101
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Cusick ME. Purification of ribonucleoproteins by a novel approach: isolation of the SSB1 ribonucleoprotein from yeast and demonstration that it has no role in mRNA splicing. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1171:176-86. [PMID: 1482680 DOI: 10.1016/0167-4781(92)90118-j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A novel approach is described to purify potential ribonucleoproteins (RNP) of yeast. The method assays a yeast RNP complex, assembled in vitro on actin pre-mRNA, by low-ionic strength acrylamide gel electrophoresis. The minimal protein components of this RNP complex were three proteins, one of 30 kDa and two at 42-44 kDa, defined by formation of the complex on biotinylated-RNA, binding of this complex to avidin-agarose, and salt elution of the protein in the biotinylated-RNP complex. Using the assay for RNP complex formation, an RNP protein was purified to homogeneity on the basis of its affinity towards single-stranded DNA and RNA. This RNP protein turned out to be identical to a known RNP protein, the single-stranded binding protein 1 (ssb1) of yeast, on the basis of identical gel electrophoretic migration, antibody cross-reactivity, and identical properties on the gel complex formation assay. In vitro mRNA splicing was normal in extracts made from a yeast strain missing ssb1 (ssb1- strain). Addition of anti-ssb1 antibody to splicing extracts made from a wild type strain did not inhibit or diminish splicing. Instead, mRNA splicing was reproducibly stimulated several fold, indicating competition between ssb1 and splicing factors for binding to single-stranded RNA in the extracts. RNP complexes still formed in the ssb1- strain, demonstrating that it would be possible to purify other RNP proteins from this strain using the gel complex formation assay.
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Affiliation(s)
- M E Cusick
- Department of Medical Biochemistry and Genetics, Texas A&M College of Medicine, College Station 77843-1114
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102
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Brown JD, Plumpton M, Beggs JD. The genetics of nuclear pre-mRNA splicing: a complex story. Antonie Van Leeuwenhoek 1992; 62:35-46. [PMID: 1444335 DOI: 10.1007/bf00584461] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The occurrence of introns in nuclear precursor RNAs (pre-mRNAs) is widespread in eukaryotes, and the splicing process that removes them is basically the same in yeasts as it is in higher eukaryotes. Splicing takes place in a very large, multi-component complex, the splicesome, and biochemical studies have been complicated by the large number of splicing factors involved. This review describes how genetic approaches used to study RNA splicing in Saccharomyces cerevisiae have complemented the biochemical studies and led to rapid advances in the field.
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Affiliation(s)
- J D Brown
- Institute of Cell and Molecular Biology, University of Edinburgh, Scotland
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103
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Apolipoprotein B mRNA editing is an intranuclear event that occurs posttranscriptionally coincident with splicing and polyadenylation. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54960-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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104
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Shannon KW, Guthrie C. Suppressors of a U4 snRNA mutation define a novel U6 snRNP protein with RNA-binding motifs. Genes Dev 1991; 5:773-85. [PMID: 1827420 DOI: 10.1101/gad.5.5.773] [Citation(s) in RCA: 126] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
U4 and U6 small nuclear RNAs are associated by an extensive base-pairing interaction that must be disrupted and reformed with each round of splicing. U4 mutations within the U4/U6 interaction domain destabilize the complex in vitro and cause a cold-sensitive phenotype in vivo. Restabilization of the U4/U6 helix by dominant (gain-of-function), compensatory mutations in U6 results in wild-type growth. Cold-insensitive growth can also be restored by two classes of recessive (loss-of-function) suppressors: (1) mutations in PRP24, which we show to be a U6-specific binding protein of the RNP-consensus family; and (2) mutations in U6, which lie outside the interaction domain and identify putative PRP24-binding sites. Destabilization of the U4/U6 helix causes the accumulation of a PRP24/U4/U6 complex, which is undetectable in wild-type cells. The loss-of-function suppressor mutations inhibit the binding of PRP24 to U6, and thus presumably promote the release of PRP24 from the PRP24/U4/U6 complex and the reformation of the base-paired U4/U6 snRNP. We propose that the PRP24/U4/U6 complex is normally a highly transient intermediate in the spliceosome cycle and that PRP24 promotes the reannealing of U6 with U4.
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Affiliation(s)
- K W Shannon
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143
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105
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Schwer B, Guthrie C. PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome. Nature 1991; 349:494-9. [PMID: 1825134 DOI: 10.1038/349494a0] [Citation(s) in RCA: 249] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The assembly of the spliceosome is an ATP-dependent process. The splicing factor PRP16 contains variations of several motifs that define the eIF-4A-like ATP-dependent RNA helicase family. The protein has now been purified and shown to exhibit RNA-dependent ATPase activity. PRP16 is required specifically for the second catalytic step of the splicing reaction in vitro. This function requires ATP binding and/or hydrolysis, which appears to be concomitant with release of the protein from the spliceosome. PRP16 may be the prototype for a set of splicing factors which use ATP to drive a cycle of conformational changes.
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Affiliation(s)
- B Schwer
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143
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106
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107
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Lührmann R, Kastner B, Bach M. Structure of spliceosomal snRNPs and their role in pre-mRNA splicing. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1087:265-92. [PMID: 2147394 DOI: 10.1016/0167-4781(90)90001-i] [Citation(s) in RCA: 323] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- R Lührmann
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg F.R.G
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108
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Abstract
It has previously been shown that a mutation of yeast 5' splice junctions at position 5 (GUAUGU) causes aberrant pre-mRNA cleavages near the correct 5' splice site. We show here that the addition of exon mutations to an aberrant cleavage site region transforms it into a functional 5' splice site both in vivo and in vitro. The aberrant mRNAs are translated in vivo. The results suggest that the highly conserved G at the 5' end of introns is necessary for the second step of splicing. Further analyses indicate that the location of the U1 snRNA-pre-mRNA pairing is not affected by the exon mutations and that the precise 5' splice site is selected independent of this pairing.
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Affiliation(s)
- B Séraphin
- Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02254
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109
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Bordonné R, Banroques J, Abelson J, Guthrie C. Domains of yeast U4 spliceosomal RNA required for PRP4 protein binding, snRNP-snRNP interactions, and pre-mRNA splicing in vivo. Genes Dev 1990; 4:1185-96. [PMID: 2145195 DOI: 10.1101/gad.4.7.1185] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
U4 small nuclear RNA (snRNA) contains two intramolecular stem-loop structures, located near each end of the molecule. The 5' stem-loop is highly conserved in structure and separates two regions of U4 snRNA that base-pair with U6 snRNA in the U4/U6 small nuclear ribonucleoprotein particle (snRNP). The 3' stem-loop is highly divergent in structure among species and lies immediately upstream of the binding site for Sm proteins. To investigate the function of these two domains, mutants were constructed that delete the yeast U4 snRNA 5' stem-loop and that replace the yeast 3' stem-loop with that from trypanosome U4 snRNA. Both mutants fail to complement a null allele of the yeast U4 gene. The defects of the mutants have been examined in heterozygous strains by native gel electrophoresis, glycerol gradient centrifugation, and immunoprecipitation. The chimeric yeast-trypanosome RNA does not associate efficiently with U6 snRNA, suggesting that the 3' stem-loop of yeast U4 snRNA might be a binding site for a putative protein that facilitates assembly of the U4/U6 complex. In contrast, the 5' hairpin deletion mutant associates efficiently with U6 snRNA. However, it does not bind the U4/U6-specific protein PRP4 and does not assemble into a U4/U5/U6 snRNA. Thus, we propose that the role of the PRP4 protein is to promote interactions between the U4/U6 snRNP and the U5 snRNP.
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Affiliation(s)
- R Bordonné
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143
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110
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Jamieson DJ, Whittaker E, King D, Anderson GJ, Beggs JD. Protein interactions in nuclear pre-mRNA splicing in Saccharomyces cerevisiae. Mol Biol Rep 1990; 14:141-2. [PMID: 2141897 DOI: 10.1007/bf00360449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- D J Jamieson
- Department of Molecular Biology, University of Edinburgh, Scotland, UK
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111
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Rymond BC, Pikielny C, Seraphin B, Legrain P, Rosbash M. Measurement and analysis of yeast pre-mRNA sequence contribution to splicing efficiency. Methods Enzymol 1990; 181:122-47. [PMID: 2116568 DOI: 10.1016/0076-6879(90)81116-c] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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112
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Cheng SC, Newman AN, Lin RJ, McFarland GD, Abelson JN. Preparation and fractionation of yeast splicing extract. Methods Enzymol 1990; 181:89-96. [PMID: 2199769 DOI: 10.1016/0076-6879(90)81114-a] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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113
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Abstract
Small, reversibly biotinylated RNAs as described here are versatile ligands for affinity chromatography of RNA-binding components. These RNAs can be attached to a solid support by binding to avidin and used as ligands, or they may be hybridized to another RNA which acts as the ligand. The incorporation of a disulfide bond in the linker arm connecting biotin to the RNA makes it possible to dissociate the RNA from avidin under mild conditions. Our results regarding the binding and elution of the biotinylated RNA may be applied to other, reversibly biotinylated molecules.
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114
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Affiliation(s)
- J L Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
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115
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Abstract
Methods for studying pre-mRNA splicing in Xenopus oocytes have been improved to allow simultaneous analysis of the splicing reaction and the formation of splicing complexes in vivo. The number, order of appearance, and dependence on intact U1 and U2 snRNPs of complexes formed in vivo on a pre-mRNA substrate are similar but not identical to those observed in vitro. The migration on native gels of the complexes formed in vivo and in vitro is, however, dissimilar. RNAase H-mediated inhibition of splicing caused by oligonucleotide microinjection can be overcome by coinjection of a gene encoding the U snRNA that is targeted for cleavage. Transcripts from the injected gene complement the defect in splicing by assembling into functionally active U snRNPs. Using this assay, mutant U2 snRNAs have been tested for their ability to function in splicing and in splicing complex formation. The results indicate that much of the U2 snRNA, including regions essential for detectable binding of the U2-specific proteins A' and B", is dispensable for splicing.
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Affiliation(s)
- J Hamm
- European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany
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116
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Goodall GJ, Filipowicz W. The AU-rich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing. Cell 1989; 58:473-83. [PMID: 2758463 DOI: 10.1016/0092-8674(89)90428-5] [Citation(s) in RCA: 250] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Plant cells do not in general process the introns of transcripts expressed from introduced vertebrate genes. By studying the processing of model introns in transfected plant protoplasts, we have investigated the special requirements for intron recognition by plant cells. Our results indicate that the requirements for intron recognition in plants are different from those of both metazoa and yeast. A synthetic intron of arbitrary sequence but incorporating splice site consensus sequences and a high proportion of U and A nucleotides, a characteristic feature of plant introns, was efficiently spliced in protoplasts. We have studied the effects of various sequence alterations and conclude that AU-rich sequences are necessary for intron recognition. In addition, we find that the criteria for branch site selection are relaxed, as they are in vertebrates, but a polypyrimidine tract is not necessary.
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Affiliation(s)
- G J Goodall
- Friedrich Miescher-Institut, Basel, Switzerland
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117
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Goyer C, Altmann M, Trachsel H, Sonenberg N. Identification and characterization of cap-binding proteins from yeast. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)83277-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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118
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Chang YH, Smith JA. Molecular Cloning and Sequencing of Genomic DNA Encoding Aminopeptidase I from Saccharomyces cerevisiae. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)83527-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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119
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Abstract
In whole cell extracts of Saccharomyces cerevisiae, incubation of precursor mRNA transcripts encoding the sequences essential in vivo for forming the 3' end of the iso-1-cytochrome c mRNA (CYC1) revealed an endonuclease activity with the characteristics required for producing the mature mRNA 3' end. The observed cleavage in vitro is (i) accurate, occurring at or near the polyadenylation site of CYC1 RNA, (ii) 30 to 50 percent efficient, (iii) adenosine triphosphate dependent, (iv) specific for the 3' ends of at least two yeast pre-mRNA's, and (v) absent with related pre-mRNA's carrying mutations that abolish correct 3' end formation in vivo. In addition, a second activity in the extract polyadenylates the product under appropriate conditions. Thus, the mature 3' ends of yeast mRNA's may be generated by endonucleolytic cleavage and polyadenylation rather than by transcription termination.
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Affiliation(s)
- J S Butler
- Department of Biochemistry, University of Rochester Medical Center, NY 14642
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120
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Ruby SW, Abelson J. An early hierarchic role of U1 small nuclear ribonucleoprotein in spliceosome assembly. Science 1988; 242:1028-35. [PMID: 2973660 DOI: 10.1126/science.2973660] [Citation(s) in RCA: 218] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Splicing of nuclear precursor messenger RNA (pre-mRNA) occurs on a large ribonucleoprotein complex, the spliceosome. Several small nuclear ribonucleoproteins (snRNP's) are subunits of this complex that assembles on the pre-mRNA. Although the U1 snRNP is known to recognize the 5' splice site, its roles in spliceosome formation and splice site alignment have been unclear. A new affinity purification method for the spliceosome is described which has provided insight into the very early stages of spliceosome formation in a yeast in vitro splicing system. Surprisingly, the U1 snRNP initially recognizes sequences at or near both splice junctions in the intron. This interaction must occur before the other snRNP's (U2, U4, U5, and U6) can join the complex. The results suggest that interaction of the two splice site regions occurs at an early stage of spliceosome formation and is probably mediated by U1 snRNP and perhaps other factors.
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Affiliation(s)
- S W Ruby
- Division of Biology, California Institute of Technology, Pasadena 91125
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121
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Noble JC, Prives C, Manley JL. Alternative splicing of SV40 early pre-mRNA is determined by branch site selection. Genes Dev 1988; 2:1460-75. [PMID: 2850262 DOI: 10.1101/gad.2.11.1460] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Splicing of SV40 early pre-mRNA to alternative large-T and small-t mRNAs involves the utilization of multiple lariat branch sites. To determine the functional significance of these sites, we constructed and analyzed a set of base substitution mutants in which the major branch acceptors were altered, either singly or in combination. The ratio of large-T to small-t mRNAs produced in vivo was found to vary by over 100-fold between different mutants. When splicing was assayed in vitro with a standard pre-RNA, which results in splicing almost exclusively to large-T mRNA, the patterns of branch site utilization were altered dramatically, although the mutations were essentially without effect on splicing efficiency. However, use of a 5' truncated pre-RNA, which results in a splicing pattern that reflects the in vivo alternative splicing potential of this pre-RNA, revealed a strong correlation between the effects of the base substitutions on branch site selection and alternative splice-site utilization. An RNase protection analysis of factor interactions with the 5' splice sites and branch sites in wild-type and mutant pre-RNAs suggests that a competition for different branch sites plays a crucial role in the assembly of 'alternative' spliceosomes, thereby controlling alternative splice-site selection.
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Affiliation(s)
- J C Noble
- Department of Biological Sciences, Columbia University, New York, New York 10027
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122
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Substitution of pre-mRNA with phosphorothioate linkages reveals a new splicing-related reaction. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)37754-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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123
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Rymond BC, Rosbash M. A chemical modification/interference study of yeast pre-mRNA spliceosome assembly and splicing. Genes Dev 1988; 2:428-39. [PMID: 3286372 DOI: 10.1101/gad.2.4.428] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A chemical modification/interference assay was used to determine the yeast pre-mRNA sequence requirements for in vitro spliceosome assembly and splicing. Modifications of any of the nucleotides within the 5' splice site and branch point (TACTAAC box) consensus sequences as well as less conserved intron and exon positions were found to inhibit assembly and/or splicing. The interference pattern of the 5' splice site and TACTAAC box lesions increased as spliceosome assembly proceeded (complex III----complex I----complex II) and as splicing proceeded, suggesting that these sequence elements play multiple roles in the assembly of yeast spliceosomes and in the removal of intervening sequences. Furthermore, modification (or mutation) of a TACTAAC-like sequence upstream of the branch point was found to inhibit the rate of spliceosome assembly, implying a possible role for degenerate branch point sequences in modulating the efficiency of spliceosome assembly.
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Affiliation(s)
- B C Rymond
- Biology Department, Brandeis University, Waltham, Massachusetts 02254
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124
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Lossky M, Anderson GJ, Jackson SP, Beggs J. Identification of a yeast snRNP protein and detection of snRNP-snRNP interactions. Cell 1987; 51:1019-26. [PMID: 2961458 DOI: 10.1016/0092-8674(87)90588-5] [Citation(s) in RCA: 155] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The RNA8 gene of Saccharomyces cerevisiae encodes an unusually large (260 kd) protein required for pre-mRNA splicing. Immunological procedures have been used to demonstrate that the RNA8 protein is in stable association with the small nuclear RNAs snR7L and snR7S, which are also known to be required for splicing and which are present in spliceosomal complexes. RNA8 is also involved in an ATP-dependent association with two other small nuclear RNAs, snR14 and snR6. It is proposed that this represents an ATP-dependent interaction between small nuclear ribonucleoprotein particles that precedes their entry into the spliceosome.
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Affiliation(s)
- M Lossky
- Department of Molecular Biology, University of Edinburgh, Scotland
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125
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Schmelzer C, Müller MW. Self-splicing of group II introns in vitro: lariat formation and 3' splice site selection in mutant RNAs. Cell 1987; 51:753-62. [PMID: 2445492 DOI: 10.1016/0092-8674(87)90098-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Deletion or substitution of the branch A residue in group II intron bl1 significantly reduces splicing activity; yet, residual exon ligation is correct, and lariats have their branch points at the normal distance from the 3' end of the intron. Mutations in the sequence facing the branch point also allow residual lariat formation; however, free 3' exons are generated with false 5' termini, all of which are within a UCACA consensus sequence located upstream or downstream of the normal 3' splice site. These results indicate that both the conserved 3' splice site APy and the spatial arrangements in stem 6 are crucial for correct 3' splice site selection.
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Affiliation(s)
- C Schmelzer
- Institut für Genetik und Mikrobiologie, Universität München, FRG
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126
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Abstract
Precursors to mRNA become substrates for splicing by being assembled into a complex multisubunit structure, the spliceosome. To study the assembly of the yeast spliceosome, intermediate complexes were separated by electrophoresis on nondenaturing polyacrylamide gels. Four splicing-dependent complexes, A1, A2-1, A2-2, and B, were observed. The order of assembly of these complexes was determined to be B----A2-1----A1----A2-2. The assembly process can be blocked at complex A1 by addition of 5 mM EDTA or by carrying out the assembly process in heat-inactivated rna2 extracts. The snRNA composition of the complexes was determined by hybridization with probes for five yeast snRNAs. snR14 (U4) was only found in complex A2-1, snR6 (U6) and snR7 (U5) were in complexes A1, A2-1, and A2-2, whereas snR20 (U2) was in all four of the complexes. snR19 (U1) was not present in any of the complexes. Hybridization with these probes was also employed to detect snRNPs present in yeast splicing extracts. We found that snR6, snR7, and snR14 were present together in a large complex. This complex underwent an ATP-dependent dissociation to give snR7 and snR6-snR14 complexes. snR19 and snR20 are present in distinct RNPs but the mobility of these is not affected by ATP. A mechanism for spliceosome assembly is proposed.
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Affiliation(s)
- S C Cheng
- Division of Biology, California Institute of Technology, Pasadena 91125
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127
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Siliciano PG, Jones MH, Guthrie C. Saccharomyces cerevisiae has a U1-like small nuclear RNA with unexpected properties. Science 1987; 237:1484-7. [PMID: 3306922 DOI: 10.1126/science.3306922] [Citation(s) in RCA: 106] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Previous experiments indicated that only a small subset of the approximately equal to 24 small nuclear RNAs (snRNAs) in Saccharomyces cerevisiae have binding sites for the Sm antigen, a hallmark of metazoan small nuclear ribonucleoproteins (snRNPs) involved in pre-messenger RNA splicing. Antibodies from human serum to Sm proteins were used to show that four snRNAs (snR7, snR14, snR19, and snR20) can be immunoprecipitated from yeast extracts. Three of these four, snR7, snR14, and snR20, have been shown to be analogs of mammalian U5, U4, and U2, respectively. Several regions of significant homology to U1 (164 nucleotides) have now been found in cloned and sequenced snR19 (568 nucleotides). These include ten out of ten matches to the 5' end of U1, the site known to interact with the 5' splice site of mammalian introns. Surprisingly, the precise conservation of this sequence precludes perfect complementarity between snR19 and the invariant yeast 5' junction (GTATGT), which differs from the mammalian consensus at the fourth position (GTPuAGT).
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128
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Price JV. Origin of the phosphate at the ligation junction produced by self-splicing of Tetrahymena thermophila pre-ribosomal RNA. J Mol Biol 1987; 196:217-21. [PMID: 3656445 DOI: 10.1016/0022-2836(87)90522-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The exons of the self-splicing pre-ribosomal RNA of Tetrahymena thermophila are joined accurately in vitro, even when only 33 nucleotides of the natural 5' exon and 38 nucleotides of the natural 3' exon remain. RNA fingerprint analysis was used to identify the unique ribonuclease T1 oligonucleotide generated by exon ligation. Secondary digests of the ligation junction oligonucleotide with ribonuclease A confirmed the identity of the fragment and demonstrated that the phosphate group that forms the phosphodiester bond at the ligation junction is derived from the 5' position of a uridine nucleotide in the RNA. This observation supports the prediction that the splice junction phosphate is derived from the 3' splice site. These results emphasize the mechanistic similarities of RNA splicing reactions of the group I introns, group II introns and nuclear pre-mRNA introns.
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Affiliation(s)
- J V Price
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder 80309
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129
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Sharp PA. Biology, oncology, and RNA splicing. Cancer 1987; 59:1697-708. [PMID: 3548941 DOI: 10.1002/1097-0142(19870515)59:10<1697::aid-cncr2820591004>3.0.co;2-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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130
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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; 1:238-46. [PMID: 3315850 DOI: 10.1101/gad.1.3.238] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
To investigate the importance of sequences between the yeast (Saccharomyces cerevisiae) branch point (TACTAAC box) and 3' splice site (AG), we generated a series of pre-mRNA substrates that differed in the length of RNA retained on the 3' side of the TACTAAC box. These pre-mRNAs were compared as substrates for the first step of in vitro splicing (5' cleavage and lariat formation) and in vitro spliceosome assembly (complex formation) in a whole-cell yeast extract. The results indicate that for rp51A pre-mRNA at least 29 nucleotides of RNA on the 3' side of the TACTAAC box are required for 5' cleavage and lariat formation, as smaller substrates fail to manifest any detectable cleavage or ligation events. Analysis of splicing complex assembly indicates that these smaller substrates undergo efficient yet incomplete complex formation; they are blocked at a late stage of spliceosome assembly, the complex I to complex II transition (Pikielny et al. 1986), a result which suggests that the failure to form lariats is due to a specific assembly defect. The lariat formation block (and assembly defect) can be relieved by the addition of ribohomopolymer "tails" to the 3' end of the shortened rp51A pre-mRNAs, and similar results were obtained with shortened actin pre-mRNAs. The results of this study indicate that this region of the pre-mRNA serves a specific function late in in vitro spliceosome assembly.
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Affiliation(s)
- B C Rymond
- Department of Biology, Brandeis University, Waltham, Massachusetts 02254
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131
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Lin RJ, Lustig AJ, Abelson J. Splicing of yeast nuclear pre-mRNA in vitro requires a functional 40S spliceosome and several extrinsic factors. Genes Dev 1987; 1:7-18. [PMID: 3322937 DOI: 10.1101/gad.1.1.7] [Citation(s) in RCA: 112] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We have previously shown that extracts prepared from most of the yeast temperature-sensitive rna mutants are heat sensitive for pre-mRNA splicing in vitro, and that the products of the corresponding RNA genes are essential for the early stages of the splicing region. In this report, we demonstrate that most heat-inactivated mutant extracts do not form the spliceosome, suggesting that their gene products are likely to be involved in spliceosome formation. Heat-inactivated rna2 extracts, on the other hand, do form a splicing-dependent 40S complex containing uncleaved pre-mRNA exclusively. The pre-mRNA in the 40S complex can be converted to the splicing products in the presence of ATP and complementing extracts. These results demonstrate that: (1) the 40S complex formed in heat-inactivated rna2 extracts is a spliceosome (termed the rna2 delta spliceosome), (2) the spliceosome is a functional intermediate in the splicing pathway, and (3) the splicing process can be dissected into two steps, spliceosome formation and cleavage-ligation reactions. Additional results indicate that at least two extrinsic factors, as well as the RNA2 gene product, are required for complementation of the rna2 delta spliceosome. A three-step mechanism for nuclear pre-mRNA splicing in yeast is proposed.
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Affiliation(s)
- R J Lin
- Division of Biology, California Institute of Technology, Pasadena 91125
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132
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Abstract
A small set of distinctive short RNA molecules are found in the nuclei of all higher eukaryotic cells and yeast, in protein complexes known as 'small nuclear ribonucleoprotein particles', or snRNPs. Recent work has confirmed early suggestions that these particles form part of the machinery by which primary RNA transcripts are processed to their mature, functional form. In particular, snRNPs have been shown to be an integral part of the 'spliceosome', a multi-component complex involved in the removal of intron sequences from the coding regions of messenger RNA precursors.
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133
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Abstract
A general mechanism for the splicing of nuclear messenger RNA precursors in eukaryotic cells has been widely accepted. This mechanism, which generates lariat RNAs possessing a branch site, seems related to the RNA-catalyzed reactions of self-splicing introns. The splicing of nuclear messenger RNA precursors involves the formation of a multicomponent complex, the spliceosome. This splicing body contains at least three different small nuclear ribonucleoprotein particles (snRNPs), U2, U5, and U4 + U6. A complex containing precursor RNA and the U2 snRNP particle is a likely intermediate in the formation of the spliceosome.
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134
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Beggs JD, Lossky M, Jackson SP, Anderson GJ. Identification of a snRNP protein in Saccharomyces cerevisiae. Mol Biol Rep 1987. [DOI: 10.1007/bf00356905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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135
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Gerke V, Steitz JA. A protein associated with small nuclear ribonucleoprotein particles recognizes the 3' splice site of premessenger RNA. Cell 1986; 47:973-84. [PMID: 2946421 DOI: 10.1016/0092-8674(86)90812-3] [Citation(s) in RCA: 242] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A HeLa cell nuclear extract active in splicing of pre-mRNA has been fractionated to identify the component that interacts with the 3' splice site. The activity that binds this region in an RNAase T1 protection assay copurifies with a 70 kd protein which is recognized by anti-Sm antibodies. Protein blots probed with labeled mRNA precursors either containing or lacking an intact 3' splice site reveal that the 70 kd polypeptide can bind pre-mRNA after immobilization on nitrocellulose and that it shows a preference for sequences located between the 3' splice junction and the site of lariat formation. Cofractionation during chromatography and immunoprecipitation by anti-2,2,7-trimethylguanosine antibodies demonstrate that the 3' splice site binding component associates with small nuclear ribonucleoprotein particles in low (1 mM) but not high (15 mM) Mg++ concentrations.
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136
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Abstract
The yeast rna mutations (rna2-rna11) are a set of temperature-sensitive mutations that result in the accumulation of intron-containing mRNA precursors at the restrictive temperature. We have used the yeast in vitro splicing system to investigate the role of products of the RNA genes in mRNA splicing. We have tested the heat lability of the in vitro mRNA splicing reaction in extracts isolated from mutant and wild-type cells. Extracts isolated from seven of the nine rna mutants demonstrated heat lability in this assay, while most wild-type extracts were stable under the conditions utilized. We have also demonstrated that heat inactivation usually results in the specific loss of an exchangeable component by showing that most combinations of heat-inactivated extracts from different mutants complement one another. In three cases (rna2, rna5, and rna11), the linkage of the in vitro defect to the rna mutations was ascertained by a combination of reversion, tetrad, and in vitro complementation analyses. Furthermore, each heat-inactivated extract was capable of complementation by at least one fraction of the wild-type splicing system. Thus many of the RNA genes are likely to code for products directly involved in and essential for mRNA splicing.
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137
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Pikielny CW, Rymond BC, Rosbash M. Electrophoresis of ribonucleoproteins reveals an ordered assembly pathway of yeast splicing complexes. Nature 1986; 324:341-5. [PMID: 3537805 DOI: 10.1038/324341a0] [Citation(s) in RCA: 233] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Three splicing complexes formed with a yeast pre-messenger RNA during in vitro splicing can be resolved by non-denaturing gel electrophoresis after incubation in the presence of non-specific competitor RNA. The time course of the appearance of these complexes and their composition suggest that they represent an ordered pathway of splicing complex assembly.
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138
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Murphy WJ, Watkins KP, Agabian N. Identification of a novel Y branch structure as an intermediate in trypanosome mRNA processing: evidence for trans splicing. Cell 1986; 47:517-25. [PMID: 3779835 DOI: 10.1016/0092-8674(86)90616-1] [Citation(s) in RCA: 296] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We present evidence that addition of the 35 nucleotide spliced leader (SL) to the 5' end of T. brucei mRNAs occurs via trans RNA splicing. A 100 nucleotide fragment of the 135 base SL RNA (100-mer) is revealed by S1 nuclease analysis of total and poly(A)+ RNA. This 100-mer is not detected by Northern hybridization analysis, indicating that it does not exist free in the cell. The 5' end of the 100-mer maps precisely to the conserved splice junction sequence of the SL RNA. Purified debranching enzyme releases this 100-mer RNA as a free, 100 nucleotide species. This indicates that the 100-mer is covalently linked to poly(A)+ RNA by a 2'-5' phosphodiester bond, that the branched intermediate has a discontinuous intron or Y structure (rather than a lariat), which is expected of a trans-spliced mRNA, and that the SL RNA is indeed the donor of the SL sequence to trypanosome mRNAs.
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139
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Ares M. U2 RNA from yeast is unexpectedly large and contains homology to vertebrate U4, U5, and U6 small nuclear RNAs. Cell 1986; 47:49-59. [PMID: 3530502 DOI: 10.1016/0092-8674(86)90365-x] [Citation(s) in RCA: 141] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
I have determined the structure of the gene from Saccharomyces cerevisiae coding for the yeast homolog of vertebrate U2 snRNA. Surprisingly, the RNA is 1175 nucleotides long, six times larger than U2 RNAs from other organisms, including Schizosaccharomyces pombe. Nearly 100 nucleotides of the large RNA share sequence homology and potential secondary structure with metazoan U2. The large RNA also contains homology to vertebrate U4, U5, and U6 snRNAs, implying a "poly-snRNP" structure for the RNP containing the large RNA. The gene LSR1, encoding the large RNA, is essential for growth, suggesting that the yeast spliceosome can be dissected using genetic approaches. The different organization of spliceosomal RNA may underlie differences in splicing between yeast and metazoans.
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141
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Abstract
Two different methods have been devised for the analysis and purification of spliceosomes formed in a yeast in vitro splicing system. The first method relies on the electrophoretic separation of ribonucleoprotein particles in composite acrylamide-agarose gels. A large fraction of added substrate is located in spliceosomes, the formation of which can be shown to be dependent on the presence of both a yeast 5' splice junction and a TACTAAC box on the RNA substrate. The second method relies on oligo(dT)-cellulose chromatography of spliceosomes formed with a polyadenylated substrate. Purification of spliceosomes by either method indicates that at least three small nuclear RNAs, approximately 160, 185, and 215 nucleotides in length, are specifically associated with yeast spliceosomes.
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142
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Fouser LA, Friesen JD. Mutations in a yeast intron demonstrate the importance of specific conserved nucleotides for the two stages of nuclear mRNA splicing. Cell 1986; 45:81-93. [PMID: 3513966 DOI: 10.1016/0092-8674(86)90540-4] [Citation(s) in RCA: 129] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mutations were introduced at all positions of the internal conserved sequence (ICS) and at three positions in the 5' junction sequence of a Saccharomyces cerevisiae actin intron contained within an actin-thymidine kinase fusion gene. Stage I of splicing is reduced by changes at all these positions. C or A replacement at the fifth nucleotide of the 5' sequence reduces the fidelity of RNA cleavage at the 5' exon-intron junction and results in an accumulation of aberrant lariat intermediate. Stage II of splicing is affected by changes in the first and second residues of the 5' sequence and in the penultimate position of the ICS. An A to G transition at the branch point of the ICS causes a major accumulation of lariat intermediate.
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