by forcing cell state changes such as the epithelial-to-mesenchymal transition. Our study reconciles previous conflicting views in the p53 field, by demonstrating that although the majority of p53 DNA binding is conserved across cell types, there is a small set of cell line specific binding sites that depend on cell state.