Identification and characterization of genes susceptible to transcriptional cross-talk between the hypoxia and dioxin signaling cascades.

The aryl hydrocarbon receptor (AHR) and hypoxia inducible factors (HIFs) are transcription factors that control the adaptive response to toxicants such as dioxins and decreases in available oxygen, respectively. The AHR and HIFs utilize the same heterodimeric partner, the aryl hydrocarbon nuclear translocator (ARNT) for proper function. This requirement raises the possibility that cross-talk exists between these critical signaling systems. Single gene and reporter assays have yielded conflicting results regarding the nature of the competition for ARNT. Therefore, to determine the extent of cross-talk between the AHR and HIFs, a comprehensive analysis was performed using global gene expression analysis. The results identified 767 and 430 transcripts that are sensitive to cobalt chloride and 2,3,7,8-tetrachlorodibenzo-rho-dioxin (TCDD) stimulation, respectively, with 308 and 176, respectively, exhibiting sensitivity to cross-talk. The overlap between these two sets consists of 33 unique transcripts, including the classic target genes CYP1A1, carbonic anhydrase IX, and those involved in lipid metabolism and coagulation. Computational analysis of the regulatory region of these genes identified complex relationships between HIFs, AHR, and their respective response elements as well as other DNA motifs, including the SRF, Sp-1, NF-kB, and AP-2 binding sites. These results suggest that HIF-AHR cross-talk is limited to genes with regulatory regions that contain specific motifs and architectures.

[1]  Y. Zou,et al.  Hypoxia-associated Induction of Early Growth Response-1 Gene Expression* , 1999, The Journal of Biological Chemistry.

[2]  B. Ebert,et al.  Hypoxia and Mitochondrial Inhibitors Regulate Expression of Glucose Transporter-1 via Distinct Cis-acting Sequences (*) , 1995, The Journal of Biological Chemistry.

[3]  G. Semenza,et al.  Transcriptional regulation of genes encoding glycolytic enzymes by hypoxia-inducible factor 1. , 1994, The Journal of biological chemistry.

[4]  P. Schumacker,et al.  Mitochondrial dysfunction resulting from loss of cytochrome c impairs cellular oxygen sensing and hypoxic HIF-alpha activation. , 2005, Cell metabolism.

[5]  J. Hogenesch,et al.  The PAS superfamily: sensors of environmental and developmental signals. , 2000, Annual review of pharmacology and toxicology.

[6]  C. Bradfield,et al.  Molecular characterization of the murine Ahr gene. Organization, promoter analysis, and chromosomal assignment. , 1993, The Journal of biological chemistry.

[7]  Michael I. Wilson,et al.  C. elegans EGL-9 and Mammalian Homologs Define a Family of Dioxygenases that Regulate HIF by Prolyl Hydroxylation , 2001, Cell.

[8]  W. Farrar,et al.  Transcriptional crosstalk between nuclear receptors and cytokine signal transduction pathways in immunity. , 2004, Cellular & molecular immunology.

[9]  A. Lund,et al.  Cardiac hypertrophy in aryl hydrocarbon receptor null mice is correlated with elevated angiotensin II, endothelin-1, and mean arterial blood pressure. , 2003, Toxicology and applied pharmacology.

[10]  Edgar Wingender,et al.  TRANSFAC, TRANSPATH and CYTOMER as starting points for an ontology of regulatory networks. , 2004, In silico biology.

[11]  P. du Souich,et al.  Effect of hypoxia on cytochrome P450 activity and expression. , 2004, Current drug metabolism.

[12]  M. Gassmann,et al.  Oxygen- and dioxin-regulated gene expression in mouse hepatoma cells. , 1997, Kidney international.

[13]  Paul C Boutros,et al.  dbZach: A MIAME-compliant toxicogenomic supportive relational database. , 2006, Toxicological sciences : an official journal of the Society of Toxicology.

[14]  C. Bradfield,et al.  Liver Deformation in Ahr-Null Mice: Evidence for Aberrant Hepatic Perfusion In Early Development , 2006, Molecular Pharmacology.

[15]  L D Burgoon,et al.  Comparative analysis of dioxin response elements in human, mouse and rat genomic sequences. , 2004, Nucleic acids research.

[16]  C. Bradfield,et al.  A competitive binding assay for 2,3,7,8-tetrachlorodibenzo-p-dioxin and related ligands of the Ah receptor. , 1988, Molecular pharmacology.

[17]  G. Semenza,et al.  Characterization of hypoxia-inducible factor 1 and regulation of DNA binding activity by hypoxia. , 1993, The Journal of biological chemistry.

[18]  G. Semenza,et al.  Structural and functional analysis of hypoxia-inducible factor 1. , 1997, Kidney international.

[19]  Rafael A. Irizarry,et al.  A Model-Based Background Adjustment for Oligonucleotide Expression Arrays , 2004 .

[20]  T. Werner,et al.  MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. , 1995, Nucleic acids research.

[21]  M. Walker,et al.  Aryl hydrocarbon receptor null mice develop cardiac hypertrophy and increased hypoxia-inducible factor-1α in the absence of cardiac hypoxia , 2007, Cardiovascular Toxicology.

[22]  P. Schumacker,et al.  Mitochondrial complex III is required for hypoxia-induced ROS production and cellular oxygen sensing. , 2005, Cell metabolism.

[23]  Fumio Tajima,et al.  Determination of window size for analyzing DNA sequences , 1991, Journal of Molecular Evolution.

[24]  S. McKnight,et al.  A Conserved Family of Prolyl-4-Hydroxylases That Modify HIF , 2001, Science.

[25]  Joaquín Dopazo,et al.  GEPAS: a web-based resource for microarray gene expression data analysis , 2003, Nucleic Acids Res..

[26]  J. Hogenesch,et al.  Characterization of a Subset of the Basic-Helix-Loop-Helix-PAS Superfamily That Interacts with Components of the Dioxin Signaling Pathway* , 1997, The Journal of Biological Chemistry.

[27]  R. Johnson,et al.  Gene expression profiling of the hypoxia signaling pathway in hypoxia-inducible factor 1alpha null mouse embryonic fibroblasts. , 2003, Gene expression.

[28]  J. Giesy,et al.  Interactions between aryl hydrocarbon receptor (AhR) and hypoxia signaling pathways. , 2001, Environmental toxicology and pharmacology.

[29]  G. Semenza,et al.  Hypoxia-inducible factor 1 is a basic-helix-loop-helix-PAS heterodimer regulated by cellular O2 tension. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Chun-chung Lee,et al.  The Plasminogen Activator Inhibitor-1 Gene Is Induced by Cell Adhesion through the MEK/ERK Pathway , 2003, Journal of Biomedical Science.

[31]  R. Pollenz,et al.  Analysis of aryl hydrocarbon receptor-mediated signaling during physiological hypoxia reveals lack of competition for the aryl hydrocarbon nuclear translocator transcription factor. , 1999, Molecular pharmacology.

[32]  O. Hankinson,et al.  Identification of the Ah Receptor Nuclear Translocator Protein (Arnt) as a Component of the DNA Binding Form of the Ah Receptor , 1992, Science.

[33]  C Gennings,et al.  Empirical Bayes Gene Screening Tool for Time-Course or Dose–Response Microarray Data , 2004, Journal of biopharmaceutical statistics.

[34]  J. Caro,et al.  Hypoxia regulatory elements of the human vascular endothelial growth factor gene. , 1994, Cellular & molecular biology research.

[35]  A. Lund,et al.  Characterizing the role of endothelin-1 in the progression of cardiac hypertrophy in aryl hydrocarbon receptor (AhR) null mice. , 2006, Toxicology and applied pharmacology.

[36]  M. Gassmann,et al.  Functional interference between hypoxia and dioxin signal transduction pathways: competition for recruitment of the Arnt transcription factor , 1996, Molecular and cellular biology.

[37]  J. P. Whitlock,et al.  A Novel Cytoplasmic Protein That Interacts with the Ah Receptor, Contains Tetratricopeptide Repeat Motifs, and Augments the Transcriptional Response to 2,3,7,8-Tetrachlorodibenzo-p-dioxin* , 1997, The Journal of Biological Chemistry.

[38]  Massimo Zeviani,et al.  Oxygen sensing requires mitochondrial ROS but not oxidative phosphorylation. , 2005, Cell metabolism.

[39]  Ross Ihaka,et al.  Gentleman R: R: A language for data analysis and graphics , 1996 .

[40]  R. Tibshirani,et al.  Empirical bayes methods and false discovery rates for microarrays , 2002, Genetic epidemiology.

[41]  J. Pouysségur,et al.  HIF prolyl‐hydroxylase 2 is the key oxygen sensor setting low steady‐state levels of HIF‐1α in normoxia , 2003, The EMBO journal.

[42]  G. Semenza,et al.  Hypoxia Response Elements in the Aldolase A, Enolase 1, and Lactate Dehydrogenase A Gene Promoters Contain Essential Binding Sites for Hypoxia-inducible Factor 1* , 1996, The Journal of Biological Chemistry.

[43]  J. Whitlock,et al.  Induction of hepatic cytochrome P450 gene expression by 2,3,7,8-tetrachlorodibenzo-p-dioxin. , 1989, Molecular biology & medicine.

[44]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[45]  P. Ratcliffe,et al.  Regulation of HIF by the von Hippel‐Lindau Tumour Suppressor: Implications for Cellular Oxygen Sensing , 2001, IUBMB life.