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Post-Transcriptional Regulation by STAR Proteins pp 123–141Cite as

The Branchpoint Binding Protein

In and Out of the Spliceosome Cycle

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Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 693))

Abstract

The Saccharomyces cerevisiae branchpoint binding protein (BBP) is a 53 kDa pre-mRNA processing factor with characteristic STAR/GSG protein organization. This includes a central RNA binding site composed of an extended Type I KH domain with an adjacent QUA2 motif. Downstream of KH-QUA2 are two CCHC-type zinc knuckles and a proline-rich C-terminal interaction domain (Fig. 1A). The QUA1 homodimerization motif found upstream of the KH-QUA2 sequence in other STAR/GSG family members is absent in BBP and replaced by a site for the phylogenetically conserved binding partner, Mud2/U2AF65. BBP’s name reflects the fact that it binds the conserved RNA sequence, UACUAAC, called the branchpoint motif found near the 3′ end of yeast introns. This sequence contains the catalytic adenosine (underlined) which directs the first RNA transesterification reaction in splicing chemistry. BBP recruitment to the branchpoint initiates a series of spliceosomal subunit addition and rearrangement events that ultimately configures the active site of this enzyme.1 The mammalian homolog, ZF M1/ZNF162/D11S636/SF1 (henceforth, SF1), was first identified in a screen for genes associated with Type 1 multiple endocrine neoplasia2 and was subsequently shown to act similarly to BBP in mammalian splicing.3,4 BBP/SF1 is essential for viability in organisms spanning the evolutionary spectrum from yeast to Caenorhabditis elegans to mice. In addition, mice heterozygous for a SF1 knockout allele show enhanced susceptibility to azoxymethane-induced colon tumorigenesis5 adding BBP/SF1 to the growing list of RNA processing factors implicated in genetic disease.6 Summarized below is our current understanding of BBP structure and its proposed multifaceted contribution to mRNA biogenesis and function. Reference to SF1 will be made to fill gaps in our understanding of BBP and to highlight areas of clear similarity or difference between yeast and mammals.

Domain organization of the BBP/SF1 splicing factor. A) Schematic representation of BBP. Indicated are the ULM domain-containing region that mediates Mud2 association (Heterodimerization); the RNA binding element (KH_QUA2), two CCHC zinc knuckles (Zn) and the positions conforming to the Smy2 binding site, PPG{F/I/L/M/V}. The Smy2 sequences overlap a clathrin adaptor appendage domain that has not been scored for function in BBP. B) Alignment of the yeast BBP and human SF1 proteins using Blossom 62 matrix with identities shaded black and conserved residues shaded gray. Shown above BBP is the ULM sub-sequence critical to the SF1/U2AF65 interaction, the location of the KIS phosphorylation motif and the βααββ αα secondary structures (thick dashed line) of the KH-QUA2 motif. Also shown are the two loop sequences that contribute to the RNA binding channel (^) and the six Smy2 binding sites (*).

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References

  1. Wahl MC, Will CL, Luhrmann R. The spliceosome: design principles of a dynamic RNP machine. Cell 2009; 136(4):701–718.

    CAS  PubMed  Google Scholar 

  2. Toda T, Iida A, Miwa T et al. Isolation and characterization of a novel gene encoding nuclear protein at a locus (D11S636) tightly linked to multiple endocrine neoplasia type 1 (MEN1). Hum Mol Genet 1994; 3(3):465–470.

    CAS  PubMed  Google Scholar 

  3. Kramer A. Purification of splicing factor SF1, a heat-stable protein that functions in the assembly of a presplicing complex. Mol Cell Biol 1992; 12(10):4545–4552.

    CAS  PubMed  Google Scholar 

  4. Rain JC, Rafi Z, Rhani Z et al. Conservation of functional domains involved in RNA binding and proteinprotein interactions in human and Saccharomyces cerevisiae pre-mRNA splicing factor SF1. RNA 1998; 4(5):551–565.

    CAS  PubMed  Google Scholar 

  5. Shitashige M, Satow R, Honda K et al. Increased susceptibility of Sf1(+/−) mice to azoxymethane-induced colon tumorigenesis. Cancer Sci 2007; 98(12):1862–1867.

    CAS  PubMed  Google Scholar 

  6. Lukong KE, Chang KW, Khandjian EW et al. RNA-binding proteins in human genetic disease. Trends Genet 2008; 24(8):416–425.

    CAS  PubMed  Google Scholar 

  7. Abovich N, Rosbash M. Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals. Cell 1997; 89(3):403–412.

    CAS  PubMed  Google Scholar 

  8. Zamore PD, Patton JG, Green MR. Cloning and domain structure of the mammalian splicing factor U2AF. Nature 1992; 355(6361):609–614.

    CAS  PubMed  Google Scholar 

  9. Rutz B, Seraphin B. A dual role for BBP/ScSF1 in nuclear pre-mRNA retention and splicing. EBMO J 2000; 19(8):1873–1886.

    CAS  Google Scholar 

  10. Wang Q, Zhang L, Lynn B et al. A BBP-Mud2p heterodimer mediates branchpoint recognition and influences splicing substrate abundance in budding yeast. Nucleic Acids Res 2008; 36(8):2787–2798.

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  12. Michaud S, Reed R. A functional association between the 5′ and 3′ splice site is established in the earliest prespliceosome complex (E) in mammals. Genes Dev 1993; 7(6):1008–1020.

    CAS  PubMed  Google Scholar 

  13. Michaud S, Reed R. An ATP-independent complex commits pre-mRNA to the mammalian spliceosome assembly pathway. Genes Dev 1991; 5(12B):2534–2546.

    CAS  PubMed  Google Scholar 

  14. Berglund JA, Fleming ML, Rosbash M. The KH domain of the branchpoint sequence binding protein determines specificity for the pre-mRNA branchpoint sequence. RNA 1998; 4(8):998–1006.

    CAS  PubMed  Google Scholar 

  15. Garrey SM, Voelker R, Berglund JA. An extended RNA binding site for the yeast branch point-binding protein and the role of its zinc knuckle domains in RNA binding. J Biol Chem 2006; 281(37):27443–27453.

    CAS  PubMed  Google Scholar 

  16. Buratti E, Baralle FE. Influence of RNA secondary structure on the pre-mRNA splicing process. Mol Cell Biol 2004; 24(24):10505–10514.

    CAS  PubMed  Google Scholar 

  17. Grishin NV. KH domain: one motif, two folds. Nucleic Acids Res 2001; 29(3):638–643.

    CAS  PubMed  Google Scholar 

  18. Liu Z, Luyten I, Bottomley MJ et al. Structural basis for recognition of the intron branch site RNA by splicing factor 1. Science 2001; 294(5544):1098–1102.

    CAS  PubMed  Google Scholar 

  19. Garrey SM, Cass DM, Wandler AM et al. Transposition of two amino acids changes a promiscuous RNA binding protein into a sequence-specific RNA binding protein. RNA 2008; 14(1):78–88.

    CAS  PubMed  Google Scholar 

  20. Berglund JA, Chua K, Abovich N et al. The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAC. Cell 1997; 89(5):781–787.

    CAS  PubMed  Google Scholar 

  21. Keller EB, Noon WA. Intron splicing: a conserved internal signal in introns of animal pre-mRNAs. Proc Natl Acad Sci USA 1984; 81(23):7417–7420.

    CAS  PubMed  Google Scholar 

  22. Wang Z, Burge CB. Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA 2008; 14(5):802–813.

    CAS  PubMed  Google Scholar 

  23. Fromont-Racine M, Rain JC, Legrain P. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens [see comments]. Nat Genet 1997; 16(3):277–282.

    CAS  PubMed  Google Scholar 

  24. Berglund JA, Abovich N, Rosbash M. A cooperative interaction between U2AF65 and mBBP/SF1 facilitates branchpoint region recognition. Genes Dev 1998; 12(6):858–867.

    CAS  PubMed  Google Scholar 

  25. Abovich N, Liao XC, Rosbash M. The yeast MUD2 protein: an interaction with PRP11 defines a bridge between commitment complexes and U2 snRNP addition. Genes Dev 1994; 8(7):843–854.

    CAS  PubMed  Google Scholar 

  26. Clark TA, Sugnet CW, Ares M Jr. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 2002; 296(5569):907–910.

    CAS  PubMed  Google Scholar 

  27. Kielkopf CL, Lucke S, Green MR. U2AF homology motifs: protein recognition in the RRM world. Genes Dev 2004; 18(13):1513–1526.

    CAS  PubMed  Google Scholar 

  28. Jenkins JL, Shen H, Green MR et al. Solution conformation and thermodynamic characteristics of RNA binding by the splicing factor U2AF65. J Biol Chem 2008; 283(48):33641–33649.

    CAS  PubMed  Google Scholar 

  29. Gaur RK, Valcarcel J, Green MR. Sequential recognition of the pre-mRNA branch point by U2AF65 and a novel spliceosome-associated 28-kDa protein. RNA 1995; 1(4):407–417.

    CAS  PubMed  Google Scholar 

  30. Banerjee H, Rahn A, Davis W et al. Sex lethal and U2 small nuclear ribonucleoprotein auxiliary factor (U2AF65) recognize polypyrimidine tracts using multiple modes of binding. RNA 2003; 9(1):88–99.

    CAS  PubMed  Google Scholar 

  31. Valcarcel J, Gaur RK, Singh R et al. Interaction of U2AF65 RS region with pre-mRNA branch point and promotion of base pairing with U2 snRNA [corrected] [published erratum appears in Science 1996; 274(5284):21]. Science 1996; 273(5282):1706–1709.

    CAS  PubMed  Google Scholar 

  32. Selenko P, Gregorovic G, Sprangers R et al. Structural basis for the molecular recognition between human splicing factors U2AF65 and SF1/mBBP. Mol Cell 2003; 11(4):965–976.

    CAS  PubMed  Google Scholar 

  33. Wang X, Bruderer S, Rafi Z et al. Phosphorylation of splicing factor SF1 on Ser20 by cGMP-dependent protein kinase regulates spliceosome assembly. EBMO J 1999; 18(16):4549–4559.

    CAS  Google Scholar 

  34. Corsini L, Bonnal S, Basquin J et al. U2AF-homology motif interactions are required for alternative splicing regulation by SPF45. Nat Struct Mol Biol 2007; 14(7):620–629.

    CAS  PubMed  Google Scholar 

  35. Rain JC, Legrain P. In vivo commitment to splicing in yeast involves the nucleotide upstream from the branch site conserved sequence and the Mud2 protein. EBMO J 1997; 16(7):1759–1771.

    CAS  Google Scholar 

  36. Rymond BC, Torrey DD, Rosbash M. A novel role for the 3′ region of introns in pre-mRNA splicing of Saccharomyces cerevisiae. Genes Dev 1987; 1(3):238–246.

    CAS  PubMed  Google Scholar 

  37. Rutz B, Seraphin B. Transient interaction of BBP/ScSF1 and Mud2 with the splicing machinery affects the kinetics of spliceosome assembly. RNA 1999; 5(6):819–831.

    CAS  PubMed  Google Scholar 

  38. Zamore PD, Green MR. Identification, purification and biochemical characterization of U2 small nuclear ribonucleoprotein auxiliary factor. Proc Natl Acad Sci USA 1989; 86(23):9243–9247.

    CAS  PubMed  Google Scholar 

  39. Wu S, Romfo CM, Nilsen TW et al. Functional recognition of the 3′ splice site AG by the splicing factor U2AF35. Nature 1999; 402(6763):832–835.

    CAS  PubMed  Google Scholar 

  40. Zorio DA, Blumenthal T. Both subunits of U2AF recognize the 3′ splice site in Caenorhabditis elegans. Nature 1999; 402(6763):835–838.

    CAS  PubMed  Google Scholar 

  41. Merendino L, Guth S, Bilbao D et al. Inhibition of msl-2 splicing by Sex-lethal reveals interaction between U2AF35 and the 3′ splice site AG. Nature 1999; 402(6763):838–841.

    CAS  PubMed  Google Scholar 

  42. Huang T, Vilardell J, Query CC. Prespliceosome formation in S.pombe requires a stable complex of SF1-U2AF(59)-U2AF(23). EBMO J 2002; 21(20):5516–5526.

    CAS  Google Scholar 

  43. Rino J, Desterro JM, Pacheco TR et al. Splicing factors SF1 and U2AF associate in extraspliceosomal complexes. Mol Cell Biol 2008; 28(9):3045–3057.

    CAS  PubMed  Google Scholar 

  44. Linder P. Dead-box proteins: a family affair—active and passive players in RNP-remodeling. Nucleic Acids Res 2006; 34(15):4168–4180.

    CAS  PubMed  Google Scholar 

  45. Smith DJ, Query CC, Konarska MM. “Nought may endure but mutability“: spliceosome dynamics and the regulation of splicing. Mol Cell 2008; 30(6):657–666.

    CAS  PubMed  Google Scholar 

  46. Puig O, Gottschalk A, Fabrizio P et al. Interaction of the U1 snRNP with nonconserved intronic sequences affects 5′ splice site selection. Genes Dev 1999; 13(5):569–580.

    CAS  PubMed  Google Scholar 

  47. Zhang D, Rosbash M. Identification of eight proteins that cross-link to pre-mRNA in the yeast commitment complex. Genes Dev 1999; 13(5):581–592.

    PubMed  Google Scholar 

  48. Colot HV, Stutz F, Rosbash M. The yeast splicing factor Mud13p is a commitment complex component and corresponds to CBP20, the small subunit of the nuclear cap-binding complex. Genes Dev 1996; 10(13):1699–1708.

    CAS  PubMed  Google Scholar 

  49. Lewis JD, Gorlich D, Mattaj IW. A yeast cap binding protein complex (yCBC) acts at an early step in pre mRNA splicing. Nucleic Acids Res 1996; 24(17):3332–3336.

    CAS  PubMed  Google Scholar 

  50. Hage R, Tung L, Du H et al. A targeted bypass screen identifies Ynl187p, Prp42p, Snu71p and Cbp80p for stable U1 snRNP/Pre-mRNA interaction. Mol Cell Biol 2009; 29(14):3941–3952.

    CAS  PubMed  Google Scholar 

  51. Du H, Rosbash M. The U1 snRNP protein U1C recognizes the 5′ splice site in the absence of base pairing. Nature 2002; 419(6902):86–90.

    CAS  PubMed  Google Scholar 

  52. Balzer RJ, Henry MF. Snu56p is required for Mer1p-activated meiotic splicing. Mol Cell Biol 2008; 28(8):2497–2508.

    CAS  PubMed  Google Scholar 

  53. Corsini L, Hothorn M, Stier G et al. Dimerization and protein binding specificity of the U2AF homology motif of the splicing factor Puf60. J Biol Chem 2009; 284(1):630–639.

    CAS  PubMed  Google Scholar 

  54. Wang Q, Rymond BC. Rds3p is required for stable U2 snRNP recruitment to the splicing apparatus. Molecular and Cellular Biology 2003; 23(20):7339–7349.

    CAS  PubMed  Google Scholar 

  55. Wang Q, He J, Lynn B et al. Interactions of the Yeast SF3b Splicing Factor. Mol Cell Biol 2005; 25(24):10745–10754.

    CAS  PubMed  Google Scholar 

  56. Dziembowski A, Ventura AP, Rutz B et al. Proteomic analysis identifies a new complex required for nuclear pre-mRNA retention and splicing. EBMO J 2004; 23(24):4847–4856.

    CAS  Google Scholar 

  57. Gozani O, Potashkin J, Reed R. A potential role for U2AF-SAP 155 interactions in recruiting U2 snRNP to the branch site. Mol Cell Biol 1998; 18(8):4752–4760.

    CAS  PubMed  Google Scholar 

  58. Spadaccini R, Reidt U, Dybkov O et al. Biochemical and NMR analyses of an SF3b155-p14-U2AF-RNA interaction network involved in branch point definition during pre-mRNA splicing. RNA 2006; 12(3):410–425.

    CAS  PubMed  Google Scholar 

  59. Hastings ML, Allemand E, Duelli DM et al. Control of pre-mRNA splicing by the general splicing factors PUF60 and U2AF65. PLoS ONE 2007; 2(6):e538.

    PubMed  Google Scholar 

  60. Das BK, Xia L, Palandjian L et al. Characterization of a protein complex containing spliceosomal proteins SAPs 49, 130, 145 and 155. Mol Cell Biol 1999; 19(10):6796–6802.

    CAS  PubMed  Google Scholar 

  61. Gozani O, Feld R, Reed R. Evidence that sequence-independent binding of highly conserved U2 snRNP proteins upstream of the branch site is required for assembly of spliceosomal complex A. Genes Dev 1996; 10(2):233–243.

    CAS  PubMed  Google Scholar 

  62. Xu YZ, Newnham CM, Kameoka S et al. Prp5 bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA. EBMO J 2004; 23(2):376–385.

    Google Scholar 

  63. Perriman R, Barta I, Voeltz GK et al. ATP requirement for Prp5p function is determined by Cus2p and the structure of U2 small nuclear RNA. Proc Natl Acad Sci USA 2003; 100(24):13857–13862.

    CAS  PubMed  Google Scholar 

  64. Perriman RJ, Ares M Jr. Rearrangement of competing U2 RNA helices within the spliceosome promotes multiple steps in splicing. Genes Dev 2007; 21(7):811–820.

    CAS  PubMed  Google Scholar 

  65. Xu YZ, Query CC. Competition between the ATPase Prp5 and branch region-U2 snRNA pairing modulates the fidelity of spliceosome assembly. Mol Cell 2007; 28(5):838–849.

    CAS  PubMed  Google Scholar 

  66. Strasser K, Masuda S, Mason P et al. TREX is a conserved complex coupling transcription with messenger RNA export. Nature 2002; 417(6886):304–308.

    PubMed  Google Scholar 

  67. Shen H, Zheng X, Shen J et al. Distinct activities of the DExD/H-box splicing factor hUAP56 facilitate stepwise assembly of the spliceosome. Genes Dev 2008; 22(13):1796–1803.

    CAS  PubMed  Google Scholar 

  68. Kelly SM, Corbett AH. Messenger RNA export from the nucleus: a series of molecular wardrobe changes. Traffic 2009; 10(9):1199–1208.

    CAS  PubMed  Google Scholar 

  69. Abruzzi KC, Lacadie S, Rosbash M. Biochemical analysis of TREX complex recruitment to intronless and intron-containing yeast genes. EBMO J 2004; 23(13):2620–2631.

    CAS  Google Scholar 

  70. Kistler AL, Guthrie C. Deletion of MUD2, the yeast homolog of U2AF65, can bypass the requirement for sub2, an essential spliceosomal ATPase. Genes Dev 2001; 15(1):42–49.

    CAS  PubMed  Google Scholar 

  71. Libri D, Graziani N, Saguez C et al. Multiple roles for the yeast SUB2/yUAP56 gene in splicing. Genes Dev 2001; 15(1):36–41.

    CAS  PubMed  Google Scholar 

  72. Pandit S, Wang D, Fu XD. Functional integration of transcriptional and RNA processing machineries. Curr Opin Cell Biol 2008; 20(3):260–265.

    CAS  PubMed  Google Scholar 

  73. Moore MJ, Proudfoot NJ. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 2009; 136(4):688–700.

    CAS  PubMed  Google Scholar 

  74. Tardiff DF, Rosbash M. Arrested yeast splicing complexes indicate stepwise snRNP recruitment during in vivo spliceosome assembly. RNA 2006; 12(6):968–979.

    CAS  PubMed  Google Scholar 

  75. Pandya-Jones A, Black DL. Co-transcriptional splicing of constitutive and alternative exons. RNA 2009; 15(10):1896–1908.

    CAS  PubMed  Google Scholar 

  76. Gornemann J, Kotovic KM, Hujer K et al. Co-transcriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex. Mol Cell 2005; 19(1):53–63.

    PubMed  Google Scholar 

  77. Kotovic KM, Lockshon D, Boric L et al. Co-transcriptional recruitment of the U1 snRNP to intron-containing genes in yeast. Mol Cell Biol 2003; 23(16):5768–5779.

    CAS  PubMed  Google Scholar 

  78. Lacadie SA, Rosbash M. Co-transcriptional spliceosome assembly dynamics and the role of U1 snRNA:5′ss base pairing in yeast. Mol Cell 2005; 19(1):65–75.

    CAS  PubMed  Google Scholar 

  79. Lacadie SA, Tardiff DF, Kadener S et al. In vivo commitment to yeast co-transcriptional splicing is sensitive to transcription elongation mutants. Genes Dev 2006; 20(15):2055–2066.

    CAS  PubMed  Google Scholar 

  80. Moore MJ, Schwartzfarb EM, Silver PA et al. Differential recruitment of the splicing machinery during transcription predicts genome-wide patterns of mRNA splicing. Mol Cell 2006; 24(6):903–915.

    CAS  PubMed  Google Scholar 

  81. Swinburne IA, Meyer CA, Liu XS et al. Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription. Genome Res 2006; 16(7):912–921.

    CAS  PubMed  Google Scholar 

  82. Listerman I, Sapra AK, Neugebauer KM. Co-transcriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells. Nat Struct Mol Biol 2006; 13(9):815–822.

    CAS  PubMed  Google Scholar 

  83. Sapra AK, Anko ML, Grishina I et al. SR protein family members display diverse activities in the formation of nascent and mature mRNPs in vivo. Mol Cell 2009; 34(2):179–190.

    CAS  PubMed  Google Scholar 

  84. Stevens SW, Ryan DE, Ge HY et al. Composition and functional characterization of the yeast spliceosomal penta-snRNP. Mol Cell 2002; 9(1):31–44.

    CAS  PubMed  Google Scholar 

  85. Behzadnia N, Hartmuth K, Will CL et al. Functional spliceosomal A complexes can be assembled in vitro in the absence of a penta-snRNP. RNA 2006; 12(9):1738–1746.

    CAS  PubMed  Google Scholar 

  86. Greenleaf AL. Positive patches and negative noodles: linking RNA processing to transcription? Trends Biochem Sci 1993; 18(4):117–119.

    CAS  PubMed  Google Scholar 

  87. Natalizio BJ, Robson-Dixon ND, Garcia-Blanco MA. The Carboxyl-terminal Domain of RNA Polymerase II Is Not Sufficient to Enhance the Efficiency of Pre-mRNA Capping or Splicing in the Context of a Different Polymerase. J Biol Chem 2009; 284(13):8692–8702.

    CAS  PubMed  Google Scholar 

  88. Bushnell DA, Cramer P, Kornberg RD. Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution. Proc Natl Acad Sci USA 2002; 99(3):1218–1222.

    CAS  PubMed  Google Scholar 

  89. Morris DP, Greenleaf AL. The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem 2000; 275(51):39935–39943.

    CAS  PubMed  Google Scholar 

  90. Lin KT, Lu RM, Tarn WY. The WW domain-containing proteins interact with the early spliceosome and participate in pre-mRNA splicing in vivo. Mol Cell Biol 2004; 24(20):9176–9185.

    CAS  PubMed  Google Scholar 

  91. Grainger RJ, Beggs JD. Prp8 protein: at the heart of the spliceosome. RNA 2005; 11(5):533–557.

    CAS  PubMed  Google Scholar 

  92. Jobert L, Pinzon N, Van Herreweghe E et al. Human U1 snRNA forms a new chromatin-associated snRNP with TAF15. EMBO Rep 2009; 10(5):494–500.

    CAS  PubMed  Google Scholar 

  93. de la Mata M, Alonso CR, Kadener S et al. A slow RNA polymerase II affects alternative splicing in vivo. Mol Cell 2003; 12(2):525–532.

    PubMed  Google Scholar 

  94. Howe KJ, Kane CM, Ares M Jr. Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae. RNA 2003; 9(8):993–1006.

    CAS  PubMed  Google Scholar 

  95. Kornblihtt AR, Schor IE, Allo M et al. When chromatin meets splicing. Nat Struct Mol Biol 2009; 16(9):902–903.

    CAS  PubMed  Google Scholar 

  96. Pleiss JA, Whitworth GB, Bergkessel M et al. Transcript specificity in yeast pre-mRNA splicing revealed by mutations in core spliceosomal components. PLoS Biol 2007; 5(4):e90.

    PubMed  Google Scholar 

  97. Tanackovic G, Kramer A. Human splicing factor SF3a, but not SF1, is essential for pre-mRNA splicing in vivo. Mol Biol Cell 2005; 16(3):1366–1377.

    CAS  PubMed  Google Scholar 

  98. Wilmes GM, Bergkessel M, Bandyopadhyay S et al. A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol Cell 2008; 32(5):735–746.

    CAS  PubMed  Google Scholar 

  99. Houseley J, LaCava J, Tollervey D. RNA-quality control by the exosome. Nat Rev Mol Cell Biol 2006; 7(7):529–539.

    CAS  PubMed  Google Scholar 

  100. Tardiff DF, Lacadie SA, Rosbash M. A genome-wide analysis indicates that yeast pre-mRNA splicing is predominantly post-transcriptional. Mol Cell 2006; 24(6):917–929.

    CAS  PubMed  Google Scholar 

  101. Legrain P, Rosbash M. Some cis-and trans-acting mutants for splicing target pre-mRNA to the cytoplasm. Cell 1989; 57(4):573–583.

    CAS  PubMed  Google Scholar 

  102. Abovich N, Legrain P, Rosbash M. The yeast PRP6 gene encodes a U4/U6 small nuclear ribonucleoprotein particle (snRNP) protein and the PRP9 gene encodes a protein required for U2 snRNP binding. Mol Cell Biol 1990; 10(12):6417–6425.

    CAS  PubMed  Google Scholar 

  103. Scherrer FW Jr, Spingola M. A subset of Mer1p-dependent introns requires Bud13p for splicing activation and nuclear retention. RNA 2006; 12(7):1361–1372.

    CAS  PubMed  Google Scholar 

  104. Spingola M, Armisen J, Ares M Jr. Mer1p is a modular splicing factor whose function depends on the conserved U2 snRNP protein Snu17p. Nucleic Acids Res 2004; 32(3):1242–1250.

    CAS  PubMed  Google Scholar 

  105. Will CL, Schneider C, MacMillan AM et al. A novel U2 and U11/U12 snRNP protein that associates with the pre-mRNA branch site. EBMO J 2001; 20(16):4536–4546.

    CAS  Google Scholar 

  106. Gottschalk A, Bartels C, Neubauer G et al. A novel yeast U2 snRNP protein, Snu17p, is required for the first catalytic step of splicing and for progression of spliceosome assembly. Mol Cell Biol 2001; 21(9):3037–3046.

    CAS  PubMed  Google Scholar 

  107. Kotake Y, Sagane K, Owa T et al. Splicing factor SF3b as a target of antitumor natural product pladienolide. Nature Chemical Genetics 2007; 3.

    Google Scholar 

  108. Kaida D, Motoyoshi H, Tashiro E et al. Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA. Nature Chemical Genetics 2007; 3.

    Google Scholar 

  109. Palancade B, Zuccolo M, Loeillet S et al. Pml39, a novel protein of the nuclear periphery required for nuclear retention of improper messenger ribonucleoparticles. Mol Biol Cell 2005; 16(11):5258–5268.

    CAS  PubMed  Google Scholar 

  110. Casolari JM, Silver PA. Guardian at the gate: preventing unspliced pre-mRNA export. Trends in Cell Biology 2004; 14(5):222–225.

    CAS  PubMed  Google Scholar 

  111. Galy V, Gadal O, Fromont-Racine M et al. Nuclear retention of unspliced mRNAs in yeast is mediated by perinuclear Mlp1. Cell 2004; 116(1):63–73.

    CAS  PubMed  Google Scholar 

  112. Sommer P, Nehrbass U. Quality control of messenger ribonucleoprotein particles in the nucleus and at the pore. Curr Opin Cell Biol 2005; 17(3):294–301.

    CAS  PubMed  Google Scholar 

  113. Bruno I, Wilkinson MF. P-bodies react to stress and nonsense. Cell 2006; 125(6):1036–1038.

    CAS  PubMed  Google Scholar 

  114. McKee AE, Silver PA. Systems perspectives on mRNA processing. Cell Res 2007; 17(7):581–590.

    CAS  PubMed  Google Scholar 

  115. Lareau LF, Brooks AN, Soergel DA et al. The coupling of alternative splicing and nonsense-mediated mRNA decay. Adv Exp Med Biol 2007; 623:190–211.

    PubMed  Google Scholar 

  116. Rebbapragada I, Lykke-Andersen J. Execution of nonsense-mediated mRNA decay: what defines a substrate? Curr Opin Cell Biol 2009; 21(3):394–402.

    CAS  PubMed  Google Scholar 

  117. Chang YF, Imam JS, Wilkinson MF. The nonsense-mediated decay RNA surveillance pathway. Annu Rev Biochem 2007; 76:51–74.

    CAS  PubMed  Google Scholar 

  118. McGlincy NJ, Smith CW. Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense? Trends Biochem Sci 2008; 33(8):385–393.

    CAS  PubMed  Google Scholar 

  119. Ni JZ, Grate L, Donohue JP et al. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev 2007; 21(6):708–718.

    CAS  PubMed  Google Scholar 

  120. Pleiss JA, Whitworth GB, Bergkessel M et al. Rapid, transcript-specific changes in splicing in response to environmental stress. Mol Cell 2007; 27(6):928–937.

    CAS  PubMed  Google Scholar 

  121. Sayani S, Janis M, Lee CY et al. Widespread impact of nonsense-mediated mRNA decay on the yeast intronome. Mol Cell 2008; 31(3):360–370.

    CAS  PubMed  Google Scholar 

  122. Henras AK, Soudet J, Gerus M et al. The post-transcriptional steps of eukaryotic ribosome biogenesis. Cell Mol Life Sci 2008; 65(15):2334–2359.

    CAS  PubMed  Google Scholar 

  123. Halbeisen RE, Gerber AP. Stress-Dependent Coordination of Transcriptome and Translatome in Yeast. PLoS Biol 2009; 7(5):e105.

    PubMed  Google Scholar 

  124. Zaman S, Lippman SI, Zhao X et al. How Saccharomyces responds to nutrients. Annu Rev Genet 2008; 42:27–81.

    CAS  PubMed  Google Scholar 

  125. Kofler M, Motzny K, Freund C. GYF domain proteomics reveals interaction sites in known and novel target proteins. Mol Cell Proteomics 2005; 4(11):1797–1811.

    CAS  PubMed  Google Scholar 

  126. Georgiev A, Sjostrom M, Wieslander A. Binding specificities of the GYF domains from two Saccharomyces cerevisiae Paralogs. Protein Eng Des Sel 2007.

    Google Scholar 

  127. Parker R, Sheth U. P bodies and the control of mRNA translation and degradation. Mol Cell 2007; 25(5):635–646.

    CAS  PubMed  Google Scholar 

  128. Kofler MM, Freund C. The GYF domain. Febs J 2006; 273(2):245–256.

    CAS  PubMed  Google Scholar 

  129. Cosentino GP, Schmelzle T, Haghighat A et al. Eap1p, a novel eukaryotic translation initiation factor 4E-associated protein in Saccharomyces cerevisiae. Mol Cell Biol 2000; 20(13):4604–4613.

    CAS  PubMed  Google Scholar 

  130. Chang W, Zaarour RF, Reck-Peterson S et al. Myo2p, a class V myosin in budding yeast, associates with a large ribonucleic acid-protein complex that contains mRNAs and subunits of the RNA-processing body. RNA 2008; 14(3):491–502.

    CAS  PubMed  Google Scholar 

  131. Paquin N, Chartrand P. Local regulation of mRNA translation: new insights from the bud. Trends Cell Biol 2008; 18(3):105–111.

    CAS  PubMed  Google Scholar 

  132. Paquin N, Menade M, Poirier G et al. Local activation of yeast ASH1 mRNA translation through phosphorylation of Khd1p by the casein kinase Yck1p. Mol Cell 2007; 26(6):795–809.

    CAS  PubMed  Google Scholar 

  133. Hasegawa Y, Irie K, Gerber AP. Distinct roles for Khd1p in the localization and expression of bud-localized mRNAs in yeast. RNA 2008; 14(11):2333–2347.

    CAS  PubMed  Google Scholar 

  134. Sezen B, Seedorf M, Schiebel E. The SESA network links duplication of the yeast centrosome with the protein translation machinery. Genes Dev 2009; 23(13):1559–1570.

    CAS  PubMed  Google Scholar 

  135. Huh WK, Falvo JV, Gerke LC et al. Global analysis of protein localization in budding yeast. Nature 2003; 425(6959):686–691.

    CAS  PubMed  Google Scholar 

  136. Fleischer TC, Weaver CM, McAfee KJ et al. Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes. Genes Dev 2006; 20(10):1294–1307.

    CAS  PubMed  Google Scholar 

  137. Hogan DJ, Riordan DP, Gerber AP et al. Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol 2008; 6(10):e255.

    PubMed  Google Scholar 

  138. Chenard CA, Richard S. New implications for the QUAKING RNA binding protein in human disease. J Neurosci Res 2008; 86(2):233–242.

    CAS  PubMed  Google Scholar 

  139. Sette C, Messina V, Paronetto MP. Sam68: A New STAR in the Male Fertility Firmament. J Androl 2009.

    Google Scholar 

  140. Volk T, Israeli D, Nir R et al. Tissue development and RNA control: “HOW“ is it coordinated? Trends Genet 2008; 24(2):94–101.

    CAS  PubMed  Google Scholar 

  141. Ohno G, Hagiwara M, Kuroyanagi H. STAR family RNA-binding protein ASD-2 regulates developmental switching of mutually exclusive alternative splicing in vivo. Genes Dev 2008; 22(3):360–374.

    CAS  PubMed  Google Scholar 

  142. Stoss O, Olbrich M, Hartmann AM et al. The STAR/GSG family protein rSLM-2 regulates the selection of alternative splice sites. J Biol Chem 2001; 276(12):8665–8673.

    CAS  PubMed  Google Scholar 

  143. Chawla G, Lin CH, Han A et al. Sam68 regulates a set of alternatively spliced exons during neurogenesis. Mol Cell Biol 2009; 29(1):201–213.

    CAS  PubMed  Google Scholar 

  144. Paronetto MP, Achsel T, Massiello A et al. The RNA-binding protein Sam68 modulates the alternative splicing of Bcl-x. J Cell Biol 2007; 176(7):929–939.

    CAS  PubMed  Google Scholar 

  145. Saccomanno L, Loushin C, Jan E et al. The STAR protein QKI-6 is a translational repressor. Proc Natl Acad Sci USA 1999; 96(22):12605–12610.

    CAS  PubMed  Google Scholar 

  146. Lee MH, Schedl T. Translation repression by GLD-1 protects its mRNA targets from nonsense-mediated mRNA decay in C. elegans. Genes Dev 2004; 18(9):1047–1059.

    CAS  PubMed  Google Scholar 

  147. Larocque D, Pilotte J, Chen T et al. Nuclear retention of MBP mRNAs in the quaking viable mice. Neuron 2002; 36(5):815–829.

    CAS  PubMed  Google Scholar 

  148. Galarneau A, Richard S. The STAR RNA binding proteins GLD-1, QKI, SAM68 and SLM-2 bind bipartite RNA motifs. BMC Mol Biol 2009; 10:47.

    PubMed  Google Scholar 

  149. Lukong KE, Richard S. Sam68, the KH domain-containing superSTAR. Biochim Biophys Acta 2003; 1653(2):73–86.

    CAS  PubMed  Google Scholar 

  150. Ryder SP, Frater LA, Abramovitz DL et al. RNA target specificity of the STAR/GSG domain post-transcriptional regulatory protein GLD-1. Nat Struct Mol Biol 2004; 11(1):20–28.

    CAS  PubMed  Google Scholar 

  151. Pascual M, Vicente M, Monferrer L et al. The Muscleblind family of proteins: an emerging class of regulators of developmentally programmed alternative splicing. Differentiation 2006; 74(2–3):65–80.

    CAS  PubMed  Google Scholar 

  152. Shepard PJ, Hertel KJ. The SR protein family. Genome Biol 2009; 10(10):242.

    PubMed  Google Scholar 

  153. Keene JD. RNA regulons: coordination of post-transcriptional events. Nat Rev Genet 2007; 8(7):533–543.

    CAS  PubMed  Google Scholar 

  154. Gama-Carvalho M, Barbosa-Morais NL, Brodsky AS et al. Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors. Genome Biol 2006; 7(11):R113.

    PubMed  Google Scholar 

  155. Blanchette M, Labourier E, Green RE et al. Genome-wide analysis reveals an unexpected function for the Drosophila splicing factor U2AF50 in the nuclear export of intronless mRNAs. Mol Cell 2004; 14(6):775–786.

    CAS  PubMed  Google Scholar 

  156. Allemand E, Batsche E, Muchardt C. Splicing, transcription and chromatin: a menage a trois. Curr Opin Genet Dev 2008; 18(2):145–151.

    CAS  PubMed  Google Scholar 

  157. Zhong XY, Wang P, Han J et al. SR proteins in vertical integration of gene expression from transcription to RNA processing to translation. Mol Cell 2009; 35(1):1–10.

    CAS  PubMed  Google Scholar 

  158. Pandit S, Lynn B, Rymond BC. Inhibition of a spliceosome turnover pathway suppresses splicing defects. Proc Natl Acad Sci USA 2006; 103(37):13700–13705.

    CAS  PubMed  Google Scholar 

  159. Pandit S, Paul S, Zhang L et al. Spp382p interacts with multiple yeast splicing factors, including possible regulators of Prp43 DExD/H-Box protein function. Genetics 2009; 183(1):195–206.

    CAS  PubMed  Google Scholar 

  160. Ohi MD, Link AJ, Ren L et al. Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors and snRNAs. Mol Cell Biol 2002; 22(7):2011–2024.

    CAS  PubMed  Google Scholar 

  161. Wang Q, Hobbs K, Lynn B et al. The Clf1p splicing factor promotes spliceosome assembly through N-terminal tetratricopeptide repeat contacts. J Biol Chem 2003; 278(10):7875–7883.

    CAS  PubMed  Google Scholar 

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  1. Biology Department, University of Kentucky, 675 Rose Street, Lexington, Kentucky, 40506-0225, USA

    Brian C. Rymond

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  1. Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel

    Talila Volk BSc, MSc, PhD

  2. Department of Molecular Genetics and Microbiology, Institute of Cell and Molecular Biology, University of Texas at Austin, Austin, Texas, USA

    Karen Artzt BA, PhD

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Rymond, B.C. (2010). The Branchpoint Binding Protein. In: Volk, T., Artzt, K. (eds) Post-Transcriptional Regulation by STAR Proteins. Advances in Experimental Medicine and Biology, vol 693. Springer, Boston, MA. https://doi.org/10.1007/978-1-4419-7005-3_9

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