Genome-Wide ChIPseq Analysis of AhR, COUP-TF, and HNF4 Enrichment in TCDD-Treated Mouse Liver

Abstract

The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor known for mediating the toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and related compounds. Although the canonical mechanism of AhR activation involves heterodimerization with the aryl hydrocarbon receptor nuclear translocator, other transcriptional regulators that interact with AhR have been identified. Enrichment analysis of motifs in AhR-bound genomic regions implicated co-operation with COUP transcription factor (COUP-TF) and hepatocyte nuclear factor 4 (HNF4). The present study investigated AhR, HNF4α and COUP-TFII genomic binding and effects on gene expression associated with liver-specific function and cell differentiation in response to TCDD. Hepatic ChIPseq data from male C57BL/6 mice at 2 h after oral gavage with 30 µg/kg TCDD were integrated with bulk RNA-sequencing (RNAseq) time-course (2–72 h) and dose–response (0.01–30 µg/kg) datasets to assess putative AhR, HNF4α and COUP-TFII interactions associated with differential gene expression. Functional enrichment analysis of differentially expressed genes (DEGs) identified differential binding enrichment for AhR, COUP-TFII, and HNF4α to regions within liver-specific genes, suggesting intersections associated with the loss of liver-specific functions and hepatocyte differentiation. Analysis found that the repression of liver-specific, HNF4α target and hepatocyte differentiation genes, involved increased AhR and HNF4α binding with decreased COUP-TFII binding. Collectively, these results suggested TCDD-elicited loss of liver-specific functions and markers of hepatocyte differentiation involved interactions between AhR, COUP-TFII and HNF4α.

TCDD dysregulation of lncRNA expression, liver zonation and intercellular communication across the liver lobule

“…2,3,7,8-Tetrachlorodibenzo- p -dioxin (TCDD) is a persistent hepatotoxic environmental chemical that directly binds to aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor that dysregulates hundreds of genes 1, 2 . TCDD-activated AhR translocates to the nucleus, where it heterodimerizes with Arnt and then binds to chromatin at thousands of regulatory sequences controlling transcription of linked target genes 3 . TCDD also induces AhR-dependent nongenomic signaling via changes in intracellular Ca 2+ and activation of the tyrosine kinase src and downstream kinases 4, 5 .…”

DegCre: Probabilistic association of differential gene expression with regulatory regions

“…Such knowledge, however, is of high value for both basic and applied biology. Examples include better interpretation of how genetic variation in a CRE leads to molecular and phenotypic effect (Ulirsch et al 2016; van Arensbergen et al 2019; Song et al 2019; Nasser et al 2021) and better prediction of the effects of perturbations, such as drug treatment, on gene expression levels in a cell or tissue (Thormann et al 2018; Carleton et al 2020; Cholico et al 2022).…”

Dose-dependent disruption of hepatic zonation by 2,3,7,8-tetrachlorodibenzo-p-dioxin in mice: integration of single-nuclei RNA sequencing and spatial transcriptomics

“…Our previous work has suggested a global loss of hepatic function following TCDD treatment, especially functions associated with hepatocyte metabolism (Nault et al , 2021; Nault et al , 2017a). Moreover, it is established that AHR activation by TCDD perturbs mechanisms associated with the maintenance of zonation including HNF4α binding and Wnt signaling (Cholico et al , 2022; Moreno-Marin et al , 2018; Yang et al , 2022). In this study we aimed to further characterize the cell-cell interactions in the mouse liver that were disrupted by TCDD and resulted in the loss of hepatic zonation.…”