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Origin and evolution of new exons in the rodent zinc finger protein 39 gene

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Chinese Science Bulletin

Abstract

The origin of new structures and functions is an important process in evolution. In the past decades, we have obtained some preliminary knowledge of the origin and evolution of new genes. However, as the basic unit of genes, the origin and evolution of exons remain unclear. Because young exons retain the footprints of origination, they can be good materials for studying origin and evolution of new exons. In this paper, we report two young exons in a zinc finger protein gene of rodents. Since they are unique sequences in mouse and rat genome and no homologous sequences were found in the orthologous genes of human and pig, the young exons might originate after the divergence of primates and rodents through exonization of intronic sequences. Strong positive selection was detected in the new exons between mouse and rat, suggesting that these exons have undergone significant functional divergence after the separation of the two species. On the other hand, population genetics data of mouse demonstrate that the new exons have been subject to functional constraint, indicating an important function of the new exons in mouse. Functional analyses suggest that these new exons encode a nuclear localization signal peptide, which may mediate new ways of nuclear protein transport. To our knowledge, this is the first example of the origin and evolution of young exons.

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References

  1. Li, X., Yang, S., Peng, L. X. et al., Origin and evolution of new genes, Chinese Science Bulletin, 2004, 49(16): 1219–1225.

    Google Scholar 

  2. Long, M., Betran, E., Thornton, K. et al., The origin of new genes: Glimpses from the young and old, Nat. Rev. Genet., 2003, 4(11): 865–875.

    Article  PubMed  CAS  Google Scholar 

  3. Nekrutenko, A., Li, W. H., Assessment of compositional heterogeneity within and between eukaryotic genomes, Genome Res., 2000, 10(12): 1986–1995.

    Article  PubMed  CAS  Google Scholar 

  4. Rogalla, P., Kazmierczak, B., Flohr, A. M. et al., Back to the roots of a new exon—the molecular archaeology of a SP100 splice variant, Genomics, 2000, 63(1): 117–122.

    Article  PubMed  CAS  Google Scholar 

  5. Letunic, I., Copley, R. R., Bork, P., Common exon duplication in animals and its role in alternative splicing, Hum. Mol. Genet., 2002, 11(13): 1561–1567.

    Article  PubMed  CAS  Google Scholar 

  6. Ast, G., How did alternative splicing evolve? Nat. Rev. Genet., 2004, 5(10): 773–782.

    Article  PubMed  CAS  Google Scholar 

  7. Makalowski, W., Mitchell, G. A., Labuda, D., Alu sequences in the coding regions of mRNA: A source of protein variability, Trends Genet, 1994, 10(6): 188–193.

    Article  PubMed  CAS  Google Scholar 

  8. Kondrashov, F. A., Koonin, E. V., Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences, Trends Genet, 2003, 19(3): 115–119.

    Article  PubMed  CAS  Google Scholar 

  9. Wang, W., Brunet, F. G., Nevo, E. et al., Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster, Proc. Natl. Acad. Sci. USA, 2002, 99(7): 4448–4453.

    Article  PubMed  CAS  Google Scholar 

  10. Wang, W., Yu, H., Long, M., Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species, Nat. Genet, 2004, 36(5): 523–527.

    Article  PubMed  CAS  Google Scholar 

  11. Looman, C., Abrink, M., Mark, C. et al., KRAB zinc finger proteins: An analysis of the molecular mechanisms governing their increase in numbers and complexity during evolution, Mol. Biol. Evol., 2002, 19(12): 2118–2130.

    PubMed  CAS  Google Scholar 

  12. Shannon, M., Hamilton, A. T., Gordon, L. et al., Differential expansion of zinc-finger transcription factor loci in homologous human and mouse gene clusters, Genome Res., 2003, 13(6A): 1097–1110.

    Article  PubMed  CAS  Google Scholar 

  13. Urrutia, R., KRAB-containing zinc-finger repressor proteins, Genome Biol., 2003, 4(10): 231.

    Article  PubMed  Google Scholar 

  14. Jordan, I. K., Wolf, Y. I., Koonin, E. V., No simple dependence between protein evolution rate and the number of protein-protein interactions: Only the most prolific interactors tend to evolve slowly, BMC Evol. Biol., 2003, 3: 1.

    Article  PubMed  Google Scholar 

  15. Kumar, S., Tamura, K., Nei, M., MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment, Brief Bioinform., 2004, 5(2): 150–163.

    Article  PubMed  CAS  Google Scholar 

  16. Rozas, J., Sánchez-DelBarrio, J. C., Messeguer, X. et al., DnaSP, DNA polymorphism analyses by the coalescent and other methods, Bioinformatics, 2003, 19: 2496–2497.

    Article  PubMed  CAS  Google Scholar 

  17. Tajima, F., Statistical method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, 1989, 123(3): 585–95.

    PubMed  CAS  Google Scholar 

  18. Fu, Y. X., Li, W. H., Statistical tests of neutrality of mutations, Genetics, 1993, 133(3): 693–709.

    PubMed  CAS  Google Scholar 

  19. Zhou, Q., Wang, W., Detecting natural selection at the DNA level, Zoological Research, 2004, 25(1): 73–80.

    CAS  Google Scholar 

  20. O’Brien, S. J., Eizirik, E., Murphy, W. J., Genomics. On choosing mammalian genomes for sequencing, Science, 2001, 292(5525): 2264–2266.

    Article  PubMed  CAS  Google Scholar 

  21. Springer, M. S., Murphy, W. J., Eizirik, E. et al., Placental mammal diversification and the Cretaceous-Tertiary boundary, Proc. Natl. Acad. Sci. USA, 2003, 100(3): 1056–1061.

    Article  PubMed  CAS  Google Scholar 

  22. Cokol, M., Nair, R., Rost, B., Finding nuclear localization signals, EMBO Rep., 2000, 1(5): 411–415.

    Article  PubMed  CAS  Google Scholar 

  23. Dingwall, C., Laskey, R. A., Protein import into the cell nucleus, Annu. Rev. Cell Biol., 1986, 2: 367–390.

    Article  PubMed  CAS  Google Scholar 

  24. Fontes, M. R., The, T., Toth, G. et al., Role of flanking sequences and phosphorylation in the recognition of the simian-virus-40 large T-antigen nuclear localization sequences by importin-alpha, Biochem. J., 2003, 375: 339–349.

    Article  PubMed  CAS  Google Scholar 

  25. Moede, T., Leibiger, B., Pour, H. G. et al., Identification of a nuclear localization signal, RRMKWKK, in the homeodomain transcription factor PDX-1, FEBS Lett, 1999, 461(3): 229–234.

    Article  PubMed  CAS  Google Scholar 

  26. Boulikas, T., Nuclear localization signals (NLS), Crit Rev. Eukaryot. Gene Expr., 1993, 3(3): 193–227.

    PubMed  CAS  Google Scholar 

  27. Pandya, K., Townes, T. M., Basic residues within the Kruppel zinc finger DNA binding domains are the critical nuclear localization determinants of EKLF/KLF-1, J. Biol. Chem., 2002, 277(18): 16304–16312.

    Article  PubMed  CAS  Google Scholar 

  28. Shomron, N., Reznik, M., Ast, G., Splicing factor hSlu7 contains a unique functional domain required to retain the protein within the nucleus, Mol. Biol. Cell., 2004, 15(8): 3782–3795.

    Article  PubMed  CAS  Google Scholar 

  29. Somasekaram, A., Jarmuz, A., How, A. et al., Intracellular localization of human cytidine deaminase. Identification of a functional nuclear localization signal, J. Biol. Chem., 1999, 274(40): 28405–28412.

    Article  PubMed  CAS  Google Scholar 

  30. Dingwall, C., Dilworth, S. M., Black, S. J. et al., Nucleoplasmin cDNA sequence reveals polyglutamic acid tracts and a cluster of sequences homologous to putative nuclear localization signals, EMBO J., 1987, 6(1): 69–74.

    PubMed  CAS  Google Scholar 

  31. Efthymiadis, A., Shao, H., Hubner, S. et al., Kinetic characterization of the human retinoblastoma protein bipartite nuclear localization sequence (NLS) in vivo and in vitro. A comparison with the SV40 large T-antigen NLS, J. Biol. Chem., 1997, 272(35): 22134–22139.

    Article  PubMed  CAS  Google Scholar 

  32. Fahrenkrog, B., Aebi, U., The nuclear pore complex: Nucleocytoplasmic transport and beyond, Nat. Rev. Mol. Cell Biol., 2003, 4(10): 757–766.

    PubMed  CAS  Google Scholar 

  33. Sauer, F., Fondell, J. D., Ohkuma, Y. et al., Control of transcription by Kruppel through interactions with TFIIB and TFIIE beta, Nature, 1995a, 375(6527): 162–164.

    Article  PubMed  CAS  Google Scholar 

  34. Sauer, F., Jackie, H., Heterodimeric Drosophila gap gene protein complexes acting as transcriptional repressors, EMBO J., 1995b, 14(19): 4773–4780.

    PubMed  CAS  Google Scholar 

  35. Noce, T., Fujiwara, Y., Sezaki, M. et al., Expression of a mouse zinc finger protein gene in both permatocytes and oocytes during meiosis, Dev. Biol., 1993, 153(2): 356–367.

    Article  Google Scholar 

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Correspondence to Wen Wang.

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These authors contributed equally to this work.

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Peng, L., Zheng, H., Li, X. et al. Origin and evolution of new exons in the rodent zinc finger protein 39 gene. Chin.Sci.Bull. 50, 1126–1130 (2005). https://doi.org/10.1360/982004-743

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  • DOI: https://doi.org/10.1360/982004-743

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