Global Analyses to Identify Direct Transcriptional Targets of p53

Methods Mol Biol. 2021;2267:19-56. doi: 10.1007/978-1-0716-1217-0_3.


The transcription factor p53 controls a gene expression program with pleiotropic effects on cell biology including cell cycle arrest and apoptosis. Identifying direct p53 target genes within this network and determining how they influence cell fate decisions downstream of p53 activation is a prerequisite for designing therapeutic approaches that target p53 to effectively kill cancer cells. Here we describe a comprehensive multi-omics approach for identifying genes that are direct transcriptional targets of p53. We provide detailed procedures for measuring global RNA polymerase activity, defining p53 binding sites across the genome, and quantifying changes in steady-state mRNA in response to p53 activation.

Keywords: ChIP-seq; GRO-seq; Gene Expression; Nutlin; RNA-seq; Sequencing; Transcription; Transcriptome; p53.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Cell Line
  • Chromatin Immunoprecipitation Sequencing / methods*
  • Genomics / methods*
  • Humans
  • RNA-Seq / methods*
  • Transcriptional Activation
  • Transcriptome*
  • Tumor Suppressor Protein p53 / metabolism*


  • Tumor Suppressor Protein p53