Cell context dependent p53 genome-wide binding patterns and enrichment at repeats

PLoS One. 2014 Nov 21;9(11):e113492. doi: 10.1371/journal.pone.0113492. eCollection 2014.

Abstract

The p53 ability to elicit stress specific and cell type specific responses is well recognized, but how that specificity is established remains to be defined. Whether upon activation p53 binds to its genomic targets in a cell type and stress type dependent manner is still an open question. Here we show that the p53 binding to the human genome is selective and cell context-dependent. We mapped the genomic binding sites for the endogenous wild type p53 protein in the human cancer cell line HCT116 and compared them to those we previously determined in the normal cell line IMR90. We report distinct p53 genome-wide binding landscapes in two different cell lines, analyzed under the same treatment and experimental conditions, using the same ChIP-seq approach. This is evidence for cell context dependent p53 genomic binding. The observed differences affect the p53 binding sites distribution with respect to major genomic and epigenomic elements (promoter regions, CpG islands and repeats). We correlated the high-confidence p53 ChIP-seq peaks positions with the annotated human repeats (UCSC Human Genome Browser) and observed both common and cell line specific trends. In HCT116, the p53 binding was specifically enriched at LINE repeats, compared to IMR90 cells. The p53 genome-wide binding patterns in HCT116 and IMR90 likely reflect the different epigenetic landscapes in these two cell lines, resulting from cancer-associated changes (accumulated in HCT116) superimposed on tissue specific differences (HCT116 has epithelial, while IMR90 has mesenchymal origin). Our data support the model for p53 binding to the human genome in a highly selective manner, mobilizing distinct sets of genes, contributing to distinct pathways.

Publication types

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

MeSH terms

  • Binding Sites
  • Cell Line
  • Chromatin Immunoprecipitation
  • DNA / metabolism*
  • Epigenesis, Genetic
  • Genome, Human*
  • HCT116 Cells
  • Humans
  • Long Interspersed Nucleotide Elements*
  • Organ Specificity
  • Tumor Suppressor Protein p53 / genetics
  • Tumor Suppressor Protein p53 / metabolism*

Substances

  • TP53 protein, human
  • Tumor Suppressor Protein p53
  • DNA

Grants and funding

The work described in the manuscript was performed at Brookhaven National Laboratory supported by a grant DE AC02 98CH10886 from the U.S. Department of Energy, Low Dose Radiation Research Program (CWA). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.