The development of the nervous system requires the concerted actions of multiple transcription factors, yet the molecular events leading to their expression remain poorly understood. Barhl1, a mammalian homeodomain transcription factor of the BarH class, is expressed by developing inner ear hair cells, cerebellar granule cells, precerebellar neurons, and collicular neurons. Targeted gene inactivation has demonstrated a crucial role for Barhl1 in the survival and/or migration of these sensory cells and neurons. Here we report the regulatory sequences of Barhl1 necessary for directing its proper spatiotemporal expression pattern in the inner ear and central nervous system (CNS). Using a transgenic approach, we have found that high-level and cell-specific expression of Barhl1 within the inner ear and CNS depends on both its 5 promoter and 3 enhancer sequences. Further transcriptional, binding, and mutational analyses of the 5 promoter have identified two homeoprotein binding motifs that can be occupied and activated by Barhl1. Moreover, proper Barhl1 expression in inner ear hair cells and cerebellar and precerebellar neurons requires the presence of Atoh1. Together, these data delineate useful Barhl1 regulatory sequences that direct strong and specific gene expression to inner ear hair cells and CNS sensory neurons, establish a role for autoregulation in the maintenance of Barhl1 expression, and identify Atoh1 as a key upstream regulator.The mammalian Barhl1 and Barhl2 proteins belong to the BarH class of homeodomain transcription factors that are evolutionarily conserved in both invertebrate and vertebrate species ranging from Drosophila flies to humans. The factors of this class are usually expressed in the developing and adult nervous systems and are required for proper neural development and survival (4, 7, 12, 13, 15, 18-20, 24, 26-32, 34). In Drosophila, BarH1 and BarH2 are coexpressed in cells of the central nervous system (CNS) and the peripheral nervous system and are redundantly required for determining the subtypes of external sensory organs and photoreceptor and primary pigment cells during eye development (12,13,15). The vertebrate Barhl1 and Barhl2 genes similarly display overlapping yet distinct patterns of expression in the CNS and sensory organs, thereby also playing redundant as well as distinct roles during neurogenesis (4, 7, 18-20, 24, 26-29, 31, 32, 34). For instance, Xenopus Barhl2 is expressed in the developing neural plate and retina during Xenopus embryogenesis and plays a key role in patterning the neural plate and specifying retinal ganglion cells (27,29).The functions of mammalian Barhl genes during murine neurogenesis have been extensively investigated previously. In the developing mouse inner ear, Barhl1 but not Barhl2 is specifically expressed in all hair cells of the cochlear and vestibular systems (4, 18). The targeted disruption of Barhl1 leads to hearing loss as a result of the age-related progressive degeneration of inner and outer hair cells in the organ of Corti (18), demonstr...