Characterization of the p53 cistrome--DNA binding cooperativity dissects p53's tumor suppressor functions

PLoS Genet. 2013;9(8):e1003726. doi: 10.1371/journal.pgen.1003726. Epub 2013 Aug 15.

Abstract

p53 protects us from cancer by transcriptionally regulating tumor suppressive programs designed to either prevent the development or clonal expansion of malignant cells. How p53 selects target genes in the genome in a context- and tissue-specific manner remains largely obscure. There is growing evidence that the ability of p53 to bind DNA in a cooperative manner prominently influences target gene selection with activation of the apoptosis program being completely dependent on DNA binding cooperativity. Here, we used ChIP-seq to comprehensively profile the cistrome of p53 mutants with reduced or increased cooperativity. The analysis highlighted a particular relevance of cooperativity for extending the p53 cistrome to non-canonical binding sequences characterized by deletions, spacer insertions and base mismatches. Furthermore, it revealed a striking functional separation of the cistrome on the basis of cooperativity; with low cooperativity genes being significantly enriched for cell cycle and high cooperativity genes for apoptotic functions. Importantly, expression of high but not low cooperativity genes was correlated with superior survival in breast cancer patients. Interestingly, in contrast to most p53-activated genes, p53-repressed genes did not commonly contain p53 binding elements. Nevertheless, both the degree of gene activation and repression were cooperativity-dependent, suggesting that p53-mediated gene repression is largely indirect and mediated by cooperativity-dependently transactivated gene products such as CDKN1A, E2F7 and non-coding RNAs. Since both activation of apoptosis genes with non-canonical response elements and repression of pro-survival genes are crucial for p53's apoptotic activity, the cistrome analysis comprehensively explains why p53-induced apoptosis, but not cell cycle arrest, strongly depends on the intermolecular cooperation of p53 molecules as a possible safeguard mechanism protecting from accidental cell killing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Apoptosis / genetics*
  • Base Sequence
  • Binding Sites / genetics
  • Cell Cycle Checkpoints / genetics*
  • Cell Division
  • Cyclin-Dependent Kinase Inhibitor p21 / genetics
  • Cyclin-Dependent Kinase Inhibitor p21 / metabolism
  • DNA Damage / genetics
  • E2F7 Transcription Factor / genetics
  • E2F7 Transcription Factor / metabolism
  • Gene Expression Regulation, Neoplastic
  • Humans
  • Neoplasms / genetics*
  • Neoplasms / metabolism
  • Protein Binding / genetics
  • RNA, Untranslated / genetics
  • RNA, Untranslated / metabolism
  • Transcriptional Activation
  • Tumor Suppressor Protein p53 / genetics*
  • Tumor Suppressor Protein p53 / metabolism

Substances

  • CDKN1A protein, human
  • Cyclin-Dependent Kinase Inhibitor p21
  • E2F7 Transcription Factor
  • E2F7 protein, human
  • RNA, Untranslated
  • Tumor Suppressor Protein p53

Associated data

  • GEO/GSM545807
  • GEO/GSM545808
  • GEO/GSM545809

Grant support

This work was supported by funds to TS by the Deutsche Forschungsgemeinschaft (DFG TR17, TR81, KFO 210), European Research Council, Deutsche Krebshilfe, Behring-Röntgen-Stiftung, Deutsche José Carreras Leukämie Stiftung, the Priority Research Program Tumor & Inflammation (LOEWE) and the Universities of Giessen and Marburg Lung Center (LOEWE). KS acknowledges support by the mentoring program SciMento. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.