title: Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells.
abstract: The effects of diverse stresses on promoter selectivity and transcription regulation by the tumor suppressor p53 are poorly understood. We have taken a comprehensive approach to characterizing the human p53 network that includes p53 levels, binding, expression and chromatin changes under diverse stresses. Human osteosarcoma U2OS cells treated with anti-cancer drugs Doxorubicin (DXR) or Nutlin-3 (Nutlin) led to strikingly different p53 gene binding patterns based on chromatin immunoprecipitation with high-throughput sequencing experiments. Although two contiguous RRRCWWGYYY decamers is the consensus binding motif, p53 can bind a single decamer and function in vivo. Although the number of sites bound by p53 was six times greater for Nutlin than DXR, expression changes induced by Nutlin were much less dramatic compared with DXR. Unexpectedly, the solvent dimethylsulphoxide (DMSO) alone induced p53 binding to many sites common to DXR; however, this binding had no effect on target gene expression. Together, these data imply a two-stage mechanism for p53 transactivation where p53 binding only constitutes the first stage. Furthermore, both p53 binding and transactivation were associated with increased active histone modification histone H3 lysine 4 trimethylation. We discovered 149 putative new p53 target genes including several that are relevant to tumor suppression, revealing potential new targets for cancer therapy and expanding our understanding of the p53 regulatory network.
authors.affiliation: Chromosome Stability Group, Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Research Triangle Park, NC 27709, USA, Systems Biology Group, Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Research Triangle Park, NC 27709, USA, William G. Enloe High School, Raleigh, NC 27610, USA and Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Menendez
authors.forename: Thuy-Ai
authors.initials: TA
authors.lastname: Nguyen
authors.forename: Johannes M
authors.initials: JM
authors.lastname: Freudenberg
authors.forename: Viju J
authors.initials: VJ
authors.lastname: Mathew
authors.forename: Carl W
authors.initials: CW
authors.lastname: Anderson
authors.forename: Raja
authors.initials: R
authors.lastname: Jothi
authors.forename: Michael A
authors.initials: MA
authors.lastname: Resnick
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology; D001665:Binding Sites; D016384:Consensus Sequence; D004273:DNA, Neoplasm / Q000235:genetics / Q000378:metabolism*; D004121:Dimethyl Sulfoxide / Q000494:pharmacology; D004317:Doxorubicin / Q000494:pharmacology; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D016158:Genes, p53; D045325:HCT116 Cells; D006657:Histones / Q000235:genetics / Q000378:metabolism; D006801:Humans; D007093:Imidazoles / Q000494:pharmacology; D008745:Methylation; D059372:Nucleotide Motifs; D012516:Osteosarcoma / Q000235:genetics / Q000473:pathology; D010879:Piperazines / Q000494:pharmacology; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D015533:Transcriptional Activation; D016159:Tumor Suppressor Protein p53 / Q000235:genetics / Q000378:metabolism*
chemical_list: D000970:Antineoplastic Agents; D004273:DNA, Neoplasm; D006657:Histones; D007093:Imidazoles; D010879:Piperazines; D016159:Tumor Suppressor Protein p53; C482205:nutlin 3; D004317:Doxorubicin; D004121:Dimethyl Sulfoxide