PHOX2A is a paired-like homeodomain transcription factor that participates in specifying the autonomic nervous system. It is also involved in the transcriptional control of the noradrenergic neurotransmitter phenotype as it regulates the gene expression of tyrosine hydroxylase and dopamine--hydroxylase. The results of this study show that the human orthologue of PHOX2A is also capable of regulating the transcription of the human ␣3 nicotinic acetylcholine receptor gene, which encodes the ligand-binding subunit of the ganglionic type nicotinic receptor. In particular, we demonstrated by chromatin immunoprecipitation and DNA pulldown assays that PHOX2A assembles on the SacI-NcoI region of ␣3 promoter and, by cotransfection experiments, that it exerts its transcriptional effects by acting through the 60-bp minimal promoter. PHOX2A does not seem to bind to DNA directly, and its DNA binding domain seems to be partially dispensable for the regulation of ␣3 gene transcription. However, as suggested by the findings of our co-immunoprecipitation assays, it may establish direct or indirect protein-protein interactions with Sp1, thus regulating the expression of ␣3 through a DNA-independent mechanism. As the ␣3 subunit is expressed in every terminally differentiated ganglionic cell, this is the first example of a "pan-autonomic" gene whose expression is regulated by PHOX2 proteins.The high degree of cellular heterogeneity of the mammalian nervous system is because of distinct specification and differentiation processes that mainly rely on transcriptional control mechanisms mediated by transcription factors having discrete temporal patterns of region-specific and cell type-specific expression.PHOX2A and PHOX2B are paired-like homeodomain proteins that have been shown to play a pivotal role in the development of the three peripheral divisions of the autonomic nervous system (1). They are also expressed in all of the noradrenergic neurons of the brainstem, in some cranial sensory ganglia that participate in autonomic reflexes, and in a subset of cranial motor neurons (2). None of the components of the autonomic nervous system develop properly in Phox2b knock-out mice (3), whereas Phox2a null mutants show an apparently less severe phenotype that only involves the agenesis of the Locus coeruleus and atrophy of the cranial sensory ganglia (4); nevertheless, they do not feed and die on the day of birth. The different phenotypes of Phox2 knock-out mutants along with their asynchronous onset of expression during development underscore that the two factors are not functionally equivalent. This has been more directly demonstrated by reciprocal gene replacement experiments (5) that led to the conclusion that biochemical differences may be responsible for the specific function of each paralogue.It is worth noting that PHOX2 proteins are also involved in the transcriptional control of the neurotransmitter phenotype (6); they play a fundamental role in the terminal differentiation of the orthosympathetic system as they regulate the gene...