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Cells need oxygen (O2) to meet their metabolic demands. Highly efficient systems of O2-sensing have evolved to initiate responses enabling cells to adapt their metabolism to reduced O2 availability. Of central importance is the activation of hypoxia-inducible factor-1 (HIF-1), a transcription factor complex that controls the expression of genes the products of which regulate glucose uptake and metabolism, vasotonus and angiogenesis, oxygen capacity of the blood as well as cell growth and death. Activation of HIF-1 requires the accumulation and nuclear translocation of the HIF-1alpha subunit, its dimerization with HIF-1beta and the binding of co-activator proteins such as p300. In this study we investigated the three-dimensional (3D) distribution of HIF-1alpha within the nucleus and assigned its localization to known nuclear compartments. Using two-photon microscopy we determined the colocalization of HIF-1alpha and -beta subunits within nuclear domains as well as overlaps between HIF-1alpha and p300. Our data provide information on the nuclear distribution of HIF-1alpha with respect to subnuclear domains that could serve as specific locations for hypoxia-induced gene expression.