Genomewide analysis of aryl hydrocarbon receptor binding targets reveals an extensive array of gene clusters that control morphogenetic and developmental programs.
BACKGROUND
The vertebrate aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that regulates cellular responses to environmental polycyclic and halogenated compounds. The naive receptor is believed to reside in an inactive cytosolic complex that translocates to the nucleus and induces transcription of xenobiotic detoxification genes after activation by ligand.


OBJECTIVE
We conducted an integrative genomewide analysis of AHR gene targets in mouse hepatoma cells and determined whether AHR regulatory functions may take place in the absence of an exogenous ligand.


METHODS
The network of AHR-binding targets in the mouse genome was mapped through a multipronged approach involving chromatin immunoprecipitation/chip and global gene expression signatures. The findings were integrated into a prior functional knowledge base from Gene Ontology, interaction networks, Kyoto Encyclopedia of Genes and Genomes pathways, sequence motif analysis, and literature molecular concepts.


RESULTS
We found the naive receptor in unstimulated cells bound to an extensive array of gene clusters with functions in regulation of gene expression, differentiation, and pattern specification, connecting multiple morphogenetic and developmental programs. Activation by the ligand displaced the receptor from some of these targets toward sites in the promoters of xenobiotic metabolism genes.


CONCLUSIONS
The vertebrate AHR appears to possess unsuspected regulatory functions that may be potential targets of environmental injury.
Sartor
Maureen A
MA
Laboratory for Statistical Genomics and Systems Biology, Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45220, USA.
Schnekenburger
Michael
M
Marlowe
Jennifer L
JL
Reichard
John F
JF
Wang
Ying
Y
Fan
Yunxia
Y
Ma
Ci
C
Karyala
Saikumar
S
Halbleib
Danielle
D
Liu
Xiangdong
X
Medvedovic
Mario
M
Puga
Alvaro
A
D000818:Animals; D001665:Binding Sites / Q000235:genetics; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation; D020869:Gene Expression Profiling; D051379:Mice; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics* / Q000502:physiology; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D011485:Protein Binding / Q000235:genetics / Q000502:physiology; D018336:Receptors, Aryl Hydrocarbon / Q000378:metabolism*
D018336:Receptors, Aryl Hydrocarbon