With the aid of microarray and PCR analysis, this investigation sought expression profiles of BDNF-regulated genes in Cultured mouse cerebellar granule cells and addressed their relevance to gene regulation in developing granule cells in vivo. Many of the BDNF-upregulated and downregulated genes identified were upregulated and downregulated, respectively, during cerebellar development. This developmental change was, at least partly, prevented in the TrkB receptor-deficient cerebellum. The BDNF-upregulated genes were distributed in either postmigratory or both premigratory and postinigratory granule cells at postnatal day 8 (P8) and were still present in mature granule cells at P21. In contrast, the BDNF-downregulated genes were predominantly expressed in premigratory granule cells at P8 and disappeared at P21. Furthermore, many of the BDNF-Upregulated gene products are implicated in signaling cascades of N-methyl-D-aspartate receptors and MAP kinase. The results indicate that BDNF signaling plays a pivotal role in promoting gene expression in granule cell development and maturation. (c) 2006 Elsevier Inc. All rights reserved.