Functional genomic analysis of non-canonical DNA regulatory elements of the aryl hydrocarbon receptor.

Abstract

The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that is activated by environmental toxicants, like halogenated and polycyclic aromatic hydrocarbons, and then binds to DNA and regulates gene expression. AHR is involved in various physiological processes, including liver and immune system function, cell cycle regulation, oncogenesis, and metabolism. In the canonical pathway, AHR binds to a consensus DNA sequence (GCGTC), termed the xenobiotic response element (XRE), recruits protein coregulators, and regulates target gene expression. Emerging evidence suggests that AHR may regulate gene expression via an additional pathway, by binding to a non-consensus DNA sequence (GGGA) termed the non- consensus XRE (NC-XRE). The prevalence of NC-XRE motifs in the genome is not known. Studies using chromatin immunoprecipitation and reporter genes provide indirect evidence of AHR-NC-XRE interactions, but direct evidence for an AHR-NC-XRE interaction that regulates transcription in a natural genomic context is lacking. Here, we analyzed AHR binding to NC-XRE DNA on a genome-wide scale in mouse liver. We integrated ChIP-seq and RNA-seq data and identified putative AHR target genes with NC-XRE motifs in regulatory regions. We found that NC-XRE motifs are present in 82% of AHR-bound DNA, which are significantly enriched relative to random genomic regions. These AHR-bound regions include, but are not limited to, promoters and enhancers of AHR target genes. To obtain direct evidence of AHR regulation via this non-canonical pathway, we performed functional genomics on the mouse Serpine1 gene, a putative AHR target via NC-XRE. Deleting NC-XRE motifs from the Serpine1 promoter reduced the upregulation of Serpine1 by TCDD, an AHR ligand. We conclude that AHR upregulates Serpine1 via NC-XRE DNA. Taken together, our results provide the first direct evidence of AHR-mediated gene regulation via NC-XRE in a natural genomic context. These findings enhance our understanding of AHR-bound DNA regions and their influence on target gene expression. Our results will also improve our ability to identify AHR target genes and their physiological relevance.