High-Resolution Genome-wide Mapping of AHR and ARNT Binding Sites by ChIP-Seq

Abstract

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.

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.…”

Regulation of pyruvate metabolism and human disease

“…However, under hypoxic conditions, hydroxylation does not occur, stabilizing HIF1α and targeting it for translocation into the nucleus [141, 145]. HIF1β, on the other hand, is a constitutively expressed transcription factor which is involved in several other signaling pathways, most notably the detoxification of polyaromatic hydrocarbons [149]. Several hundred genes are transcriptionally regulated by HIF1.…”