The Drosophila melanogaster gene Dscam is essential for axon guidance and has 38,016 possible alternative splice forms. This diversity can potentially be used to distinguish cells. We analyzed the Dscam mRNA isoforms expressed by different cell types and individual cells. The choice of splice variants expressed is regulated both spatially and temporally. Different subtypes of photoreceptors express broad yet distinctive spectra of Dscam isoforms. Single-cell RT-PCR documented that individual cells express several different Dscam isoforms and allowed an estimation of the diversity that is present. For example, we estimate that each R3/R4 photoreceptor cell expresses 14-50 distinct mRNAs chosen from the spectrum of thousands of splice variants distinctive of its cell type. Thus, the Dscam repertoire of each cell is different from those of its neighbors, providing a potential mechanism for generating unique cell identity in the nervous system and elsewhere. To circumvent these technical difficulties, we used an approach that combined a customized oligonucleotide microarray, isolation of distinct populations of cells and sensitive RT-PCR that allowed examination of Dscam expression by single cells. Here we show that Dscam alternative splicing is differentially regulated both during development and in different tissues. A given cell type expresses a broad, yet distinctive, spectrum of splice variants. Individual cells express a unique repertoire of Dscam splice variants. We estimate that individual R3/R4 photoreceptors express 14-50 distinct mRNA molecules chosen from a subset of thousands of Dscam isoforms characteristic of the population. This would ensure that the Dscam repertoire of each cell is different from those of its neighbors.
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RESULTS
A microarray for analyzing Dscam alternative splicingThe genomic structure of Dscam 1 is shown in Figure 1a. There are four alternatively spliced exons. In this study we focused on three alternatively spliced exons, which may create many possible isoforms (Fig. 1a): the cluster in exon 4 has 12 alternative exons, the cluster in exon 6 has 48 alternative exons and the cluster in exon 9 has 33 alternative exons. Each of these highly variable exons can form a portion of an immunoglobulin domain in the extracellular region of the protein. We designed a microarray containing probes for all 93 alternative exons in these three clusters. We amplified cloned DNAs (whose identities were confirmed by sequencing) by PCR to create a reference library that equally represents all the alternative exons present in the microarray. To test the specificity of the different probes in the microarray, we used combinations of RNAs in controlled amounts (Fig. 1b). RNA samples were in vitro transcribed from cloned cDNAs containing different combinations of exons 4, 6 and 9. We carried out a quantitative analysis of four independent experiments in which eight different samples were combined in different amounts spanning two orders of magnitude. Throughout this study, we expressed sample...