Bcl11A/Evi9/CTIP1, a Kruppel-like zinc finger gene, plays an important role in B-cell development. In addition to expression in B lymphocytes, Bcl11A/Evi9/CTIP1 is also highly expressed in the brain, although its function there is still unclear. In the present study, regional and subcellular distributions of Bcl11A/Evi9/CTIP1 in rat brain were investigated by immunostaining and biochemical fractionation. Using antibodies recognizing the first 18 amino acid residues of Bcl11A/Evi9/CTIP1, the distribution of 2 isoforms of Bcl11A/Evi9/CTIP1 gene products, Bcl11A-L/Evi9a and Bcl11A-S/Evi9c, was examined. In rat brain, both Bcl11A-L/Evi9a and Bcl11A-S/Evi9c were expressed, although the amount of Bcl11A-S/Evi9c protein was higher. Bcl11A-S/Evi9c was widely expressed in different regions of the rat brain. In contrast, Bcl11A-L/Evi9a was more restricted, being expressed in the cerebral cortex, hippocampus, and olfactory bulb. At the subcellular level, biochemical fractionation and confocal analysis of adult rat brain revealed that, in addition to being in the nuclei of neurons, fractions of Bcl11A-L/Evi9a and Bcl11A-S/Evi9c could be found in extranuclear locations. Double staining with the synaptic marker synaptophysin indicated a synaptic distribution of Bcl11A/Evi9/CTIP1. Postsynaptic density was also biochemically purified and subjected to immunoblotting using Bcl11A/Evi9/CTIP1 antibodies. The results showed that Bcl11A-L/Evi9a was enriched in the PSD I and PSD II fractions. In contrast, only a trace amount of Bcl11A-S was detected in PSD fractions. Our study also indicated that a fraction of Bcl11A/Evi9/CTIP1 was present in the cytoplasm, even at synapses. To regulate gene expression in the nuclei, nuclear translocation of Bcl11A/Evi9/CTIP1 may be one of the mechanisms controlling neuronal Bcl11A/Evi9/CTIP1 function. Copyright (c) 2007 Wiley-Liss, Inc.