Production of the amyloid -peptide (A) via sequential proteolytic cleavage of the amyloid precursor protein by -and ␥-secretases is strongly implicated in the pathogenesis of Alzheimer disease. The -secretase that executes the first cleavage event is a transmembrane aspartyl protease known as -site amyloid precursor protein-cleaving enzyme 1 (BACE1). BACE1 pre-mRNA is alternatively spliced through the use of alternative splice sites in exons 3 and 4, although the significance of these splicing events is unclear. Here, we quantitatively measured relative levels of BACE1 transcripts and identified a novel splice variant of BACE1. We found a subtle but significant difference in BACE1 splicing between brain and pancreas, indicating the cellular environment can affect BACE1 alternative splicing. Furthermore, we have shown that BACE1 proteins translated from alternatively spliced transcripts have dramatically reduced -secretase activity and promotion of BACE1 alternative splicing reduces A production. These findings illustrate the importance of BACE1 alternative splicing in affecting the level of A produced in cells and suggest that targeting regulation of BACE1 alternative splicing is a potential therapeutic strategy for lowering -secretase activity.Deposition of extracellular plaques in the brain is a hallmark of Alzheimer disease (AD) 2 pathology. The major component of these plaques is the amyloid -peptide (A), a hydrophobic peptide usually 40 or 42 amino acids in length and prone to aggregation (1, 2). A is produced by sequential proteolysis of the amyloid precursor protein (APP) by -and ␥-secretases (3, 4). -site APP-cleaving enzyme 1 (BACE1) is the primary transmembrane aspartyl protease responsible for -secretase activity in the brain and carries out the first cleavage step leading to A production (5-9). Moreover, BACE1 protein and activity levels are elevated in AD brains relative to controls, further suggesting its involvement in AD pathogenesis (10 -14).Elimination or reduction of BACE1 activity in order to slow A production is an attractive therapeutic strategy for AD. Although the brains of Bace1 knock-out mice do not produce A and these mice appear relatively healthy (15-17), there is evidence that complete absence of BACE1 may cause reduced myelination as well as some cognitive deficits in mice (18 -20). However, partial reduction of BACE1 has been shown to dramatically reduce plaque deposition and synaptic deficits in APP transgenic mouse models (20 -22). Although a number of BACE1 inhibitors have been developed, identification of a selective compound that is potent in vivo and practical for clinical development has proven challenging (23, 24).The BACE1 gene is composed of nine exons, and its pre-mRNA was previously found to undergo alternative splicing (25-27). BACE1 mRNA is most highly expressed in brain and pancreas (5-9), and alternatively spliced transcripts of BACE1 have been identified in both tissues (26,27). Normal splicing of BACE1 results in production of the full-length 50...