High-resolution genome-wide mapping of AHR and ARNT binding sites by ChIP-Seq

Toxicol Sci. 2012 Dec;130(2):349-61. doi: 10.1093/toxsci/kfs253. Epub 2012 Aug 17.


The aryl hydrocarbon receptor (AHR) and AHR nuclear translocator (ARNT) activated complex regulates genes in response to the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). AHR has also emerged as a potential therapeutic target for the treatment of human diseases and different cancers, including breast cancer. To better understand AHR and ARNT signaling in breast cancer cells, we used chromatin immunoprecipitation linked to high-throughput sequencing to identify AHR- and ARNT-binding sites across the genome in TCDD-treated MCF-7 cells. We identified 2594 AHR-bound, 1352 ARNT-bound, and 882 AHR/ARNT cobound regions. No significant differences in the genomic distribution of AHR and ARNT were observed. Approximately 60% of the cobound regions contained at least one core an aryl hydrocarbon response element (AHRE), 5'-GCGTG-3'. AHR/ARNT peak density was the highest within 1 kb of transcription start sites (TSS); however, a number of AHR/ARNT cobound regions were located as far as 100 kb from TSS. De novo motif discovery identified a symmetrical variation of the AHRE (5'-GTGCGTG-3'), as well as FOXA1 and SP1 binding motifs. Microarray analysis identified 104 TCDD-responsive genes where 98 genes were upregulated by TCDD. Of the 104 regulated genes, 69 (66.3%) were associated with an AHR- or ARNT-bound region within 100 kb of their TSS. Overall our study identified AHR/ARNT cobound regions across the genome, revealed the importance but not absolute requirement for an AHRE in AHR/ARNT interactions with DNA, and identified a modified AHRE motif, thereby increasing our understanding of AHR/ARNT signaling pathway.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aryl Hydrocarbon Receptor Nuclear Translocator / genetics*
  • Aryl Hydrocarbon Receptor Nuclear Translocator / metabolism
  • Basic Helix-Loop-Helix Transcription Factors / drug effects
  • Basic Helix-Loop-Helix Transcription Factors / genetics*
  • Basic Helix-Loop-Helix Transcription Factors / metabolism
  • Binding Sites
  • Breast Neoplasms / genetics*
  • Breast Neoplasms / metabolism
  • Chromatin Immunoprecipitation*
  • Environmental Pollutants / toxicity
  • Female
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic / drug effects
  • Gene Regulatory Networks
  • Hepatocyte Nuclear Factor 3-alpha / metabolism
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • MCF-7 Cells
  • Nucleotide Motifs
  • Oligonucleotide Array Sequence Analysis
  • Polychlorinated Dibenzodioxins / toxicity
  • Receptors, Aryl Hydrocarbon / drug effects
  • Receptors, Aryl Hydrocarbon / genetics*
  • Receptors, Aryl Hydrocarbon / metabolism
  • Response Elements
  • Sequence Analysis, DNA*
  • Signal Transduction
  • Sp1 Transcription Factor / metabolism


  • AHR protein, human
  • ARNT protein, human
  • Basic Helix-Loop-Helix Transcription Factors
  • Environmental Pollutants
  • FOXA1 protein, human
  • Hepatocyte Nuclear Factor 3-alpha
  • Polychlorinated Dibenzodioxins
  • Receptors, Aryl Hydrocarbon
  • Sp1 Transcription Factor
  • Aryl Hydrocarbon Receptor Nuclear Translocator