528 Aid et al. Fig. 1. Exon/intron structure and alternative transcripts of mouse and rat BDNF genes. A: Rat BDNF gene structure as described by Tim- musk et al. (1993). Exons are shown as boxes and introns are shown as lines. B: The new arrangement of exons and introns of mouse and rat BDNF genes as determined by analyzing genomic and mRNA sequence data using bioinformatics, 50 RACE, and RT-PCR. The schematic rep- resentation of BDNF transcripts in relation to the gene is shown below the gene structure. Protein coding regions are shown as solid boxes and untranslated regions are shown as open boxes. Each of the eight 50 untranslated exons is spliced to the common 30 protein coding exon IX. In addition, transcription can be initiated in the intron before the protein coding exon, which results in IXA transcripts containing 50 extended coding exon. Each transcription unit may use one of the two alternative polyadenylation signals in the 30 exon (arrows). For exon II, three differ- ent transcript variants, IIA, IIB, and IIC, are generated as a result of using alternative splice-donor sites in exon II (arrows marked A, B, and C). levels peaked at postnatal (P) day 1 in mouse and embry- onic day 21 in rat and decreased slightly during postnatal development (Fig. 2A,B). BDNF exon II mRNA splice variants A, B, and C revealed differential expression pat- terns in brain both in mouse and in rat, and their expres- sion was not detected in peripheral tissues. In cerebellum, exon IIA transcript was the most abundant; in hippocam- pus, all three exon II splice variants were expressed at similar levels. Overall brain-speciﬁc expression pattern of mouse and rat novel BDNF exon III transcripts resembled that of BDNF exon II (Fig. 2A,B). In murine nonneural tissues, low levels of exon III transcripts were detected only in spleen and kidney, and, in rat, exon III transcripts were detected in thymus. BDNF exon IV and exon VI mRNAs (formerly exons III and IV, Timmusk et al., 1993) were observed at signiﬁcant levels in developing mouse and rat brain already at E13, the earliest develop- mental stage studied. Both in mouse and in rat, BDNF exon IV and exon VI mRNA levels increased gradually during embryonic and postnatal development and de- creased slightly in adult brain. In adult brain, exon IV and exon VI transcripts were detected in all analyzed brain regions both in mouse and in rat. Exon IV and exon VI transcripts exhibited wide patterns of expression in mouse and rat nonneural tissues, with the highest levels in heart and lung (Fig. 2A,B). In both mouse and rat, BDNF novel exons V, VII, and VIII, were expressed at relatively low levels during brain development, broadly in adult peripheral tissues, and differentially in adult brain regions (Fig. 2A,B). In spite of the fact that mouse BDNF mRNA containing exons VII and VIII in the same transcript has been submit- ted to NCBI GenBank (AY231132), we failed to detect similar mRNAs in any of mouse or rat tissue studied. Expression of the novel BDNF exon IXA tran- scripts was detected in rodent brain during embryonic Journal of Neuroscience Research DOI 10.1002/jnr