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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Niall P. Keegan,
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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2
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Broeders M, Smits K, Goynuk B, Oussoren E, van den Hout HJMP, Bergsma AJ, van der Ploeg AT, Pijnappel WWMP. A Generic Assay to Detect Aberrant ARSB Splicing and mRNA Degradation for the Molecular Diagnosis of MPS VI. Mol Ther Methods Clin Dev 2020; 19:174-185. [PMID: 33209960 PMCID: PMC7648089 DOI: 10.1016/j.omtm.2020.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/11/2020] [Indexed: 12/16/2022]
Abstract
Identification and characterization of disease-associated variants in monogenic disorders is an important aspect of diagnosis, genetic counseling, prediction of disease severity, and development of therapy. However, the effects of disease-associated variants on pre-mRNA splicing and mRNA degradation are difficult to predict and often missed. Here we present a generic assay for unbiased identification and quantification of arylsulfatase B (ARSB) mRNA for molecular diagnosis of patients with mucopolysaccharidosis VI (MPS VI). We found that healthy control individuals have inefficient ARSB splicing because of natural skipping of exon 5 and inclusion of two pseudoexons in introns 5 and 6. Analyses of 12 MPS VI patients with 10 different genotypes resulted in identification of a 151-bp intron inclusion caused by the c.1142+2T>C variant and detection of low ARSB expression from alleles with the c.629A>G variant. A special case showed skipping of exon 4 and low ARSB expression. Although no disease-associated DNA variant could be identified in this patient, the molecular diagnosis could be made based on RNA. These results highlight the relevance of RNA-based analyses to establish a molecular diagnosis of MPS VI. We speculate that inefficient natural splicing of ARSB may be a target for therapy based on promotion of canonical splicing.
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Affiliation(s)
- Mike Broeders
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Kasper Smits
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Busra Goynuk
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Esmee Oussoren
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Hannerieke J M P van den Hout
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Atze J Bergsma
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Ans T van der Ploeg
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - W W M Pim Pijnappel
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, 3015 GE Rotterdam, the Netherlands
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3
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Patsali P, Mussolino C, Ladas P, Floga A, Kolnagou A, Christou S, Sitarou M, Antoniou MN, Cathomen T, Lederer CW, Kleanthous M. The Scope for Thalassemia Gene Therapy by Disruption of Aberrant Regulatory Elements. J Clin Med 2019; 8:jcm8111959. [PMID: 31766235 PMCID: PMC6912506 DOI: 10.3390/jcm8111959] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/22/2019] [Accepted: 11/04/2019] [Indexed: 12/17/2022] Open
Abstract
The common IVSI-110 (G>A) β-thalassemia mutation is a paradigm for intronic disease-causing mutations and their functional repair by non-homologous end joining-mediated disruption. Such mutation-specific repair by disruption of aberrant regulatory elements (DARE) is highly efficient, but to date, no systematic analysis has been performed to evaluate disease-causing mutations as therapeutic targets. Here, DARE was performed in highly characterized erythroid IVSI-110(G>A) transgenic cells and the disruption events were compared with published observations in primary CD34+ cells. DARE achieved the functional correction of β-globin expression equally through the removal of causative mutations and through the removal of context sequences, with disruption events and the restriction of indel events close to the cut site closely resembling those seen in primary cells. Correlation of DNA-, RNA-, and protein-level findings then allowed the extrapolation of findings to other mutations by in silico analyses for potential repair based on the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9, Cas12a, and transcription activator-like effector nuclease (TALEN) platforms. The high efficiency of DARE and unexpected freedom of target design render the approach potentially suitable for 14 known thalassemia mutations besides IVSI-110(G>A) and put it forward for several prominent mutations causing other inherited diseases. The application of DARE, therefore, has a wide scope for sustainable personalized advanced therapy medicinal product development for thalassemia and beyond.
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Affiliation(s)
- Petros Patsali
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus; (P.P.); (A.F.); (M.K.)
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center–University of Freiburg, 79106 Freiburg, Germany; (C.M.); (T.C.)
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Petros Ladas
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus; (P.P.); (A.F.); (M.K.)
- Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus
| | - Argyro Floga
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus; (P.P.); (A.F.); (M.K.)
- Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus
| | - Annita Kolnagou
- Thalassemia Clinic Paphos, Paphos General Hospital, 8100 Paphos, Cyprus;
| | - Soteroula Christou
- Thalassemia Clinic Nicosia, Archbishop Makarios III Hospital, 1474 Nicosia, Cyprus;
| | - Maria Sitarou
- Thalassemia Clinic Larnaca, Larnaca General Hospital, 6301 Larnaca, Cyprus;
| | - Michael N. Antoniou
- Department of Medical and Molecular Genetics, King’s College London, London SE1 9RT, UK;
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center–University of Freiburg, 79106 Freiburg, Germany; (C.M.); (T.C.)
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Carsten Werner Lederer
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus; (P.P.); (A.F.); (M.K.)
- Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus
- Correspondence: ; Tel.: +357-22-392-764
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus; (P.P.); (A.F.); (M.K.)
- Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus
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4
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Agouti I, Bennani M, Ahmed A, Barakat A, Mohamed K, Badens C. Thalassemia intermedia due to a novel mutation in the second intervening sequence of the beta-globin gene. Hemoglobin 2008; 31:433-8. [PMID: 17994377 DOI: 10.1080/03630260701613210] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We describe a new beta-thalassemia (thal) mutation in the beta-globin gene of an 8-year-old Moroccan boy. This homozygous mutation produces a phenotype of thalassemia intermedia and is associated with the Mediterranean haplotype IX. We discuss the pathophysiological consequences of this mutation which is located near the 3' end of the second intervening sequence (IVS-II) of the beta-globin gene.
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Affiliation(s)
- Imane Agouti
- Laboratoire de Biologie Appliquée, Faculté des Sciences et Techniques, Tanger, Maroc
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5
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Xie SY, Ren ZR, Zhang JZ, Guo XB, Wang QX, Wang S, Lin D, Gong XL, Li W, Huang SZ, Zeng F, Zeng YT. Restoration of the balanced alpha/beta-globin gene expression in beta654-thalassemia mice using combined RNAi and antisense RNA approach. Hum Mol Genet 2007; 16:2616-25. [PMID: 17716993 DOI: 10.1093/hmg/ddm218] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The beta-thalassemia is associated with abnormality in beta-globin gene, leading to imbalanced synthesis of alpha-/beta-globin chains. Consequently, the excessive free alpha-globin chains precipitate to the erythrocyte membrane, resulting in hemolytic anemia. We have explored post-transcriptional strategies aiming at alpha-globin reduction and beta-globin enrichment on beta(654) (Hbb(th-4)/Hbb(+)) mouse, carrying a human splicing-deficient beta-globin allele (Hbb(th-4)). Lentiviral vectors of short hairpin RNA (shRNA) targeting alpha-globin and/or antisense RNA facilitating beta-globin correct splicing were microinjected into beta(654) single-cell embryos. Three transgenic strains were generated, as alpha(i)-Hbb(th-4)/Hbb(+)(shRNA), beta(a)-Hbb(th-4)/Hbb(+)(antisense) and alpha(i)beta(a)-Hbb(th-4)/Hbb(+)(both shRNA and antisense). Without notable abnormalities, all the founders and their offsprings showed sustained amelioration of hematologic parameters, ineffective erythropoiesis and extramedullary hematopoiesis. Augmented effects appeared in alpha(i)beta(a)-Hbb(th-4)/Hbb(+), which correlated with a better-balanced alpha-/beta-globin mRNA level. Among the transgenic mice integrated with shRNA and antisense RNA, one homozygous mouse (Hbb(th-4)/Hbb(th-4)) had been viable, and the 3-week survival rate for heterozygotes (Hbb(th-4)/Hbb(+)) was 97%, compared with 45.4% for untreated. Our data have demonstrated the feasibility of techniques for beta-thalassemia therapy by balancing the synthesis of alpha-/beta-globin chains.
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Affiliation(s)
- Shu-Yang Xie
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
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6
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Vacek MM, Ma H, Gemignani F, Lacerra G, Kafri T, Kole R. High-level expression of hemoglobin A in human thalassemic erythroid progenitor cells following lentiviral vector delivery of an antisense snRNA. Blood 2003; 101:104-11. [PMID: 12393543 DOI: 10.1182/blood-2002-06-1869] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutations at nucleotides 654, 705, or 745 in intron 2 of the human beta-globin gene activate aberrant 3' and 5' splice sites within the intron and prevent correct splicing of beta-globin pre-mRNA, resulting in inhibition of beta-globin synthesis and in consequence beta-thalassemia. Transfection of HeLa cells expressing the 3 thalassemic mutants with modified U7 snRNA (U7.623), containing a sequence antisense to a region between the aberrant splice sites, reduced the incorrect splicing of pre-mRNA and led to increased levels of the correctly spliced beta-globin mRNA and protein. A lentiviral vector carrying the U7.623 gene was effective in restoration of correct splicing in the model cell lines for at least 6 months. Importantly, the therapeutic value of this system was demonstrated in hematopoietic stem cells and erythroid progenitor cells from a patient with IVS2-745/IVS2-1 thalassemia. Twelve days after transduction of the patient cells with the U7.623 lentiviral vector, the levels of correctly spliced beta-globin mRNA and hemoglobin A were approximately 25-fold over background. These results should be regarded as a proof of principle for lentiviral vector-based gene therapy for beta-thalassemia.
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Affiliation(s)
- Marla M Vacek
- Curriculum in Genetics and Molecular Biology, University of North Carolina Gene Therapy Center, Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 27599, USA
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7
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Suwanmanee T, Sierakowska H, Lacerra G, Svasti S, Kirby S, Walsh CE, Fucharoen S, Kole R. Restoration of human beta-globin gene expression in murine and human IVS2-654 thalassemic erythroid cells by free uptake of antisense oligonucleotides. Mol Pharmacol 2002; 62:545-53. [PMID: 12181431 DOI: 10.1124/mol.62.3.545] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Correct human beta-globin mRNA has been restored in erythroid cells from transgenic mice carrying the human gene with beta-globin IVS2-654 splice mutation and from thalassemia patients with the IVS2-654/beta(E) genotype. This was accomplished in a dose- and time-dependent manner by free uptake of morpholino oligonucleotide antisense to the aberrant splice site at position 652 of intron 2 in beta-globin pre-mRNA. Under optimal conditions of oligonucleotide uptake, the maximal levels of correct human beta-globin mRNA and hemoglobin A in patients' erythroid cells were 77 and 54%, respectively. These levels of correction were equal to, if not higher than, those obtained by syringe loading of the oligonucleotide into the cells. Comparison of splicing correction results with the cellular uptake of fluorescein-labeled oligonucleotide indicated that the levels of mRNA and hemoglobin A correlate well with the nuclear localization of the oligonucleotide and the degree of erythroid differentiation of cultured cells. Similar but not as pronounced results were obtained after the oligonucleotide treatment of bone marrow cells from IVS2-654 mouse. The effectiveness of the free antisense morpholino oligonucleotide in restoration of correct splicing of IVS2-654 pre-mRNA in cultured erythropoietic cells from transgenic mice and thalassemic patients suggests the applicability of this or similar compounds in in vivo experiments and possibly in treatment of thalassemia.
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Affiliation(s)
- Thipparat Suwanmanee
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7295, USA
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8
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Lacerra G, Sierakowska H, Carestia C, Fucharoen S, Summerton J, Weller D, Kole R. Restoration of hemoglobin A synthesis in erythroid cells from peripheral blood of thalassemic patients. Proc Natl Acad Sci U S A 2000; 97:9591-6. [PMID: 10944225 PMCID: PMC16909 DOI: 10.1073/pnas.97.17.9591] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mononuclear cells from peripheral blood of thalassemic patients were treated with morpholino oligonucleotides antisense to aberrant splice sites in mutant beta-globin precursor mRNAs (pre-mRNAs). The oligonucleotides restored correct splicing and translation of beta-globin mRNA, increasing the hemoglobin (Hb) A synthesis in erythroid cells from patients with IVS2-654/beta(E), IVS2-745/IVS2-745, and IVS2-745/IVS2-1 genotypes. The maximal Hb A level for repaired IVS2-745 mutation was approximately 30% of normal; Hb A was still detectable 9 days after a single treatment with oligonucleotide. Thus, expression of defective beta-globin genes was repaired and significant level of Hb A was restored in a cell population that would be targeted in clinical applications of this approach.
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Affiliation(s)
- G Lacerra
- Lineberger Comprehensive Cancer Center and Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599-7295, USA
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9
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Schmajuk G, Sierakowska H, Kole R. Antisense oligonucleotides with different backbones. Modification of splicing pathways and efficacy of uptake. J Biol Chem 1999; 274:21783-9. [PMID: 10419493 DOI: 10.1074/jbc.274.31.21783] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A novel, positive read-out assay that quantifies only sequence-specific nuclear activity of antisense oligonucleotides was used to evaluate morpholino and 2'-O-methyl sugar-phosphate oligonucleotides. The assay is based on modification of the splicing pathway of human beta-globin pre-mRNA. In addition, scrape-loading of cells with oligonucleotides allows the separate assessment of intracellular antisense activity of the oligonucleotides and their ability to penetrate the cell membrane barrier. The results show that, with scrape-loading, the morpholino oligonucleotides were approximately 3-fold more effective in their intrinsic antisense activity than alternating phosphodiester/phosphorothioate 2'-O-methyl-oligoribonucleotides and 6-9- and almost 200-fold more effective than the exclusively phosphorothioate and phosphodiester derivatives, respectively. The morpholino oligonucleotides were over 20-fold more effective than the phosphorothioate 2'-O-methyl-oligoribonucleotides in free uptake from the culture media. The antisense activity of the morpholino oligonucleotides was detectable not only in monolayer HeLa cells but also in suspension K562 cells. Time course experiments suggest that both the free uptake and efflux of morpholino oligonucleotides are slow.
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Affiliation(s)
- G Schmajuk
- Lineberger Comprehensive Cancer Center and Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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10
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Sierakowska H, Montague M, Agrawal S, Kole R. Restoration of ß-Globin Gene Expression in Mammalian Cells by Antisense Oligonucleotides That Modify the Aberrant Splicing Patierns of Thalassemic Pre-mRNAs. ACTA ACUST UNITED AC 1997. [DOI: 10.1080/07328319708006154] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Sierakowska H, Sambade MJ, Agrawal S, Kole R. Repair of thalassemic human beta-globin mRNA in mammalian cells by antisense oligonucleotides. Proc Natl Acad Sci U S A 1996; 93:12840-4. [PMID: 8917506 PMCID: PMC24007 DOI: 10.1073/pnas.93.23.12840] [Citation(s) in RCA: 181] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In one form of beta-thalassemia, a genetic blood disorder, a mutation in intron 2 of the beta-globin gene (IVS2-654) causes aberrant splicing of beta-globin pre-mRNA and, consequently, beta-globin deficiency. Treatment of mammalian cells stably expressing the IVS2-654 human beta-globin gene with antisense oligonucleotides targeted at the aberrant splice sites restored correct splicing in a dose-dependent fashion, generating correct human beta-globin mRNA and polypeptide. Both products persisted for up to 72 hr posttreatment. The oligonucleotides modified splicing by a true antisense mechanism without overt unspecific effects on cell growth and splicing of other pre-mRNAs. This novel approach in which antisense oligonucleotides are used to restore rather than to down-regulate the activity of the target gene is applicable to other splicing mutants and is of potential clinical interest.
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Affiliation(s)
- H Sierakowska
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill 27599, USA
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12
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13
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Youssoufian H, Kazazian HH, Patel A, Aronis S, Tsiftis G, Hoyer LW, Antonarakis SE. Mild hemophilia A associated with a cryptic donor splice site mutation in intron 4 of the factor VIII gene. Genomics 1988; 2:32-6. [PMID: 2838411 DOI: 10.1016/0888-7543(88)90106-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Hemophilia A, an X-linked disease caused by deficiency of factor VIII, is characterized by variation in clinical severity and coagulation activity. This variation is though to reflect heterogeneity of mutations in the factor VIII gene. Here we describe a CG-to-CA mutation within a potential cryptic donor splice site in intron 4 of the factor VIII gene from a patient with mild disease. This mutation makes the cryptic sequence resemble more closely the consensus sequence for donor splice sites. We infer that the mutation activates the cryptic donor splice site, which in turn causes a defect in RNA processing.
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Affiliation(s)
- H Youssoufian
- Department of Pediatrics, Johns Hopkins University of School of Medicine, Baltimore, Maryland 21205
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14
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Tatei K, Takemura K, Tanaka H, Masaki T, Ohshima Y. Recognition of 5' and 3' splice site sequences in pre-mRNA studied with a filter binding technique. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)60862-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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15
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Ohshima Y, Gotoh Y. Signals for the selection of a splice site in pre-mRNA. Computer analysis of splice junction sequences and like sequences. J Mol Biol 1987; 195:247-59. [PMID: 3656413 DOI: 10.1016/0022-2836(87)90647-4] [Citation(s) in RCA: 205] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
To evaluate the importance of the surrounding nucleotide sequence in the selection of a splice site for mRNA, we have carried out computer studies of eukaryotic protein genes whose entire nucleotide sequences were available. A splice site-like sequence that has a significant homology to the consensus splice junction sequences is frequently found within an intron and exon. It is found that the higher the homology of a candidate donor site sequence to the nine-nucleotide consensus sequence, the higher is its probability of being a donor site. For most of the donors, the stability of presumed base-pairing with U1-RNA is higher than that of donor-like sequences, if any, in the adjacent exon and intron. However, homology of a candidate acceptor sequence to the 15-nucleotide consensus is a poor criterion of an acceptor site. The presence of a sequence that could serve as a branch-point 18 to 37 nucleotides before an acceptor does not seem to be critical in distinguishing it from an acceptor-like sequence. For genes of human, rat, mouse and chicken, respectively, nucleotide frequencies around splice junctions of many genes have been calculated. They seem to be different at some positions around a donor site from species to species. The acceptors for these vertebrates have longer pyrimidine-rich regions than the previous consensus sequence. The newly derived nucleotide frequencies were used as the standard to calculate the weighted homology score of a candidate splice site sequence in a gene of the four species. This weighted homology score of the 40 to 60-nucleotide intron-exon sequence is a much better criterion of an acceptor. These results suggest that the most important signal in the selection of a splice resides in the surrounding nucleotide sequence. It is also suggested that the surrounding nucleotide sequence alone is not generally sufficient for the selection.
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Affiliation(s)
- Y Ohshima
- Institute of Biological Sciences, University of Tsukuba, Ibaraki-ken, Japan
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