Abstract
BackgroundThe aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor (TF) that mediates responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Integration of TCDD-induced genome-wide AhR enrichment, differential gene expression and computational dioxin response element (DRE) analyses further elucidate the hepatic AhR regulatory network.ResultsGlobal ChIP-chip and gene expression analyses were performed on hepatic tissue from immature ovariectomized mice orally gavaged with 30 μg/kg TCDD. ChIP-chip analysis identified 14,446 and 974 AhR enriched regions (1% false discovery rate) at 2 and 24 hrs, respectively. Enrichment density was greatest in the proximal promoter, and more specifically, within ± 1.5 kb of a transcriptional start site (TSS). AhR enrichment also occurred distal to a TSS (e.g. intergenic DNA and 3' UTR), extending the potential gene expression regulatory roles of the AhR. Although TF binding site analyses identified over-represented DRE sequences within enriched regions, approximately 50% of all AhR enriched regions lacked a DRE core (5'-GCGTG-3'). Microarray analysis identified 1,896 number of TCDD-responsive genes (|fold change| ≥ 1.5, P1(t) > 0.999). Integrating this gene expression data with our ChIP-chip and DRE analyses only identified 625 differentially expressed genes that involved an AhR interaction at a DRE. Functional annotation analysis of differentially regulated genes associated with AhR enrichment identified overrepresented processes related to fatty acid and lipid metabolism and transport, and xenobiotic metabolism, which are consistent with TCDD-elicited steatosis in the mouse liver.ConclusionsDetails of the AhR regulatory network have been expanded to include AhR-DNA interactions within intragenic and intergenic genomic regions. Moreover, the AhR can interact with DNA independent of a DRE core suggesting there are alternative mechanisms of AhR-mediated gene regulation.
Highlights
The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor (TF) that mediates responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)
Identification and Characterization of TCDD-Elicited AhR Enrichment In order to identify regions of AhR enrichment induced by TCDD across the genome, Chromatin Immunoprecipitation (ChIP)-chip assays were performed using hepatic tissue from immature ovariectomized mice orally gavaged with 30 μg/kg TCDD for 2 and 24 hrs
Note that the probes are unevenly tiled throughout the genome, resulting in gaps in genome coverage that may coincide with dioxin response element (DRE) core locations that may affect AhR enriched region identification
Summary
The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor (TF) that mediates responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Integration of TCDD-induced genome-wide AhR enrichment, differential gene expression and computational dioxin response element (DRE) analyses further elucidate the hepatic AhR regulatory network. The aryl hydrocarbon receptor (AhR) is a ligand activated transcription factor (TF) belonging to the basic-helixloop-helix-PAS (bHLH-PAS) family of proteins that serve as environmental sensors [1]. The activated AhR complex heterodimerizes with the aryl hydrocarbon nuclear translocator (ARNT), another bHLH-PAS family member, and binds dioxin response elements (DREs) containing the substitution intolerant 5’-GCGTG-3’ core sequence to regulate changes in gene expression [4,7]. Genome-wide location analyses further suggest that TF binding at cis-regulatory enhancers in intergenic DNA regions of the genome may have functional significance [10,17,23,24]
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