Hypoxia-inducible factor 1␣ (HIF-1␣) and the HIF-like factor (HLF) are two highly related basic Helix-LoopHelix/Per-Arnt-Sim (bHLH/PAS) homology transcription factors that undergo dramatically increased function at low oxygen levels. Despite strong similarities in their activation mechanisms (e.g. they both undergo rapid hypoxia-induced protein stabilization, bind identical target DNA sequences, and induce synthetic reporter genes to similar degrees), they are both essential for embryo survival via distinct functions during vascularization (HIF-1␣) or catecholamine production (HLF). It is currently unknown how such specificity of action is achieved. We report here that DNA binding by HLF, but not by HIF-1␣, is dependent upon reducing redox conditions. In vitro DNA binding and mammalian two-hybrid assays showed that a unique cysteine in the DNA-binding basic region of HLF is a target for the reducing activity of redox factor Ref- Cells of aerobic organisms depend upon a plentiful supply of oxygen for energy production, and consequently, a number of mechanisms have evolved to sense and respond to disruptions of oxygen homeostasis. Although several signal transduction and gene regulatory mechanisms have been established to operate in response to oxidative stresses induced by intracellular oxygen radical production or cell penetration by oxidants, mammalian gene regulatory pathways that respond to hypoxia (low oxygen) have only recently begun to be understood. Analysis of hypoxia-induced activation of the erythropoietin gene led to the cloning of HIF-1␣ 1 (1), a transcription factor that exhibits marked increases in stability and transcription potency at low intracellular oxygen levels (for a recent review, see Ref.2). HIF-1␣ is a member of a bHLH protein subfamily that contains PAS dimerization domains juxtaposed with the bHLH. A number of bHLH/PAS factors have now been cloned and found to have crucial roles in physiological functions as diverse as xenobiotic metabolism (the dioxin or Ah receptor), maintenance of circadian rhythms (Clock and Period), and neurogenesis (Single-minded) (for a recent review, see Ref.3). Like the dioxin receptor, HIF-1␣ responds to environmental cues to form a functional heterodimer with a general bHLH/ PAS partner protein, Arnt (Ah receptor nuclear translocator). A closely related factor, the HIF-like factor (HLF (4); also known as EPAS1 (endothelial PAS1) (5), HIF-related factor (6), and MOP2 (member of PAS family 2) (7)), shares 48% amino acid identity with HIF-1␣ and is correspondingly induced by hypoxia to form a transcriptionally active HLF/Arnt heterodimer. In vitro mechanistic analysis of HIF-1␣ and HLF revealed that they dimerize with Arnt with similar affinities (4); bind to the same consensus hypoxia response elements found in genes such as erythropoietin (EPO) and vascular endothelial growth factor; and in transient transfection assays, activate reporter genes with similar intensities when under hypoxic stress (4,5,8). RNA and protein blot analyses showed both HLF and HIF-1␣...