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Stochastic yet biased expression of multiple Dscam splice variants by individual cells

Nature Genetics volume 36, pages 240–246 (2004)Cite this article

Abstract

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.

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Figure 1: Developmental regulation of alternative splicing.
Figure 2: A large number of different Dscam isoforms is expressed by homogeneous cell populations.
Figure 3: Independent confirmation of microarray results using restriction endonuclease analyses of cloned cDNAs.
Figure 4: Dscam expression in hemocytes and several clonally derived S2 cell lines.
Figure 5: Single cells express multiple Dscam isoforms.
Figure 6: Single photoreceptors from the same class express different Dscam repertoires.

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References

  1. Schmucker, D. et al. Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 101, 671–684 (2000).

    Article  CAS  Google Scholar 

  2. Wang, J., Zugates, C.T., Liang, I.H., Lee, C.H. & Lee, T. Drosophila Dscam is required for divergent segregation of sister branches and suppresses ectopic bifurcation of axons. Neuron 33, 559–571 (2002).

    Article  CAS  Google Scholar 

  3. Hummel, T. et al. Axonal targeting of olfactory receptor neurons in Drosophila is controlled by Dscam. Neuron 37, 221–231 (2003).

    Article  CAS  Google Scholar 

  4. Celotto, A.M. & Graveley, B.R. Alternative splicing of the Drosophila Dscam pre-mRNA is both temporally and spatially regulated. Genetics 159, 599–608 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Brand, A.H. & Perrimon, N. Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118, 401–415 (1993).

    CAS  PubMed  Google Scholar 

  6. Jasper, H. et al. A genomic switch at the transition from cell proliferation to terminal differentiation in the Drosophila eye. Dev. Cell 3, 511–521 (2002).

    Article  CAS  Google Scholar 

  7. Cooper, M.T. & Bray, S.J. R7 photoreceptor specification requires Notch activity. Curr. Biol. 10, 1507–1510 (2000).

    Article  CAS  Google Scholar 

  8. Lee, C.H., Herman, T., Clandinin, T.R., Lee, R. & Zipursky, S.L. N-cadherin regulates target specificity in the Drosophila visual system. Neuron 30, 437–450 (2001).

    Article  CAS  Google Scholar 

  9. Franc, N.C., Heitzler, P., Ezekowitz, R.A. & White, K. Requirement for croquemort in phagocytosis of apoptotic cells in Drosophila. Science 284, 1991–1994 (1999).

    Article  CAS  Google Scholar 

  10. Ramet, M. et al. Drosophila scavenger receptor CI is a pattern recognition receptor for bacteria. Immunity 15, 1027–1038 (2001).

    Article  CAS  Google Scholar 

  11. Boutros, M., Agaisse, H. & Perrimon, N. Sequential activation of signaling pathways during innate immune responses in Drosophila. Dev. Cell 3, 711–722 (2002).

    Article  CAS  Google Scholar 

  12. Samakovlis, C., Asling, B., Boman, H.G., Gateff, E. & Hultmark, D. In vitro induction of cecropin genes—an immune response in a Drosophila blood cell line. Biochem. Biophys. Res. Commun. 188, 1169–1175 (1992).

    Article  CAS  Google Scholar 

  13. Echalier, G. Drosophila cells in culture (Academic, San Diego, 1997).

    Google Scholar 

  14. Goto, A. et al. A Drosophila haemocyte-specific protein, hemolectin, similar to human von Willebrand factor. Biochem. J. 359, 99–108 (2001).

    Article  CAS  Google Scholar 

  15. Rhoades, K.L. et al. Allele-specific expression patterns of interleukin-2 and Pax-5 revealed by a sensitive single-cell RT-PCR analysis. Curr. Biol. 10, 789–792 (2000).

    Article  CAS  Google Scholar 

  16. Mostoslavsky, R. et al. Kappa chain monoallelic demethylation and the establishment of allelic exclusion. Genes Dev. 12, 1801–1811 (1998).

    Article  CAS  Google Scholar 

  17. Klickstein, L.B., Neve, R.L., Golemis, E.A. & Gyuris, J. Conversion of mRNA into double-stranded cDNA. in Current Protocols in Molecular Biology vol. 1 (eds. Ausubel, F.M. et al.) (John Wiley & Sons, 1995).

    Google Scholar 

  18. Zdobnov, E.M. et al. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 298, 149–159 (2002).

    Article  CAS  Google Scholar 

  19. Barlow, G.M., Micales, B., Chen, X.N., Lyons, G.E. & Korenberg, J.R. Mammalian DSCAMs: roles in the development of the spinal cord, cortex, and cerebellum? Biochem. Biophys. Res. Commun. 293, 881–891 (2002).

    Article  CAS  Google Scholar 

  20. Tabuchi, K. & Sudhof, T.C. Structure and evolution of neurexin genes: insight into the mechanism of alternative splicing. Genomics 79, 849–859 (2002).

    Article  CAS  Google Scholar 

  21. Wu, Q. et al. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Genome Res. 11, 389–404 (2001).

    Article  CAS  Google Scholar 

  22. Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306–2309 (2000).

    Article  CAS  Google Scholar 

  23. Lin, D.M. & Goodman, C.S. Ectopic and increased expression of Fasciclin II alters motoneuron growth cone guidance. Neuron 13, 507–523 (1994).

    Article  CAS  Google Scholar 

  24. Lee, T. & Luo, L. Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis. Neuron 22, 451–461 (1999).

    Article  CAS  Google Scholar 

  25. Ashburner, M. Drosophila: A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1989).

    Google Scholar 

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Acknowledgements

We thank members of the laboratories of A.C. and P. Garrity for suggestions and discussion during the course of this work, T. Volkert for help in the design and printing of microarrays at the Center for Microarray Technology at the Whitehead Institute, B. Chazaro and J. Love for help with hybridizations and scanning, N. Watson for help with confocal microscopy at the W. M. Keck microscopy facility at the Whitehead Institute, G. Paradis for help with FACS experiments, The Bloomington Stock Center and P. Garrity laboratory for providing D. melanogaster stocks, several laboratories for providing the different cell lines (S2 from T. Orr-Weaver and I. Rebay, Kc from S. Bell, Mbn-2 from D. Hultmart), T. DiCesare for help with figure preparation and P. Garrity and S.L. Zipursky for critical reading of the manuscript and for sharing data before publication.

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  1. Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, 02142, Massachusetts, USA

    Guilherme Neves, Jacob Zucker, Mark Daly & Andrew Chess

  2. Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA

    Andrew Chess

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  1. Guilherme Neves
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Correspondence to Andrew Chess.

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Neves, G., Zucker, J., Daly, M. et al. Stochastic yet biased expression of multiple Dscam splice variants by individual cells. Nat Genet 36, 240–246 (2004). https://doi.org/10.1038/ng1299

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