Differential regulation of the transcriptional activities of hypoxia-inducible factor 1 alpha (HIF-1α) and HIF-2α in stem cells

Transcriptional responses to hypoxia are primarily mediated by hypoxia-inducible factors (HIFs), HIF-1 alpha and HIF-2 alpha. The HIF-1 alpha and HIF-2 alpha subunits are structurally similar in their DNA binding and dimerization domains but differ in their transactivation domains, implying they may have unique target genes and require distinct transcriptional cofactors. Our previous results demonstrated that HIF-1 alpha and HIF-2 alpha regulate distinct target genes. Here, we report that HIF-2 alpha is not transcriptionally active in embryonic stem (ES) cells, as well as possible inhibition by a HIF-2 alpha-specific transcriptional repressor. Using DNA microarray analysis of hypoxia-inducible genes in wild-type (WT), Hif-1 alpha(-/-), and Hif-2 alpha(-/-) ES cells, we show that HIF-1 alpha induces a large number of both confirmed and novel hypoxia-inducible genes, while HIF-2a does not activate any of its previously described targets. We further demonstrate that inhibition of HIF-2a function occurs at the level of transcription cofactor recruitment to endogenous target gene promoters. Overexpression of WT and, notably, a DNA-binding-defective HIF-2 alpha mutant restores endogenous HIF-2a protein activity, suggesting that ES cells express a HIF-2 alpha-specific corepressor that can be titrated by overexpressed HIF-2 alpha protein. HIF-2 alpha repression may explain why patients with mutations in the VHL tumor suppressor gene display cancerous lesions in specific tissue types.