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A regulator of Dscam mutually exclusive splicing fidelity

Nature Structural & Molecular Biology volume 14, pages 1134–1140 (2007)Cite this article

Abstract

The Down syndrome cell adhesion molecule (Dscam) gene has essential roles in neural wiring and pathogen recognition in Drosophila melanogaster. Dscam encodes 38,016 distinct isoforms via extensive alternative splicing. The 95 alternative exons in Dscam are organized into clusters that are spliced in a mutually exclusive manner. The exon 6 cluster contains 48 variable exons and uses a complex system of competing RNA structures to ensure that only one variable exon is included. Here we show that the heterogeneous nuclear ribonucleoprotein hrp36 acts specifically within, and throughout, the exon 6 cluster to prevent the inclusion of multiple exons. Moreover, hrp36 prevents serine/arginine-rich proteins from promoting the ectopic inclusion of multiple exon 6 variants. Thus, the fidelity of mutually exclusive splicing in the exon 6 cluster is governed by an intricate combination of alternative RNA structures and a globally acting splicing repressor.

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Figure 1: hrp36 is required for mutually exclusive splicing fidelity in the exon 6 cluster of Dscam.
Figure 2: hrp36 functions in a cluster-specific manner.
Figure 3: hrp36 is the only major hnRNP protein that regulates the fidelity of exon 6 mutually exclusive splicing.
Figure 4: hrp36 binds to exon 6 variants.
Figure 5: hrp36 binds to Dscam pre-mRNA throughout the entire exon 6 cluster.
Figure 6: hrp36 prevents ectopic exon 6 inclusion by SR proteins.
Figure 7: Model for the mechanism by which hrp36 prevents the inclusion of multiple exon 6 variants.

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Acknowledgements

We thank members of the Graveley lab for discussions and comments on the manuscript. This work was funded by the Crick-Jacobs Center for Theoretical and Computational Biology (G.W.Y.), a long-term fellowship from the Human Frontier Science Program to M.B., and grants from the US National Institutes of Health to D.C.R. (GM61987) and B.R.G. (GM62561 and GM67842).

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Author notes

  1. Marco Blanchette & Yiannis Savva

    Present address: Present addresses: The Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA (M.B.) and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, Rhode Island 02912, USA (Y.S.).,

Authors and Affiliations

  1. Department of Genetics and Developmental Biology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, 06030-3301, Connecticut, USA

    Sara Olson, Jung Park, Yiannis Savva & Brenton R Graveley

  2. Department of Molecular and Cell Biology, University of California, 16 Barker Hall, Berkeley, 94720-3204, California, USA

    Marco Blanchette & Donald C Rio

  3. Center for Integrative Genomics, University of California, 16 Barker Hall, Berkeley, 94720-3204, California, USA

    Marco Blanchette & Donald C Rio

  4. Crick-Jacobs Center for Theoretical and Computational Biology, Salk Institute, 10010 North Torrey Pines Road, La Jolla, 92037, California, USA

    Gene W Yeo

  5. Illumina Inc., 9885 Towne Centre Drive, San Diego, 92121-1975, California, USA

    Joanne M Yeakley

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Contributions

S.O., M.B., J.P., Y.S. and J.M.Y. performed the experiments; S.O., M.B., J.P., Y.S., J.M.Y., D.C.R. and B.R.G. designed the experiments; S.O., M.B., J.P., Y.S., J.M.Y., G.W.Y., D.C.R. and B.R.G. analyzed the data; B.R.G. wrote the paper with input from all authors.

Corresponding author

Correspondence to Brenton R Graveley.

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Competing interests

J.M.Y. is employed by Illumina, Inc. She also performed assays and provided reagents for the DASL assays.

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Supplementary Figures 1 and 2 and Supplementary Discussion (PDF 1194 kb)

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Olson, S., Blanchette, M., Park, J. et al. A regulator of Dscam mutually exclusive splicing fidelity. Nat Struct Mol Biol 14, 1134–1140 (2007). https://doi.org/10.1038/nsmb1339

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