Integration of Genome-Wide Computation DRE Search, AhR ChIP-chip and Gene Expression Analyses of TCDD-Elicited Responses in the Mouse Liver

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.

Empirical likelihood tests for nonparametric detection of differential expression from RNA-seq data

“…Results showing KEGG (Ogata et al, 1999;Kanehisa and Goto, 2000;Kanehisa et al, 2002) pathways that are significantly enriched in our set of DE genes are tabulated in Table 3. In agreement with Salisbury et al (2014), we find that a known 2, 3, 7, 8 tetrachlorodibenzo-p-dioxin (TCDD) pathway is enriched in the set of DE genes, namely metabolism of xenobiotics by cytochrome P450 (Dere et al, 2011;Lo and Matthews, 2012).…”

Pax3 and Pax7 Play Essential Safeguard Functions against Environmental Stress-Induced Birth Defects

“…Accordingly, it was shown that AHR directly binds the first intron of p21 in vitro (Barnes-Ellerbe et al, 2004;Dere et al, 2011;Lo and Matthews, 2012). Importantly, despite p21 expression being upregulated, all TCDD-treated Pax3 GFP/+ embryos developed normally, suggesting that additional GRNs downstream of PAX3 are also regulating craniofacial development.…”

A distal enhancer controls cytokine-dependent human cPLA2α gene expression

“…Analogous to our results on C/EBP ␤ , ChIP analysis has shown that the PHOX2A transcription factor can also associate with and regulate the human ␣ 3 nicotinic receptor subunit promoter through a DNA-independent mechanism ( 69 ). Furthermore, genomewide ChIP-chip arrays and ChIP-seq data for AhR indicates that ‫ف‬ 50% of the AhR-enriched regions lack any dioxin response element (DRE) ( 70 ). We therefore believe that C/EBP ␤ functions as a transcriptional activator through interaction with a large transcription complex, including p300, independent of DNA binding.…”