The instability of the hepatocyte phenotype in vitro has limited the ability to quantitatively investigate regulation of stress responses of the liver. Here, we adopt a tissue-engineering approach to form stable liver tissue in vitro by forming collagen "sandwich" cultures of transgenic murine hepatocytes harboring a regulatory gene of interest flanked by loxP sites. The floxed gene is excised in a subset of cultures by transfection with adenovirus carrying the gene for Cre-recombinase, thereby generating wild-type and null liver tissues from a single animal. In this study, we specifically investigated the role of hypoxia inducible factor 1 alpha (HIF-1alpha) in the hepatocellular response to hypoxia. Using high-density oligonucleotide arrays, we examined genome-wide gene expression after 8 h of hypoxia in wild-type and HIF- 1alpha null hepatocyte cultures. We identified more than 130 genes differentially expressed under hypoxia involved in metabolic adaptation, angiogenic signaling, immediate early response, and cell cycle regulation. Real-time polymerase chain reaction analysis verified that known hypoxia-responsive genes such as glucose transporter-1 and vascular endothelial growth factor were induced in a HIF-1alpha-dependent manner under hypoxia. Our results demonstrate the potential to integrate in vitro tissue models with transgenic and microarray technologies for the study of physiologic stress responses.