Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Splicing double: insights from the second spliceosome

Nature Reviews Molecular Cell Biology volume 4, pages 960–970 (2003)Cite this article

Key Points

  • The genomes of most multicellular organisms contain a new class of introns that have non-canonical consensus sequences. These minor-class introns occur extremely rarely and are not restricted to the genes of a particular functional class.

  • Minor-class introns are spliced by a distinct, low-abundance splicing machinery that includes four small nuclear ribonucleoprotein particles (snRNPs; U11, U12, U4atac and U6atac) that are functionally analogous to the well-characterized major-class U1, U2, U4 and U6 snRNPs. The U5 snRNP is common to both spliceosomes.

  • The two spliceosomes have remarkable mechanistic similarities that enhance our understanding of the inner workings of the spliceosome. Although the sequences of the major- and minor-class small nuclear RNAs are significantly diverged, they have highly analogous secondary structures, snRNP–snRNP interactions and snRNP–pre-messenger RNA interactions. Some of the most conserved features of the two spliceosomes are thought to be involved in catalysis of the splicing reaction.

  • Although minor-class introns are rare within the genome of any given species, they are found in most metazoan taxa that have been examined, including vertebrates, insects and cnidarians (jellyfish), and plants. Phylogenetic analysis of U12-type introns shows that they can be conserved at homologous positions in homologous genes of species that diverged up to a billion years ago. Perhaps most surprising is the observation of minor-class introns at non-homologous positions in paralogous genes.

  • Spliceosomal factors that are bound to adjacent major-class introns are thought to form bridging interactions across exons, defining the exons as recognition units and preventing the unintended skipping of exons or introns. Evidence suggests that similar exon-spanning interactions also occur between spliceosomes that are assembled on adjacent minor- and major-class introns. Also, the incompatibility of minor- and major-class donor and acceptor splice sites has given rise to unique patterns of alternative splicing.

  • Phylogenetic analysis of minor-class introns has led to the conclusion that they must have occurred much more frequently earlier in evolutionary history, and were either lost or converted to major-class introns over time. It has been proposed that the few minor-class introns that have resisted conversion or loss could have functional roles that are indispensable to the cells that have them.

Abstract

Almost 20 years after the discovery of introns and RNA splicing, a second spliceosome was uncovered. Although this new spliceosome is structurally and functionally analogous to the well-characterized major-class splicing apparatus, it mediates the excision of a minor class of evolutionarily conserved introns that have non-canonical consensus sequences. This unanticipated diversity in the splicing machinery is refining both the mechanistic understanding and evolutionary models of RNA splicing.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Pre-mRNA splicing occurs by two sequential trans-esterification reactions.
Figure 2: Pathways of assembly and catalysis of the major-class and minor-class spliceosomes.
Figure 3: Consensus sequences of major-class and minor-class introns.
Figure 4: Sequences and predicted secondary structures of the human spliceosomal snRNAs.
Figure 5: The phylogenetic distribution of minor-class introns.
Figure 6: Comparison of U2–U6 and U12–U6atac interactions at the catalytic core of the two spliceosomes.

Similar content being viewed by others

References

  1. Burge, C. B., Tuschl, T. & Sharp, P. A. in The RNA World 2nd edn (eds Gesteland, R. F., Cech, T. R. & Atkins, J. F.) 525–560 (Cold Spring Harbor Laboratory Press, New York, 1999).

    Google Scholar 

  2. Kreivi, J. P. & Lamond, A. I. RNA splicing: unexpected spliceosome diversity. Curr. Biol. 6, 802–805 (1996).

    CAS  PubMed  Google Scholar 

  3. Mount, S. M. AT-AC introns: an ATtACk on dogma. Science 271, 1690–1692 (1996).

    CAS  PubMed  Google Scholar 

  4. Nilsen, T. W. A parallel spliceosome. Science 273, 1813 (1996).

    CAS  PubMed  Google Scholar 

  5. Tarn, W. Y. & Steitz, J. A. Pre-mRNA splicing: the discovery of a new spliceosome doubles the challenge. Trends Biochem. Sci. 22, 132–137 (1997).

    CAS  PubMed  Google Scholar 

  6. Wu, Q. & Krainer, A. R. AT-AC pre-mRNA splicing mechanisms and conservation of minor introns in voltage-gated ion channel genes. Mol. Cell. Biol. 19, 3225–3236 (1999).

    CAS  PubMed Central  PubMed  Google Scholar 

  7. Moore, M. J., Query, C. C. & Sharp, P. A. in The RNA World 1st edn (eds Gesteland, R. F. & Atkins, J. F.) 303–357 (Cold Spring Harbor Laboratory Press, New York, 1993).

    Google Scholar 

  8. Nilsen, T. W. in RNA Structure and Function (eds Simmons, R. W. & Grunberg-Menago, M.) 279–307 (Cold Spring Harbor Laboratory Press, New York, 1998).

    Google Scholar 

  9. Staley, J. P. & Guthrie, C. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 92, 315–326 (1998).

    CAS  PubMed  Google Scholar 

  10. Reed, R. Initial splice-site recognition and pairing during pre-mRNA splicing. Curr. Opin. Genet. Dev. 6, 215–220 (1996).

    CAS  PubMed  Google Scholar 

  11. Konarska, M. M. & Sharp, P. A. Interactions between small nuclear ribonucleoprotein particles in formation of spliceosomes. Cell 49, 763–774 (1987).

    CAS  PubMed  Google Scholar 

  12. Wyatt, J. R., Sontheimer, E. J. & Steitz, J. A. Site-specific cross-linking of mammalian U5 snRNP to the 5′ splice site before the first step of pre-mRNA splicing. Genes Dev. 6, 2542–2553 (1992).

    CAS  PubMed  Google Scholar 

  13. Lamond, A. I., Konarska, M. M., Grabowski, P. J. & Sharp, P. A. Spliceosome assembly involves the binding and release of U4 small nuclear ribonucleoprotein. Proc. Natl Acad. Sci. USA 85, 411–415 (1988).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Wassarman, D. A. & Steitz, J. A. Interactions of small nuclear RNAs with precursor messenger RNA during in vitro splicing. Science 257, 1918–1925 (1992).

    CAS  PubMed  Google Scholar 

  15. Datta, B. & Weiner, A. M. Genetic evidence for base pairing between U2 and U6 snRNA in mammalian mRNA splicing. Nature 352, 821–824 (1991).

    CAS  PubMed  Google Scholar 

  16. Hausner, T. P., Giglio, L. M. & Weiner, A. M. Evidence for base-pairing between mammalian U2 and U6 small nuclear ribonucleoprotein particles. Genes Dev. 4, 2146–2156 (1990).

    CAS  PubMed  Google Scholar 

  17. Madhani, H. D. & Guthrie, C. A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome. Cell 71, 803–817 (1992).

    CAS  PubMed  Google Scholar 

  18. Wu, J. A. & Manley, J. L. Base pairing between U2 and U6 snRNAs is necessary for splicing of a mammalian pre-mRNA. Nature 352, 818–821 (1991).

    CAS  PubMed  Google Scholar 

  19. Newman, A. & Norman, C. Mutations in yeast U5 snRNA alter the specificity of 5′ splice-site cleavage. Cell 65, 115–123 (1991).

    CAS  PubMed  Google Scholar 

  20. Newman, A. J. & Norman, C. U5 snRNA interacts with exon sequences at 5′ and 3′ splice sites. Cell 68, 743–754 (1992).

    CAS  PubMed  Google Scholar 

  21. Sontheimer, E. J. & Steitz, J. A. The U5 and U6 small nuclear RNAs as active site components of the spliceosome. Science 262, 1989–1996 (1993).

    CAS  PubMed  Google Scholar 

  22. Jackson, I. J. A reappraisal of non-consensus mRNA splice sites. Nucleic Acids Res. 19, 3795–3798 (1991).

    CAS  PubMed Central  PubMed  Google Scholar 

  23. Hall, S. L. & Padgett, R. A. Conserved sequences in a class of rare eukaryotic nuclear introns with non-consensus splice sites. J. Mol. Biol. 239, 357–365 (1994). The first proposal that a distinct spliceosome might excise a variant class of pre-mRNA introns, the splice-site sequences of which diverge from the established consensus. The participation of low-abundance snRNAs U11 and U12 was suggested on the basis of their complementarity to common sequences at the 5′ end and putative branch point of four of the new introns.

    CAS  PubMed  Google Scholar 

  24. Montzka, K. A. & Steitz, J. A. Additional low-abundance human small nuclear ribonucleoproteins: U11, U12, etc. Proc. Natl Acad. Sci. USA 85, 8885–8889 (1988). The discovery of the low-abundance U11 and U12 snRNPs and their association to form the U11–U12 di-snRNP in extracts of human cells.

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Dietrich, R. C., Incorvaia, R. & Padgett, R. A. Terminal intron dinucleotide sequences do not distinguish between U2- and U12-dependent introns. Mol. Cell 1, 151–160 (1997). This study showed that the terminal dinucleotides of U12-type introns can be /GT and AG/, as in the major-class introns, and that U12-type introns can instead be defined on the basis of longer consensus sequences at the 5′ end and the branch point.

    CAS  PubMed  Google Scholar 

  26. Sharp, P. A. & Burge, C. B. Classification of introns: U2-type or U12-type. Cell 91, 875–879 (1997).

    CAS  PubMed  Google Scholar 

  27. Wu, Q. & Krainer, A. R. Splicing of a divergent subclass of AT-AC introns requires the major spliceosomal snRNAs. RNA 3, 586–601 (1997).

    CAS  PubMed Central  PubMed  Google Scholar 

  28. Burge, C. B., Padgett, R. A. & Sharp, P. A. Evolutionary fates and origins of U12-type introns. Mol. Cell 2, 773–785 (1998). A genomic database analysis identified 56 different genes containing U12-type introns in various eukaryotic taxa and detected switching of AT-AC to GT-AG termini in U12-type introns, as well as conversion of U12-type to U2-type introns in homologous genes. A fission/fusion model for the evolutionary origin of the two different splicing systems was proposed.

    CAS  PubMed  Google Scholar 

  29. Levine, A. & Durbin, R. A computational scan for U12-dependent introns in the human genome sequence. Nucleic Acids Res. 29, 4006–4013 (2001).

    CAS  PubMed Central  PubMed  Google Scholar 

  30. Otake, L. R. Thesis, Yale Univ. (2001).

  31. Berget, S. M. Exon recognition in vertebrate splicing. J. Biol. Chem. 270, 2411–2414 (1995).

    CAS  PubMed  Google Scholar 

  32. Talerico, M. & Berget, S. M. Intron definition in splicing of small Drosophila introns. Mol. Cell. Biol. 14, 3434–3445 (1994).

    CAS  PubMed Central  PubMed  Google Scholar 

  33. Wu, Q. & Krainer, A. R. U1-mediated exon definition interactions between AT-AC and GT-AG introns. Science 274, 1005–1008 (1996). The first evidence that splicing of pre-mRNAs containing both U12-type and U2-type introns can be coordinated by exon-definition interactions.

    CAS  PubMed  Google Scholar 

  34. Tarn, W. Y. & Steitz, J. A. A novel spliceosome containing U11, U12, and U5 snRNPs excises a minor class (AT-AC) intron in vitro. Cell 84, 801–811 (1996). The first description of an in vitro system that could remove an AT-AC intron provided evidence for the predicted interaction of U12 with the branch site and for the additional participation of the U11 and U5, but not the U4 and U6 snRNPs.

    CAS  PubMed  Google Scholar 

  35. McConnell, T. S., Cho, S. J., Frilander, M. J. & Steitz, J. A. Branchpoint selection in the splicing of U12-dependent introns in vitro. RNA 8, 579–586 (2002).

    CAS  PubMed Central  PubMed  Google Scholar 

  36. Yu, Y. T. & Steitz, J. A. Site-specific crosslinking of mammalian U11 and u6atac to the 5′ splice site of an AT-AC intron. Proc. Natl Acad. Sci. USA 94, 6030–6035 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Tarn, W. Y. & Steitz, J. A. Highly diverged U4 and U6 small nuclear RNAs required for splicing rare AT-AC introns. Science 273, 1824–1832 (1996). The identification and characterization of two new low-abundance snRNPs, U4atac and U6atac, allowed documentation of interactions between U6atac and U12 parallel to those previously proposed for U6 and U2 to occur in the spliceosomal active site and to juxtapose an intron's 5′ splice site and branch point for the first step of the splicing reaction.

    CAS  PubMed  Google Scholar 

  38. Hall, S. L. & Padgett, R. A. Requirement of U12 snRNA for in vivo splicing of a minor class of eukaryotic nuclear pre-mRNA introns. Science 271, 1716–1718 (1996). Mutations in the conserved branch-point sequence of an AT-AC intron were suppressed by compensatory mutations in U12, providing the first in vivo evidence for the U12-type splicing machinery.

    CAS  PubMed  Google Scholar 

  39. Kolossova, I. & Padgett, R. A. U11 snRNA interacts in vivo with the 5′ splice site of U12-dependent (AU-AC) pre-mRNA introns. RNA 3, 227–233 (1997).

    CAS  PubMed Central  PubMed  Google Scholar 

  40. Incorvaia, R. & Padgett, R. A. Base pairing with U6atac snRNA is required for 5′ splice site activation of U12-dependent introns in vivo. RNA 4, 709–718 (1998).

    CAS  PubMed Central  PubMed  Google Scholar 

  41. Otake, L. R., Scamborova, P., Hashimoto, C. & Steitz, J. A. The divergent U12-type spliceosome is required for pre-mRNA splicing and is essential for development in Drosophila. Mol. Cell 9, 439–446 (2002). P-element-mediated disruptions of the single loci encoding U12 and U6atac in D. melanogaster caused lethality during the embryonic and third instar larval stages, respectively, and defects in the excision of U12-type introns from several transcripts.

    CAS  PubMed  Google Scholar 

  42. Brow, D. A. & Guthrie, C. Spliceosomal RNA U6 is remarkably conserved from yeast to mammals. Nature 334, 213–218 (1988).

    CAS  PubMed  Google Scholar 

  43. Makarov, E. M. et al. Small nuclear ribonucleoprotein remodeling during catalytic activation of the spliceosome. Science 298, 2205–2208 (2002).

    CAS  PubMed  Google Scholar 

  44. Massenet, S., Mougin, A. & Branlant, C. in The Modification and Editing of RNA (eds Grosjean, H. & Benne, R.) 201–228 (ASM Press, Washington D.C., 1998).

    Google Scholar 

  45. Massenet, S. et al. Pseudouridine mapping in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (snRNAs) reveals that pseudouridine synthase pus1p exhibits a dual substrate specificity for U2 snRNA and tRNA. Mol. Cell. Biol. 19, 2142–2154 (1999).

    CAS  PubMed Central  PubMed  Google Scholar 

  46. Szkukalek, A., Myslinski, E., Mougin, A., Luhrmann, R. & Branlant, C. Phylogenetic conservation of modified nucleotides in the terminal loop 1 of the spliceosomal U5 snRNA. Biochimie 77, 16–21 (1995).

    CAS  PubMed  Google Scholar 

  47. Yu, Y. T., Shu, M. D. & Steitz, J. A. Modifications of U2 snRNA are required for snRNP assembly and pre-mRNA splicing. EMBO J. 17, 5783–5795 (1998).

    CAS  PubMed Central  PubMed  Google Scholar 

  48. Massenet, S. & Branlant, C. A limited number of pseudouridine residues in the human atac spliceosomal UsnRNAs as compared to human major spliceosomal UsnRNAs. RNA 5, 1495–1503 (1999).

    CAS  PubMed Central  PubMed  Google Scholar 

  49. Will, C. L. & Luhrmann, R. in Eukaryotic mRNA Processing (ed. Krainer, A. R.) 130–173 (IRL Press, Oxford, 1997).

    Google Scholar 

  50. Will, C. L. & Luhrmann, R. Spliceosomal UsnRNP biogenesis, structure and function. Curr. Opin. Cell Biol. 13, 290–301 (2001).

    CAS  PubMed  Google Scholar 

  51. Golas, M. M., Sander, B., Will, C. L., Luhrmann, R. & Stark, H. Molecular architecture of the multiprotein splicing factor SF3b. Science 300, 980–984 (2003).

    CAS  PubMed  Google Scholar 

  52. Query, C. C., Strobel, S. A. & Sharp, P. A. Three recognition events at the branch-site adenine. EMBO J. 15, 1392–1402 (1996).

    CAS  PubMed Central  PubMed  Google Scholar 

  53. Will, C. L. et al. A novel U2 and U11/U12 snRNP protein that associates with the pre-mRNA branch site. EMBO J. 20, 4536–4546 (2001).

    CAS  PubMed Central  PubMed  Google Scholar 

  54. Will, C. L., Schneider, C., Reed, R. & Luhrmann, R. Identification of both shared and distinct proteins in the major and minor spliceosomes. Science 284, 2003–2005 (1999). Analysis of 20 proteins associated with the U11–U12 di-snRNP showed that not only the U5 snRNP, but several protein components are shared by the major-class and minor-class spliceosomes.

    CAS  PubMed  Google Scholar 

  55. Schneider, C., Will, C. L., Makarova, O. V., Makarov, E. M. & Luhrmann, R. Human U4/U6.U5 and U4atac/U6atac.U5 tri-snRNPs exhibit similar protein compositions. Mol. Cell. Biol. 22, 3219–3229 (2002).

    CAS  PubMed Central  PubMed  Google Scholar 

  56. Nottrott, S. et al. Functional interaction of a novel 15.5kD [U4/U6.U5] tri-snRNP protein with the 5′ stem-loop of U4 snRNA. EMBO J. 18, 6119–6133 (1999).

    CAS  PubMed Central  PubMed  Google Scholar 

  57. Luo, H. R., Moreau, G. A., Levin, N. & Moore, M. J. The human Prp8 protein is a component of both U2- and U12-dependent spliceosomes. RNA 5, 893–908 (1999).

    CAS  PubMed Central  PubMed  Google Scholar 

  58. Cavalier-Smith, T. Intron phylogeny: a new hypothesis. Trends Genet. 7, 145–148 (1991).

    CAS  PubMed  Google Scholar 

  59. Cech, T. R. The generality of self-splicing RNA: relationship to nuclear mRNA splicing. Cell 44, 207–210 (1986).

    CAS  PubMed  Google Scholar 

  60. Jacquier, A. Self-splicing group II and nuclear pre-mRNA introns: how similar are they? Trends Biochem. Sci. 15, 351–354 (1990).

    CAS  PubMed  Google Scholar 

  61. Sharp, P. A. On the origin of RNA splicing and introns. Cell 42, 397–400 (1985).

    CAS  PubMed  Google Scholar 

  62. Sharp, P. A. 'Five easy pieces'. Science 254, 663 (1991).

    CAS  PubMed  Google Scholar 

  63. Bonen, L. & Vogel, J. The ins and outs of group II introns. Trends Genet. 17, 322–331 (2001).

    CAS  PubMed  Google Scholar 

  64. Dai, L. & Zimmerly, S. Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior. Nucleic Acids Res. 30, 1091–1102 (2002).

    CAS  PubMed Central  PubMed  Google Scholar 

  65. Mattick, J. S. Introns: evolution and function. Curr. Opin. Genet. Dev. 4, 823–831 (1994).

    CAS  PubMed  Google Scholar 

  66. Weiner, A. M. mRNA splicing and autocatalytic introns: distant cousins or the products of chemical determinism? Cell 72, 161–164 (1993).

    CAS  PubMed  Google Scholar 

  67. Moore, M. J. & Sharp, P. A. Evidence for two active sites in the spliceosome provided by stereochemistry of pre-mRNA splicing. Nature 365, 364–368 (1993).

    CAS  PubMed  Google Scholar 

  68. Padgett, R. A., Podar, M., Boulanger, S. C. & Perlman, P. S. The stereochemical course of group II intron self-splicing. Science 266, 1685–1688 (1994).

    CAS  PubMed  Google Scholar 

  69. Sontheimer, E. J., Gordon, P. M. & Piccirilli, J. A. Metal ion catalysis during group II intron self-splicing: parallels with the spliceosome. Genes Dev. 13, 1729–1741 (1999).

    CAS  PubMed Central  PubMed  Google Scholar 

  70. Hetzer, M., Wurzer, G., Schweyen, R. J. & Mueller, M. W. Trans-activation of group II intron splicing by nuclear U5 snRNA. Nature 386, 417–420 (1997).

    CAS  PubMed  Google Scholar 

  71. Parker, R., Siliciano, P. G. & Guthrie, C. Recognition of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA. Cell 49, 229–239 (1987).

    CAS  PubMed  Google Scholar 

  72. Schmelzer, C. & Schweyen, R. J. Self-splicing of group II introns in vitro: mapping of the branch point and mutational inhibition of lariat formation. Cell 46, 557–565 (1986).

    CAS  PubMed  Google Scholar 

  73. Abramovitz, D. L., Friedman, R. A. & Pyle, A. M. Catalytic role of 2′-hydroxyl groups within a group II intron active site. Science 271, 1410–1413 (1996).

    CAS  PubMed  Google Scholar 

  74. Jarrell, K. A., Dietrich, R. C. & Perlman, P. S. Group II intron domain 5 facilitates a trans-splicing reaction. Mol. Cell. Biol. 8, 2361–2366 (1988).

    CAS  PubMed Central  PubMed  Google Scholar 

  75. Konforti, B. B. et al. Ribozyme catalysis from the major groove of group II intron domain 5. Mol. Cell 1, 433–441 (1998).

    CAS  PubMed  Google Scholar 

  76. Peebles, C. L., Zhang, M., Perlman, P. S. & Franzen, J. S. Catalytically critical nucleotide in domain 5 of a group II intron. Proc. Natl Acad. Sci. USA 92, 4422–4426 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Yu, Y. T., Maroney, P. A., Darzynkiwicz, E. & Nilsen, T. W. U6 snRNA function in nuclear pre-mRNA splicing: a phosphorothioate interference analysis of the U6 phosphate backbone. RNA 1, 46–54 (1995).

    CAS  PubMed Central  PubMed  Google Scholar 

  78. Shukla, G. C. & Padgett, R. A. A catalytically active group II intron domain 5 can function in the U12-dependent spliceosome. Mol. Cell 9, 1145–1150 (2002). Evidence that the catalytic cores of the group-II self-splicing intron and the major- and minor-class spliceosomes are related was provided by functionally replacing a U6atac stem-loop with D5 of the group-II intron in an in vivo splicing assay.

    CAS  PubMed  Google Scholar 

  79. Shukla, G. C. & Padgett, R. A. The intramolecular stem-loop structure of U6 snRNA can functionally replace the U6atac snRNA stem-loop. RNA 7, 94–105 (2001).

    CAS  PubMed Central  PubMed  Google Scholar 

  80. Shukla, G. C. & Padgett, R. A. Conservation of functional features of U6atac and U12 snRNAs between vertebrates and higher plants. RNA 5, 525–538 (1999).

    CAS  PubMed Central  PubMed  Google Scholar 

  81. Sun, J. S. & Manley, J. L. A novel U2-U6 snRNA structure is necessary for mammalian mRNA splicing. Genes Dev. 9, 843–854 (1995).

    CAS  PubMed  Google Scholar 

  82. Fabrizio, P. & Abelson, J. Thiophosphates in yeast U6 snRNA specifically affect pre-mRNA splicing in vitro. Nucleic Acids Res. 20, 3659–3664 (1992).

    CAS  PubMed Central  PubMed  Google Scholar 

  83. Fortner, D. M., Troy, R. G. & Brow, D. A. A stem/loop in U6 RNA defines a conformational switch required for pre-mRNA splicing. Genes Dev. 8, 221–233 (1994).

    CAS  PubMed  Google Scholar 

  84. Madhani, H. D. & Guthrie, C. Randomization-selection analysis of snRNAs in vivo: evidence for a tertiary interaction in the spliceosome. Genes Dev. 8, 1071–1086 (1994).

    CAS  PubMed  Google Scholar 

  85. McPheeters, D. S. & Abelson, J. Mutational analysis of the yeast U2 snRNA suggests a structural similarity to the catalytic core of group I introns. Cell 71, 819–831 (1992).

    CAS  PubMed  Google Scholar 

  86. Wolff, T. & Bindereif, A. Conformational changes of U6 RNA during the spliceosome cycle: an intramolecular helix is essential both for initiating the U4-U6 interaction and for the first step of splicing. Genes Dev. 7, 1377–1389 (1993).

    CAS  PubMed  Google Scholar 

  87. Wolff, T., Menssen, R., Hammel, J. & Bindereif, A. Splicing function of mammalian U6 small nuclear RNA: conserved positions in central domain and helix I are essential during the first and second step of pre-mRNA splicing. Proc. Natl Acad. Sci. USA 91, 903–907 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. Parker, R. & Siliciano, P. G. Evidence for an essential non-Watson–Crick interaction between the first and last nucleotides of a nuclear pre-mRNA intron. Nature 361, 660–662 (1993).

    CAS  PubMed  Google Scholar 

  89. Wassarman, K. M. & Steitz, J. A. The low-abundance U11 and U12 small nuclear ribonucleoproteins (snRNPs) interact to form a two-snRNP complex. Mol. Cell. Biol. 12, 1276–1285 (1992).

    CAS  PubMed Central  PubMed  Google Scholar 

  90. Frilander, M. J. & Steitz, J. A. Initial recognition of U12-dependent introns requires both U11/5′ splice-site and U12/branchpoint interactions. Genes Dev. 13, 851–863 (1999). Strong cooperativity was documented for binding of the 5′ splice site and branch-point sequence by U11 and U12 snRNPs during pre-spliceosome formation on a U12-type intron, indicating greater rigidity in the intron recognition process for minor- versus major-class splicing.

    CAS  PubMed Central  PubMed  Google Scholar 

  91. Ruskin, B., Zamore, P. D. & Green, M. R. A factor, U2AF, is required for U2 snRNP binding and splicing complex assembly. Cell 52, 207–219 (1988).

    CAS  PubMed  Google Scholar 

  92. Frilander, M. J. & Steitz, J. A. Dynamic exchanges of RNA interactions leading to catalytic core formation in the U12-dependent spliceosome. Mol. Cell 7, 217–226 (2001).

    CAS  PubMed  Google Scholar 

  93. Hertel, K. J. & Maniatis, T. Serine-arginine (SR)-rich splicing factors have an exon-independent function in pre-mRNA splicing. Proc. Natl Acad. Sci. USA 96, 2651–2655 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  94. Kandels-Lewis, S. & Seraphin, B. Involvement of U6 snRNA in 5′ splice site selection. Science 262, 2035–2039 (1993).

    CAS  PubMed  Google Scholar 

  95. Kuhn, A. N., Li, Z. & Brow, D. A. Splicing factor Prp8 governs U4/U6 RNA unwinding during activation of the spliceosome. Mol. Cell 3, 65–75 (1999).

    CAS  PubMed  Google Scholar 

  96. Lesser, C. F. & Guthrie, C. Mutations in U6 snRNA that alter splice site specificity: implications for the active site. Science 262, 1982–1988 (1993).

    CAS  PubMed  Google Scholar 

  97. Staley, J. P. & Guthrie, C. An RNA switch at the 5′ splice site requires ATP and the DEAD box protein Prp28p. Mol. Cell 3, 55–64 (1999).

    CAS  PubMed  Google Scholar 

  98. Stephens, R. M. & Schneider, T. D. Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. J. Mol. Biol. 228, 1124–1136 (1992).

    CAS  PubMed  Google Scholar 

  99. Dietrich, R. C., Peris, M. J., Seyboldt, A. S. & Padgett, R. A. Role of the 3′ splice site in U12-dependent intron splicing. Mol. Cell. Biol. 21, 1942–1952 (2001).

    CAS  PubMed Central  PubMed  Google Scholar 

  100. Kuo, H. C., Nasim, F. H. & Grabowski, P. J. Control of alternative splicing by the differential binding of U1 small nuclear ribonucleoprotein particle. Science 251, 1045–1050 (1991).

    CAS  PubMed  Google Scholar 

  101. Robberson, B. L., Cote, G. J. & Berget, S. M. Exon definition may facilitate splice site selection in RNAs with multiple exons. Mol. Cell. Biol. 10, 84–94 (1990).

    CAS  PubMed Central  PubMed  Google Scholar 

  102. Wu, Q. & Krainer, A. R. Purine-rich enhancers function in the AT-AC pre-mRNA splicing pathway and do so independently of intact U1 snRNP. RNA 4, 1664–1673 (1998). Enhancer sequences located in exons were shown to stimulate splicing of U12-type introns, as they do for U2-type introns.

    CAS  PubMed Central  PubMed  Google Scholar 

  103. Black, D. L. Protein diversity from alternative splicing: a challenge for bioinformatics and post-genome biology. Cell 103, 367–370 (2000).

    CAS  PubMed  Google Scholar 

  104. Black, D. L. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72, 291–336 (2003).

    CAS  PubMed  Google Scholar 

  105. Grabowski, P. J. & Black, D. L. Alternative RNA splicing in the nervous system. Prog. Neurobiol. 65, 289–308 (2001).

    CAS  PubMed  Google Scholar 

  106. Smith, C. W. & Valcarcel, J. Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem. Sci. 25, 381–388 (2000).

    CAS  PubMed  Google Scholar 

  107. Dietrich, R. C., Shukla, G. C., Fuller, J. D. & Padgett, R. A. Alternative splicing of U12-dependent introns in vivo responds to purine-rich enhancers. RNA 7, 1378–1388 (2001). By constructing artificial minigenes, the authors showed that U12-type introns can participate in alternative splicing and that the splicing pattern can be influenced by exonic enhancer elements.

    CAS  PubMed Central  PubMed  Google Scholar 

  108. Hastings, M. L. & Krainer, A. R. Functions of SR proteins in the U12-dependent AT-AC pre-mRNA splicing pathway. RNA 7, 471–82 (2001).

    CAS  PubMed Central  PubMed  Google Scholar 

  109. Hastings, M. L., Wilson, C. M. & Munroe, S. H. A purine-rich intronic element enhances alternative splicing of thyroid hormone receptor mRNA. RNA 7, 859–874 (2001).

    CAS  PubMed Central  PubMed  Google Scholar 

  110. Lam, B. J. & Hertel, K. J. A general role for splicing enhancers in exon definition. RNA 8, 1233–1241 (2002).

    CAS  PubMed Central  PubMed  Google Scholar 

  111. Lynch, M. & Richardson, A. O. The evolution of spliceosomal introns. Curr. Opin. Genet. Dev. 12, 701–710 (2002). A theoretical framework for the phylogenetic and physical distribution of introns is presented, including the idea that the progenitor eukaryote had spliceosomal introns that diverged early on into two distinct classes.

    CAS  PubMed  Google Scholar 

  112. Spafford, J. D., Spencer, A. N. & Gallin, W. J. A putative voltage-gated sodium channel α-subunit (PpSCN1) from the hydrozoan jellyfish, Polyorchis penicillatus: structural comparisons and evolutionary considerations. Biochem. Biophys. Res. Commun. 244, 772–780 (1998).

    CAS  PubMed  Google Scholar 

  113. Spafford, J. D., Spencer, A. N. & Gallin, W. J. Genomic organization of a voltage-gated Na+ channel in a hydrozoan jellyfish: insights into the evolution of voltage-gated Na+ channel genes. Recept. Channels 6, 493–506 (1999).

    CAS  PubMed  Google Scholar 

  114. Patel, A. A., McCarthy, M. & Steitz, J. A. The splicing of U12-type introns can be a rate-limiting step in gene expression. EMBO J. 21, 3804–3815 (2002). Data from a quantitative RT-PCR assay showed that U12-type introns are removed more slowly than neighbouring U2-type introns from pre-mRNAs in both human and Drosophila cells, and that minor-class introns thereby serve to lower the abundance of the RNA and protein products of a gene.

    CAS  PubMed Central  PubMed  Google Scholar 

  115. Shukla, G. C., Cole, A. J., Dietrich, R. C. & Padgett, R. A. Domains of human U4atac snRNA required for U12-dependent splicing in vivo. Nucleic Acids Res. 30, 4650–4657 (2002).

    CAS  PubMed Central  PubMed  Google Scholar 

  116. Hirose, Y. & Manley, J. L. RNA polymerase II and the integration of nuclear events. Genes Dev. 14, 1415–1429 (2000).

    CAS  PubMed  Google Scholar 

  117. Misteli, T. & Spector, D. L. RNA polymerase II targets pre-mRNA splicing factors to transcription sites in vivo. Mol. Cell 3, 697–705 (1999).

    CAS  PubMed  Google Scholar 

  118. Proudfoot, N. Connecting transcription to messenger RNA processing. Trends Biochem. Sci. 25, 290–293 (2000).

    CAS  PubMed  Google Scholar 

  119. Baserga, S. J. & Steitz, J. A. in The RNA World 1st edn (eds Gesteland, R. F. & Atkins, J. F.) 359–381 (Cold Spring Harbor Laboratory Press, New York, 1993).

    Google Scholar 

  120. Padgett, R. A. & Shukla, G. C. A revised model for U4atac/U6atac snRNA base pairing. RNA 8, 125–128 (2002).

    CAS  PubMed Central  PubMed  Google Scholar 

Download references

Acknowledgements

We thank C. B. Burge, R. A. Padgett, R. Luhrmann, M. Frilander, A. Krainer and R. Durbin for sharing unpublished information. We appreciate the critical reading of the manuscript by R. A. Padgett, K. Tycowski, L. Szewczak, T. Hirose and R. Lytle.

Author information

Authors and Affiliations

  1. Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, 295 Congress Avenue, New Haven, 06536, Connecticut, USA

    Abhijit A. Patel & Joan A. Steitz

Authors
  1. Abhijit A. Patel
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Joan A. Steitz
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Joan A. Steitz.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Related links

Related links

DATABASES

FlyBase

prospero

LocusLink

Huntingtin

p14

SF3b

U2AF

Swiss-Prot

Prp8

Glossary

INTRON

An intervening non-coding sequence that interrupts two exons and that must be excised from pre-messenger RNA transcripts before translation.

EXON

The segment of a pre-messenger RNA transcript that contains protein-coding sequence and/or the 5′ or 3′ untranslated sequences, which must be spliced together with other exons to produce a mature messenger RNA.

SPLICEOSOME

A large complex that consists of five splicing small nuclear ribonucleoprotein particles as well as numerous protein factors. It mediates the excision of introns from pre-messenger RNA transcripts and ligates exon ends to produce mature mRNAs.

SMALL NUCLEAR RIBONUCLEOPROTEIN PARTICLE

(snRNP). A particle that is found in the cell nucleus and consists of a tight complex between a short RNA molecule (<∼300 nucleotides) and one or more proteins. SnRNPs are involved in pre-mRNA processing and transfer RNA biogenesis.

LARIAT

An RNA, the 5′ end of which is joined by a phosphodiester linkage to the 2′ hydroxyl of an internal nucleotide, thereby creating a lasso-shaped molecule.

METAZOAN

Refers to all animal species that contain multiple cells differentiated into tissues and organs.

INTRON BRANCH SITE

The adenosine residue near the 3′ end of an intron the 2′ hydroxyl group of which becomes linked to the 5′ end of the intron during the first step of splicing.

INTRON-DEFINITION MODEL

A model that proposes the initial pairwise interaction of spliceosomal components across introns, defining intron units that subsequently interact to promote spliceosome assembly and catalysis.

EXON-DEFINITION MODEL

A model in which exon units, rather than intron units, are initially defined by pairing of spliceosomal components across exons.

PSEUDOURIDYLATION

The conversion of a uridine residue within an RNA chain into a pseudouridine residue, which requires the scission and reattachment of the base to the sugar.

SM PROTEIN

A protein that belongs to a group of seven core proteins that are common to the splicing small nuclear ribonucleoprotein particles (except for U6 and U6atac, which have Sm-like proteins). Several are recognized by anti-Sm antibodies that are produced by patients with the autoimmune disease systemic lupus erythematosus.

GROUP II INTRONS

A rare class of autocatalytic introns, the excision of which is assisted by, but does not require, trans-acting protein factors.

RIBOZYME

An enzyme that consists of RNA.

SR FAMILY OF PROTEINS

A group of essential protein splicing factors with one or more RNA-recognition motif and a region containing arginine/serine (S/R) dipeptide repeats, which facilitate spliceosome assembly onto a pre-messenger RNA.

PARALOGOUS GENES

Genes for which sequence similarity is the result of gene duplication within the same species and that encode proteins that carry out similar, but not identical functions.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Patel, A., Steitz, J. Splicing double: insights from the second spliceosome. Nat Rev Mol Cell Biol 4, 960–970 (2003). https://doi.org/10.1038/nrm1259

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrm1259

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing