AhR also directly interacts with COUP TF to repress ER mediated gene expression. De Novo Motif Analysis Approximately 50% of enriched regions lacked the DRE core sequence suggesting AhR interacts with DNA using alternate strategies. De novo motif ana lysis of these regions using the Gibbs motif sampler in CisGenome identified over representation of comparable repetitive elements in both the intergenic and intragenic DNA regions. Comparison of over represented non repetitive motifs to existing TF binding motifs in JASPAR and TRANSFAC using STAMP identified similarities to Inhibitors,Modulators,Libraries COUP TF, hepato cyte nuclear factor 4, liver receptor homolog 1 and PPAR binding sites. Interestingly, COUP TF and HNF4 belong to the NR2F family identified in the TFBS over representation analy sis of all AhR enriched regions.

The presence of these binding motifs in non DRE containing regions of AhR enrichment further Inhibitors,Modulators,Libraries suggests that AhR DNA interactions occur through a tethering mechanism invol ving other TFs or by tertiary looping of DNA. Of the 10,369 enrichments Anacetrapib identified in the intragenic DNA Inhibitors,Modulators,Libraries regions, 43. 8% contained a DRE core at 2 hrs, and 52. 4% at 24 hrs. These intragenic AhR enriched regions mapped to 5,307 and 591 unique genes at 2 and 24 hrs, respectively. Molecular and cellular functional analysis using Ingenuity Pathway Analysis found these genes to be associated with lipid and carbohydrate metabolism, small molecule biochemistry, cell cycle and gene expression based on a Fishers Exact Test p value 0. 01. Furthermore, 63. 5 and 56.

2% of the genes associated with AhR enrichment at 2 and 24 hrs, respectively, contained a DRE core within the region of enrichment. The higher percen tage of genes containing a DRE core compared to enriched regions with a DRE core is due to multiple regions of AhR enrichment associated with a single gene. The remaining genes with significant AhR enrichment were targeted independently Inhibitors,Modulators,Libraries of a DRE core. At both 2 and 24 hrs, 575 genes had AhR enrichment, with 513 possessing DRE cores in the AhR enriched region. Only 16 genes exhibited AhR enrich ment solely at 24 hrs, with three containing a DRE core. In contrast, 4,732 genes possessed significant AhR enrichment with 60. 4% containing a DRE core within the region of enrichment at 2 hrs. Due to the large overlap of enriched regions at 2 and 24 hrs, the remaining analysis focuses predominantly on the AhR enrichment at 2 hr.

Comparison of Transcriptional Responses with AhR Enrichment Gene expression analysis at 2, 4, 8, 12, 18, 24, 72, and 168 hrs identified 1,896 unique differentially expressed genes 0. 999 at one or more time points. Of the 1,896 TCDD responsive genes, 900 genes possessed significant AhR enrichment within the intragenic region. Moreover, of the 900 genes exhibiting AhR enrichment at 2 hrs, 625 contained a DRE core sequence, suggest ing these responses are AhR mediated.