The hypothalamus is a key regulatory unit of the neuroendocrine system and plays an essential role in energy balance and reproduction. Despite its important role, the molecular mechanisms underlying hypothalamic development are not fully understood. Here, we report molecular analyses of a newly identified murine homeobox gene, Bsx/Bsx1a, that is expressed in the developing and postnatal hypothalamus. We demonstrate that BSX1A is a DNA binding protein and a transcriptional activator. Transcriptional reporter assays identified the C-terminal region of BSX1A as an activation domain. We have isolated an alternative splice form of Bsx1a, designated Bsx1b, which retains the N-terminal region but lacks the homeodomain. Analyses of subcellular localization using transfected cell lines revealed that BSX1A and BSX1B localize in the nuclei and cytoplasm, respectively. Immunohistochemical analyses suggested that both BSX1A and BSX1B are expressed in the neonatal hypothalamus. Taking these data together, we propose that alternative RNA splicing is involved in hypothalamic development/function.The hypothalamus-pituitary axis is a major component of the neuroendocrine system that controls the homeostasis of energy balance and reproduction. Disturbances of hypothalamic functions cause a variety of human health problems that include growth retardation, obesity, infertility, and hormoneregulated tumor progression. Much has been elucidated in the development of the pituitary in terms of transcriptional regulation; however, relatively little is known about the development of hypothalamic neurons (4,5,16,28,31,35).Although the hypothalamus consists of several cell types located in different regions, only a few transcription factors have been identified that are expressed in the developing hypothalamus. Brn-2 encodes a POU domain transcription factor, and its targeted mutation results in the loss of corticotropin-releasing hormone (CRH), vasopressin (AVP), and oxytocin (OT) in Brn-2-expressing cells. The homozygous mutant mice die in the neonatal period with a decrease in size and weight (18,26). The basic helix-loop-helix (bHLH)-Per-ArntSim transcription factor Sim1 is expressed in the paraventricular, the supraoptic, and the anterior periventricular nuclei. In Sim1 homozygous mutant mice, OT-, AVP-, thyrotropin-releasing hormone-, CRH-, and somatostatin (SS)-secreting neurons are absent in the Sim1-expressing regions (15). The Sim1 mutant mice die within 24 h after birth. Thus, the phenotype of Sim1 mutant mice overlaps with but is more severe than that of Brn-2 mutant mice. The Sim1 mutant hypothalamus fails to express Brn-2 during development, suggesting that a part of the phenotype of Sim1 mutant mice is due to loss of Brn-2 and that BRN-2 acts downstream of SIM1. Another bHLH-Per-ArntSim transcription factor, Arnt-2, is also involved in hypothalamic development. Arnt-2 mutant mice show a strikingly similar phenotype to the Sim1-deficient mice, consistent with the finding that SIM1 and ARNT-2 form a heterodimer complex in vivo (...