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The U1 snRNP protein U1C recognizes the 5′ splice site in the absence of base pairing


Splicing of precursor messenger RNA takes place in the spliceosome, a large RNA/protein macromolecular machine1. Spliceosome assembly occurs in an ordered pathway in vitro and is conserved between yeast and mammalian systems. The earliest step is commitment complex formation in yeast or E complex formation in mammals, which engages the pre-mRNA in the splicing pathway and involves interactions between U1 small nuclear ribonucleoprotein (snRNP) and the pre-mRNA 5′ splice site2,3. Complex formation depends on highly conserved base pairing between the 5′ splice site and the 5′ end of U1 snRNA, both in vivo and in vitro4,5,6,7. U1 snRNP proteins also contribute to U1 snRNP activity8,9,10. Here we show that U1 snRNP lacking the 5′ end of its snRNA retains 5′-splice-site sequence specificity. We also show that recombinant yeast U1C protein, a U1 snRNP protein, selects a 5′-splice-site-like sequence in which the first four nucleotides, GUAU, are identical to the first four nucleotides of the yeast 5′-splice-site consensus sequence. We propose that a U1C 5′-splice-site interaction precedes pre-mRNA/U1 snRNA base pairing and is the earliest step in the splicing pathway.

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Figure 1: In vitro selection with U1 snRNP.
Figure 2: Site-specific crosslinking of commitment complex proteins to the 5′-splice-site region in the presence and absence of pre-mRNA/U1snRNA base pairing.
Figure 3: Characterization of complex formation in different extracts and at different temperatures.
Figure 4: Characterization of sequence specificity of recombinant yU1C.
Figure 5: yU1C binding to single-stranded (ss) RNA and duplex substrates.


  1. Burge, C. B., Tuschl, T. & Sharp, P. A. in The RNA World II (eds Gesteland, R. R., Cech, T. R. & Atkins, J. F.) 525–560 (Cold Spring Laboratory Harbor Press, Cold Spring Harbor, 1999)

    Google Scholar 

  2. Séraphin, B. & Rosbash, M. Identification of functional U1 snRNA–pre-mRNA complexes committed to spliceosome assembly and splicing. Cell 59, 349–358 (1989)

    Article  Google Scholar 

  3. Michaud, S. & Reed, R. An ATP-independent complex commits pre-mRNA to the mammalian spliceosome assembly pathway. Genes Dev. 5, 2534–2546 (1991)

    CAS  Article  Google Scholar 

  4. Lerner, M. R., Boyle, J. A., Mount, S. M., Wolin, S. & Steitz, J. A. Are snRNPs involved in splicing? Nature 283, 220–224 (1980)

    ADS  CAS  Article  Google Scholar 

  5. Zhuang, Y. & Weiner, A. M. A compensatory base change in U1 snRNA suppresses a 5′ splice site mutation. Cell 46, 827–835 (1986)

    CAS  Article  Google Scholar 

  6. Séraphin, B., Kretzner, L. & Rosbash, M. A U1 snRNA:pre-mRNA base pairing interaction is required early in yeast spliceosome assembly but does not uniquely define the 5′ cleavage site. EMBO J. 7, 2533–2538 (1988)

    Article  Google Scholar 

  7. Siliciano, P. G. & Guthrie, C. 5′ splice site selection in yeast: genetic alterations in base-pairing with U1 reveal additional requirements. Genes Dev. 2, 1258–1267 (1988)

    CAS  Article  Google Scholar 

  8. Zhang, D. & Rosbash, M. Identification of eight proteins that cross-link to pre-mRNA in the yeast commitment complex. Genes Dev. 13, 581–592 (1999)

    Article  Google Scholar 

  9. Puig, O., Gottschalk, A., Fabrizio, P. & Séraphin, B. Interaction of the U1 snRNP with nonconserved intronic sequences affects 5′ splice site selection. Genes Dev. 13, 569–580 (1999)

    CAS  Article  Google Scholar 

  10. Chen, J. Y. et al. Specific alterations of U1-C protein or U1 small nuclear RNA can eliminate the requirement of Prp28p, an essential DEAD box splicing factor. Mol. Cell 7, 227–232 (2001)

    CAS  Article  Google Scholar 

  11. Du, H. & Rosbash, M. Yeast U1 snRNP-pre-mRNA complex formation without U1snRNA–pre-mRNA base pairing. RNA 7, 133–142 (2001)

    CAS  Article  Google Scholar 

  12. Lund, M. & Kjems, J. Defining a 5′ splice site by functional selection in the presence and absence of U1 snRNA 5′ end. RNA 8, 166–179 (2002)

    CAS  Article  Google Scholar 

  13. Heinrichs, V., Bach, M., Winkelmann, G. & Lührmann, R. U1-specific protein C needed for efficient complex formation of U1 snRNP with a 5′ splice site. Science 247, 69–72 (1990)

    ADS  CAS  Article  Google Scholar 

  14. Jamison, S. F. et al. U1 snRNP–ASF/SF2 interaction and 5′ splice site recognition: characterization of required elements. Nucleic Acids Res. 23, 3260–3267 (1995)

    CAS  Article  Google Scholar 

  15. Tang, J., Abovich, N., Fleming, M., Séraphin, B. & Rosbash, M. Identification and characterization of a yeast homolog of U1 snRNP-specific protein C. EMBO J. 16, 4082–4091 (1997)

    CAS  Article  Google Scholar 

  16. Traub, P. & Nomura, M. Structure and function of Escherichia coli ribosomes. VI. Mechanism of assembly of 30S ribosomes studied in vitro. J. Mol. Biol. 40, 391–413 (1969)

    CAS  Article  Google Scholar 

  17. Crispino, J. D., Blencowe, B. J. & Sharp, P. A. Complementation by SR proteins of pre-mRNA splicing reactions depleted of U1 snRNP. Science 265, 1866–1869 (1994)

    ADS  CAS  Article  Google Scholar 

  18. Tarn, W. Y. & Steitz, J. A. SR proteins can compensate for the loss of U1 snRNP functions in vitro. Genes Dev. 8, 2704–2717 (1994)

    CAS  Article  Google Scholar 

  19. Konforti, B. B. & Konarska, M. M. A short 5′ splice site RNA oligo can participate in both steps of splicing in mammalian extracts. RNA 1, 815–827 (1995)

    CAS  Google Scholar 

  20. Crispino, J. D. & Sharp, P. A. A U6 snRNA:pre-mRNA interaction can be rate-limiting for U1-independent splicing. Genes Dev. 9, 2314–2323 (1995)

    CAS  Article  Google Scholar 

  21. Crispino, J. D., Mermoud, J. E., Lamond, A. I. & Sharp, P. A. Cis-acting elements distinct from the 5′ splice site promote U1-independent pre-mRNA splicing. RNA 2, 664–673 (1996)

    CAS  Google Scholar 

  22. Valcarcel, J., Gaur, R. K., Singh, R. & Green, M. R. Interaction of U2AF65 RS region with pre-mRNA branch point and promotion of base pairing with U2 snRNA. Science 273, 1706–1709 (1996)

    ADS  CAS  Article  Google Scholar 

  23. Abovich, N. & Rosbash, M. Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals. Cell 89, 403–412 (1997)

    CAS  Article  Google Scholar 

  24. Berglund, J. A., Chua, K., Abovich, N., Reed, R. & Rosbash, M. The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC. Cell 89, 781–787 (1997)

    CAS  Article  Google Scholar 

  25. Herschlag, D. Implications of ribozyme kinetics for targeting the cleavage of specific RNA molecules in vivo: more isn't always better. Proc. Natl Acad. Sci. USA 88, 6921–6925 (1991)

    ADS  CAS  Article  Google Scholar 

  26. Rossi, F. et al. Involvement of U1 small nuclear ribonucleoproteins (snRNP) in 5′ splice site–U1 snRNP interaction. J. Biol. Chem. 271, 23985–23991 (1996)

    CAS  Article  Google Scholar 

  27. Reyes, J. L., Kois, P., Konforti, B. B. & Konarska, M. M. The canonical GU dinucleotide at the 5′ splice site is recognized by p220 of the U5 snRNP within the spliceosome. RNA 2, 213–225 (1996)

    CAS  Google Scholar 

  28. Maroney, P. A., Romfo, C. M. & Nilsen, T. W. Functional recognition of 5′ splice site by U4/U6.U5 tri-snRNP defines a novel ATP-dependent step in early spliceosome assembly. Mol. Cell 6, 317–328 (2000)

    CAS  Article  Google Scholar 

  29. Johnson, T. L. & Abelson, J. Characterization of U4 and U6 interactions with the 5′ splice site using a S. cerevisiae in vitro trans-splicing system. Genes Dev. 15, 1957–1970 (2001)

    CAS  Article  Google Scholar 

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We thank current and ex-colleagues for discussions, and B. Séraphin and M. Moore for comments on the manuscript. H.D. was supported by a Charles A. King Trust Fellowship. The work was also supported by the National Institutes of Health.

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Correspondence to Michael Rosbash.

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Du, H., Rosbash, M. The U1 snRNP protein U1C recognizes the 5′ splice site in the absence of base pairing. Nature 419, 86–90 (2002).

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