Journal of Neuroscience Research 85:525–535 (2007) Mouse and Rat BDNF Gene Structure and Expression Revisited Tamara Aid, Anna Kazantseva, Marko Piirsoo, Kaia Palm, and To˜ nis Timmusk* Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia Brain-derived neurotrophic factor (BDNF) has important functions in the development of the nervous system and in brain plasticity-related processes such as memory, learning, and drug addiction. Despite the fact that the function and regulation of rodent BDNF gene expression have received close attention during the last decade, knowledge of the structural organization of mouse and rat BDNF gene has remained incomplete. We have iden- tiﬁed and characterized several mouse and rat BDNF transcripts containing novel 50 untranslated exons and introduced a new numbering system for mouse and rat BDNF exons. According to our results both mouse and rat BDNF gene consist of eight 50 untranslated exons and one protein coding 30 exon. Transcription of the gene results in BDNF transcripts containing one of the eight 50 exons spliced to the protein coding exon and in a tran- script containing only 50 extended protein coding exon. We also report the distinct tissue-speciﬁc expression proﬁles of each of the mouse and rat 50 exon-speciﬁc transcripts in different brain regions and nonneural tissues. In addition, we show that kainic acid-induced seizures that lead to changes in cellular Ca2+ levels as well as inhibition of DNA methylation and histone deacetylation contribute to the dif- ferential regulation of the expression of BDNF transcripts. Finally, we conﬁrm that mouse and rat BDNF gene loci do not encode antisense mRNA transcripts, suggesting that mechanisms of regulation for rodent and human BDNF genes differ substantially. VC 2006 Wiley-Liss, Inc. Key words: BDNF; exon; promoter; DNA methylation; histone deacetylation; calcium; kainic acid Brain-derived neurotrophic factor (BDNF) is a mem- ber of the neurotrophin family consisting of small secreted proteins that play important roles in the development of the nervous system in vertebrates (for recent reviews see Bibel and Barde, 2000; Binder and Scharfman, 2004; Chao et al., 2006). BDNF supports the survival and differentia- tion of speciﬁc populations of embryonic neurons in vivo, and growing evidence indicates that BDNF is also involved in several functions in adulthood, including neu- ronal homeostasis and brain plasticity-related processes such as memory, learning (Tyler et al., 2002; Yamada et al., 2002), and drug addiction (Bolanos and Nestler, 2004). Alterations in BDNF expression in speciﬁc neuron subpopulations contribute to various pathologies, includ- ing depression, epilepsy, and Alzheimer’s, Huntington’s, ' 2006 Wiley-Liss, Inc. and Parkinson’s diseases (Bibel and Barde, 2000; Murer et al., 2001; Binder and Scharfman, 2004; Castren, 2004; Cattaneo et al., 2005; Russo-Neustadt and Chen, 2005). In addition to BDNF, the neurotrophin family in- cludes nerve growth factor, neurotrophin-3, and neuro- trophin-4/5 (Binder, 2004). All neurotrophins bind to p75NGFR receptor but selectively interact with their indi- vidual high-afﬁnity protein kinase receptors of the trk (tropomyosin-related kinase) family (Kaplan and Miller, 2000; Chao, 2003; Teng and Hempstead, 2004). BDNF mediates its biological effects via TrkB and p75NGFR receptors. Binding of mature BDNF protein to TrkB and p75NGFR promotes cell survival, neurite outgrowth, syn- aptic transmission, plasticity, and cell migration (Dechant and Barde, 2002). Uncleaved precursor BDNF protein (pro-BDNF) has altered binding characteristics and dis- tinct biological activity in comparison with mature BDNF protein (Lee et al., 2001; Teng et al., 2005). In mouse and rat, BDNF mRNA is expressed throughout development and differentially in adult tissues (Ernfors et al., 1990; Hofer et al., 1990; Hohn et al., 1990). In the brain, BDNF mRNA and protein expres- sion becomes detectable during embryonic development, reaching the highest levels by days 10–14 postnatally and decreasing thereafter. In the adult animal, BDNF is ex- pressed throughout the brain, with the highest levels in the neurons of hippocampus (Ernfors et al., 1990; Hofer et al., 1990; Kawamoto et al., 1996; Conner et al., 1997; Yan et al., 1997). Neuronal BDNF expression is affected by many stimuli, such as g-aminobutyric acid (GABA)- ergic and glutamatergic neurotransmission and membrane depolarization through calcium-mediated pathways (Zafra et al., 1990, 1991; Ghosh et al., 1994; Shieh and Ghosh, Sequence data from this article have been deposited in the GenBank Data libraries under Accession Nos. EF125669-EF125690. Contract grant sponsor: Wellcome Trust; Contract grant number: 067952; Contract grant sponsor: Estonian Ministry of Education and Research; Contract grant number: 0222602 (to T.T.). *Correspondence to: To˜nis Timmusk, Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 19086 Tallinn, Estonia. E-mail: tonis.timmusk@ttu.ee Received 25 April 2006; Revised 16 August 2006; Accepted 12 October 2006 Published online 5 December 2006 in Wiley InterScience (www. interscience.wiley.com). DOI: 10.1002/jnr.21139