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Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity

A Corrigendum to this article was published on 01 January 2005

Abstract

Splice acceptors with the genomic NAGNAG motif may cause NAG insertion-deletions in transcripts, occur in 30% of human genes and are functional in at least 5% of human genes. We found five significant biases indicating that their distribution is nonrandom and that they are evolutionarily conserved and tissue-specific. Because of their subtle effects on mRNA and protein structures, these splice acceptors are often overlooked or underestimated, but they may have a great impact on biology and disease.

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Figure 1: Alternative splicing at NAGNAG acceptors.

References

  1. Garcia-Blanco, M.A., Baraniak, A.P. & Lasda, E.L. Nat. Biotechnol. 22, 535–546 (2004).

    Article  CAS  Google Scholar 

  2. Long, M. & Deutsch, M. Mol. Biol. Evol. 16, 1528–1534 (1999).

    Article  CAS  Google Scholar 

  3. Ferranti, P., Lilla, S., Chianese, L. & Addeo, F. J. Protein Chem. 18, 595–602 (1999).

    Article  CAS  Google Scholar 

  4. Rogina, B. & Upholt, W.B. Biochem. Mol. Biol. Int. 35, 825–831 (1995).

    CAS  PubMed  Google Scholar 

  5. Li, L. & Howe, G.A. Plant Mol. Biol. 46, 409–419 (2001).

    Article  CAS  Google Scholar 

  6. Zhang, H.B. & Blumenthal, T. RNA 2, 380–388 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Sugnet, C.W., Kent, W.J., Ares, M. Jr. & Haussler, D. Pac. Symp. Biocomput. 2004, 66–77 (2004).

    Google Scholar 

  8. Stamm, S. et al. DNA Cell Biol. 19, 739–756 (2000).

    Article  CAS  Google Scholar 

  9. Ma, B., Elkayam, T., Wolfson, H. & Nussinov, R. Proc. Natl. Acad. Sci. USA 100, 5772–5777 (2003).

    Article  CAS  Google Scholar 

  10. Chen, S., Anderson, K. & Moore, M.J. Proc. Natl. Acad. Sci. USA 97, 593–598 (2000).

    Article  CAS  Google Scholar 

  11. Resch, A. et al. J. Proteome Res. 3, 76–83 (2004).

    Article  CAS  Google Scholar 

  12. Condorelli, G., Bueno, R. & Smith, R.J. J. Biol. Chem. 269, 8510–8516 (1994).

    CAS  PubMed  Google Scholar 

  13. Karinch, A.M., deMello, D.E. & Floros, J. Biochem. J. 321, 39–47 (1997).

    Article  CAS  Google Scholar 

  14. Neves, G., Zucker, J., Daly, M. & Chess, A. Nat. Genet. 36, 240–246 (2004).

    Article  CAS  Google Scholar 

  15. Zavolan, M. et al. Genome Res. 13, 1290–1300 (2003).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank I. Görlich and M.-L. Schmidt for technical assistance. This work was supported by grants from the German Ministry of Education and Research to S.S. and to M.P. as well as from the Deutsche Forschungsgemeinschaft to M.P.

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Correspondence to Matthias Platzer.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Table 1

RefSeq entries containing NAGNAG acceptors in the CDS. (XLS 1356 kb)

Supplementary Table 2

Intron phases and splice site scores of human observed and confirmed NAGNAG acceptors. (XLS 22 kb)

Supplementary Table 3

Number of observed and confirmed tandem acceptors for 4 species. (XLS 10 kb)

Supplementary Table 4

Human NAGNAG acceptors in the CDS with a mouse ortholog identified. (XLS 733 kb)

Supplementary Table 5

Pfam domains with a biased distribution between proteins derived from genes with confirmed and without NAGNAG acceptors. (XLS 12 kb)

Supplementary Table 6

Human RefSeq entries with two or three confirmed tandem acceptors in the CDS. (XLS 14 kb)

Supplementary Note (PDF 17 kb)

Supplementary Methods (PDF 12 kb)

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Hiller, M., Huse, K., Szafranski, K. et al. Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity. Nat Genet 36, 1255–1257 (2004). https://doi.org/10.1038/ng1469

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