Basal forebrain cholinergic neurons (BFCN) participate in processes of learning, memory, and attention. Little is known about the genes expressed by BFCN and the extracellular signals that control their expression. Previous studies showed that bone morphogenetic protein (BMP) 9 induces and maintains the cholinergic phenotype of embryonic BFCN. We measured gene expression patterns in septal cultures of embryonic day 14 mice and rats grown in the presence or absence of BMP9 by using species-specific microarrays and validated the RNA expression data of selected genes by immunoblot and immunocytochemistry analysis of their protein products. BMP9 enhanced the expression of multiple genes in a time-dependent and, in most cases, reversible manner. The set of BMP9-responsive genes was concordant between mouse and rat and included genes encoding cell-cycle͞growth control proteins, transcription factors, signal transduction molecules, extracellular matrix, and adhesion molecules, enzymes, transporters, and chaperonins. BMP9 induced the p75 neurotrophin receptor (NGFR), a marker of BFCN, and Cntf and Serpinf1, two trophic factors for cholinergic neurons, suggesting that BMP9 creates a trophic environment for BFCN. To determine whether the genes induced by BMP9 in culture were constituents of the BFCN transcriptome, we purified BFCN from embryonic day 18 mouse septum by using fluorescence-activated cell sorting of NGFR ؉ cells and profiled mRNA expression of these and NGFR ؊ cells. Approximately 30% of genes induced by BMP9 in vitro were overexpressed in purified BFCN, indicating that they belong to the BFCN transcriptome in situ and suggesting that BMP signaling contributes to maturation of BFCN in vivo.nerve growth factor receptor ͉ neuronal development ͉ septum ͉ microarray ͉ fluorescence-activated cell sorting B one morphogenetic proteins (BMPs) play critical roles in the development of the nervous system, and there is growing evidence that BMPs regulate the expression of neurotransmitter phenotype, including the cholinergic phenotype (1-4) of basal forebrain cholinergic neurons (BFCN) that project to the neocortex and hippocampus and are important in the processes of attention, learning, and memory (5). Previous studies identified multiple BMP-regulated target genes in a variety of cells, including nervous tissue. However, although BMP target genes have been characterized in the specification of catecholaminergic and serotonergic neurons (6, 7), little is known about BMP target genes implicated in BFCN determination. BFCN are defined by their neuroanatomical location and the neurotransmitter that they synthesize and release, i.e., acetylcholine. The latter process requires a concerted expression of three genes, encoding choline acetyltransferase (Chat), the vesicular acetylcholine transporter (Vacht), and the choline transporter 1 (Cht1). Several additional features of these cells include expression of acetylcholinesterase, the neurotrophin receptors NGFR and TRKA, the expression of certain neurotransmitter receptors (...