Dioxin-responsive AHRE-II gene battery: identification by phylogenetic footprinting

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Abstract

We identified a set of genes that respond to dioxins through the recently discovered AHRE-II (“XRE-II”) enhancer element. A total of 36 genes containing AHRE-II motifs conserved across human, mouse, and rat gene orthologs were identified by genome-wide transcription-factor binding-site searches and phylogenetic footprinting. Microarray experiments on liver from rats treated with 2,3,7,8-tetrachlorodibenzo-p-dioxin revealed statistically significant changes in mRNA levels for 13 of these 36 genes after three hours and 15 genes after 19 h. The set of responsive genes was functionally characterized by ontological analysis and found to be enriched in ion-channels and transporters. Our identification of 36 putatively AHRE-II-regulated genes highlights the regulatory versatility of the aryl hydrocarbon receptor (AHR) and the ability of the AHR and its dimerization partner, ARNT, to act both as a ligand-activated transcription-factor (on AHRE-I) and as a ligand-activated coactivator (on AHRE-II). Collectively, these results demonstrate that the AHRE-II induction mechanism is employed by multiple genes and provide the first categorization of the gene battery of a ligand-activated coactivator.

Section snippets

Materials and methods

Extraction of genomic sequence. Complete genomic sequences were downloaded from the University of California, Santa Cruz (UCSC Golden Path) genome browser at http://genome.ucsc.edu. The releases used were: hg16 (human: NCBI build 34), mm4 (mouse: NCBI build 32), and rn3 (rat: Baylor v3.1). For each build we also downloaded the refLink and refFlat annotation tables which link LocusLink identifiers with gene symbols and with genomic locations, respectively. These tables were parsed with Perl

Motivation for phylogenetic footprinting

It is feasible to search all genes for all known transcription-factor binding-sites (TFBSs). Unfortunately the vast majority of binding-sites identified in this type of comprehensive search are biologically inactive false-positives. For example, TATA-box sequences are predicted to occur once every 250 bp throughout the entire genome. Some workers in the field have postulated a “Futility Theorem” saying that, to a first-approximation, all predicted TFBSs are non-functional [37]. Various methods

Discussion

Novel dioxin-responsive genes have been identified previously, both in microarray studies [42], [43], [44], [45] and by the careful study of individual genes and their promoters [46]. We combined these two approaches by using both genome-wide transcription-factor binding-site searches and genome-wide mRNA expression profiling. The use of phylogenetic footprinting across the three best-characterized mammalian genomes helped refine the candidate list of AHRE-II-regulated genes by 15-fold. Our

Acknowledgments

We thank the BioPerl, BioConductor, and DBI user support groups for implementation advice, Ms. Lan He for outstanding technical support with Affymetrix arrays, and Dr. Rafal Kustra for helpful discussions on statistical analyses. This study was funded by Grant MOP-57903 from the Canadian Institutes of Health Research to A.B.O., by Grant 200980 from the Academy of Finland to R.P. and Grant 53307 from the Academy of Finland Centre of Excellence Program to J.T.

References (48)

  • J.A. Walisser et al.

    Patent ductus venosus and dioxin resistance in mice harboring a hypomorphic Arnt allele

    J. Biol. Chem.

    (2004)
  • A. Kobayashi et al.

    Cooperative interaction between AhR.Arnt and Sp1 for the drug-inducible expression of CYP1A1 gene

    J. Biol. Chem.

    (1996)
  • L. Zhang et al.

    Ah receptor regulation of mouse Cyp1B1 is additionally modulated by a second novel complex that forms at two AhR response elements

    Toxicol. Appl. Pharmacol.

    (2003)
  • K. Sogawa et al.

    A novel induction mechanism of the rat CYP1A2 gene mediated by Ah receptor-Arnt heterodimer

    Biochem. Biophys. Res. Commun.

    (2004)
  • S.L. Baldauf

    Phylogeny for the faint of heart: a tutorial

    Trends Genet.

    (2003)
  • A. Puga et al.

    The transcriptional signature of dioxin in human hepatoma HepG2 cells

    Biochem. Pharmacol.

    (2000)
  • F.W. Frueh et al.

    Use of cDNA microarrays to analyze dioxin-induced changes in human liver gene expression

    Toxicol. Lett.

    (2001)
  • J. Guo et al.

    Expression of genes in the TGF-beta signaling pathway is significantly deregulated in smooth muscle cells from aorta of aryl hydrocarbon receptor knockout mice

    Toxicol. Appl. Pharmacol.

    (2004)
  • D. Demozay et al.

    Fatty aldehyde dehydrogenase: potential role in oxidative stress protection and regulation of its gene expression by insulin

    J. Biol. Chem.

    (2004)
  • O. Hankinson

    The aryl hydrocarbon receptor complex

    Annu. Rev. Pharmacol. Toxicol.

    (1995)
  • T.V. Beischlag et al.

    Recruitment of the NCoA/SRC-1/p160 family of transcriptional coactivators by the aryl hydrocarbon receptor/aryl hydrocarbon receptor nuclear translocator complex

    Mol. Cell. Biol.

    (2002)
  • J.C. Rowlands et al.

    Trans-activation by the human aryl hydrocarbon receptor and aryl hydrocarbon receptor nuclear translocator proteins: direct interactions with basal transcription factors

    Mol. Pharmacol.

    (1996)
  • D.B. Carlson et al.

    A dynamic role for the Ah receptor in cell signaling? Insights from a diverse group of Ah receptor interacting proteins

    J. Biochem. Mol. Toxicol.

    (2002)
  • T. Shimada et al.

    Arylhydrocarbon receptor-dependent induction of liver and lung cytochromes P450 1A1, 1A2, and 1B1 by polycyclic aromatic hydrocarbons and polychlorinated biphenyls in genetically engineered C57BL/6J mice

    Carcinogenesis

    (2002)
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    Abbreviations: We use the term AHRE to refer to the specific genomic regulatory nucleotide sequences that respond to the AH receptor and its agonist ligands. AHRE also is known as DRE (dioxin response element) or xenobiotic responsive element (XRE). AHR, aryl hydrocarbon receptor; ALDH3A2, aldehyde dehydrogenase 3A2; AnoC, anomalous Cyp1b1 complex; ARNT, aryl hydrocarbon receptor nuclear translocator; ER, estrogen receptor; LAC, ligand-activated coactivator; TCDD, 2,3,7,8-tetrachlorodibenzo-p-dioxin; TFBS, transcription-factor binding-site; TSS, transcription start site.

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