The pcdh alpha/CNR gene comprises a diverse array of neuronal cell-surface proteins of the cadherin superfamily, although very little is known about their role in neural development. Here we provide the first in-depth characterization of pcdhl alpha in zebrafish. Whole-mount immunocytochemistry demonstrates that a large proportion of endogenous Cytoplasmic domain immunoreactivity is present in the nucleus, suggesting that endoproteolytic cleavage and nuclear translocation of the intracellular domain are important aspects of pcdhl alpha activity in vivo, Using whole-mount immunocytochemistry and BAC-based expression of Pcdh1 alpha-GFP fusion proteins,we find that Pcdhl alpha does not appear to form stable, synaptic puncta at early stages of synaptogenesis. We also demonstrate that the presence of the Pcdhl alpha cytoplasmic domain is essential for normal function. Truncation of Pcdhl alpha proteins, Using splice-blocking antisense morpholinos to prevent the addition of the common intracellular domain to the entire pcdhl alpha cluster, results in neuronal apoptosis throughout the developing brain and spinal cord, demonstrating an essential role for pcdhl alpha in early neural development.This cell death phenotype can be attenuated by the expression of a soluble Pcdhl alpha cytoplasmic domain. (C) 2008 Elsevier Inc. All rights reserved.