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A day in the life of the spliceosome

An Erratum to this article was published on 11 March 2014

This article has been updated

Key Points

  • Spliceosomal snRNAs are transcribed from specialized promoters, which recruit RNA polymerase II cofactors that aid in proper 3′ end maturation of these non-polyadenylated transcripts.

  • Like most non-coding RNAs, small nuclear RNAs (snRNAs) use cognate antisense elements to interact with their nucleic acid targets via base pairing.

  • Assembly of functional small nuclear ribonucleoproteins (snRNPs) involves a series of non-functional intermediates that are often sequestered in subcellular compartments that are distinct from their sites of action.

  • snRNP function requires multiple protein partners (such as DExD/H helicases or WD box proteins) the roles of which may include modulating RNA structure or tethering an enzyme.

  • snRNPs recognize specific sequences in pre-mRNAs and assemble into the spliceosome in a stepwise manner. The splicing reaction itself is catalysed by U6/U2 snRNA complex that resembles a self-splicing ribozyme.

  • Alternative splicing is typically regulated by multiple cis-elements and trans-factors, which form complex interaction networks that may provide a great deal of regulatory plasticity.

  • Pre-mRNA splicing can be regulated throughout the entire spliceosomal assembly pathway, although the early steps are the main stages of regulation.

Abstract

One of the most amazing findings in molecular biology was the discovery that eukaryotic genes are discontinuous, with coding DNA being interrupted by stretches of non-coding sequence. The subsequent realization that the intervening regions are removed from pre-mRNA transcripts via the activity of a common set of small nuclear RNAs (snRNAs), which assemble together with associated proteins into a complex known as the spliceosome, was equally surprising. How do cells coordinate the assembly of this molecular machine? And how does the spliceosome accurately recognize exons and introns to carry out the splicing reaction? Insights into these questions have been gained by studying the life cycle of spliceosomal snRNAs from their transcription, nuclear export and re-import to their dynamic assembly into the spliceosome. This assembly process can also affect the regulation of alternative splicing and has implications for human disease.

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Figure 1: Comparison of transcription and processing of snRNAs and mRNAs.
Figure 2: Maturation of snRNAs requires nuclear and cytoplasmic regulatory steps.
Figure 3: Assisted assembly of Sm-class snRNPs.
Figure 4: Step-wise assembly of the spliceosome and catalytic steps of splicing.
Figure 5: Regulation of alternative splicing.

Change history

  • 11 March 2014

    In table 1 (page 116) of the above article, the secondary structure of the snRNAs (small nuclear RNAs) for the U4–U6 di–snRNP (small nuclear ribonucleoprotein) was incorrect. This has now been rectified in the online version of the article. Nature Reviews Molecular Cell Biology apologizes for any confusion caused to readers.

References

  1. 1

    Berget, S. M., Moore, C. & Sharp, P. A. Spliced segments at the 5′ terminus of adenovirus 2 late mRNA. Proc. Natl Acad. Sci. USA 74, 3171–3175 (1977).

    CAS  PubMed  Article  Google Scholar 

  2. 2

    Chow, L. T., Gelinas, R. E., Broker, T. R. & Roberts, R. J. An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger RNA. Cell 12, 1–8 (1977).

    CAS  PubMed  Article  Google Scholar 

  3. 3

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  4. 4

    Will, C. L. & Luhrmann, R. Spliceosome structure and function. Cold Spring Harb. Perspect. Biol. 3, a003707 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  5. 5

    Jurica, M. S. & Moore, M. J. Pre-mRNA splicing: awash in a sea of proteins. Mol. Cell 12, 5–14 (2003).

    CAS  PubMed  Article  Google Scholar 

  6. 6

    Matera, A. G., Terns, R. M. & Terns, M. P. Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nature Rev. Mol. Cell Biol. 8, 209–220 (2007).

    CAS  Article  Google Scholar 

  7. 7

    Henry, R. W., Mittal, V., Ma, B., Kobayashi, R. & Hernandez, N. SNAP19 mediates the assembly of a functional core promoter complex (SNAPc) shared by RNA polymerases II and III. Genes Dev. 12, 2664–2672 (1998).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  8. 8

    Hung, K. H. & Stumph, W. E. Regulation of snRNA gene expression by the Drosophila melanogaster small nuclear RNA activating protein complex (DmSNAPc). Crit. Rev. Biochem. Mol. Biol. 46, 11–26 (2011).

    CAS  PubMed  Article  Google Scholar 

  9. 9

    Hernandez, N. & Weiner, A. M. Formation of the 3′ end of U1 snRNA requires compatible snRNA promoter elements. Cell 47, 249–258 (1986).

    CAS  PubMed  Article  Google Scholar 

  10. 10

    Egloff, S. et al. The integrator complex recognizes a new double mark on the RNA polymerase II carboxyl-terminal domain. J. Biol. Chem. 285, 20564–20569 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  11. 11

    Egloff, S. et al. Serine-7 of the RNA polymerase II CTD is specifically required for snRNA gene expression. Science 318, 1777–1779 (2007).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  12. 12

    Baillat, D. et al. Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II. Cell 123, 265–276 (2005). Identifies the complex that carries out pre-snRNA 3′-end processing.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  13. 13

    Chen, J. et al. An RNAi screen identifies additional members of the Drosophila Integrator complex and a requirement for cyclin C/Cdk8 in snRNA 3′-end formation. RNA 18, 2148–2156 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  14. 14

    Weiner, A. M. E Pluribus Unum: 3′ end formation of polyadenylated mRNAs, histone mRNAs, and U snRNAs. Mol. Cell 20, 168–170 (2005).

    CAS  PubMed  Article  Google Scholar 

  15. 15

    Mandel, C. R. et al. Polyadenylation factor CPSF-73 is the pre-mRNA 3′-end-processing endonuclease. Nature 444, 953–956 (2006).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  16. 16

    Ezzeddine, N. et al. A subset of Drosophila integrator proteins is essential for efficient U7 snRNA and spliceosomal snRNA 3′-end formation. Mol. Cell. Biol. 31, 328–341 (2011).

    CAS  PubMed  Article  Google Scholar 

  17. 17

    Boon, K. L. et al. prp8 mutations that cause human retinitis pigmentosa lead to a U5 snRNP maturation defect in yeast. Nature Struct. Mol. Biol. 14, 1077–1083 (2007).

    CAS  Article  Google Scholar 

  18. 18

    Murphy, M. W., Olson, B. L. & Siliciano, P. G. The yeast splicing factor Prp40p contains functional leucine-rich nuclear export signals that are essential for splicing. Genetics 166, 53–65 (2004).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  19. 19

    Tkacz, I. D. et al. Identification of novel snRNA-specific Sm proteins that bind selectively to U2 and U4 snRNAs in Trypanosoma brucei. RNA 13, 30–43 (2007).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  20. 20

    Palfi, Z. et al. SMN-assisted assembly of snRNP-specific Sm cores in trypanosomes. Genes Dev. 23, 1650–1664 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  21. 21

    Jae, N. et al. snRNA-specific role of SMN in trypanosome snRNP biogenesis in vivo. RNA Biol. 8, 90–100 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  22. 22

    Hernandez-Verdun, D., Roussel, P., Thiry, M., Sirri, V. & Lafontaine, D. L. The nucleolus: structure/function relationship in RNA metabolism. Wiley Interdiscip. Rev. RNA 1, 415–431 (2010).

    CAS  PubMed  Article  Google Scholar 

  23. 23

    Ohno, M. Size matters in RNA export. RNA Biol. 9, 1413–1417 (2012).

    CAS  PubMed  Article  Google Scholar 

  24. 24

    Cullen, B. R. Nuclear RNA export. J. Cell Sci. 116, 587–597 (2003).

    PubMed  Article  Google Scholar 

  25. 25

    Ohno, M., Segref, A., Kuersten, S. & Mattaj, I. W. Identity elements used in export of mRNAs. Mol. Cell 9, 659–671 (2002).

    CAS  PubMed  Article  Google Scholar 

  26. 26

    Masuyama, K., Taniguchi, I., Kataoka, N. & Ohno, M. RNA length defines RNA export pathway. Genes Dev. 18, 2074–2085 (2004).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  27. 27

    Fuke, H. & Ohno, M. Role of poly (A) tail as an identity element for mRNA nuclear export. Nucleic Acids Res. 36, 1037–1049 (2008).

    CAS  PubMed  Article  Google Scholar 

  28. 28

    McCloskey, A. Taniguchi, I., Shinmyozu, K. & Ohno, M. hnRNP C tetramer measures RNA length to classify RNA polymerase II transcripts for export. Science 335, 1643–1646 (2012). First identification of a specific function for the non-shuttling hnRNP C-type proteins in RNA export.

    CAS  PubMed  Article  Google Scholar 

  29. 29

    Izaurralde, E. et al. A nuclear cap binding protein complex involved in pre-mRNA splicing. Cell 78, 657–668 (1994).

    CAS  PubMed  Article  Google Scholar 

  30. 30

    Ohno, M., Segref, A., Bachi, A., Wilm, M. & Mattaj, I. W. PHAX, a mediator of U snRNA nuclear export whose activity is regulated by phosphorylation. Cell 101, 187–198 (2000).

    CAS  PubMed  Article  Google Scholar 

  31. 31

    Hallais, M. et al. CBC–ARS2 stimulates 3′-end maturation of multiple RNA families and favors cap-proximal processing. Nature Struct. Mol. Biol. 20, 1358–1366 (2013). Shows that Ars2 forms 5′ cap-binding subcomplexes that participate in 3′-end processing of three distinct classes of transcript.

    CAS  Article  Google Scholar 

  32. 32

    Fornerod, M., Ohno, M., Yoshida, M. & Mattaj, I. W. CRM1 is an export receptor for leucine-rich nuclear export signals. Cell 90, 1051–1060 (1997).

    CAS  PubMed  Article  Google Scholar 

  33. 33

    Smith, K. P. & Lawrence, J. B. Interactions of U2 gene loci and their nuclear transcripts with Cajal (coiled) bodies: evidence for PreU2 within Cajal bodies. Mol. Biol. Cell 11, 2987–2998 (2000).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  34. 34

    Suzuki, T., Izumi, H. & Ohno, M. Cajal body surveillance of U snRNA export complex assembly. J. Cell Biol. 190, 603–612 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  35. 35

    Boulon, S. et al. PHAX and CRM1 are required sequentially to transport U3 snoRNA to nucleoli. Mol. Cell 16, 777–787 (2004).

    CAS  PubMed  Article  Google Scholar 

  36. 36

    Frey, M. R. & Matera, A. G. RNA-mediated interaction of Cajal bodies and U2 snRNA genes. J. Cell Biol. 154, 499–509 (2001).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  37. 37

    Lemm, I. et al. Ongoing U snRNP biogenesis is required for the integrity of Cajal bodies. Mol. Biol. Cell 17, 3221–3231 (2006).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  38. 38

    Matera, A. G., Izaguire-Sierra, M., Praveen, K. & Rajendra, T. K. Nuclear bodies: random aggregates of sticky proteins or crucibles of macromolecular assembly? Dev. Cell 17, 639–647 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  39. 39

    Kitao, S. et al. A compartmentalized phosphorylation/dephosphorylation system that regulates U snRNA export from the nucleus. Mol. Cell. Biol. 28, 487–497 (2008).

    CAS  PubMed  Article  Google Scholar 

  40. 40

    Meister, G., Buhler, D., Pillai, R., Lottspeich, F. & Fischer, U. A multiprotein complex mediates the ATP-dependent assembly of spliceosomal U snRNPs. Nature Cell Biol. 3, 945–949 (2001).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  41. 41

    Pellizzoni, L., Yong, J. & Dreyfuss, G. Essential role for the SMN complex in the specificity of snRNP assembly. Science 298, 1775–1779 (2002).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  42. 42

    Massenet, S., Pellizzoni, L., Paushkin, S., Mattaj, I. W. & Dreyfuss, G. The SMN complex is associated with snRNPs throughout their cytoplasmic assembly pathway. Mol. Cell. Biol. 22, 6533–6541 (2002).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  43. 43

    Narayanan, U., Ospina, J. K., Frey, M. R., Hebert, M. D. & Matera, A. G. SMN, the spinal muscular atrophy protein, forms a pre-import snRNP complex with snurportin1 and importin β. Hum. Mol. Genet. 11, 1785–1795 (2002).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  44. 44

    Mouaikel, J. et al. Interaction between the small-nuclear-RNA cap hypermethylase and the spinal muscular atrophy protein, survival of motor neuron. EMBO Rep. 4, 616–622 (2003).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  45. 45

    Meister, G. et al. Methylation of Sm proteins by a complex containing PRMT5 and the putative U snRNP assembly factor pICln. Curr. Biol. 11, 1990–1994 (2001).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  46. 46

    Friesen, W. J. et al. The methylosome, a 20S complex containing JBP1 and pICln, produces dimethylarginine-modified Sm proteins. Mol. Cell. Biol. 21, 8289–8300 (2001).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  47. 47

    Grimm, C. et al. Structural basis of assembly chaperone-mediated snRNP formation. Mol. Cell 49, 692–703 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  48. 48

    Chari, A. et al. An assembly chaperone collaborates with the SMN complex to generate spliceosomal snRNPs. Cell 135, 497–509 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  49. 49

    Yong, J., Kasim, M., Bachorik, J. L., Wan, L. & Dreyfuss, G. Gemin5 delivers snRNA precursors to the SMN complex for snRNP biogenesis. Mol. Cell 38, 551–562 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  50. 50

    Raker, V. A., Plessel, G. & Luhrmann, R. The snRNP core assembly pathway: identification of stable core protein heteromeric complexes and an snRNP subcore particle in vitro. EMBO J. 15, 2256–2269 (1996).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  51. 51

    Kambach, C. et al. Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs. Cell 96, 375–387 (1999).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  52. 52

    Leung, A. K., Nagai, K. & Li, J. Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis. Nature 473, 536–539 (2011). Co-crystal structure of U4 snRNA construct with an Sm core definitively shows that the RNA passes through the hole in the Sm ring.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  53. 53

    Kroiss, M. et al. Evolution of an RNP assembly system: a minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogaster. Proc. Natl Acad. Sci. USA 105, 10045–10050 (2008). Shows that both human and fruitfly SMN–GEMIN2 heterodimers are sufficient for mediating Sm core assembly in vitro.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  54. 54

    Zhang, R. et al. Structure of a key intermediate of the SMN complex reveals Gemin2's crucial function in snRNP assembly. Cell 146, 384–395 (2011). Together with reference 46, these papers identify key intermediates in the Sm core assembly pathway, highlighting an unexpected role for GEMIN2.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  55. 55

    Liu, Q., Fischer, U., Wang, F. & Dreyfuss, G. The spinal muscular atrophy disease gene product, SMN, and its associated protein SIP1 are in a complex with spliceosomal snRNP proteins. Cell 90, 1013–1021 (1997).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  56. 56

    Buhler, D., Raker, V., Luhrmann, R. & Fischer, U. Essential role for the tudor domain of SMN in spliceosomal U snRNP assembly: implications for spinal muscular atrophy. Hum. Mol. Genet. 8, 2351–2357 (1999).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  57. 57

    Pellizzoni, L., Charroux, B. & Dreyfuss, G. SMN mutants of spinal muscular atrophy patients are defective in binding to snRNP proteins. Proc. Natl Acad. Sci. USA 96, 11167–11172 (1999).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  58. 58

    Hannus, S., Buhler, D., Romano, M., Seraphin, B. & Fischer, U. The Schizosaccharomyces pombe protein Yab8p and a novel factor, Yip1p, share structural and functional similarity with the spinal muscular atrophy-associated proteins SMN and SIP1. Hum. Mol. Genet. 9, 663–674 (2000).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  59. 59

    Rajendra, T. K. et al. A Drosophila melanogaster model of spinal muscular atrophy reveals a function for SMN in striated muscle. J. Cell Biol. 176, 831–841 (2007).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  60. 60

    Shpargel, K. B. & Matera, A. G. Gemin proteins are required for efficient assembly of Sm-class ribonucleoproteins. Proc. Natl Acad. Sci. USA 102, 17372–17377 (2005). Assays individual Gemins, as well as a panel of SMN missense mutants for ability to carry out Sm core assembly, showing that certain SMA-causing alleles are functional, whereas others are not.

    CAS  PubMed  Article  Google Scholar 

  61. 61

    Selenko, P. et al. SMN Tudor domain structure and its interaction with the Sm proteins. Nature Struct. Biol. 8, 27–31 (2001).

    CAS  PubMed  Article  Google Scholar 

  62. 62

    Lorson, C. L. et al. SMN oligomerization defect correlates with spinal muscular atrophy severity. Nature Genet. 19, 63–66 (1998).

    CAS  PubMed  Article  Google Scholar 

  63. 63

    Martin, R., Gupta, K., Ninan, N. S., Perry, K. & Van Duyne, G. D. The survival motor neuron protein forms soluble glycine zipper oligomers. Structure 20, 1929–1939 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  64. 64

    Fischer, U. & Luhrmann, R. An essential signaling role for the m3G cap in the transport of U1 snRNP to the nucleus. Science 249, 786–790 (1990).

    CAS  PubMed  Article  Google Scholar 

  65. 65

    Narayanan, U., Achsel, T., Luhrmann, R. & Matera, A. G. Coupled in vitro import of U snRNPs and SMN, the spinal muscular atrophy protein. Mol. Cell 16, 223–234 (2004).

    CAS  PubMed  Article  Google Scholar 

  66. 66

    Fischer, U., Sumpter, V., Sekine, M., Satoh, T. & Luhrmann, R. Nucleo-cytoplasmic transport of U snRNPs: definition of a nuclear location signal in the Sm core domain that binds a transport receptor independently of the m3G cap. EMBO J. 12, 573–583 (1993).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  67. 67

    Huber, J. et al. Snurportin1, an m3G-cap-specific nuclear import receptor with a novel domain structure. EMBO J. 17, 4114–4126 (1998).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  68. 68

    Palacios, I., Hetzer, M., Adam, S. A. & Mattaj, I. W. Nuclear import of U snRNPs requires importin β. EMBO J. 16, 6783–6792 (1997).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  69. 69

    Fischer, U., Liu, Q. & Dreyfuss, G. The SMN–SIP1 complex has an essential role in spliceosomal snRNP biogenesis. Cell 90, 1023–1029 (1997).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  70. 70

    Neubauer, G. et al. Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. Nature Genet. 20, 46–50 (1998).

    CAS  PubMed  Article  Google Scholar 

  71. 71

    Trinkle-Mulcahy, L. et al. Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. J. Cell Biol. 183, 223–239 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  72. 72

    Herold, N. et al. Conservation of the protein composition and electron microscopy structure of Drosophila melanogaster and human spliceosomal complexes. Mol. Cell. Biol. 29, 281–301 (2009).

    CAS  PubMed  Article  Google Scholar 

  73. 73

    Matera, A. G. & Shpargel, K. B. Pumping RNA: nuclear bodybuilding along the RNP pipeline. Curr. Opin. Cell Biol. 18, 317–324 (2006).

    CAS  PubMed  Article  Google Scholar 

  74. 74

    Stanek, D. & Neugebauer, K. M. The Cajal body: a meeting place for spliceosomal snRNPs in the nuclear maze. Chromosoma 115, 343–354 (2006).

    CAS  PubMed  Article  Google Scholar 

  75. 75

    Sleeman, J. E. & Lamond, A. I. Newly assembled snRNPs associate with coiled bodies before speckles, suggesting a nuclear snRNP maturation pathway. Curr. Biol. 9, 1065–1074 (1999).

    CAS  PubMed  Article  Google Scholar 

  76. 76

    Lamond, A. I. & Spector, D. L. Nuclear speckles: a model for nuclear organelles. Nature Rev. Mol. Cell Biol. 4, 605–612 (2003).

    CAS  Article  Google Scholar 

  77. 77

    Ospina, J. K. et al. Cross-talk between snurportin1 subdomains. Mol. Biol. Cell 16, 4660–4671 (2005).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  78. 78

    Jady, B. E. et al. Modification of Sm small nuclear RNAs occurs in the nucleoplasmic Cajal body following import from the cytoplasm. EMBO J. 22, 1878–1888 (2003).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  79. 79

    Nesic, D., Tanackovic, G. & Kramer, A. A role for Cajal bodies in the final steps of U2 snRNP biogenesis. J. Cell Sci. 117, 4423–4433 (2004).

    CAS  PubMed  Article  Google Scholar 

  80. 80

    Schaffert, N., Hossbach, M., Heintzmann, R., Achsel, T. & Luhrmann, R. RNAi knockdown of hPrp31 leads to an accumulation of U4/U6 di-snRNPs in Cajal bodies. EMBO J. 23, 3000–3009 (2004).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  81. 81

    Novotny, I., Blazikova, M., Stanek, D., Herman, P. & Malinsky, J. In vivo kinetics of U4/U6. U5 tri-snRNP formation in Cajal bodies. Mol. Biol. Cell 22, 513–523 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  82. 82

    Stanek, D. & Neugebauer, K. M. Detection of snRNP assembly intermediates in Cajal bodies by fluorescence resonance energy transfer. J. Cell Biol. 166, 1015–1025 (2004).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  83. 83

    Stanek, D., Rader, S. D., Klingauf, M. & Neugebauer, K. M. Targeting of U4/U6 small nuclear RNP assembly factor SART3/p110 to Cajal bodies. J. Cell Biol. 160, 505–516 (2003).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  84. 84

    Strzelecka, M., Oates, A. C. & Neugebauer, K. M. Dynamic control of Cajal body number during zebrafish embryogenesis. Nucleus 1, 96–108 (2010).

    PubMed  PubMed Central  Article  Google Scholar 

  85. 85

    Takata, H., Nishijima, H., Maeshima, K. & Shibahara, K. The integrator complex is required for integrity of Cajal bodies. J. Cell Sci. 125, 166–175 (2012).

    CAS  PubMed  Article  Google Scholar 

  86. 86

    Tucker, K. E. et al. Residual Cajal bodies in coilin knockout mice fail to recruit Sm snRNPs and SMN, the spinal muscular atrophy gene product. J. Cell Biol. 154, 293–307 (2001).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  87. 87

    Liu, J. L. et al. Coilin is essential for Cajal body organization in Drosophila melanogaster. Mol. Biol. Cell 20, 1661–1670 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  88. 88

    Walker, M. P., Tian, L. & Matera, A. G. Reduced viability, fertility and fecundity in mice lacking the cajal body marker protein, coilin. PLoS ONE 4, e6171 (2009).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  89. 89

    Strzelecka, M. et al. Coilin-dependent snRNP assembly is essential for zebrafish embryogenesis. Nature Struct. Mol. Biol. 17, 403–409 (2010).

    CAS  Article  Google Scholar 

  90. 90

    Spector, D. L. & Lamond, A. I. Nuclear speckles. Cold Spring Harb. Perspect. Biol. 3, a000646 (2011).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  91. 91

    Hall, L. L., Smith, K. P., Byron, M. & Lawrence, J. B. Molecular anatomy of a speckle. Anat. Rec. A Discov. Mol. Cell. Evol. Biol. 288, 664–675 (2006).

    PubMed  PubMed Central  Article  Google Scholar 

  92. 92

    Girard, C. et al. Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion. Nature Commun. 3, 994 (2012).

    Article  CAS  Google Scholar 

  93. 93

    Valadkhan, S. Role of the snRNAs in spliceosomal active site. RNA Biol. 7, 345–353 (2010).

    CAS  PubMed  Article  Google Scholar 

  94. 94

    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).

    CAS  PubMed  Article  Google Scholar 

  95. 95

    Wiesner, S., Stier, G., Sattler, M. & Macias, M. J. Solution structure and ligand recognition of the WW domain pair of the yeast splicing factor Prp40. J. Mol. Biol. 324, 807–822 (2002).

    CAS  PubMed  Article  Google Scholar 

  96. 96

    Morris, D. P. & Greenleaf, A. L. The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II. J. Biol. Chem. 275, 39935–39943 (2000).

    CAS  PubMed  Article  Google Scholar 

  97. 97

    Gornemann, J. et al. Cotranscriptional spliceosome assembly and splicing are independent of the Prp40p WW domain. RNA 17, 2119–2129 (2011).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  98. 98

    Staknis, D. & Reed, R. SR proteins promote the first specific recognition of Pre-mRNA and are present together with the U1 small nuclear ribonucleoprotein particle in a general splicing enhancer complex. Mol. Cell. Biol. 14, 7670–7682 (1994).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  99. 99

    Cho, S. et al. Interaction between the RNA binding domains of Ser-Arg splicing factor 1 and U1–70K snRNP protein determines early spliceosome assembly. Proc. Natl Acad. Sci. USA 108, 8233–8238 (2011).

    CAS  PubMed  Article  Google Scholar 

  100. 100

    Pabis, M. et al. The nuclear cap-binding complex interacts with the U4/U6. U5 tri-snRNP and promotes spliceosome assembly in mammalian cells. RNA 19, 1054–1063 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  101. 101

    Fox-Walsh, K. L. et al. The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Proc. Natl Acad. Sci. USA 102, 16176–16181 (2005).

    CAS  PubMed  Article  Google Scholar 

  102. 102

    Xiao, X., Wang, Z., Jang, M. & Burge, C. B. Coevolutionary networks of splicing cis-regulatory elements. Proc. Natl Acad. Sci. USA 104, 18583–18588 (2007).

    CAS  PubMed  Article  Google Scholar 

  103. 103

    Sterner, D. A., Carlo, T. & Berget, S. M. Architectural limits on split genes. Proc. Natl Acad. Sci. USA 93, 15081–15085 (1996).

    CAS  PubMed  Article  Google Scholar 

  104. 104

    De Conti, L., Baralle, M. & Buratti, E. Exon and intron definition in pre-mRNA splicing. Wiley Interdiscip. Rev. RNA 4, 49–60 (2013).

    CAS  PubMed  Article  Google Scholar 

  105. 105

    Bonnal, S. et al. RBM5/Luca-15/H37 regulates Fas alternative splice site pairing after exon definition. Mol. Cell 32, 81–95 (2008).

    CAS  PubMed  Article  Google Scholar 

  106. 106

    Sharma, S., Kohlstaedt, L. A., Damianov, A., Rio, D. C. & Black, D. L. Polypyrimidine tract binding protein controls the transition from exon definition to an intron defined spliceosome. Nature Struct. Mol. Biol. 15, 183–191 (2008). Demonstrates that an early step in spliceosome assembly (transition from exon definition to intron definition complex) is a key stage for splicing regulation.

    CAS  Article  Google Scholar 

  107. 107

    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  Article  Google Scholar 

  108. 108

    Raghunathan, P. L. & Guthrie, C. RNA unwinding in U4/U6 snRNPs requires ATP hydrolysis and the DEIH-box splicing factor Brr2. Curr. Biol. 8, 847–855 (1998).

    CAS  PubMed  Article  Google Scholar 

  109. 109

    Ilagan, J. O., Chalkley, R. J., Burlingame, A. L. & Jurica, M. S. Rearrangements within human spliceosomes captured after exon ligation. RNA 19, 400–412 (2013)

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  110. 110

    Schwer, B. & Gross, C. H. Prp22, a DExH-box RNA helicase, plays two distinct roles in yeast pre-mRNA splicing. EMBO J. 17, 2086–2094 (1998).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  111. 111

    Fourmann, J. B. et al. Dissection of the factor requirements for spliceosome disassembly and the elucidation of its dissociation products using a purified splicing system. Genes Dev. 27, 413–428 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  112. 112

    Abelson, J. et al. Conformational dynamics of single pre-mRNA molecules during in vitro splicing. Nature Struct. Mol. Biol. 17, 504–512 (2010).

    CAS  Article  Google Scholar 

  113. 113

    Hoskins, A. A. et al. Ordered and dynamic assembly of single spliceosomes. Science 331, 1289–1295 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  114. 114

    Tseng, C. K. & Cheng, S. C. Both catalytic steps of nuclear pre-mRNA splicing are reversible. Science 320, 1782–1784 (2008).

    CAS  PubMed  Article  Google Scholar 

  115. 115

    Yang, F. et al. Splicing proofreading at 5′ splice sites by ATPase Prp28p. Nucleic Acids Res. 41, 4660–4670 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  116. 116

    Malca, H., Shomron, N. & Ast, G. The U1 snRNP base pairs with the 5′ splice site within a penta–snRNP complex. Mol. Cell. Biol. 23, 3442–3455 (2003).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  117. 117

    Stevens, S. W. et al. Composition and functional characterization of the yeast spliceosomal penta–snRNP. Mol. Cell 9, 31–44 (2002).

    CAS  PubMed  Article  Google Scholar 

  118. 118

    Gornemann, J., Kotovic, K. M., Hujer, K. & Neugebauer, K. M. Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex. Mol. Cell 19, 53–63 (2005). Development of a novel chromatin immunoprecipitation assay to investigate co-transcriptional spliceosome assembly, demonstrating a role for the CBC in recruitment of snRNPs to nascent pre-mRNA transcripts.

    PubMed  Article  CAS  Google Scholar 

  119. 119

    Behzadnia, N., Hartmuth, K., Will, C. L. & Luhrmann, R. Functional spliceosomal A complexes can be assembled in vitro in the absence of a penta–snRNP. RNA 12, 1738–1746 (2006).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  120. 120

    Schneider, M. et al. Exon definition complexes contain the tri-snRNP and can be directly converted into B-like precatalytic splicing complexes. Mol. Cell 38, 223–235 (2010). Together with reference 116, these studies suggest the existence of alternative spliceosome assembly pathways.

    CAS  PubMed  Article  Google Scholar 

  121. 121

    Madhani, H. D. & Guthrie, C. Dynamic RNA–RNA interactions in the spliceosome. Annu. Rev. Genet. 28, 1–26 (1994).

    CAS  PubMed  Article  Google Scholar 

  122. 122

    Valadkhan, S., Mohammadi, A., Wachtel, C. & Manley, J. L. Protein-free spliceosomal snRNAs catalyze a reaction that resembles the first step of splicing. RNA 13, 2300–2311 (2007).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  123. 123

    Valadkhan, S., Mohammadi, A., Jaladat, Y. & Geisler, S. Protein-free small nuclear RNAs catalyze a two-step splicing reaction. Proc. Natl Acad. Sci. USA 106, 11901–11906 (2009). Together with reference 122, demonstrates that protein-free U6/U2 snRNA constructs can recognize 5′ splice site and branch point sequence to carry out the first and second steps of splicing.

    CAS  PubMed  Article  Google Scholar 

  124. 124

    Marcia, M. & Pyle, A. M. Visualizing group II intron catalysis through the stages of splicing. Cell 151, 497–507 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  125. 125

    Toor, N., Keating, K. S. & Pyle, A. M. Structural insights into RNA splicing. Curr. Opin. Struct. Biol. 19, 260–266 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  126. 126

    Toor, N., Keating, K. S., Taylor, S. D. & Pyle, A. M. Crystal structure of a self-spliced group II intron. Science 320, 77–82 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  127. 127

    Fica, S. M. et al. RNA catalyses nuclear pre-mRNA splicing. Nature 503, 229–234 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  128. 128

    Butcher, S. E. The spliceosome and its metal ions. Met. Ions Life Sci. 9, 235–251 (2011).

    CAS  PubMed  Article  Google Scholar 

  129. 129

    Cordin, O., Hahn, D. & Beggs, J. D. Structure, function and regulation of spliceosomal RNA helicases. Curr. Opin. Cell Biol. 24, 431–438 (2012).

    CAS  PubMed  Article  Google Scholar 

  130. 130

    Small, E. C., Leggett, S. R., Winans, A. A. & Staley, J. P. The EF-G-like GTPase Snu114p regulates spliceosome dynamics mediated by Brr2p, a DExD/H box ATPase. Mol. Cell 23, 389–399 (2006).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  131. 131

    Galej, W. P., Oubridge, C., Newman, A. J. & Nagai, K. Crystal structure of Prp8 reveals active site cavity of the spliceosome. Nature 493, 638–643 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  132. 132

    Schellenberg, M. J. et al. A conformational switch in PRP8 mediates metal ion coordination that promotes pre-mRNA exon ligation. Nature Struct. Mol. Biol. 20, 728–734 (2013).

    CAS  Article  Google Scholar 

  133. 133

    Mozaffari-Jovin, S. et al. Inhibition of RNA helicase Brr2 by the C-terminal tail of the spliceosomal protein Prp8. Science 341, 80–84 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  134. 134

    Ohrt, T. et al. Molecular dissection of step 2 catalysis of yeast pre-mRNA splicing investigated in a purified system. RNA 19, 902–915 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  135. 135

    Sun, H. & Chasin, L. A. Multiple splicing defects in an intronic false exon. Mol. Cell. Biol. 20, 6414–6425 (2000).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  136. 136

    Matlin, A. J., Clark, F. & Smith, C. W. Understanding alternative splicing: towards a cellular code. Nature Rev. Mol. Cell Biol. 6, 386–398 (2005).

    CAS  Article  Google Scholar 

  137. 137

    Wang, Z. & Burge, C. B. Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA 14, 802–813 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  138. 138

    Bessonov, S., Anokhina, M., Will, C. L., Urlaub, H. & Luhrmann, R. Isolation of an active step I spliceosome and composition of its RNP core. Nature 452, 846–850 (2008).

    CAS  PubMed  Article  Google Scholar 

  139. 139

    Zhou, Z., Licklider, L. J., Gygi, S. P. & Reed, R. Comprehensive proteomic analysis of the human spliceosome. Nature 419, 182–185 (2002). Identifies more than 100 proteins in the active spliceosome, many more than the known protein components of snRNPs.

    CAS  PubMed  Article  Google Scholar 

  140. 140

    Hegele, A. et al. Dynamic protein–protein interaction wiring of the human spliceosome. Mol. Cell 45, 567–580 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  141. 141

    Izquierdo, J. M. et al. Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition. Mol. Cell 19, 475–484 (2005).

    CAS  PubMed  Article  Google Scholar 

  142. 142

    Sharma, S., Maris, C., Allain, F. H. & Black, D. L. U1 snRNA directly interacts with polypyrimidine tract-binding protein during splicing repression. Mol. Cell 41, 579–588 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  143. 143

    Chiou, N. T., Shankarling, G. & Lynch, K. W. HnRNP L and hnRNP A1 induce extended U1 snRNA interactions with an exon to repress spliceosome assembly. Mol. Cell 49, 972–982 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  144. 144

    House, A. E. & Lynch, K. W. An exonic splicing silencer represses spliceosome assembly after ATP-dependent exon recognition. Nature Struct. Mol. Biol. 13, 937–944 (2006).

    CAS  Article  Google Scholar 

  145. 145

    McCullough, A. J. & Berget, S. M. G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection. Mol. Cell. Biol. 17, 4562–4571 (1997).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  146. 146

    Chou, M. Y., Rooke, N., Turck, C. W. & Black, D. L. hnRNP H is a component of a splicing enhancer complex that activates a c-src alternative exon in neuronal cells. Mol. Cell. Biol. 19, 69–77 (1999).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  147. 147

    Chen, C. D., Kobayashi, R. & Helfman, D. M. Binding of hnRNP H to an exonic splicing silencer is involved in the regulation of alternative splicing of the rat β-tropomyosin gene. Genes Dev. 13, 593–606 (1999).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  148. 148

    Caputi, M. & Zahler, A. M. Determination of the RNA binding specificity of the heterogeneous nuclear ribonucleoprotein (hnRNP) H/H′/F/2H9 family. J. Biol. Chem. 276, 43850–43859 (2001).

    CAS  PubMed  Article  Google Scholar 

  149. 149

    Ule, J. et al. An RNA map predicting Nova-dependent splicing regulation. Nature 444, 580–586 (2006).

    CAS  PubMed  Article  Google Scholar 

  150. 150

    Wang, Y. et al. A complex network of factors with overlapping affinities represses splicing through intronic elements. Nature Struct. Mol. Biol. 20, 36–45 (2013). Suggests that interactions between various cis -acting elements and trans -acting factors form a complex network that controls context-dependent splicing.

    Article  CAS  Google Scholar 

  151. 151

    Borah, S., Wong, A. C. & Steitz, J. A. Drosophila hnRNP A1 homologs Hrp36/Hrp38 enhance U2-type versus U12-type splicing to regulate alternative splicing of the prospero twintron. Proc. Natl Acad. Sci. USA 106, 2577–2582 (2009).

    CAS  PubMed  Article  Google Scholar 

  152. 152

    Wang, Z. et al. Systematic identification and analysis of exonic splicing silencers. Cell 119, 831–845 (2004).

    CAS  PubMed  Article  Google Scholar 

  153. 153

    Yu, Y. et al. Dynamic regulation of alternative splicing by silencers that modulate 5′ splice site competition. Cell 135, 1224–1236 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  154. 154

    Donahue, C. P., Muratore, C., Wu, J. Y., Kosik, K. S. & Wolfe, M. S. Stabilization of the tau exon 10 stem loop alters pre-mRNA splicing. J. Biol. Chem. 281, 23302–23306 (2006).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  155. 155

    Graveley, B. R. Mutually exclusive splicing of the insect Dscam pre-mRNA directed by competing intronic RNA secondary structures. Cell 123, 65–73 (2005). A great example of how RNA structures can have a leading role in controlling a complicated regimen of mutally exclusive splicing.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  156. 156

    Yang, Y. et al. RNA secondary structure in mutually exclusive splicing. Nature Struct. Mol. Biol. 18, 159–168 (2011).

    CAS  Article  Google Scholar 

  157. 157

    Wang, X. et al. An RNA architectural locus control region involved in Dscam mutually exclusive splicing. Nature Commun. 3, 1255 (2012).

    Article  CAS  Google Scholar 

  158. 158

    Bleichert, F. & Baserga, S. J. The long unwinding road of RNA helicases. Mol. Cell 27, 339–352 (2007).

    CAS  PubMed  Article  Google Scholar 

  159. 159

    Honig, A., Auboeuf, D., Parker, M. M., O'Malley, B. W. & Berget, S. M. Regulation of alternative splicing by the ATP-dependent DEAD-box RNA helicase p72. Mol. Cell. Biol. 22, 5698–5707 (2002).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  160. 160

    Lee, C. G. RH70, a bidirectional RNA helicase, co-purifies with U1snRNP. J. Biol. Chem. 277, 39679–39683 (2002).

    CAS  PubMed  Article  Google Scholar 

  161. 161

    Weeks, K. M. Advances in RNA structure analysis by chemical probing. Curr. Opin. Struct. Biol. 20, 295–304 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  162. 162

    Khodor, Y. L. et al. Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila. Genes Dev. 25, 2502–2512 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  163. 163

    Ip, J. Y. et al. Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Res. 21, 390–401 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  164. 164

    Roberts, G. C., Gooding, C., Mak, H. Y., Proudfoot, N. J. & Smith, C. W. Co-transcriptional commitment to alternative splice site selection. Nucleic Acids Res. 26, 5568–5572 (1998).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  165. 165

    Kornblihtt, A. R. et al. Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nature Rev. Mol. Cell Biol. 14, 153–165 (2013).

    CAS  Article  Google Scholar 

  166. 166

    Brugiolo, M., Herzel, L. & Neugebauer, K. M. Counting on co-transcriptional splicing. F1000Prime Rep. 5, 9 (2013).

    PubMed  PubMed Central  Article  Google Scholar 

  167. 167

    Wang, Y., Ma, M., Xiao, X. & Wang, Z. Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules. Nature Struct. Mol. Biol. 19, 1044–1052 (2012).

    CAS  Article  Google Scholar 

  168. 168

    Spellman, R., Llorian, M. & Smith, C. W. Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1. Mol. Cell 27, 420–434 (2007).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  169. 169

    Boutz, P. L. et al. A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev. 21, 1636–1652 (2007).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  170. 170

    Barash, Y. et al. Deciphering the splicing code. Nature 465, 53–59 (2010).

    CAS  PubMed  Article  Google Scholar 

  171. 171

    Nilsen, T. W. & Graveley, B. R. Expansion of the eukaryotic proteome by alternative splicing. Nature 463, 457–463 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  172. 172

    Nilsen, T. W. The spliceosome: the most complex macromolecular machine in the cell? BioEssays 25, 1147–1149 (2003).

    PubMed  Article  Google Scholar 

  173. 173

    Singh, R. K. & Cooper, T. A. Pre-mRNA splicing in disease and therapeutics. Trends Mol. Med. 18, 472–482 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  174. 174

    Padgett, R. A. New connections between splicing and human disease. Trends Genet. 28, 147–154 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  175. 175

    Tanackovic, G. et al. PRPF mutations are associated with generalized defects in spliceosome formation and pre-mRNA splicing in patients with retinitis pigmentosa. Hum. Mol. Genet. 20, 2116–2130 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  176. 176

    Utz, V. M., Beight, C. D., Marino, M. J., Hagstrom, S. A. & Traboulsi, E. I. Autosomal dominant retinitis pigmentosa secondary to pre-mRNA splicing-factor gene PRPF31 (RP11): review of disease mechanism and report of a family with a novel 3-base pair insertion. Ophthalm. Genet. 34, 183–188 (2013).

    CAS  Article  Google Scholar 

  177. 177

    Pena, V., Liu, S., Bujnicki, J. M., Luhrmann, R. & Wahl, M. C. Structure of a multipartite protein–protein interaction domain in splicing factor prp8 and its link to retinitis pigmentosa. Mol. Cell 25, 615–624 (2007).

    CAS  PubMed  Article  Google Scholar 

  178. 178

    He, H. et al. Mutations in U4atac snRNA, a component of the minor spliceosome, in the developmental disorder MOPD I. Science 332, 238–240 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  179. 179

    Lorson, C. L., Hahnen, E., Androphy, E. J. & Wirth, B. A single nucleotide in the SMN gene regulates splicing and is responsible for spinal muscular atrophy. Proc. Natl Acad. Sci. USA 96, 6307–6311 (1999).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  180. 180

    Schrank, B. et al. Inactivation of the survival motor neuron gene, a candidate gene for human spinal muscular atrophy, leads to massive cell death in early mouse embryos. Proc. Natl Acad. Sci. USA 94, 9920–9925 (1997).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  181. 181

    Gabanella, F. et al. Ribonucleoprotein assembly defects correlate with spinal muscular atrophy severity and preferentially affect a subset of spliceosomal snRNPs. PLoS ONE 2, e921 (2007).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  182. 182

    Praveen, K., Wen, Y. & Matera, A. G. A. Drosophila model of spinal muscular atrophy uncouples snRNP biogenesis functions of survival motor neuron from locomotion and viability defects. Cell Rep. 1, 624–631 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  183. 183

    Garcia, E. L., Lu, Z., Meers, M. P., Praveen, K. & Matera, A. G. Developmental arrest of Drosophila survival motor neuron (Smn) mutants accounts for differences in expression of minor intron-containing genes. RNA 19, 1510–1516 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  184. 184

    Baumer, D. et al. Alternative splicing events are a late feature of pathology in a mouse model of spinal muscular atrophy. PLoS Genet. 5, e1000773 (2009). Together with references 182 and 183, these studies show that SMA phenotypes can be uncoupled from global splicing deficits. Using a missense allele that is active in Sm core assembly, reference 184 reveals a separation of SMN functions.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  185. 185

    Cazzola, M., Rossi, M. & Malcovati, L. Biologic and clinical significance of somatic mutations of SF3B1 in myeloid and lymphoid neoplasms. Blood 121, 260–269 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  186. 186

    Yoshida, K. et al. Frequent pathway mutations of splicing machinery in myelodysplasia. Nature 478, 64–69 (2011).

    CAS  Article  Google Scholar 

  187. 187

    Chesnais, V. et al. Spliceosome mutations in myelodysplastic syndromes and chronic myelomonocytic leukemia. Oncotarget 3, 1284–1293 (2012).

    PubMed  PubMed Central  Article  Google Scholar 

  188. 188

    Dhir, A., Buratti, E., van Santen, M. A., Luhrmann, R. & Baralle, F. E. The intronic splicing code: multiple factors involved in ATM pseudoexon definition. EMBO J. 29, 749–760 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  189. 189

    Lewandowska, M. A., Stuani, C., Parvizpur, A., Baralle, F. E. & Pagani, F. Functional studies on the ATM intronic splicing processing element. Nucleic Acids Res. 33, 4007–4015 (2005).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  190. 190

    Pagani, F. et al. A new type of mutation causes a splicing defect in ATM. Nature Genet. 30, 426–429 (2002).

    CAS  PubMed  Article  Google Scholar 

  191. 191

    Gunderson, S. I., Polycarpou-Schwarz, M. & Mattaj, I. W. U1 snRNP inhibits pre-mRNA polyadenylation through a direct interaction between U1 70K and poly(A) polymerase. Mol. Cell 1, 255–264 (1998).

    CAS  PubMed  Article  Google Scholar 

  192. 192

    Langemeier, J., Radtke, M. & Bohne, J. U1 snRNP-mediated poly(A) site suppression: beneficial and deleterious for mRNA fate. RNA Biol. 10, 180–184 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  193. 193

    Kaida, D. et al. U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. Nature 468, 664–668 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  194. 194

    Almada, A. E., Wu, X., Kriz, A. J., Burge, C. B. & Sharp, P. A. Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature 499, 360–363 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  195. 195

    Berg, M. G. et al. U1 snRNP determines mRNA length and regulates isoform expression. Cell 150, 53–64 (2012). Together with reference 193, these genome-wide analyses illustrate a pervasive, non-splicing role for U1 snRNP in selection of the site of pre-mRNA 3′-end cleavage and polyadenylation.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  196. 196

    Peterson, M. L., Bingham, G. L. & Cowan, C. Multiple features contribute to the use of the immunoglobulin M secretion-specific poly(A) signal but are not required for developmental regulation. Mol. Cell. Biol. 26, 6762–6771 (2006).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  197. 197

    Hall-Pogar, T., Liang, S., Hague, L. K. & Lutz, C. S. Specific trans-acting proteins interact with auxiliary RNA polyadenylation elements in the COX-2 3′-UTR. RNA 13, 1103–1115 (2007).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  198. 198

    Luo, W. et al. The conserved intronic cleavage and polyadenylation site of CstF-77 gene imparts control of 3′ end processing activity through feedback autoregulation and by U1 snRNP. PLoS Genet. 9, e1003613 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  199. 199

    Michaeli, S. Trans-splicing in trypanosomes: machinery and its impact on the parasite transcriptome. Future Microbiol. 6, 459–474 (2011).

    CAS  PubMed  Article  Google Scholar 

  200. 200

    Lasda, E. L. & Blumenthal, T. Trans-splicing. Wiley Interdiscip. Rev. RNA 2, 417–434 (2011).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  201. 201

    Bruzik, J. P. & Maniatis, T. Spliced leader RNAs from lower eukaryotes are trans-spliced in mammalian cells. Nature 360, 692–695 (1992).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  202. 202

    Smith, E. R. et al. The little elongation complex regulates small nuclear RNA transcription. Mol. Cell 44, 954–965 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  203. 203

    Fabrizio, P. et al. The evolutionarily conserved core design of the catalytic activation step of the yeast spliceosome. Mol. Cell 36, 593–608 (2009).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

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Acknowledgements

Research in the authors' laboratories is supported by US National Institutes of Health grants R01-GM053034 and R01-NS041617 (to A.G.M.), as well as R01-CA158283 and R21-AR061640 (to Z.W.). The authors apologize to those whose work could not be discussed owing to space limitations.

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Correspondence to A. Gregory Matera or Zefeng Wang.

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The authors declare no competing financial interests.

PowerPoint slides

Glossary

Splice site

The short sequences at exon–intron junctions of pre-mRNA, which include the 5′ splice (splice donor) site and the 3′ splice (splice acceptor) site located at the beginning and the end of an intron, respectively.

Heterogeneous nuclear RNP

(hnRNP). A diverse class of ribonucleoproteins (RNPs) located in the cell nucleus, and primarily involved in post-transcriptional regulation of mRNAs. The hnRNP proteins are a class of RNA-binding factors, many of which shuttle between the nucleus and cytoplasm, that are involved in regulating the processing, stability and subcellular transport of mRNPs.

Cajal bodies

Nuclear substructures that are highly enriched in pre-mRNA splicing factors. They are thought to function as sites of ribonucleoprotein assembly and remodelling.

Tudor domain

A conserved protein structural motif that is thought to bind to methylated arginine or lysine residues, promoting physical interactions with its target protein.

Nuclear speckles

Sub-nuclear structures highly enriched in pre-mRNA-splicing factors. At the ultrastructural level, they correspond to domains known as interchromatin granule clusters.

SR proteins

Proteins that contain a domain with repeats of serine (S) and arginine (R) residues and one or more RNA-recognition motifs. SR proteins are best known for their ability to bind exonic splicing enhancers and activate splicing, although some SR proteins also regulate transcription.

Branch point

A loosely conserved short sequence usually located 15–50 nucleotides upstream of the 3′ splice site, before a region rich in pyrimidines (cytosine and uracil). Most branch points include an adenine nucleotide as the site of lariat formation.

Exon definition

One of two different modes of initial splice site pairing at the early stage of splicing (the other being intron definition). During exon definition, the U1 and U2 small nuclear ribonucleoproteins (snRNPs) interact to pair the splice sites across an exon. For some small introns, the U1 and U2 snRNPs interact to pair the splice sites across introns.

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Matera, A., Wang, Z. A day in the life of the spliceosome. Nat Rev Mol Cell Biol 15, 108–121 (2014). https://doi.org/10.1038/nrm3742

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