Transcription is essential for neurite and axon outgrowth during development. Recent work points to the involvement of nuclear factor of activated T cells (NFAT) in the regulation of genes important for axon growth and guidance. However, NFAT has not been reported to directly control the transcription of axon outgrowth-related genes. To identify transcriptional targets, we performed an in silico promoter analysis and found a putative NFAT site within the GAP-43 promoter. Using in vitro and in vivo experiments, we demonstrated that NFAT-3 regulates GAP-43, but unexpectedly, does not promote but represses the expression of GAP-43 in neurons and in the developing brain. Specifically, in neuron-like PC-12 cells and in cultured cortical neurons, the overexpression of NFAT-3 represses GAP-43 activation mediated by neurotrophin signaling. Using chromatin immunoprecipitation assays, we also show that prior to neurotrophin activation, endogenous NFAT-3 occupies the GAP-43 promoter in PC-12 cells, in cultured neurons, and in the mouse brain. Finally, we observe that NFAT-3 is required to repress the physiological expression of GAP-43 and other proaxon outgrowth genes in specific developmental windows in the mouse brain. Taken together, our data reveal an unexpected role for NFAT-3 as a direct transcriptional repressor of GAP-43 expression and suggest a more general role for NFAT-3 in the control of the neuronal outgrowth program.Transcription involves many protein-protein and protein-DNA interactions. This allows for the integration of multiple signaling pathways by a limited set of transcription factors that work in combination to either activate or repress genes relevant to the current cellular signaling context (1, 2). These diverse "inputs" are integrated by the binding of transcriptional activators/repressors along with their coactivators/repressors and the modification of chromatin itself to result in the final "output" of a unique nucleoprotein complex capable of either inducing or repressing transcription (3). Transcription is therefore a key regulation point as it allows for the integration of diverse and subtle cellular context during neural development (4, 5).Not surprisingly, axon sprouting and outgrowth are under tight transcriptional control, and the expression of pro-axon growth genes is limited to appropriate spatial and temporal stages of neural development. Therefore, an examination of how changing developmental cues are integrated at the level of transcription might reveal novel mechanisms that regulate axon sprouting and outgrowth.One gene involved in axon outgrowth and guidance is GAP-43 (growth-associated protein 43), a neurotrophin-dependent membrane-bound phosphoprotein highly expressed during the development of the nervous system (6 -8). It is found localized to the axon and growth cones of developing neurons and shows preferential expression in the forebrain and in highly plastic central nervous system regions such as the olfactory bulb, hippocampus, dorsal root ganglia, and ascending sensory pat...