Cytochrome c oxidase (COX) is one of only four bigenomic proteins in mammalian cells, having ten subunits encoded in the nuclear genome and three in the mitochondrial DNA. The mechanism of its bigenomic control is not well understood. The ten nuclear subunits are on different chromosomes, and the possibility of their coordinate regulation by the same transcription factor(s) deserves serious consideration. The present study tested our hypothesis that nuclear respiratory factor 1 (NRF-1) serves such a role in subunit coordination. Following in silico analysis of murine nuclear-encoded COX subunit promoters, electrophoretic mobility shift and supershift assays indicated NRF-1 binding to all ten promoters. In vivo chromatin immunoprecipitation assays also showed NRF-1 binding to all ten promoters in murine neuroblastoma cells. Site-directed mutagenesis of putative NRF-1 binding sites confirmed the functionality of NRF-1 binding on all ten COX promoters. These sites are highly conserved among mice, rats, and humans. Silencing of NRF-1 with RNA interference reduced all ten COX subunit mRNAs and mRNAs of other genes involved in mitochondrial biogenesis. We conclude that NRF-1 plays a significant role in coordinating the transcriptional regulation of all ten nuclearencoded COX subunits in neurons. Moreover, NRF-1 is known to activate mitochondrial transcription factors A and B, thereby indirectly regulating the expressions of the three mitochondrial-encoded COX subunits. Thus, NRF-1 and our previously described NRF-2 prove to be the two key bigenomic coordinators for transcriptional regulation of all cytochrome c oxidase subunits in neurons. Possible interactions between the NRFs will be investigated in the future.Cytochrome c oxidase or complex IV is a large transmembrane protein located in the inner mitochondrial membrane of eukaryotes and plasma membrane of prokaryotes. It is the terminal enzyme of the electron transport chain, catalyzing the transfer of electrons from reduced cytochrome c to molecular oxygen to form water. The important outcome of this reaction is the generation of ATP through the coupled process of oxidative phosphorylation. Neurons are highly dependent upon ATP for their activity and functions (1). Approximately 90% of ATP generated in the brain is synthesized in the mitochondria via oxidative phosphorylation (2). The activity of this enzyme is reduced in neurodegenerative diseases, such as Alzheimer disease (3, 4). Among respiratory chain deficiencies presented in infancy and early childhood in humans, cytochrome c oxidase (COX) 2 deficiency is the most commonly diagnosed (5). COX deficiency is found with different clinical phenotypes primarily affecting organs with high energy demand, such as the brain, skeletal muscle, heart, and kidney (6).COX is a complex of 13 different subunits, 3 of which (I, II, and III) are encoded in the mitochondrial DNA, and the remaining 10 are nuclear-encoded (7). To form a functional holoenzyme with 1:1 stoichiometry, exact coordination is essential between the two...