The heterodimeric transcription factor hypoxia-inducible factor (HIF) plays an important role in the progression of a number of processes in which O 2 availability is compromised and, as such, has become an increasingly attractive therapeutic target. Although tremendous progress has been made in recent years in unraveling the mechanisms underlying O 2 -dependent regulation of HIF through its O 2 -dependent degradation domain and C-terminal transactivation domain, our understanding of the contributions of other structural elements, particularly the Per/ARNT/Sim (PAS)-A and PAS-B domains, to the activity of HIF is incomplete. Using insights derived from the recently determined solution structures of the HIF PAS-B domains as a starting point, we have explored the function(s) of the HIF-2␣ PAS domains via mutational analysis. In contrast to recent models, our data reveal that both PAS domains of the HIF-␣ subunit are necessary for heterodimer formation but are not required to mediate other HIF functions in which PAS domains have been implicated. Because disruption of individual PAS domains compromise HIF function independent of the mechanism of HIF induction, these data demonstrate the potential utility of targeting these domains for therapeutic applications.A pathway to sense and respond to changes in O 2 availability is expressed in virtually every mammalian cell, contributing to a host of developmental, physiological, and pathophysiological processes (reviewed in Ref. 1). This ubiquitous hypoxic response pathway involves changes in gene expression mediated through the induction of hypoxiainducible transcription factors (HIFs).2 HIFs are obligate heterodimers composed of single copies of ␣-and -subunits, the latter of which is also called the aryl hydrocarbon receptor nuclear translocator (ARNT) (2). The mammalian genome contains three HIF-␣ genes, HIF-1␣, HIF-2␣ (also called endothelial Per/ARNT/Sim (PAS) domain protein 1 or HIF-like factor), and HIF-3␣ (3-5), that share similar domain structures but likely serve nonoverlapping physiological roles (6, 7).Although the HIF- subunit is essentially insensitive to O 2 availability, both the accumulation and activity of the HIF-␣ subunit are acutely induced in response to low O 2 levels (reviewed in Ref. 8). Briefly, multiple proline residues within the oxygen-dependent degradation domain (9) of the ␣-subunit are selectively hydroxylated under normoxic conditions (10, 11) and subsequently recognized by the product of the von Hippel-Lindau tumor suppressor gene (pVHL). pVHL is a component of a ubiquitin-protein ligase complex that tags the ␣-subunit for rapid proteasomal degradation (12-16). A second independent O 2 -dependent hydroxylation activity directed toward an asparagine residue within the C-terminal transactivation domain of the ␣-subunit blocks coactivator recruitment under normoxic conditions (17). By virtue of their utilization of O 2 as a substrate, the prolyl (18 -20) and asparaginyl hydroxylases (21, 22) that regulate HIF are potential "oxygen sensors" ...