1
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Gallagher PG, Maksimova Y, Lezon-Geyda K, Newburger PE, Medeiros D, Hanson RD, Rothman J, Israels S, Wall DA, Sidonio RF, Sieff C, Gowans LK, Mittal N, Rivera-Santiago R, Speicher DW, Baserga SJ, Schulz VP. Aberrant splicing contributes to severe α-spectrin-linked congenital hemolytic anemia. J Clin Invest 2019; 129:2878-2887. [PMID: 31038472 DOI: 10.1172/jci127195] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The etiology of severe hemolytic anemia in most patients with recessive hereditary spherocytosis (rHS) and the related disorder hereditary pyropoikilocytosis (HPP) is unknown. Whole exome sequencing of DNA from probands of 24 rHS or HPP kindreds identified numerous mutations in erythrocyte membrane α-spectrin (SPTA1). Twenty-eight mutations were novel, with null alleles frequently found in trans to missense mutations. No mutations were identified in a third of SPTA1 alleles (17/48). Whole genome sequencing revealed linkage disequilibrium between the common rHS-linked α-spectrinBug Hill polymorphism and a rare intron 30 variant in all 17 mutation-negative alleles. In vitro minigene studies and in vivo splicing analyses revealed the intron 30 variant changes a weak alternate branch point (BP) to a strong BP. This change leads to increased utilization of an alternate 3' splice acceptor site, perturbing normal α-spectrin mRNA splicing and creating an elongated mRNA transcript. In vivo mRNA stability studies revealed the newly created termination codon in the elongated transcript activates nonsense mediated decay leading to spectrin deficiency. These results demonstrate a unique mechanism of human genetic disease contributes to the etiology of a third of cases of rHS, facilitating diagnosis and treatment of severe anemia, and identifying a new target for therapeutic manipulation.
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Affiliation(s)
- Patrick G Gallagher
- Department of Pediatrics.,Department of Genetics, and.,Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | | | - Peter E Newburger
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Desiree Medeiros
- Kapiolani Medical Center for Women & Children, Honolulu, Hawaii, USA
| | | | - Jennifer Rothman
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Sara Israels
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Donna A Wall
- Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Robert F Sidonio
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Colin Sieff
- Harvard Medical School, Dana-Farber and Boston Children's, Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - L Kate Gowans
- Beaumont Children's Hospital, Royal Oak, Michigan, USA
| | - Nupur Mittal
- Department of Pediatrics, Rush University Medical Center, Chicago, Illinois, USA
| | - Roland Rivera-Santiago
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - David W Speicher
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Susan J Baserga
- Department of Genetics, and.,Departments of Molecular Biophysics and Biochemistry and Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
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2
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Paggi JM, Bejerano G. A sequence-based, deep learning model accurately predicts RNA splicing branchpoints. RNA (NEW YORK, N.Y.) 2018; 24:1647-1658. [PMID: 30224349 PMCID: PMC6239175 DOI: 10.1261/rna.066290.118] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/10/2018] [Indexed: 05/26/2023]
Abstract
Experimental detection of RNA splicing branchpoints is difficult. To date, high-confidence experimental annotations exist for 18% of 3' splice sites in the human genome. We develop a deep-learning-based branchpoint predictor, LaBranchoR, which predicts a correct branchpoint for at least 75% of 3' splice sites genome-wide. Detailed analysis of cases in which our predicted branchpoint deviates from experimental data suggests a correct branchpoint is predicted in over 90% of cases. We use our predicted branchpoints to identify a novel sequence element upstream of branchpoints consistent with extended U2 snRNA base-pairing, show an association between weak branchpoints and alternative splicing, and explore the effects of genetic variants on branchpoints. We provide genome-wide branchpoint annotations and in silico mutagenesis scores at http://bejerano.stanford.edu/labranchor.
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Affiliation(s)
- Joseph M Paggi
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - Gill Bejerano
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
- Department of Developmental Biology, Stanford University, Stanford, California 94305, USA
- Department of Pediatrics, Stanford University, Stanford, California 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, California 94305, USA
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3
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Competition between the ATPase Prp5 and branch region-U2 snRNA pairing modulates the fidelity of spliceosome assembly. Mol Cell 2008; 28:838-49. [PMID: 18082608 DOI: 10.1016/j.molcel.2007.09.022] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 07/25/2007] [Accepted: 09/26/2007] [Indexed: 11/20/2022]
Abstract
ATPase-facilitated steps during spliceosome function have been postulated to afford opportunities for kinetic proofreading. Spliceosome assembly requires the ATPase Prp5p, whose activity might thus impact fidelity during initial intron recognition. Using alanine mutations in S. cerevisiae Prp5p, we identified a suboptimal intron whose splicing could be improved by altered Prp5p activity and then, using this intron, screened for potent prp5 mutants. These prp5 alleles specifically alter branch region selectivity, with improved splicing in vivo of suboptimal substrates correlating with reduced ATPase activity in vitro for a series of mutants in ATPase motif III (SAT). Because these effects are abrogated by compensatory U2 snRNA mutations or other changes that increase branch region-U2 pairing, these results explicitly link a fidelity event with a defined physical structure, the branch region-U2 snRNA duplex, and provide strong evidence that progression of the splicing pathway requires branch region-U2 snRNA pairing prior to Prp5p-facilitated conformational change.
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4
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De la Rosa-Rios MA, Martínez-Salazar M, Martínez-Garcia M, González-Bonilla C, Villegas-Sepúlveda N. The intron 1 of HPV 16 has a suboptimal branch point at a guanosine. Virus Res 2006; 118:46-54. [PMID: 16343675 DOI: 10.1016/j.virusres.2005.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2005] [Revised: 11/11/2005] [Accepted: 11/11/2005] [Indexed: 11/28/2022]
Abstract
The branch point sequence (BPS) of intron 1 of the HPV-16 was determined via RT-PCR in a cell free system, using lariat intermediates obtained by in vitro splicing reactions. We used synthetic E6/E7 transcripts and HeLa nuclear protein extracts to obtain the splicing intermediates. Then, a divergent oligonucleotide primer set, pairing on the lariat RNA that encompassed the 2'-5' phosphodiester bond formed between the 5' end of the intron and the BPS, was used for cDNA synthesis and PCR amplification. Subsequent RT-PCR assays revealed four splicing intermediates, made up of a major intermediary corresponding to the BPS and four cryptic branched sequences. Only intermediates bound at the 5' end of the intron are probably the authentic branch point sequence, and all of them branch at guanosine 328 instead of the typical adenosine. Unusually, the BPS of intron 1 of HPV-16 is a suboptimal sequence (AGUGAGU) that differs from the eukaryotic consensus BPS, which correlates with the splicing profile observed for early transcripts of HPV-16 in tumors and tumor derived cell lines. The implications of this unusual branch point sequence for splicing of the HPV-16 pre-mRNA are discussed.
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5
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Lacadie SA, Rosbash M. Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA:5'ss base pairing in yeast. Mol Cell 2005; 19:65-75. [PMID: 15989965 DOI: 10.1016/j.molcel.2005.05.006] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 04/05/2005] [Accepted: 05/09/2005] [Indexed: 11/16/2022]
Abstract
To investigate the mechanism of spliceosome assembly in vivo, we performed chromatin immunoprecipitation (ChIP) analysis of U1, U2, and U5 small nuclear ribonucleoprotein particles (snRNPs) to intron-containing yeast (S. cerevisiae) genes. The snRNPs display patterns that indicate a cotranscriptional assembly model: U1 first, then U2, and the U4/U6*U5 tri-snRNP followed by U1 destabilization. cis-splicing mutations also support a role of U2 and/or the tri-snRNP in U1 destabilization. Moreover, they indicate that splicing efficiency has a major impact on cotranscriptional snRNP recruitment and suggest that cotranscriptional recruitment of U2 or the tri-snRNP is required to commit the pre-mRNA to splicing. Branchpoint (BP) mutations had a major effect on the U1 pattern, whereas 5' splice site (5'ss) mutations had a stronger effect on the U2 pattern. A 5'ss-U1 snRNA complementation experiment suggests that pairing between U1 and the 5'ss occurs after U1 recruitment and contributes to a specific U1:substrate conformation required for efficient U2 and tri-snRNP recruitment.
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Affiliation(s)
- Scott A Lacadie
- Howard Hughes Medical Institute, Biology Department MS008, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, USA
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6
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Hovhannisyan RH, Carstens RP. A novel intronic cis element, ISE/ISS-3, regulates rat fibroblast growth factor receptor 2 splicing through activation of an upstream exon and repression of a downstream exon containing a noncanonical branch point sequence. Mol Cell Biol 2005; 25:250-63. [PMID: 15601847 PMCID: PMC538792 DOI: 10.1128/mcb.25.1.250-263.2005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutually exclusive splicing of fibroblast growth factor receptor 2 (FGFR2) exons IIIb and IIIc yields two receptor isoforms, FGFR2-IIIb and -IIIc, with distinctly different ligand binding properties. Several RNA cis elements in the intron (intron 8) separating these exons have been described that are required for splicing regulation. Using a heterologous splicing reporter, we have identified a new regulatory element in this intron that confers cell-type-specific inclusion of an unrelated exon that mirrors its ability to promote cell-type-specific inclusion of exon IIIb. This element promoted inclusion of exon IIIb while at the same time silencing exon IIIc inclusion in cells expressing FGFR2-IIIb; hence, we have termed this element ISE/ISS-3 (for "intronic splicing enhancer-intronic splicing silencer 3"). Silencing of exon IIIc splicing by ISE/ISS-3 was shown to require a branch point sequence (BPS) using G as the primary branch nucleotide. Replacing a consensus BPS with A as the primary branch nucleotide resulted in constitutive splicing of exon IIIc. Our results suggest that the branch point sequence constitutes an important component that can contribute to the efficiency of exon definition of alternatively spliced cassette exons. Noncanonical branch points may thus facilitate cell-type-specific silencing of regulated exons by flanking cis elements.
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Affiliation(s)
- Ruben H Hovhannisyan
- University of Pennsylvania School of Medicine, 700 Clinical Research Building, 415 Curie Blvd., Philadelphia, PA 19104-6144, USA
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7
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Abstract
Introns are removed from precursor messenger RNAs in the cell nucleus by a large ribonucleoprotein complex called the spliceosome. The spliceosome contains five subcomplexes called snRNPs, each with one RNA and several protein components. Interactions of the snRNPs with each other and the intron are highly dynamic, changing in an ordered progression throughout the splicing process. This allosteric cascade of interactions is programmed into the RNA and protein components of the spliceosome, and is driven by a family of DExD/H-box RNA-dependent ATPases. The dependence of cascade progression on multiple intron-recognition events likely serves to enforce the accuracy of splicing. Here, the progression of the allosteric cascade from the first recognition event to the first catalytic step of splicing is reviewed.
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Affiliation(s)
- David A Brow
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1532, USA.
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8
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Simpson CG, Thow G, Clark GP, Jennings SN, Watters JA, Brown JWS. Mutational analysis of a plant branchpoint and polypyrimidine tract required for constitutive splicing of a mini-exon. RNA (NEW YORK, N.Y.) 2002; 8:47-56. [PMID: 11873758 PMCID: PMC1370234 DOI: 10.1017/s1355838202015546] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The branchpoint sequence and associated polypyrimidine tract are firmly established splicing signals in vertebrates. In plants, however, these signals have not been characterized in detail. The potato invertase mini-exon 2 (9 nt) requires a branchpoint sequence positioned around 50 nt upstream of the 5' splice site of the neighboring intron and a U11 element found adjacent to the branchpoint in the upstream intron (Simpson et al., RNA, 2000, 6:422-433). Utilizing the sensitivity of this plant splicing system, these elements have been characterized by systematic mutation and analysis of the effect on inclusion of the mini-exon. Mutation of the branchpoint sequence in all possible positions demonstrated that branchpoints matching the consensus, CURAY, were most efficient at supporting splicing. Branchpoint sequences that differed from this consensus were still able to permit mini-exon inclusion but at greatly reduced levels. Mutation of the downstream U11 element suggested that it functioned as a polypyrimidine tract rather than a UA-rich element, common to plant introns. The minimum sequence requirement of the polypyrimidine tract for efficient splicing was two closely positioned groups of uridines 3-4 nt long (<6 nt apart) that, within the context of the mini-exon system, required being close (<14 nt) to the branchpoint sequence. The functional characterization of the branchpoint sequence and polypyrimidine tract defines these sequences in plants for the first time, and firmly establishes polypyrimidine tracts as important signals in splicing of at least some plant introns.
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Affiliation(s)
- Craig G Simpson
- Unit of Gene Expression, Scottish Crop Research Institute, Invergowrie, Dundee, United Kingdom
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9
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Ast G, Pavelitz T, Weiner AM. Sequences upstream of the branch site are required to form helix II between U2 and U6 snRNA in a trans-splicing reaction. Nucleic Acids Res 2001; 29:1741-9. [PMID: 11292847 PMCID: PMC31302 DOI: 10.1093/nar/29.8.1741] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2000] [Revised: 02/08/2001] [Accepted: 02/08/2001] [Indexed: 11/13/2022] Open
Abstract
Three different base paired stems form between U2 and U6 snRNA over the course of the mRNA splicing reaction (helices I, II and III). One possible function of U2/U6 helix II is to facilitate subsequent U2/U6 helix I and III interactions, which participate directly in catalysis. Using an in vitro trans-splicing assay, we investigated the function of sequences located just upstream from the branch site (BS). We find that these upstream sequences are essential for stable binding of U2 to the branch region, and for U2/U6 helix II formation, but not for initial U2/BS pairing. We also show that non-functional upstream sequences cause U2 snRNA stem-loop IIa to be exposed to dimethylsulfate modification, perhaps reflecting a U2 snRNA conformational change and/or loss of SF3b proteins. Our data suggest that initial binding of U2 snRNP to the BS region must be stabilized by an interaction with upstream sequences before U2/U6 helix II can form or U2 stem-loop IIa can participate in spliceosome assembly.
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Affiliation(s)
- G Ast
- Department of Human Genetics, Sackler School of Medicine, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
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10
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Li M, Pritchard PH. Characterization of the effects of mutations in the putative branchpoint sequence of intron 4 on the splicing within the human lecithin:cholesterol acyltransferase gene. J Biol Chem 2000; 275:18079-84. [PMID: 10849435 DOI: 10.1074/jbc.m910197199] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have previously identified a point mutation (intervening sequence (IVS) 4: T --> C) in the branchpoint consensus sequence of intron 4 of the lecithin:cholesterol acyltransferase (LCAT) gene in patients with fish-eye disease. To investigate the possible mechanisms responsible for the defective splicing, we made a series of mutations in the branchpoint sequence and expressed these mutants in HEK-293 cells followed by the analysis of pre-mRNA splicing using reverse transcriptase-polymerase chain reaction as well as LCAT activity assay. The results reveal that 1) the mutation of the branchpoint adenosine to any other nucleotide completely abolishes splicing; 2) the insertion of a normal branch site into the intronic sequence of the natural (IVS4-22c) or the branchpoint (IVS4-20t) mutant completely restores splicing; 3) the natural mutation can be partially rescued by making a single nucleotide change (G --> A) within the branchpoint consensus sequence; and 4) other single base changes, particularly around the branchpoint adenosine residue, significantly decrease the efficiency of splicing and thus enzyme activity. Surprisingly, the nucleotide transversion at the last position of the branchpoint sequence (i.e. IVS4-25a or -25g) results in a 2.7-fold increase in splicing efficiency. Therefore, these observations clearly establish the functional significance of the branchpoint sequence of intron 4 for the splicing of the human LCAT mRNA precursors.
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Affiliation(s)
- M Li
- Atherosclerosis Specialty Laboratory, Department of Pathology, St. Paul's Hospital and University of British Columbia, Vancouver, British Columbia, V6Z 1Y6 Canada
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11
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Lund M, Tange TO, Dyhr-Mikkelsen H, Hansen J, Kjems J. Characterization of human RNA splice signals by iterative functional selection of splice sites. RNA (NEW YORK, N.Y.) 2000; 6:528-44. [PMID: 10786844 PMCID: PMC1369934 DOI: 10.1017/s1355838200992033] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
An iterative in vitro splicing strategy was employed to select for optimal 3' splicing signals from a pool of pre-mRNAs containing randomized regions. Selection of functional branchpoint sequences in HeLa cell nuclear extract yielded a sequence motif that evolved from UAA after one round of splicing toward a UACUAAC consensus after seven rounds. A significant part of the selected sequences contained a conserved AAUAAAG motif that proved to be functional both as a polyadenylation signal and a branch site in a competitive manner. Characterization of the branchpoint in these clones to either the upstream or downstream adenosines of the AAUAAAG sequence revealed that the branching process proceeded efficiently but quite promiscuously. Surprisingly, the conserved guanosine, adjacent to the common AAUAAA polyadenylation motif, was found to be required only for polyadenylation. In an independent experiment, sequences surrounding an optimal branchpoint sequence were selected from two randomized 20-nt regions. The clones selected after six rounds of splicing revealed an extended polypyrimidine tract with a high frequency of UCCU motifs and a highly conserved YAG sequence in the extreme 3' end of the randomized insert. Mutating the 3' terminal guanosine of the intron strongly affects complex A formation, implying that the invariant AG is recognized early in spliceosome assembly.
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Affiliation(s)
- M Lund
- Department of Molecular and Structural Biology, University of Aarhus, Denmark
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12
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Massenet S, Branlant C. A limited number of pseudouridine residues in the human atac spliceosomal UsnRNAs as compared to human major spliceosomal UsnRNAs. RNA (NEW YORK, N.Y.) 1999; 5:1495-503. [PMID: 10580478 PMCID: PMC1369871 DOI: 10.1017/s1355838299991537] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Two forms of spliceosomes were found in higher eukaryotes. The major form contains the U1, U2, U4, U5, and U6 snRNAs; the minor form contains the U11, U12, U4atac, U5, and U6atac snRNAs. Assembly and function of the major form are based on a complex dynamic of UsnRNA-UsnRNA and UsnRNA-pre-mRNA interactions, and the involved UsnRNA segments are highly posttranscriptionally modified in plants and vertebrates. To further characterize the minor form of spliceosomes, we looked for the psi residues in HeLa cells' U11, U12, U4atac, and U6atac snRNAs, using chemical approaches. Four psi residues were detected in total for these four atac UsnRNAs, compared to 20 in their counterparts of the major spliceosomes. The two psi residues detected in U12 are also found in U2 snRNA. One of them belongs to the branch-site-recognition sequence. It forms one of the base pairs that bulge out the A residue, responsible for the nucleophilic attack. Conservation of this strategic psi residue probably reflects a functional role. Another psi residue was detected in a U4atac snRNA segment involved in formation of helix II with U6atac. The fourth one was detected in the additional stem-loop structure present at the 3' end of U6atac snRNA. Differences in psi content of the atac and major UsnRNAs of human cells may participate in the differentiation of the two splicing systems. Based on secondary structure similarity, U2 and U12 snRNAs on the one hand and U4 and U4atac snRNAs on the other hand may share common psi synthases.
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Affiliation(s)
- S Massenet
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 CNRS-UHP Nancy I, Faculté des Sciences, Vandoeuvre-les-Nancy, France
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13
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Fortes P, Bilbao-Cortés D, Fornerod M, Rigaut G, Raymond W, Séraphin B, Mattaj IW. Luc7p, a novel yeast U1 snRNP protein with a role in 5' splice site recognition. Genes Dev 1999; 13:2425-38. [PMID: 10500099 PMCID: PMC317023 DOI: 10.1101/gad.13.18.2425] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The characterization of a novel yeast-splicing factor, Luc7p, is presented. The LUC7 gene was identified by a mutation that causes lethality in a yeast strain lacking the nuclear cap-binding complex (CBC). Luc7p is similar in sequence to metazoan proteins that have arginine-serine and arginine-glutamic acid repeat sequences characteristic of a family of splicing factors. We show that Luc7p is a component of yeast U1 snRNP and is essential for vegetative growth. The composition of yeast U1 snRNP is altered in luc7 mutant strains. Extracts of these strains are unable to support any of the defined steps of splicing unless recombinant Luc7p is added. Although the in vivo defect in splicing wild-type reporter introns in a luc7 mutant strain is comparatively mild, splicing of introns with nonconsensus 5' splice site or branchpoint sequences is more defective in the mutant strain than in wild-type strains. By use of reporters that have two competing 5' splice sites, a loss of efficient splicing to the cap proximal splice site is observed in luc7 cells, analogous to the defect seen in strains lacking CBC. CBC can be coprecipitated with U1 snRNP from wild-type, but not from luc7, yeast strains. These data suggest that the loss of Luc7p disrupts U1 snRNP-CBC interaction, and that this interaction contributes to normal 5' splice site recognition.
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Affiliation(s)
- P Fortes
- European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
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14
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Luukkonen BG, Séraphin B. A conditional U5 snRNA mutation affecting pre-mRNA splicing and nuclear pre-mRNA retention identifies SSD1/SRK1 as a general splicing mutant suppressor. Nucleic Acids Res 1999; 27:3455-65. [PMID: 10446233 PMCID: PMC148587 DOI: 10.1093/nar/27.17.3455] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A combination of point mutations disrupting both stem 1 and stem 2 of U5 snRNA (U5AI) was found to confer a thermosensitive phenotype in vivo. In a strain expressing U5AI, pre-mRNA splicing was blocked before the first step through an inability of the mutant U5 snRNA to efficiently associate with the U4/U6 di-snRNP. Formation of early splicing complexes was not affected in extracts prepared from U5 snRNA mutant cells, while the capacity of these extracts to splice a pre-mRNA in vitro was greatly diminished. In addition, significant levels of a translation product derived from intron containing pre-mRNAs could be detected in vivo. The SSD1/SRK1 gene was identified as a multi-copy suppressor of the U5AI snRNA mutant. Single copy expression of SSD1/SRK1 was sufficient to suppress the thermosensitive phenotype, and high copy expression partially suppressed the splicing and U4/U6.U5 tri-snRNP assembly pheno-types. SSD1/SRK1 also suppressed thermosensitive mutations in the Prp18p and U1-70K proteins, while inhibiting growth of the cold sensitive U1-4U snRNA mutant at 30 degrees C. Thus we have identified SSD1/SRK1 as a general suppressor of splicing mutants.
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Affiliation(s)
- B G Luukkonen
- European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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15
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Rutz B, Séraphin B. Transient interaction of BBP/ScSF1 and Mud2 with the splicing machinery affects the kinetics of spliceosome assembly. RNA (NEW YORK, N.Y.) 1999; 5:819-31. [PMID: 10376880 PMCID: PMC1369807 DOI: 10.1017/s1355838299982286] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Removal of introns from pre-mRNA is an essential step of gene expression. The splicing reaction is catalyzed in a large complex termed the spliceosome. Introns are recognized during the early steps of spliceosome assembly with the formation of commitment complexes. Intron recognition is mediated by the interaction of splicing factors with conserved sequences present in the pre-mRNA. BBP/SF1 participates in this recognition by interacting with the pre-mRNA branch point in both yeast and mammals. This protein, which is essential in yeast, also interacts with the U2AF65/Mud2 splicing factor. However, its precise role in splicing complex formation is still unclear. We have now analyzed the presence of BBP and Mud2 in yeast splicing complexes using supershift and coprecipitation assays. We found that BBP is present together with Mud2 in commitment complex 2 (CC2), but is not detectable in commitment complex 1 (CC1). Furthermore, genetic and biochemical depletion of BBP demonstrated that it is required for CC2 formation. In addition we observed that BBP and Mud2 are not detectable in pre-spliceosomes. These are the first commitment complex components that are shown to be released during or immediately after pre-spliceosome formation. Interestingly, depletion of BBP or disruption of MUD2 had no significant effect on pre-spliceosome formation and splicing in vitro but led to a transient accumulation of CC1. These observations support a model in which BBP and Mud2 are recycled during transition from CC2 to pre-spliceosome.
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Affiliation(s)
- B Rutz
- European Molecular Biology Laboratory, Heidelberg, Germany
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16
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Massenet S, Motorin Y, Lafontaine DL, Hurt EC, Grosjean H, Branlant C. Pseudouridine mapping in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (snRNAs) reveals that pseudouridine synthase pus1p exhibits a dual substrate specificity for U2 snRNA and tRNA. Mol Cell Biol 1999; 19:2142-54. [PMID: 10022901 PMCID: PMC84007 DOI: 10.1128/mcb.19.3.2142] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Pseudouridine (Psi) residues were localized in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (UsnRNAs) by using the chemical mapping method. In contrast to vertebrate UsnRNAs, S. cerevisiae UsnRNAs contain only a few Psi residues, which are located in segments involved in intermolecular RNA-RNA or RNA-protein interactions. At these positions, UsnRNAs are universally modified. When yeast mutants disrupted for one of the several pseudouridine synthase genes (PUS1, PUS2, PUS3, and PUS4) or depleted in rRNA-pseudouridine synthase Cbf5p were tested for UsnRNA Psi content, only the loss of the Pus1p activity was found to affect Psi formation in spliceosomal UsnRNAs. Indeed, Psi44 formation in U2 snRNA was abolished. By using purified Pus1p enzyme and in vitro-produced U2 snRNA, Pus1p is shown here to catalyze Psi44 formation in the S. cerevisiae U2 snRNA. Thus, Pus1p is the first UsnRNA pseudouridine synthase characterized so far which exhibits a dual substrate specificity, acting on both tRNAs and U2 snRNA. As depletion of rRNA-pseudouridine synthase Cbf5p had no effect on UsnRNA Psi content, formation of Psi residues in S. cerevisiae UsnRNAs is not dependent on the Cbf5p-snoRNA guided mechanism.
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Affiliation(s)
- S Massenet
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR7567 CNRS-UHP, Faculté des Sciences, 54506 Vandoeuvre-les-Nancy Cédex, France
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17
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Puig O, Gottschalk A, Fabrizio P, Séraphin B. Interaction of the U1 snRNP with nonconserved intronic sequences affects 5' splice site selection. Genes Dev 1999; 13:569-80. [PMID: 10072385 PMCID: PMC316504 DOI: 10.1101/gad.13.5.569] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Intron definition and splice site selection occur at an early stage during assembly of the spliceosome, the complex mediating pre-mRNA splicing. Association of U1 snRNP with the pre-mRNA is required for these early steps. We report here that the yeast U1 snRNP-specific protein Nam8p is a component of the commitment complexes, the first stable complexes assembled on pre-mRNA. In vitro and in vivo, Nam8p becomes indispensable for efficient 5' splice site recognition when this process is impaired as a result of the presence of noncanonical 5' splice sites or the absence of a cap structure. Nam8p stabilizes commitment complexes in the latter conditions. Consistent with this, Nam8p interacts with the pre-mRNA downstream of the 5' splice site, in a region of nonconserved sequence. Substitutions in this region affect splicing efficiency and alternative splice site choice in a Nam8p-dependent manner. Therefore, Nam8p is involved in a novel mechanism by which a snRNP component can affect splice site choice and regulate intron removal through its interaction with a nonconserved sequence. This supports a model where early 5' splice recognition results from a network of interactions established by the splicing machinery with various regions of the pre-mRNA.
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Affiliation(s)
- O Puig
- Gene Expression Program, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
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18
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Luukkonen BG, Séraphin B. A role for U2/U6 helix Ib in 5' splice site selection. RNA (NEW YORK, N.Y.) 1998; 4:915-27. [PMID: 9701283 PMCID: PMC1369669 DOI: 10.1017/s1355838298980591] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Selection of pre-mRNA splice sites is a highly accurate process involving many trans-acting factors. Recently, we described a role for U6 snRNA position G52 in selection of the first intron nucleotide (+1G). Because some U2 alleles suppress U6-G52 mutations, we investigated whether the corresponding U2 snRNA region also influenced 5' splice site selection. Our results demonstrate that U2 snRNAs mutated at position U23, but not adjacent nucleotides, specifically affect 5' splice site cleavage. Furthermore, all U2 position U23 mutations are synthetic lethal with the thermosensitive U6-G52U allele. Interestingly, the U2-U23C substitution has an unprecedented hyperaccurate splicing phenotype in which cleavage of introns with a +1G substitution is reduced, whereas the strain grows with wild-type kinetics. U2 position U23 forms the first base pair with U6 position A59 in U2/U6 helix Ib. Restoration of the helical structure suppresses 5' splice site cleavage defects, showing an important role for the helix Ib structure in 5' splice site selection. U2/U6 helix Ib and helix II have recently been described as being functionally redundant. This report demonstrates a unique role for helix Ib in 5' splice site selection that is not shared with helix II.
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Affiliation(s)
- B G Luukkonen
- European Molecular Biology Laboratory, Heidelberg, Germany
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Meyer V, Oliver B, Pauli D. Multiple developmental requirements of noisette, the Drosophila homolog of the U2 snRNP-associated polypeptide SP3a60. Mol Cell Biol 1998; 18:1835-43. [PMID: 9528755 PMCID: PMC121413 DOI: 10.1128/mcb.18.4.1835] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/1997] [Accepted: 01/20/1998] [Indexed: 02/07/2023] Open
Abstract
We report the cloning of the noisette gene (noi), which encodes the Drosophila melanogaster ortholog of a U2 snRNP-associated splicing factor, SF3a60 (SAP61) in humans and PRP9p in Saccharomyces cerevisiae. Antibodies raised against human SF3a60 recognized NOI in flies, showing a nuclear localization in all the stages examined, including the embryo, the dividing cells of imaginal discs, and the larval polyploid nuclei. NOI is expressed in somatic and germinal cells of both male and female gonads. By mobilization of P transposons, we have generated a large number of noi mutations. Complete loss of function resulted in lethality at the end of embryogenesis, without obvious morphological defects. Hypomorphic alleles revealed multiple roles of noi for the survival and differentiation of male germ cells, the differentiation of female germ cells, and the development of several adult structures.
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Affiliation(s)
- V Meyer
- Department of Zoology and Animal Biology, University of Geneva, Switzerland
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20
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Luukkonen BG, Séraphin B. Genetic interaction between U6 snRNA and the first intron nucleotide in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 1998; 4:167-180. [PMID: 9570316 PMCID: PMC1369605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Nuclear pre-mRNA splicing necessitates specific recognition of the pre-mRNA splice sites. It is known that 5' splice site selection requires base pairing of U6 snRNA with intron positions 4-6. However, no factor recognizing the highly conserved 5' splice site GU has yet been identified. We have tested if the known U6 snRNA-pre-mRNA interaction could be extended to include the first intron nucleotides and the conserved 50GAG52 sequence of U6 snRNA. We observe that some combinations of 5' splice site and U6 snRNA mutations produce a specific synthetic block to the first splicing step. In addition, the U6-G52U allele can switch between two competing 5' splice sites harboring different nucleotides following the cleavage site. These results indicate that U6 snRNA position 52 interacts with the first nucleotide of the intron before 5' splice site cleavage. Some combinations of U6 snRNA and pre-mRNA mutations also blocked the second splicing step, suggesting a role for the corresponding nucleotides in a proofreading step before exon ligation. From studies in diverse organisms, various functions have been ascribed to the conserved U6 snRNA 47ACAGAG52 sequence. Our results suggest that these discrepancies might reflect variations between different experimental systems and point to an important conserved role of this sequence in the splicing reaction.
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Affiliation(s)
- B G Luukkonen
- European Molecular Biology Laboratory, Heidelberg, Germany
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Luukkonen BG, Séraphin B. Construction of an in vivo-regulated U6 snRNA transcription unit as a tool to study U6 function. RNA (NEW YORK, N.Y.) 1998; 4:231-238. [PMID: 9570323 PMCID: PMC1369612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
U6 snRNA is the only spliceosomal snRNA transcribed by RNA polymerase III in yeast. We have constructed a regulated U6 snRNA transcription unit by introducing the binding site for the Escherichia coli lacI repressor protein in the U6 snRNA promoter. GAL-induced expression of lacI protein led to a decrease in U6 snRNA levels and blocked cell growth. lacI dissociation from the promoter, and consequent U6 snRNA transcription, could be induced by addition of IPTG and repression of lacI transcription. To test the usefulness of this system in studying spliceosomal U6 snRNA function, we conditionally expressed U6 snRNAs with a single base substitution in position A51. We demonstrate that expression of the U6-A51 mutations confers a strong dominant negative phenotype as shown by severe reductions in growth rate. In these strains, splicing of endogenous pre-mRNAs was blocked before the second step.
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Affiliation(s)
- B G Luukkonen
- European Molecular Biology Laboratory, Heidelberg, Germany
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