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Liang Q, Zhang Z, Ding B, Shao Y, Ding Q, Dai J, Hu X, Wu W, Wang X. A noncanonical splicing variant c.875-5 T > G in von Willebrand factor causes in-frame exon skipping and type 2A von Willebrand disease. Thromb Res 2024; 236:51-60. [PMID: 38387303 DOI: 10.1016/j.thromres.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/16/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024]
Abstract
INTRODUCTION A novel variant involving noncanonical splicing acceptor site (c.875-5 T > G) in propeptide coding region of von Willebrand factor (VWF) was identified in a patient with type 2A von Willebrand disease (VWD), who co-inherited with a null variant (p.Tyr271*) and presented characteristic discrepancy of plasma level of VWF antigen and activity, and a selective reduction of both intermediate-molecular-weight (IMWMs) and high-molecular-weight VWF multimers (HMWMs). MATERIALS AND METHODS VWF mRNA transcripts obtained from peripheral leukocytes and platelets of the patients were investigated to analyze the consequence of c.875-5 T > G on splicing. The impact of the variant on expression and multimer assembly was further analyzed by in vitro expression studies in AtT-20 cells. The intracellular processing of VWF mutant and the Weibel-Palade bodies (WPBs) formation was evaluated by immunofluorescence staining and electron microscopy. RESULTS The mRNA transcript analysis revealed that c.875-5 T > G variant led to exon 8 skipping and an in-frame deletion of 41 amino acids in the D1 domain of VWF (p.Ser292_Glu333delinsLys), yielding a truncated propeptide. Consistent with the patient's laboratory manifestations, the AtT-20 cells transfected with mutant secreted less VWF, with the VWF antigen level in conditioned medium 47 % of wild-type. A slight retention in the endoplasmic reticulum was observed for the mutant. Almost complete loss of IMWMs and HMWMs in the medium and impaired WPBs formation in the cell, indicating truncated VWF propeptide lost its chaperon-like function for VWF multimerization and tubular storage. CONCLUSIONS The VWF splicing site variant (c.875-5 T > G) causes propeptide truncation, severely compromising VWF multimer assembly and tubular storage.
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Affiliation(s)
- Qian Liang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ziqi Zhang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Department of Molecular Biology, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Biying Ding
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yanyan Shao
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jing Dai
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaobo Hu
- Department of Molecular Biology, Shanghai Center for Clinical Laboratory, Shanghai, China.
| | - Wenman Wu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China.
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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Bakhtiar D, Vondraskova K, Pengelly RJ, Chivers M, Kralovicova J, Vorechovsky I. Exonic splicing code and coordination of divalent metals in proteins. Nucleic Acids Res 2024; 52:1090-1106. [PMID: 38055834 PMCID: PMC10853796 DOI: 10.1093/nar/gkad1161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
Exonic sequences contain both protein-coding and RNA splicing information but the interplay of the protein and splicing code is complex and poorly understood. Here, we have studied traditional and auxiliary splicing codes of human exons that encode residues coordinating two essential divalent metals at the opposite ends of the Irving-Williams series, a universal order of relative stabilities of metal-organic complexes. We show that exons encoding Zn2+-coordinating amino acids are supported much less by the auxiliary splicing motifs than exons coordinating Ca2+. The handicap of the former is compensated by stronger splice sites and uridine-richer polypyrimidine tracts, except for position -3 relative to 3' splice junctions. However, both Ca2+ and Zn2+ exons exhibit close-to-constitutive splicing in multiple tissues, consistent with their critical importance for metalloprotein function and a relatively small fraction of expendable, alternatively spliced exons. These results indicate that constraints imposed by metal coordination spheres on RNA splicing have been efficiently overcome by the plasticity of exon-intron architecture to ensure adequate metalloprotein expression.
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Affiliation(s)
- Dara Bakhtiar
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Katarina Vondraskova
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
| | - Reuben J Pengelly
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Martin Chivers
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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Zhang P, Chaldebas M, Ogishi M, Al Qureshah F, Ponsin K, Feng Y, Rinchai D, Milisavljevic B, Han JE, Moncada-Vélez M, Keles S, Schröder B, Stenson PD, Cooper DN, Cobat A, Boisson B, Zhang Q, Boisson-Dupuis S, Abel L, Casanova JL. Genome-wide detection of human intronic AG-gain variants located between splicing branchpoints and canonical splice acceptor sites. Proc Natl Acad Sci U S A 2023; 120:e2314225120. [PMID: 37931111 PMCID: PMC10655562 DOI: 10.1073/pnas.2314225120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 10/02/2023] [Indexed: 11/08/2023] Open
Abstract
Human genetic variants that introduce an AG into the intronic region between the branchpoint (BP) and the canonical splice acceptor site (ACC) of protein-coding genes can disrupt pre-mRNA splicing. Using our genome-wide BP database, we delineated the BP-ACC segments of all human introns and found extreme depletion of AG/YAG in the [BP+8, ACC-4] high-risk region. We developed AGAIN as a genome-wide computational approach to systematically and precisely pinpoint intronic AG-gain variants within the BP-ACC regions. AGAIN identified 350 AG-gain variants from the Human Gene Mutation Database, all of which alter splicing and cause disease. Among them, 74% created new acceptor sites, whereas 31% resulted in complete exon skipping. AGAIN also predicts the protein-level products resulting from these two consequences. We performed AGAIN on our exome/genomes database of patients with severe infectious diseases but without known genetic etiology and identified a private homozygous intronic AG-gain variant in the antimycobacterial gene SPPL2A in a patient with mycobacterial disease. AGAIN also predicts a retention of six intronic nucleotides that encode an in-frame stop codon, turning AG-gain into stop-gain. This allele was then confirmed experimentally to lead to loss of function by disrupting splicing. We further showed that AG-gain variants inside the high-risk region led to misspliced products, while those outside the region did not, by two case studies in genes STAT1 and IRF7. We finally evaluated AGAIN on our 14 paired exome-RNAseq samples and found that 82% of AG-gain variants in high-risk regions showed evidence of missplicing. AGAIN is publicly available from https://hgidsoft.rockefeller.edu/AGAIN and https://github.com/casanova-lab/AGAIN.
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Affiliation(s)
- Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Matthieu Chaldebas
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Fahd Al Qureshah
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Khoren Ponsin
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Yi Feng
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Baptiste Milisavljevic
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Ji Eun Han
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Marcela Moncada-Vélez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Sevgi Keles
- Division of Pediatric Allergy and Immunology, Necmettin Erbakan University, Meram Medical Faculty, Konya42080, Turkey
| | - Bernd Schröder
- Institute of Physiological Chemistry, Technische Universität Dresden, Dresden01307, Germany
| | - Peter D. Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, CardiffCF14 4XN, United Kingdom
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, CardiffCF14 4XN, United Kingdom
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris75015, France
- HHMI, New York, NY10065
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Alimohamed MZ, Boven LG, van Dijk KK, Vos YJ, Hoedemaekers YM, van der Zwaag PA, Sijmons RH, Jongbloed JD, Sikkema-Raddatz B, Westers H. SEPT–GD: A decision tree to prioritise potential RNA splice variants in cardiomyopathy genes for functional splicing assays in diagnostics. Gene 2023; 851:146984. [DOI: 10.1016/j.gene.2022.146984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 08/09/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022]
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Leman R, Parfait B, Vidaud D, Girodon E, Pacot L, Le Gac G, Ka C, Ferec C, Fichou Y, Quesnelle C, Aucouturier C, Muller E, Vaur D, Castera L, Boulouard F, Ricou A, Tubeuf H, Soukarieh O, Gaildrat P, Riant F, Guillaud‐Bataille M, Caputo SM, Caux‐Moncoutier V, Boutry‐Kryza N, Bonnet‐Dorion F, Schultz I, Rossing M, Quenez O, Goldenberg L, Harter V, Parsons MT, Spurdle AB, Frébourg T, Martins A, Houdayer C, Krieger S. SPiP: Splicing Prediction Pipeline, a machine learning tool for massive detection of exonic and intronic variant effects on mRNA splicing. Hum Mutat 2022; 43:2308-2323. [PMID: 36273432 PMCID: PMC10946553 DOI: 10.1002/humu.24491] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 10/06/2022] [Accepted: 10/18/2022] [Indexed: 01/25/2023]
Abstract
Modeling splicing is essential for tackling the challenge of variant interpretation as each nucleotide variation can be pathogenic by affecting pre-mRNA splicing via disruption/creation of splicing motifs such as 5'/3' splice sites, branch sites, or splicing regulatory elements. Unfortunately, most in silico tools focus on a specific type of splicing motif, which is why we developed the Splicing Prediction Pipeline (SPiP) to perform, in one single bioinformatic analysis based on a machine learning approach, a comprehensive assessment of the variant effect on different splicing motifs. We gathered a curated set of 4616 variants scattered all along the sequence of 227 genes, with their corresponding splicing studies. The Bayesian analysis provided us with the number of control variants, that is, variants without impact on splicing, to mimic the deluge of variants from high-throughput sequencing data. Results show that SPiP can deal with the diversity of splicing alterations, with 83.13% sensitivity and 99% specificity to detect spliceogenic variants. Overall performance as measured by area under the receiving operator curve was 0.986, better than SpliceAI and SQUIRLS (0.965 and 0.766) for the same data set. SPiP lends itself to a unique suite for comprehensive prediction of spliceogenicity in the genomic medicine era. SPiP is available at: https://sourceforge.net/projects/splicing-prediction-pipeline/.
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Affiliation(s)
- Raphaël Leman
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
- UNICAENNormandie UniversitéCaenFrance
| | - Béatrice Parfait
- Service de Génétique et Biologie Moléculaires, APHP, HUPCHôpital CochinParisFrance
| | - Dominique Vidaud
- Service de Génétique et Biologie Moléculaires, APHP, HUPCHôpital CochinParisFrance
| | - Emmanuelle Girodon
- Service de Génétique et Biologie Moléculaires, APHP, HUPCHôpital CochinParisFrance
| | - Laurence Pacot
- Service de Génétique et Biologie Moléculaires, APHP, HUPCHôpital CochinParisFrance
| | - Gérald Le Gac
- Inserm UMR1078, Genetics, Functional Genomics and BiotechnologyUniversité de Bretagne OccidentaleBrestFrance
| | - Chandran Ka
- Inserm UMR1078, Genetics, Functional Genomics and BiotechnologyUniversité de Bretagne OccidentaleBrestFrance
| | - Claude Ferec
- Inserm UMR1078, Genetics, Functional Genomics and BiotechnologyUniversité de Bretagne OccidentaleBrestFrance
| | - Yann Fichou
- Inserm UMR1078, Genetics, Functional Genomics and BiotechnologyUniversité de Bretagne OccidentaleBrestFrance
| | - Céline Quesnelle
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
| | - Camille Aucouturier
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Etienne Muller
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
| | - Dominique Vaur
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Laurent Castera
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Flavie Boulouard
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Agathe Ricou
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Hélène Tubeuf
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
- Integrative BiosoftwareRouenFrance
| | - Omar Soukarieh
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | | | - Florence Riant
- Laboratoire de Génétique, AP‐HPGH Saint‐Louis‐Lariboisière‐Fernand WidalParisFrance
| | | | - Sandrine M. Caputo
- Department of Genetics, Institut CurieParis Sciences Lettres Research UniversityParisFrance
| | | | - Nadia Boutry‐Kryza
- Unité Mixte de Génétique Constitutionnelle des Cancers FréquentsHospices Civils de LyonLyonFrance
| | - Françoise Bonnet‐Dorion
- Departement de Biopathologie Unité de Génétique ConstitutionnelleInstitut Bergonie—INSERM U1218BordeauxFrance
| | - Ines Schultz
- Laboratoire d'OncogénétiqueCentre Paul StraussStrasbourgFrance
| | - Maria Rossing
- Centre for Genomic Medicine, RigshospitaletUniversity of CopenhagenCopenhagenDenmark
| | - Olivier Quenez
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Louis Goldenberg
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Valentin Harter
- Department of BiostatisticsBaclesse Unicancer CenterCaenFrance
| | - Michael T. Parsons
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteHerstonQueenslandAustralia
| | - Amanda B. Spurdle
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteHerstonQueenslandAustralia
| | - Thierry Frébourg
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
- Department of geneticsRouen University HospitalRouenFrance
| | - Alexandra Martins
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Claude Houdayer
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
- Department of geneticsRouen University HospitalRouenFrance
| | - Sophie Krieger
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
- UNICAENNormandie UniversitéCaenFrance
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Bryen SJ, Yuen M, Joshi H, Dawes R, Zhang K, Lu JK, Jones KJ, Liang C, Wong WK, Peduto AJ, Waddell LB, Evesson FJ, Cooper ST. Prevalence, parameters, and pathogenic mechanisms for splice-altering acceptor variants that disrupt the AG exclusion zone. HGG ADVANCES 2022; 3:100125. [PMID: 35847480 PMCID: PMC9284458 DOI: 10.1016/j.xhgg.2022.100125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/19/2022] [Indexed: 10/26/2022] Open
Abstract
Predicting the pathogenicity of acceptor splice-site variants outside the essential AG is challenging, due to high sequence diversity of the extended splice-site region. Critical analysis of 24,445 intronic extended acceptor splice-site variants reported in ClinVar and the Leiden Open Variation Database (LOVD) demonstrates 41.9% of pathogenic variants create an AG dinucleotide between the predicted branchpoint and acceptor (AG-creating variants in the AG exclusion zone), 28.4% result in loss of a pyrimidine at the -3 position, and 15.1% result in loss of one or more pyrimidines in the polypyrimidine tract. Pathogenicity of AG-creating variants was highly influenced by their position. We define a high-risk zone for pathogenicity: > 6 nucleotides downstream of the predicted branchpoint and >5 nucleotides upstream from the acceptor, where 93.1% of pathogenic AG-creating variants arise and where naturally occurring AG dinucleotides are concordantly depleted (5.8% of natural AGs). SpliceAI effectively predicts pathogenicity of AG-creating variants, achieving 95% sensitivity and 69% specificity. We highlight clinical examples showing contrasting mechanisms for mis-splicing arising from AG variants: (1) cryptic acceptor created; (2) splicing silencer created: an introduced AG silences the acceptor, resulting in exon skipping, intron retention, and/or use of an alternative existing cryptic acceptor; and (3) splicing silencer disrupted: loss of a deep intronic AG activates inclusion of a pseudo-exon. In conclusion, we establish AG-creating variants as a common class of pathogenic extended acceptor variant and outline factors conferring critical risk for mis-splicing for AG-creating variants in the AG exclusion zone, between the branchpoint and acceptor.
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Affiliation(s)
- Samantha J. Bryen
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
- Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Michaela Yuen
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Himanshu Joshi
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Ruebena Dawes
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Katharine Zhang
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Jessica K. Lu
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Kristi J. Jones
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
- Department of Clinical Genetics, Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Christina Liang
- Department of Neurology, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
- Department of Neurogenetics, Northern Clinical School, Kolling Institute, University of Sydney, NSW 2065, Australia
| | - Wui-Kwan Wong
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Anthony J. Peduto
- Department of Radiology, Westmead Hospital, Western Clinical School, University of Sydney, Westmead, NSW 2145, Australia
| | - Leigh B. Waddell
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Frances J. Evesson
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Sandra T. Cooper
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
- Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
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7
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Harvey JP, Yu-Wai-Man P, Cheetham ME. Characterisation of a novel OPA1 splice variant resulting in cryptic splice site activation and mitochondrial dysfunction. Eur J Hum Genet 2022; 30:848-855. [PMID: 35534703 PMCID: PMC9259687 DOI: 10.1038/s41431-022-01102-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/01/2022] [Accepted: 04/12/2022] [Indexed: 12/13/2022] Open
Abstract
Autosomal dominant optic atrophy (DOA) is an inherited optic neuropathy that results in progressive, bilateral visual acuity loss and field defects. OPA1 is the causative gene in around 60% of cases of DOA. The majority of patients have a pure ocular phenotype, but 20% have extra-ocular features (DOA +). We report on a patient with DOA + manifesting as bilateral optic atrophy, spastic paraparesis, urinary incontinence and white matter changes in the central nervous system associated with a novel heterozygous splice variant NM_015560.2(OPA1):c.2356-1 G > T. Further characterisation, which was performed using fibroblasts obtained from a skin biopsy, demonstrated that this variant altered mRNA splicing of the OPA1 transcript, specifically a 21 base pair deletion at the start of exon 24, NM_015560.2(OPA1):p.Cys786_Lys792del. The majority of variant transcripts were shown to escape nonsense-mediated decay and modelling of the predicted protein structure suggests that the in-frame 7 amino acid deletion may affect OPA1 oligomerisation. Fibroblasts carrying the c.2356-1 G > T variant demonstrated impaired mitochondrial bioenergetics, membrane potential, increased cell death, and disrupted and fragmented mitochondrial networks in comparison to WT cells. This study suggests that the c.2356-1 G > T OPA1 splice site variant leads to a cryptic splice site activation and may manifest in a dominant-negative manner, which could account for the patient's severe syndromic phenotype.
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Affiliation(s)
- Joshua Paul Harvey
- UCL Institute of Ophthalmology, London, UK.
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.
| | - Patrick Yu-Wai-Man
- UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Cambridge Eye Unit, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK
- Department of Clinical Neurosciences, John van Geest Centre for Brain Repair and MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
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8
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Sette C, Paronetto MP. Somatic Mutations in Core Spliceosome Components Promote Tumorigenesis and Generate an Exploitable Vulnerability in Human Cancer. Cancers (Basel) 2022; 14:cancers14071827. [PMID: 35406598 PMCID: PMC8997811 DOI: 10.3390/cancers14071827] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary High throughput exome sequencing approaches have disclosed recurrent cancer-associated mutations in spliceosomal components, which drive aberrant pre-mRNA processing events and support the tumor phenotype. At the same time, mutations in spliceosome genes and aberrant splicing regulation establish a selective vulnerability of cancer cells to splicing-targeting approaches, which could be exploited therapeutically. It is conceivable that a better understanding of the mechanisms and roles of abnormal splicing in tumor metabolism will facilitate the development of a novel generation of tumor-targeting drugs. In this review, we describe recent advances in the elucidation of the biological impact and biochemical effects of somatic mutations in core spliceosome components on splicing choices and their associated targetable vulnerabilities. Abstract Alternative pre-mRNA processing enables the production of distinct mRNA and protein isoforms from a single gene, thus greatly expanding the coding potential of eukaryotic genomes and fine-tuning gene expression programs. Splicing is carried out by the spliceosome, a complex molecular machinery which assembles step-wise on mRNA precursors in the nucleus of eukaryotic cells. In the last decade, exome sequencing technologies have allowed the identification of point mutations in genes encoding splicing factors as a recurrent hallmark of human cancers, with higher incidence in hematological malignancies. These mutations lead to production of splicing factors that reduce the fidelity of the splicing process and yield splicing variants that are often advantageous for cancer cells. However, at the same time, these mutations increase the sensitivity of transformed cells to splicing inhibitors, thus offering a therapeutic opportunity for novel targeted strategies. Herein, we review the recent literature documenting cancer-associated mutations in components of the early spliceosome complex and discuss novel therapeutic strategies based on small-molecule spliceosome inhibitors that exhibit strong anti-tumor effects, particularly against cancer cells harboring mutations in spliceosomal components.
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Affiliation(s)
- Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy;
- GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, Piazza Lauro De Bosis, 6, 00135 Rome, Italy
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, IRCCS, Via del Fosso di Fiorano 64, 00143 Rome, Italy
- Correspondence:
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9
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Murphy MK, Moon JT, Skolaris AT, Mikulin JA, Wilson TJ. Evidence for the loss and recovery of SLAMF9 during human evolution: implications on Dollo's law. Immunogenetics 2021; 73:243-251. [PMID: 33616677 PMCID: PMC7898023 DOI: 10.1007/s00251-021-01208-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/05/2021] [Indexed: 11/04/2022]
Abstract
Signaling lymphocyte activation molecule family member 9 (SLAMF9) is a cell surface protein of the CD2/SLAM family of leukocyte surface receptors. It is conserved throughout mammals and has roles in the initiation of inflammatory responses and regulation of plasmacytoid dendritic cell function. Through comparison of reference sequences encoding SLAMF9 in human, mouse, and primate sequences, we have determined that the SLAMF9 gene underwent successive mutation events, resulting in the loss of the protein and subsequent recovery of a less stable version. The mutations included a single base pair deletion in the second exon and a change in the splice acceptor site of that same exon. These changes would have had the effect of creating and later repairing a frameshift in the coding sequence. These events took place since the divergence of the human lineage from the chimpanzee-human last common ancestor and represent the first known case of the functional loss and recovery of a gene within the human lineage.
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Affiliation(s)
- Maegan K Murphy
- Department of Microbiology, Miami University, 700 E. High Street, Oxford, OH, 45056, USA
| | - Justin T Moon
- Department of Microbiology, Miami University, 700 E. High Street, Oxford, OH, 45056, USA
| | - Alexis T Skolaris
- Department of Microbiology, Miami University, 700 E. High Street, Oxford, OH, 45056, USA
| | - Joseph A Mikulin
- Department of Microbiology, Miami University, 700 E. High Street, Oxford, OH, 45056, USA
| | - Timothy J Wilson
- Department of Microbiology, Miami University, 700 E. High Street, Oxford, OH, 45056, USA.
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10
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Jung H, Lee KS, Choi JK. Comprehensive characterisation of intronic mis-splicing mutations in human cancers. Oncogene 2021; 40:1347-1361. [PMID: 33420369 PMCID: PMC7892346 DOI: 10.1038/s41388-020-01614-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 11/23/2020] [Accepted: 12/10/2020] [Indexed: 12/21/2022]
Abstract
Previous studies studying mis-splicing mutations were based on exome data and thus our current knowledge is largely limited to exons and the canonical splice sites. To comprehensively characterise intronic mis-splicing mutations, we analysed 1134 pan-cancer whole genomes and transcriptomes together with 3022 normal control samples. The ratio-based splicing analysis resulted in 678 somatic intronic mutations, with 46% residing in deep introns. Among the 309 deep intronic single nucleotide variants, 245 altered core splicing codes, with 38% activating cryptic splice sites, 12% activating cryptic polypyrimidine tracts, and 36% and 12% disrupting authentic polypyrimidine tracts and branchpoints, respectively. All the intronic cryptic splice sites were created at pre-existing GT/AG dinucleotides or by GC-to-GT conversion. Notably, 85 deep intronic mutations indicated gain of splicing enhancers or loss of splicing silencers. We found that 64 tumour suppressors were affected by intronic mutations and blood cancers showed higher proportion of deep intronic mutations. In particular, a telomere maintenance gene, POT1, was recurrently mis-spliced by deep intronic mutations in blood cancers. We validated a pseudoexon activation involving a splicing silencer in POT1 by CRISPR/Cas9. Our results shed light on previously unappreciated mechanisms by which noncoding mutations acting on splicing codes in deep introns contribute to tumourigenesis.
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Affiliation(s)
- Hyunchul Jung
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea.
- Cancer Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Cambridge, UK.
| | - Kang Seon Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea.
- Penta Medix Co., Ltd., Seongnam-si, Gyeongi-do, 13449, Republic of Korea.
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11
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Nix P, Mundt E, Coffee B, Goossen E, Warf BM, Brown K, Bowles K, Roa B. Interpretation of BRCA2 Splicing Variants: A Case Series of Challenging Variant Interpretations and the Importance of Functional RNA Analysis. Fam Cancer 2021; 21:7-19. [PMID: 33469799 PMCID: PMC8799590 DOI: 10.1007/s10689-020-00224-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 12/15/2020] [Indexed: 11/13/2022]
Abstract
A substantial proportion of pathogenic variants associated with an increased risk of hereditary cancer are sequence variants affecting RNA splicing. The classification of these variants can be complex when both non-functional and functional transcripts are produced from the variant allele. We present four BRCA2 splice site variants with complex variant interpretations (BRCA2 c.68-3T>G, c.68-2A>G, c.425G>T, c.8331+2T>C). Evidence supporting a pathogenic classification is available for each variant, including in silico models, absence in population databases, and published functional data. However, comprehensive RNA analysis showed that some functional transcript may be produced by each variant. BRCA2 c.68-3T>G results in a partial splice defect. For BRCA2 c.68-2A>G and c.425G>T, aberrant splicing was shown to produce a potentially functional, in-frame transcript. BRCA2 c.8331+2T>C may utilize a functional GC donor in place of the wild-type GT donor. The severity of cancer history for carriers of these variants was also assessed using a history weighting algorithm and was not consistent with pathogenic controls (carriers of known pathogenic variants in BRCA2). Due to the conflicting evidence, our laboratory classifies these BRCA2 variants as variants of uncertain significance. This highlights the importance of evaluating new and existing evidence to ensure accurate variant classification and appropriate patient care.
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Affiliation(s)
- Paola Nix
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA.
| | - Erin Mundt
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Bradford Coffee
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | | | - Bryan M Warf
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA.,Third Wave Analytics, Inc., San Francisco, CA, USA
| | - Krystal Brown
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Karla Bowles
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Benjamin Roa
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA
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12
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Sarkar A, Yang Y, Vihinen M. Variation benchmark datasets: update, criteria, quality and applications. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5710862. [PMID: 32016318 PMCID: PMC6997940 DOI: 10.1093/database/baz117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/03/2019] [Accepted: 07/01/2019] [Indexed: 02/07/2023]
Abstract
Development of new computational methods and testing their performance has to be carried out using experimental data. Only in comparison to existing knowledge can method performance be assessed. For that purpose, benchmark datasets with known and verified outcome are needed. High-quality benchmark datasets are valuable and may be difficult, laborious and time consuming to generate. VariBench and VariSNP are the two existing databases for sharing variation benchmark datasets used mainly for variation interpretation. They have been used for training and benchmarking predictors for various types of variations and their effects. VariBench was updated with 419 new datasets from 109 papers containing altogether 329 014 152 variants; however, there is plenty of redundancy between the datasets. VariBench is freely available at http://structure.bmc.lu.se/VariBench/. The contents of the datasets vary depending on information in the original source. The available datasets have been categorized into 20 groups and subgroups. There are datasets for insertions and deletions, substitutions in coding and non-coding region, structure mapped, synonymous and benign variants. Effect-specific datasets include DNA regulatory elements, RNA splicing, and protein property for aggregation, binding free energy, disorder and stability. Then there are several datasets for molecule-specific and disease-specific applications, as well as one dataset for variation phenotype effects. Variants are often described at three molecular levels (DNA, RNA and protein) and sometimes also at the protein structural level including relevant cross references and variant descriptions. The updated VariBench facilitates development and testing of new methods and comparison of obtained performances to previously published methods. We compared the performance of the pathogenicity/tolerance predictor PON-P2 to several benchmark studies, and show that such comparisons are feasible and useful, however, there may be limitations due to lack of provided details and shared data. Database URL: http://structure.bmc.lu.se/VariBench
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Affiliation(s)
- Anasua Sarkar
- Department of Experimental Medical Science, BMC B13, Lund University, SE-22 184 Lund, Sweden
| | - Yang Yang
- School of Computer Science and Technology, Soochow University, No1. Shizi Street, Suzhou, 215006 Jiangsu, China.,Provincial Key Laboratory for Computer Information Processing Technology, No1. Shizi Street, Soochow University, Suzhou, 215006 Jiangsu, China
| | - Mauno Vihinen
- Department of Experimental Medical Science, BMC B13, Lund University, SE-22 184 Lund, Sweden
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13
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Alvarez MEV, Chivers M, Borovska I, Monger S, Giannoulatou E, Kralovicova J, Vorechovsky I. Transposon clusters as substrates for aberrant splice-site activation. RNA Biol 2020; 18:354-367. [PMID: 32965162 PMCID: PMC7951965 DOI: 10.1080/15476286.2020.1805909] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Transposed elements (TEs) have dramatically shaped evolution of the exon-intron structure and significantly contributed to morbidity, but how recent TE invasions into older TEs cooperate in generating new coding sequences is poorly understood. Employing an updated repository of new exon-intron boundaries induced by pathogenic mutations, termed DBASS, here we identify novel TE clusters that facilitated exon selection. To explore the extent to which such TE exons maintain RNA secondary structure of their progenitors, we carried out structural studies with a composite exon that was derived from a long terminal repeat (LTR78) and AluJ and was activated by a C > T mutation optimizing the 5ʹ splice site. Using a combination of SHAPE, DMS and enzymatic probing, we show that the disease-causing mutation disrupted a conserved AluJ stem that evolved from helix 3.3 (or 5b) of 7SL RNA, liberating a primordial GC 5ʹ splice site from the paired conformation for interactions with the spliceosome. The mutation also reduced flexibility of conserved residues in adjacent exon-derived loops of the central Alu hairpin, revealing a cross-talk between traditional and auxilliary splicing motifs that evolved from opposite termini of 7SL RNA and were approximated by Watson-Crick base-pairing already in organisms without spliceosomal introns. We also identify existing Alu exons activated by the same RNA rearrangement. Collectively, these results provide valuable TE exon models for studying formation and kinetics of pre-mRNA building blocks required for splice-site selection and will be useful for fine-tuning auxilliary splicing motifs and exon and intron size constraints that govern aberrant splice-site activation.
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Affiliation(s)
| | - Martin Chivers
- School of Medicine, University of Southampton, Southampton, UK
| | - Ivana Borovska
- Slovak Academy of Sciences, Institute of Molecular Physiology and Genetics, Bratislava, Slovak Republic
| | - Steven Monger
- Computational Genomics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Eleni Giannoulatou
- Computational Genomics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Jana Kralovicova
- School of Medicine, University of Southampton, Southampton, UK.,Slovak Academy of Sciences, Institute of Molecular Physiology and Genetics, Bratislava, Slovak Republic
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14
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Weisschuh N, Obermaier CD, Battke F, Bernd A, Kuehlewein L, Nasser F, Zobor D, Zrenner E, Weber E, Wissinger B, Biskup S, Stingl K, Kohl S. Genetic architecture of inherited retinal degeneration in Germany: A large cohort study from a single diagnostic center over a 9-year period. Hum Mutat 2020; 41:1514-1527. [PMID: 32531858 DOI: 10.1002/humu.24064] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/27/2020] [Accepted: 05/04/2020] [Indexed: 12/29/2022]
Abstract
We aimed to unravel the molecular genetic basis of inherited retinal degeneration (IRD) in a comprehensive cohort of patients diagnosed in the largest center for IRD in Germany. A cohort of 2,158 affected patients from 1,785 families diagnosed with IRD was analyzed by targeted next-generation sequencing (NGS). Patients with single-gene disorders (i.e., choroideremia and retinoschisis) were analyzed by Sanger sequencing and multiplex ligation-dependent probe amplification. Our study cohort accounts for ∼7% of the estimated 30,000 patients with IRD in Germany, thereby providing representative data for both the prevalence of IRDs and the mutation spectrum of IRD genes for the population in Germany. We achieved a molecular diagnostic rate of 35-95%, depending on the clinical entities, with a high detection rate for achromatopsia, retinoschisis, and choroideremia, and a low detection rate for central areolar choroidal dystrophy and macular dystrophy. A total of 1,161 distinct variants were identified, including 501 novel variants, reaffirming the known vast genetic heterogeneity of IRD in a mainly outbred European population. This study demonstrates the clinical utility of panel-based NGS in a large and highly heterogeneous cohort from an outbred population and for the first time gives a comprehensive representation of the genetic landscape of IRDs in Germany. The data are valuable and crucial for the scientific community and healthcare providers, but also for the pharmaceutical industry in the progressing field of personalized medicine and gene therapy.
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Affiliation(s)
- Nicole Weisschuh
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Carolin D Obermaier
- Praxis für Humangenetik, Tübingen, Germany.,Center for Genomics and Transcriptomics, CeGaT GmbH, Tübingen, Germany
| | - Florian Battke
- Center for Genomics and Transcriptomics, CeGaT GmbH, Tübingen, Germany
| | - Antje Bernd
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany.,Center for Ophthalmology, University Eye Hospital, University of Tübingen, Tübingen, Germany
| | - Laura Kuehlewein
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany.,Center for Ophthalmology, University Eye Hospital, University of Tübingen, Tübingen, Germany
| | - Fadi Nasser
- Center for Ophthalmology, University Eye Hospital, University of Tübingen, Tübingen, Germany
| | - Ditta Zobor
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Eberhart Zrenner
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany.,Werner Reichardt Centre for Integrative Neuroscience (CIN), University of Tübingen, Tübingen, Germany
| | - Eva Weber
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Bernd Wissinger
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Saskia Biskup
- Praxis für Humangenetik, Tübingen, Germany.,Center for Genomics and Transcriptomics, CeGaT GmbH, Tübingen, Germany
| | - Katarina Stingl
- Center for Ophthalmology, University Eye Hospital, University of Tübingen, Tübingen, Germany
| | - Susanne Kohl
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
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15
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Morín M, Borreguero L, Booth KT, Lachgar M, Huygen P, Villamar M, Mayo F, Barrio LC, Santos Serrão de Castro L, Morales C, Del Castillo I, Arellano B, Tellería D, Smith RJH, Azaiez H, Moreno Pelayo MA. Insights into the pathophysiology of DFNA10 hearing loss associated with novel EYA4 variants. Sci Rep 2020; 10:6213. [PMID: 32277154 PMCID: PMC7148344 DOI: 10.1038/s41598-020-63256-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/27/2020] [Indexed: 12/13/2022] Open
Abstract
The mutational spectrum of many genes and their contribution to the global prevalence of hereditary hearing loss is still widely unknown. In this study, we have performed the mutational screening of EYA4 gene by DHLPC and NGS in a large cohort of 531 unrelated Spanish probands and one Australian family with autosomal dominant non-syndromic hearing loss (ADNSHL). In total, 9 novel EYA4 variants have been identified, 3 in the EYA4 variable region (c.160G > T; p.Glu54*, c.781del; p.Thr261Argfs*34 and c.1078C > A; p.Pro360Thr) and 6 in the EYA-HR domain (c.1107G > T; p.Glu369Asp, c.1122G > T; p.Trp374Cys, c.1281G > A; p.Glu427Glu, c.1282-1G > A, c.1601C > G; p.S534* and an heterozygous copy number loss encompassing exons 15 to 17). The contribution of EYA4 mutations to ADNSHL in Spain is, therefore, very limited (~1.5%, 8/531). The pathophysiology of some of these novel variants has been explored. Transient expression of the c-myc-tagged EYA4 mutants in mammalian COS7 cells revealed absence of expression of the p.S534* mutant, consistent with a model of haploinsufficiency reported for all previously described EYA4 truncating mutations. However, normal expression pattern and translocation to the nucleus were observed for the p.Glu369Asp mutant in presence of SIX1. Complementary in silico analysis suggested that c.1107G > T (p.Glu369Asp), c.1281G > A (p.Glu427Glu) and c.1282-1G > A variants alter normal splicing. Minigene assays in NIH3T3 cells further confirmed that all 3 variants caused exon skipping resulting in frameshifts that lead to premature stop codons. Our study reports the first likely pathogenic synonymous variant linked to DFNA10 and provide further evidence for haploinsufficiency as the common underlying disease-causing mechanism for DFNA10-related hearing loss.
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Affiliation(s)
- Matias Morín
- Servicio de Genética, Ramón y Cajal Institute of Health Research (IRYCIS) and Biomedical Network Research Centre on Rare Diseases (CIBERER), 28034, Madrid, Spain
| | - Lucía Borreguero
- Servicio de Genética, Ramón y Cajal Institute of Health Research (IRYCIS) and Biomedical Network Research Centre on Rare Diseases (CIBERER), 28034, Madrid, Spain
| | - Kevin T Booth
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Head & Surgery, University of Iowa, Iowa City, Iowa, 52242, USA.,Harvard Medical School, Department of Neurobiology, Boston, Massachusetts, 02115, USA
| | - María Lachgar
- Servicio de Genética, Ramón y Cajal Institute of Health Research (IRYCIS) and Biomedical Network Research Centre on Rare Diseases (CIBERER), 28034, Madrid, Spain
| | - Patrick Huygen
- Department of Otorhinolaryngology, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - Manuela Villamar
- Servicio de Genética, Ramón y Cajal Institute of Health Research (IRYCIS) and Biomedical Network Research Centre on Rare Diseases (CIBERER), 28034, Madrid, Spain
| | - Fernando Mayo
- Servicio de Genética, Ramón y Cajal Institute of Health Research (IRYCIS) and Biomedical Network Research Centre on Rare Diseases (CIBERER), 28034, Madrid, Spain
| | - Luis Carlos Barrio
- Departamento de Investigación, Ramón y Cajal Institute of Health Research (IRYCIS), Unidad de Neurología Experimental, 28034, Madrid, Spain
| | - Luciana Santos Serrão de Castro
- Servicio de Genética, Ramón y Cajal Institute of Health Research (IRYCIS) and Biomedical Network Research Centre on Rare Diseases (CIBERER), 28034, Madrid, Spain
| | - Carmelo Morales
- Servicio de Otorrinolaringología, Hospital Universitario Marqués de Valdecilla, 39008, Santander, Spain
| | - Ignacio Del Castillo
- Servicio de Genética, Ramón y Cajal Institute of Health Research (IRYCIS) and Biomedical Network Research Centre on Rare Diseases (CIBERER), 28034, Madrid, Spain
| | - Beatriz Arellano
- Servicio de Otorrinolaringología, Hospital Universitario Puerta de Hierro, Majadahonda, 28922, Madrid, Spain
| | - Dolores Tellería
- Servicio de Genética, Ramón y Cajal Institute of Health Research (IRYCIS) and Biomedical Network Research Centre on Rare Diseases (CIBERER), 28034, Madrid, Spain
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Head & Surgery, University of Iowa, Iowa City, Iowa, 52242, USA
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Head & Surgery, University of Iowa, Iowa City, Iowa, 52242, USA
| | - M A Moreno Pelayo
- Servicio de Genética, Ramón y Cajal Institute of Health Research (IRYCIS) and Biomedical Network Research Centre on Rare Diseases (CIBERER), 28034, Madrid, Spain.
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16
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Wimmer K, Schamschula E, Wernstedt A, Traunfellner P, Amberger A, Zschocke J, Kroisel P, Chen Y, Callens T, Messiaen L. AG-exclusion zone revisited: Lessons to learn from 91 intronic NF1 3' splice site mutations outside the canonical AG-dinucleotides. Hum Mutat 2020; 41:1145-1156. [PMID: 32126153 PMCID: PMC7317903 DOI: 10.1002/humu.24005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/26/2020] [Accepted: 02/24/2020] [Indexed: 12/17/2022]
Abstract
Uncovering frequent motives of action by which variants impair 3′ splice site (3′ss) recognition and selection is essential to improve our understanding of this complex process. Through several mini‐gene experiments, we demonstrate that the pyrimidine (Y) to purine (R) transversion NM_000267.3(NF1):c.1722‐11T>G, although expected to weaken the polypyrimidine tract, causes exon skipping primarily by introducing a novel AG in the AG‐exclusion zone (AGEZ) between the authentic 3′ss AG and the branch point. Evaluation of 90 additional noncanonical intronic NF1 3′ss mutations confirmed that 63% of all mutations and 89% (49/55) of the single‐nucleotide variants upstream of positions ‐3 interrupt the AGEZ. Of these AGEZ‐interrupting mutations, 24/49 lead to exon skipping suggesting that absence of AG in this region is necessary for accurate 3′ss selection already in the initial steps of splicing. The analysis of 91 noncanonical NF1 3′ss mutations also shows that 90% either introduce a novel AG in the AGEZ, cause a Y>R transversion at position ‐3 or remove ≥2 Ys in the AGEZ. We confirm in a validation cohort that these three motives distinguish spliceogenic from splice‐neutral variants with 85% accuracy and, therefore, are generally applicable to select among variants of unknown significance those likely to affect splicing.
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Affiliation(s)
- Katharina Wimmer
- Institute of Human Genetics, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Esther Schamschula
- Institute of Human Genetics, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Annekatrin Wernstedt
- Institute of Human Genetics, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Pia Traunfellner
- Institute of Human Genetics, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Albert Amberger
- Institute of Human Genetics, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Johannes Zschocke
- Institute of Human Genetics, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Peter Kroisel
- Diagnostic & Research Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Yunjia Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Tom Callens
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Ludwine Messiaen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
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17
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Weisschuh N, Sturm M, Baumann B, Audo I, Ayuso C, Bocquet B, Branham K, Brooks BP, Catalá-Mora J, Giorda R, Heckenlively JR, Hufnagel RB, Jacobson SG, Kellner U, Kitsiou-Tzeli S, Matet A, Martorell Sampol L, Meunier I, Rudolph G, Sharon D, Stingl K, Streubel B, Varsányi B, Wissinger B, Kohl S. Deep-intronic variants in CNGB3 cause achromatopsia by pseudoexon activation. Hum Mutat 2019; 41:255-264. [PMID: 31544997 DOI: 10.1002/humu.23920] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/20/2019] [Accepted: 09/16/2019] [Indexed: 01/18/2023]
Abstract
Our comprehensive cohort of 1100 unrelated achromatopsia (ACHM) patients comprises a considerable number of cases (~5%) harboring only a single pathogenic variant in the major ACHM gene CNGB3. We sequenced the entire CNGB3 locus in 33 of these patients to find a second variant which eventually explained the patients' phenotype. Forty-seven intronic CNGB3 variants were identified in 28 subjects after a filtering step based on frequency and the exclusion of variants found in cis with pathogenic alleles. In a second step, in silico prediction tools were used to filter out those variants with little odds of being deleterious. This left three variants that were analyzed using heterologous splicing assays. Variant c.1663-1205G>A, found in 14 subjects, and variant c.1663-2137C>T, found in two subjects, were indeed shown to exert a splicing defect by causing pseudoexon insertion into the transcript. Subsequent screening of further unsolved CNGB3 subjects identified four additional cases harboring the c.1663-1205G>A variant which makes it the eighth most frequent CNGB3 variant in our cohort. Compound heterozygosity could be validated in ten cases. Our study demonstrates that whole gene sequencing can be a powerful approach to identify the second pathogenic allele in patients apparently harboring only one disease-causing variant.
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Affiliation(s)
- Nicole Weisschuh
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Britta Baumann
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Isabelle Audo
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France.,CHNO des Quinze-Vingts, INSERM-DHOS CIC1423, Paris, France.,Institute of Ophthalmology, University College of London, London, United Kingdom
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Beatrice Bocquet
- Centre National de Référence «Maladies Sensorielles Génétiques», Service Ophtalmologie, Hôpital Gui de Chauliac, CHRU de Montpellier, Montpellier, France.,INSERM U1051, Institute for Neurosciences of Montpellier, Montpellier, France
| | - Kari Branham
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - Brian P Brooks
- National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Roberto Giorda
- Molecular Biology Lab, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Italy
| | - John R Heckenlively
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - Robert B Hufnagel
- National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - Samuel G Jacobson
- Department of Ophthalmology, Perelman School of Medicine, Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ulrich Kellner
- Rare Retinal Disease Center, Augenzentrum Siegburg, MVZ ADTC Siegburg GmbH, Siegburg, Germany
| | - Sofia Kitsiou-Tzeli
- Department of Medical Genetics, National & Kapodistrian University of Athens, Athens, Greece
| | - Alexandre Matet
- Department of Ophthalmology, Jules-Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland
| | | | - Isabelle Meunier
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.,Centre National de Référence «Maladies Sensorielles Génétiques», Service Ophtalmologie, Hôpital Gui de Chauliac, CHRU de Montpellier, Montpellier, France
| | - Günther Rudolph
- Department of Ophthalmology, Ludwig-Maximilians-University, Munich, Germany
| | - Dror Sharon
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Katarina Stingl
- University Eye Hospital, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Berthold Streubel
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Balázs Varsányi
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary.,Department of Ophthalmology, University of Pécs Medical School, Pécs, Hungary
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
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18
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Královicová J, Ševcíková I, Stejskalová E, Obuca M, Hiller M, Stanek D, Vorechovský I. PUF60-activated exons uncover altered 3' splice-site selection by germline missense mutations in a single RRM. Nucleic Acids Res 2019; 46:6166-6187. [PMID: 29788428 PMCID: PMC6093180 DOI: 10.1093/nar/gky389] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/01/2018] [Indexed: 12/27/2022] Open
Abstract
PUF60 is a splicing factor that binds uridine (U)-rich tracts and facilitates association of the U2 small nuclear ribonucleoprotein with primary transcripts. PUF60 deficiency (PD) causes a developmental delay coupled with intellectual disability and spinal, cardiac, ocular and renal defects, but PD pathogenesis is not understood. Using RNA-Seq, we identify human PUF60-regulated exons and show that PUF60 preferentially acts as their activator. PUF60-activated internal exons are enriched for Us upstream of their 3′ splice sites (3′ss), are preceded by longer AG dinucleotide exclusion zones and more distant branch sites, with a higher probability of unpaired interactions across a typical branch site location as compared to control exons. In contrast, PUF60-repressed exons show U-depletion with lower estimates of RNA single-strandedness. We also describe PUF60-regulated, alternatively spliced isoforms encoding other U-bound splicing factors, including PUF60 partners, suggesting that they are co-regulated in the cell, and identify PUF60-regulated exons derived from transposed elements. PD-associated amino-acid substitutions, even within a single RNA recognition motif (RRM), altered selection of competing 3′ss and branch points of a PUF60-dependent exon and the 3′ss choice was also influenced by alternative splicing of PUF60. Finally, we propose that differential distribution of RNA processing steps detected in cells lacking PUF60 and the PUF60-paralog RBM39 is due to the RBM39 RS domain interactions. Together, these results provide new insights into regulation of exon usage by the 3′ss organization and reveal that germline mutation heterogeneity in RRMs can enhance phenotypic variability at the level of splice-site and branch-site selection.
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Affiliation(s)
- Jana Královicová
- University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK.,Slovak Academy of Sciences, Centre for Biosciences, 840 05 Bratislava, Slovak Republic
| | - Ivana Ševcíková
- Slovak Academy of Sciences, Centre for Biosciences, 840 05 Bratislava, Slovak Republic
| | - Eva Stejskalová
- Czech Academy of Sciences, Institute of Molecular Genetics, 142 20 Prague, Czech Republic
| | - Mina Obuca
- Czech Academy of Sciences, Institute of Molecular Genetics, 142 20 Prague, Czech Republic
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics and Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - David Stanek
- Czech Academy of Sciences, Institute of Molecular Genetics, 142 20 Prague, Czech Republic
| | - Igor Vorechovský
- University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK
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19
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Siavrienė E, Petraitytė G, Mikštienė V, Rančelis T, Maldžienė Ž, Morkūnienė A, Byčkova J, Utkus A, Kučinskas V, Preikšaitienė E. A novel CHD7 variant disrupting acceptor splice site in a patient with mild features of CHARGE syndrome: a case report. BMC MEDICAL GENETICS 2019; 20:127. [PMID: 31315586 PMCID: PMC6637606 DOI: 10.1186/s12881-019-0859-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/11/2019] [Indexed: 12/16/2022]
Abstract
Background CHARGE syndrome (MIM# 214800)—which is characterised by a number of congenital anomalies including coloboma, ear anomalies, deafness, facial anomalies, heart defects, atresia choanae, genital hypoplasia, growth retardation, and developmental delay—is caused by a heterozygous variant in the CHD7 (MIM# 608892) gene located on chromosome 8q12. We report the identification of a novel c.5535-1G > A variant in CHD7 and provide the evaluation of its effect on pre-mRNA splicing. Case presentation In this study, we report on a female presenting features of CHARGE syndrome. A novel heterozygous CHD7 variant c.5535-1G > A located in the acceptor splice site of intron 26 was identified in the proband’s DNA sample after analysis of whole exome sequencing data. In silico predictions indicating that the variant is probably pathogenic by affecting pre-mRNA splicing were verified by genetic analysis based on reverse transcription of the patient’s RNA followed by PCR amplifications performed on synthesised cDNA and Sanger sequencing. Sanger sequencing of cDNA revealed that the c.5535-1G > A variant disrupts the original acceptor splice site and activates a cryptic splice site only one nucleotide downstream of the pathogenic variant site. This change causes the omission of the first nucleotide of exon 27, leading to a frameshift in the mRNA of the CHD7 gene. Our results suggest that the alteration induces the premature truncation of the CHD7 protein (UniProtKB: Q9P2D1), thus resulting in CHARGE syndrome. Conclusion Genetic analysis of novel splice site variant underlines its importance for studying the pathogenic splicing mechanism as well as for confirming a diagnosis. Electronic supplementary material The online version of this article (10.1186/s12881-019-0859-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evelina Siavrienė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania.
| | - Gunda Petraitytė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Violeta Mikštienė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Tautvydas Rančelis
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Živilė Maldžienė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Aušra Morkūnienė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Jekaterina Byčkova
- Center of Ear, Nose and Throat Diseases, Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
| | - Algirdas Utkus
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Eglė Preikšaitienė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
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20
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Minchiotti L, Caridi G, Campagnoli M, Lugani F, Galliano M, Kragh-Hansen U. Diagnosis, Phenotype, and Molecular Genetics of Congenital Analbuminemia. Front Genet 2019; 10:336. [PMID: 31057599 PMCID: PMC6478806 DOI: 10.3389/fgene.2019.00336] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/29/2019] [Indexed: 12/25/2022] Open
Abstract
Congenital analbuminemia (CAA) is an inherited, autosomal recessive disorder with an incidence of 1:1,000,000 live birth. Affected individuals have a strongly decreased concentration, or complete absence, of serum albumin. The trait is usually detected by serum protein electrophoresis and immunochemistry techniques. However, due to the existence of other conditions in which the albumin concentrations are very low or null, analysis of the albumin (ALB) gene is necessary for the molecular diagnosis. CAA can lead to serious consequences in the prenatal period, because it can cause miscarriages and preterm birth, which often is due to oligohydramnios and placental abnormalities. Neonatally and in early childhood the trait is a risk factor that can lead to death, mainly from fluid retention and infections in the lower respiratory tract. By contrast, CAA is better tolerated in adulthood. Clinically, in addition to the low level of albumin, the patients almost always have hyperlipidemia, but they usually also have mild oedema, reduced blood pressure and fatigue. The fairly mild symptoms in adulthood are due to compensatory increment of other plasma proteins. The condition is rare; clinically, only about 90 cases have been detected worldwide. Among these, 53 have been studied by sequence analysis of the ALB gene, allowing the identification of 27 different loss of function (LoF) pathogenic variants. These include a variant in the start codon, frame-shift/insertions, frame-shift/deletions, nonsense variants, and variants affecting splicing. Most are unique, peculiar for each affected family, but one, a frame-shift deletion called Kayseri, has been found to cause about one third of the known cases allowing to presume a founder effect. This review provides an overview of the literature about CAA, about supportive and additional physiological and pharmacological information obtained from albumin-deficient mouse and rat models and a complete and up-to-date dataset of the pathogenic variants identified in the ALB gene.
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Affiliation(s)
| | - Gianluca Caridi
- Laboratory of Molecular Nephrology, Istituto Giannina Gaslini (IRCCS), Genoa, Italy
| | | | - Francesca Lugani
- Laboratory of Molecular Nephrology, Istituto Giannina Gaslini (IRCCS), Genoa, Italy
| | - Monica Galliano
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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21
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Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes. Nat Commun 2018; 9:2032. [PMID: 29795225 PMCID: PMC5966403 DOI: 10.1038/s41467-018-04110-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 04/04/2018] [Indexed: 01/04/2023] Open
Abstract
Modification of SMN2 exon 7 (E7) splicing is a validated therapeutic strategy against spinal muscular atrophy (SMA). However, a target-based approach to identify small-molecule E7 splicing modifiers has not been attempted, which could reveal novel therapies with improved mechanistic insight. Here, we chose as a target the stem-loop RNA structure TSL2, which overlaps with the 5' splicing site of E7. A small-molecule TSL2-binding compound, homocarbonyltopsentin (PK4C9), was identified that increases E7 splicing to therapeutic levels and rescues downstream molecular alterations in SMA cells. High-resolution NMR combined with molecular modelling revealed that PK4C9 binds to pentaloop conformations of TSL2 and promotes a shift to triloop conformations that display enhanced E7 splicing. Collectively, our study validates TSL2 as a target for small-molecule drug discovery in SMA, identifies a novel mechanism of action for an E7 splicing modifier, and sets a precedent for other splicing-mediated diseases where RNA structure could be similarly targeted.
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22
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Jourdy Y, Janin A, Fretigny M, Lienhart A, Négrier C, Bozon D, Vinciguerra C. Reccurrent F8 Intronic Deletion Found in Mild Hemophilia A Causes Alu Exonization. Am J Hum Genet 2018; 102:199-206. [PMID: 29357978 DOI: 10.1016/j.ajhg.2017.12.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 12/12/2017] [Indexed: 01/12/2023] Open
Abstract
Incorporation of distant intronic sequences in mature mRNA is an underappreciated cause of genetic disease. Several disease-causing pseudoexons have been found to contain repetitive elements such as Alu elements. This study describes an original pathological mechanism by which a small intronic deletion leads to Alu exonization. We identified an intronic deletion, c.2113+461_2113+473del, in the F8 intron 13, in two individuals with mild hemophilia A. In vivo and in vitro transcript analysis found an aberrant transcript, with an insertion of a 122-bp intronic fragment (c.2113_2114ins2113+477_2113+598) at the exon 13-14 junction. This out-of-frame insertion is predicted to lead to truncated protein (p.Gly705Aspfs∗37). DNA sequencing analysis found that the pseudoexon corresponds to antisense AluY element and the deletion removed a part of the poly(T)-tail from the right arm of these AluY. The heterogenous nuclear riboprotein C1/C2 (hnRNP C) is an important antisense Alu-derived cryptic exon silencer and binds to poly(T)-tracts. Disruption of the hnRNP C binding site in AluY T-tract by mutagenesis or hnRNP C knockdown using siRNA in HeLa cells reproduced the effect of c.2113+461_2113+473del. The screening of 114 unrelated families with mild hemophilia A in whom no genetic event was previously identified found a deletion in the poly(T)-tail of AluY in intron 13 in 54% of case subjects (n = 61/114). In conclusion, this study describes a deletion leading to Alu exonization found in 6.1% of families with mild hemophila A in France.
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Affiliation(s)
- Yohann Jourdy
- Service d'hématologie biologique, Centre de Biologie et Pathologie Est, Bron (69500) Hospices Civils de Lyon, France; EA 4609 Hémostase et cancer, Lyon (69008), Université Claude Bernard Lyon 1, Univ Lyon, France.
| | - Alexandre Janin
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Bron (69500), Hospices Civils de Lyon, France; Institut NeuroMyoGène, Université Claude Bernard Lyon 1, Univ Lyon, France, CNRS UMR 5510, Villeurbanne (69100), France; INSERM U1217, Villeurbanne, France
| | - Mathilde Fretigny
- Service d'hématologie biologique, Centre de Biologie et Pathologie Est, Bron (69500) Hospices Civils de Lyon, France
| | - Anne Lienhart
- Unité d'hémostase clinique, Hôpital Cardiologique Louis Pradel, Bron (69500), Hospices Civils de Lyon, France
| | - Claude Négrier
- Service d'hématologie biologique, Centre de Biologie et Pathologie Est, Bron (69500) Hospices Civils de Lyon, France; EA 4609 Hémostase et cancer, Lyon (69008), Université Claude Bernard Lyon 1, Univ Lyon, France; Unité d'hémostase clinique, Hôpital Cardiologique Louis Pradel, Bron (69500), Hospices Civils de Lyon, France
| | - Dominique Bozon
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Bron (69500), Hospices Civils de Lyon, France
| | - Christine Vinciguerra
- Service d'hématologie biologique, Centre de Biologie et Pathologie Est, Bron (69500) Hospices Civils de Lyon, France; EA 4609 Hémostase et cancer, Lyon (69008), Université Claude Bernard Lyon 1, Univ Lyon, France
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23
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Legendre M, Rodriguez-Ballesteros M, Rossi M, Abadie V, Amiel J, Revencu N, Blanchet P, Brioude F, Delrue MA, Doubaj Y, Sefiani A, Francannet C, Holder-Espinasse M, Jouk PS, Julia S, Melki J, Mur S, Naudion S, Fabre-Teste J, Busa T, Stamm S, Lyonnet S, Attie-Bitach T, Kitzis A, Gilbert-Dussardier B, Bilan F. CHARGE syndrome: a recurrent hotspot of mutations in CHD7 IVS25 analyzed by bioinformatic tools and minigene assays. Eur J Hum Genet 2017; 26:287-292. [PMID: 29255276 DOI: 10.1038/s41431-017-0007-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 08/17/2017] [Accepted: 08/29/2017] [Indexed: 11/09/2022] Open
Abstract
CHARGE syndrome is a rare genetic disorder mainly due to de novo and private truncating mutations of CHD7 gene. Here we report an intriguing hot spot of intronic mutations (c.5405-7G > A, c.5405-13G > A, c.5405-17G > A and c.5405-18C > A) located in CHD7 IVS25. Combining computational in silico analysis, experimental branch-point determination and in vitro minigene assays, our study explains this mutation hot spot by a particular genomic context, including the weakness of the IVS25 natural acceptor-site and an unconventional lariat sequence localized outside the common 40 bp upstream the acceptor splice site. For each of the mutations reported here, bioinformatic tools indicated a newly created 3' splice site, of which the existence was confirmed using pSpliceExpress, an easy-to-use and reliable splicing reporter tool. Our study emphasizes the idea that combining these two complementary approaches could increase the efficiency of routine molecular diagnosis.
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Affiliation(s)
- Marine Legendre
- Service de Génétique, Centre de Référence Anomalies du Développement de l'Ouest, CHU Poitiers, France.,EA3808 CiMoTheMA Université Poitiers, Poitiers, France
| | | | - Massimiliano Rossi
- Service de génétique, Centre de Référence Anomalies du Développement, Hospices Civils de Lyon et INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Université Claude Bernard Lyon 1, Bron, France
| | - Véronique Abadie
- Service de Pédiatrie Générale, Hôpital Necker Enfants-Malades, AP-HP, Paris, France
| | - Jeanne Amiel
- Département de Génétique, Hôpital Universitaire Necker-Enfants Malades, AP-HP, Institut Imagine, UMR-1163 INSERM-Université Paris Descartes, Paris, France
| | - Nicole Revencu
- Center for Human Genetics, Cliniques universitaires St Luc, Université catholique de Louvain, Brussels, Belgium
| | - Patricia Blanchet
- Département de Génétique Médicale, Hôpital Arnaud de Villeneuve, CHU Montpellier, France
| | - Frédéric Brioude
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S938, Centre de Recherche Saint Antoine and AP-HP, Hôpitaux Universitaires Paris Est, Hôpital Trousseau, Service d'Explorations Fonctionnelles Endocriniennes, Paris, France
| | | | - Yassamine Doubaj
- Département de Génétique Médicale, Institut National d'Hygiène, Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie de Rabat, Mohammed V University in Rabat, Rabat, Morocco
| | - Abdelaziz Sefiani
- Département de Génétique Médicale, Institut National d'Hygiène, Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie de Rabat, Mohammed V University in Rabat, Rabat, Morocco
| | | | | | - Pierre-Simon Jouk
- Département Génétique & Procréation, Hôpital Couple-Enfant, CHU Grenoble, France
| | - Sophie Julia
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, France
| | - Judith Melki
- CHU Bicêtre, Unité de Génétique Médicale and UMR-1169, Inserm, Le Kremlin Bicêtre, France
| | - Sébastien Mur
- Clinique de médecine néonatale, Hôpital Jeanne de Flandre, CHU Lille, France
| | - Sophie Naudion
- Service de Génétique Médicale, GH Pellegrin, CHU Bordeaux, France
| | | | - Tiffany Busa
- Département de Génétique Médicale, Hôpital d'enfants de la Timone, Marseille, France
| | - Stephen Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, USA
| | - Stanislas Lyonnet
- Département de Génétique, Hôpital Universitaire Necker-Enfants Malades, AP-HP, Institut Imagine, UMR-1163 INSERM-Université Paris Descartes, Paris, France
| | - Tania Attie-Bitach
- Département de Génétique, Hôpital Universitaire Necker-Enfants Malades, AP-HP, Institut Imagine, UMR-1163 INSERM-Université Paris Descartes, Paris, France
| | - Alain Kitzis
- Service de Génétique, Centre de Référence Anomalies du Développement de l'Ouest, CHU Poitiers, France.,EA3808 CiMoTheMA Université Poitiers, Poitiers, France
| | - Brigitte Gilbert-Dussardier
- Service de Génétique, Centre de Référence Anomalies du Développement de l'Ouest, CHU Poitiers, France.,EA3808 CiMoTheMA Université Poitiers, Poitiers, France
| | - Frédéric Bilan
- Service de Génétique, Centre de Référence Anomalies du Développement de l'Ouest, CHU Poitiers, France. .,EA3808 CiMoTheMA Université Poitiers, Poitiers, France.
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24
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Systematic analysis of splicing defects in selected primary immunodeficiencies-related genes. Clin Immunol 2017; 180:33-44. [DOI: 10.1016/j.clim.2017.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 02/03/2017] [Accepted: 03/23/2017] [Indexed: 12/15/2022]
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25
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Humphrey J, Emmett W, Fratta P, Isaacs AM, Plagnol V. Quantitative analysis of cryptic splicing associated with TDP-43 depletion. BMC Med Genomics 2017; 10:38. [PMID: 28549443 PMCID: PMC5446763 DOI: 10.1186/s12920-017-0274-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 05/17/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Reliable exon recognition is key to the splicing of pre-mRNAs into mature mRNAs. TDP-43 is an RNA-binding protein whose nuclear loss and cytoplasmic aggregation are a hallmark pathology in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). TDP-43 depletion causes the aberrant inclusion of cryptic exons into a range of transcripts, but their extent, relevance to disease pathogenesis and whether they are caused by other RNA-binding proteins implicated in ALS/FTD are unknown. METHODS We developed an analysis pipeline to discover and quantify cryptic exon inclusion and applied it to publicly available human and murine RNA-sequencing data. RESULTS We detected widespread cryptic splicing in TDP-43 depletion datasets but almost none in another ALS/FTD-linked protein FUS. Sequence motif and iCLIP analysis of cryptic exons demonstrated that they are bound by TDP-43. Unlike the cryptic exons seen in hnRNP C depletion, those repressed by TDP-43 cannot be linked to transposable elements. Cryptic exons are poorly conserved and inclusion overwhelmingly leads to nonsense-mediated decay of the host transcript, with reduced transcript levels observed in differential expression analysis. RNA-protein interaction data on 73 different RNA-binding proteins showed that, in addition to TDP-43, 7 specifically bind TDP-43 linked cryptic exons. This suggests that TDP-43 competes with other splicing factors for binding to cryptic exons and can repress cryptic exon inclusion. CONCLUSIONS Our quantitative analysis pipeline confirms the presence of cryptic exons during the depletion of TDP-43 but not FUS providing new insight into to RNA-processing dysfunction as a cause or consequence in ALS/FTD.
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Affiliation(s)
- Jack Humphrey
- University College London Genetics Institute, Gower Street, London, UK.
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK.
| | - Warren Emmett
- University College London Genetics Institute, Gower Street, London, UK
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
- The Francis Crick Institute, Midland Road, London, UK
| | - Pietro Fratta
- Department of Motor Neuroscience and Movement Disorders, UCL Institute of Neurology, Queen Square, London, UK
| | - Adrian M Isaacs
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK
| | - Vincent Plagnol
- University College London Genetics Institute, Gower Street, London, UK
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26
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Nozu K, Iijima K, Igarashi T, Yamada S, Kralovicova J, Nozu Y, Yamamura T, Minamikawa S, Morioka I, Ninchoji T, Kaito H, Nakanishi K, Vorechovsky I. A birth of bipartite exon by intragenic deletion. Mol Genet Genomic Med 2017; 5:287-294. [PMID: 28546999 PMCID: PMC5441408 DOI: 10.1002/mgg3.277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/03/2017] [Accepted: 01/06/2017] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Disease-causing mutations that activate transposon-derived exons without creating a new splice-site consensus have been reported rarely, but they provided unique insights into our understanding of structural motifs required for inclusion of intronic sequences in mature transcripts. METHODS We employ a combination of experimental and computational techniques to characterize the first de novo bipartite exon activation in genetic disease. RESULTS The exon originated from two separate introns as a result of an in-frame COL4A5 deletion associated with a typical Alport syndrome. The deletion encompassed exons 38 through 41 and activated a cryptic 3' and 5' splice site that were derived from intron 37 and intron 41, respectively. The deletion breakpoint was in the middle of the new exon, with considerable complementarity between the two exonic parts, potentially bringing the cryptic 3' and 5' splice site into proximity. The 3' splice site, polypyrimidine tract and the branch site of the new exon were derived from an inactive, 5' truncated LINE-1 retrotransposon. This ancient LINE-1 copy sustained a series of mutations that created the highly conserved AG dinucleotide at the 3' splice site early in primate development. The exon was fully included in mature transcripts and introduced a stop codon in the shortened COL4A5 mRNA, illustrating pitfalls of inferring disease severity from DNA mutation alone. CONCLUSION These results expand the repertoire of mutational mechanisms that alter RNA processing in genetic disease and illustrate the extraordinary versatility of transposed elements in shaping the new exon-intron structure and the phenotypic variability.
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Affiliation(s)
- Kandai Nozu
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Kazumoto Iijima
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Toru Igarashi
- Department of PediatricsNippon Medical School HospitalTokyoJapan
| | - Shiro Yamada
- Department of PediatricsTokai University Oiso HospitalOisoJapan.,Division of Human GeneticsNational Institute of GeneticsMishimaJapan
| | | | - Yoshimi Nozu
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Tomohiko Yamamura
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Shogo Minamikawa
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Ichiro Morioka
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Takeshi Ninchoji
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Hiroshi Kaito
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Koichi Nakanishi
- Department of PediatricsWakayama Medical UniversityWakayamaJapan
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27
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Cancer-associated SF3B1 mutants recognize otherwise inaccessible cryptic 3' splice sites within RNA secondary structures. Oncogene 2016; 36:1123-1133. [PMID: 27524419 PMCID: PMC5311031 DOI: 10.1038/onc.2016.279] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 06/14/2016] [Accepted: 07/01/2016] [Indexed: 02/08/2023]
Abstract
Recurrent mutations in core splicing factors have been reported in several clonal disorders, including cancers. Mutations in SF3B1, a component of the U2 splicing complex, are the most common. SF3B1 mutations are associated with aberrant pre-mRNA splicing using cryptic 3’ splice sites (3’SS) but the mechanism of their selection is not clear. To understand how cryptic 3’SS are selected, we performed comprehensive analysis of transcriptome-wide changes to splicing and gene expression associated with SF3B1 mutations in patient samples as well as an experimental model of inducible expression. Hundreds of cryptic 3’SS were detectable across the genome in cells expressing mutant SF3B1. These 3’SS are typically sequestered within RNA secondary structures and poorly accessible compared to their corresponding canonical 3’SS. We hypothesized that these cryptic 3’SS are inaccessible during normal splicing catalysis and that this constraint is overcome in spliceosomes containing mutant SF3B1. This model of secondary structure-dependent selection of cryptic 3’SS was found across multiple clonal processes associated with SF3B1 mutations (myelodysplastic syndrome and chronic lymphocytic leukemia). We validated our model predictions in mini-gene splicing assays. Additionally, we found deregulated expression of proteins with relevant functions in splicing factor-related diseases both in association with aberrant splicing and without corresponding splicing changes. Our results show that SF3B1 mutations are associated with a distinct splicing program shared across multiple clonal processes and define a biochemical mechanism for altered 3’SS choice.
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28
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Caridi G, Thomas W, Campagnoli M, Lugani F, Galliano M, Minchiotti L. A novel splicing mutation in the albumin gene (c.270+1G>T) causes analbuminaemia in a German infant. Ann Clin Biochem 2015; 53:615-9. [PMID: 26543026 DOI: 10.1177/0004563215618223] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2015] [Indexed: 12/25/2022]
Abstract
Congenital analbuminaemia is a rare autosomal recessive disorder manifested by the presence of a very low amount of circulating serum albumin. The clinical diagnosis may be challenging because of the absence of unambiguous symptoms and because hypoalbuminemia may have many causes different from a genetic lack of the protein. We describe the clinical and molecular characterization of a new case of congenital analbuminaemia in an infant of apparently non-consanguineous parents from Treves, Germany. For molecular diagnosis, we used our strategy, based on the screening of the albumin gene by single-strand conformation polymorphism, heteroduplex analysis and direct DNA sequencing, which revealed that the proband is homozygous and both parents are heterozygous, for a novel G > T transversion at nucleotide c.270+ 1, the first base of intron 3. The mutation inactivates the strongly conserved GT dinucleotide at the 5' splice site consensus sequence of this intron. In conclusion, we report the clinical findings and the molecular defect of this case, which contributes to a better understanding of the biological mechanism of congenital analbuminaemia.
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Affiliation(s)
- Gianluca Caridi
- Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini IRCCS, Genova, Italy
| | - Wolfgang Thomas
- Department of Pediatrics, Klinikum Mutterhaus der Borromaeerinnen, Trier, Germany
| | | | - Francesca Lugani
- Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini IRCCS, Genova, Italy
| | - Monica Galliano
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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29
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Kralovicova J, Knut M, Cross NCP, Vorechovsky I. Identification of U2AF(35)-dependent exons by RNA-Seq reveals a link between 3' splice-site organization and activity of U2AF-related proteins. Nucleic Acids Res 2015; 43:3747-63. [PMID: 25779042 PMCID: PMC4402522 DOI: 10.1093/nar/gkv194] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 02/24/2015] [Indexed: 01/05/2023] Open
Abstract
The auxiliary factor of U2 small nuclear RNA (U2AF) is a heterodimer consisting of 65- and 35-kD proteins that bind the polypyrimidine tract (PPT) and AG dinucleotides at the 3′ splice site (3′ss). The gene encoding U2AF35 (U2AF1) is alternatively spliced, giving rise to two isoforms U2AF35a and U2AF35b. Here, we knocked down U2AF35 and each isoform and characterized transcriptomes of HEK293 cells with varying U2AF35/U2AF65 and U2AF35a/b ratios. Depletion of both isoforms preferentially modified alternative RNA processing events without widespread failure to recognize 3′ss or constitutive exons. Over a third of differentially used exons were terminal, resulting largely from the use of known alternative polyadenylation (APA) sites. Intronic APA sites activated in depleted cultures were mostly proximal whereas tandem 3′UTR APA was biased toward distal sites. Exons upregulated in depleted cells were preceded by longer AG exclusion zones and PPTs than downregulated or control exons and were largely activated by PUF60 and repressed by CAPERα. The U2AF(35) repression and activation was associated with a significant interchange in the average probabilities to form single-stranded RNA in the optimal PPT and branch site locations and sequences further upstream. Although most differentially used exons were responsive to both U2AF subunits and their inclusion correlated with U2AF levels, a small number of transcripts exhibited distinct responses to U2AF35a and U2AF35b, supporting the existence of isoform-specific interactions. These results provide new insights into function of U2AF and U2AF35 in alternative RNA processing.
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Affiliation(s)
- Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Marcin Knut
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Nicholas C P Cross
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury SP2 8BJ, UK
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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30
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Soemedi R, Vega H, Belmont JM, Ramachandran S, Fairbrother WG. Genetic variation and RNA binding proteins: tools and techniques to detect functional polymorphisms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:227-66. [PMID: 25201108 DOI: 10.1007/978-1-4939-1221-6_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
At its most fundamental level the goal of genetics is to connect genotype to phenotype. This question is asked at a basic level evaluating the role of genes and pathways in genetic model organism. Increasingly, this question is being asked in the clinic. Genomes of individuals and populations are being sequenced and compared. The challenge often comes at the stage of analysis. The variant positions are analyzed with the hope of understanding human disease. However after a genome or exome has been sequenced, the researcher is often deluged with hundreds of potentially relevant variations. Traditionally, amino-acid changing mutations were considered the tractable class of disease-causing mutations; however, mutations that disrupt noncoding elements are the subject of growing interest. These noncoding changes are a major avenue of disease (e.g., one in three hereditary disease alleles are predicted to affect splicing). Here, we review some current practices of medical genetics, the basic theory behind biochemical binding and functional assays, and then explore technical advances in how variations that alter RNA protein recognition events are detected and studied. These advances are advances in scale-high-throughput implementations of traditional biochemical assays that are feasible to perform in any molecular biology laboratory. This chapter utilizes a case study approach to illustrate some methods for analyzing polymorphisms. The first characterizes a functional intronic SNP that deletes a high affinity PTB site using traditional low-throughput biochemical and functional assays. From here we demonstrate the utility of high-throughput splicing and spliceosome assembly assays for screening large sets of SNPs and disease alleles for allelic differences in gene expression. Finally we perform three pilot drug screens with small molecules (G418, tetracycline, and valproic acid) that illustrate how compounds that rescue specific instances of differential pre-mRNA processing can be discovered.
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Affiliation(s)
- Rachel Soemedi
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
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31
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Vihinen M. Majority vote and other problems when using computational tools. Hum Mutat 2014; 35:912-4. [PMID: 24915749 DOI: 10.1002/humu.22600] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/28/2014] [Indexed: 11/06/2022]
Abstract
Computational tools are essential for most of our research. To use these tools, one needs to know how they work. Problems in application of computational methods to variation analysis can appear at several stages and affect, for example, the interpretation of results. Such cases are discussed along with suggestions how to avoid them. The applications include incomplete reporting of methods, especially about the use of prediction tools; method selection on unscientific grounds and without consulting independent method performance assessments; extending application area of methods outside their intended purpose; use of the same data several times for obtaining majority vote; and filtering of datasets so that variants of interest are excluded. All these issues can be avoided by discontinuing the use software tools as black boxes.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, BMC D10, Lund University, Lund, Sweden
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32
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Characterization of NOL7 gene point mutations, promoter methylation, and protein expression in cervical cancer. Int J Gynecol Pathol 2014; 31:15-24. [PMID: 22123719 DOI: 10.1097/pgp.0b013e318220ba16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
NOL7 is a putative tumor suppressor gene localized to 6p23, a region with frequent loss of heterozygosity in a number of cancers, including cervical cancer (CC). We have previously demonstrated that reintroduction of NOL7 into CC cells altered the angiogenic phenotype and suppressed tumor growth in vivo by 95%. Therefore, to understand its mechanism of inactivation in CC, we investigated the genetic and epigenetic regulation of NOL7. NOL7 mRNA and protein levels were assessed in 13 CC cell lines and 23 consecutive CC specimens by real-time quantitative polymerase chain reaction, western blotting, and immunohistochemistry. Methylation of the NOL7 promoter was analyzed by bisulfite sequencing and mutations were identified through direct sequencing. A CpG island with multiple CpG dinucleotides spanned the 5' untranslated region and first exon of NOL7. However, bisulfite sequencing failed to identify persistent sites of methylation. Mutational sequencing revealed that 40% of the CC specimens and 31% of the CC cell lines harbored somatic mutations that may affect the in vivo function of NOL7. Endogenous NOL7 mRNA and protein expression in CC cell lines were significantly decreased in 46% of the CC cell lines. Finally, immunohistochemistry demonstrated strong NOL7 nucleolar staining in normal tissues that decreased with histologic progression toward CC. NOL7 is inactivated in CC in accordance with the Knudson 2-hit hypothesis through loss of heterozygosity and mutation. Together with evidence of its in vivo tumor suppression, these data support the hypothesis that NOL7 is the legitimate tumor suppressor gene located on 6p23.
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33
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Igudin EL, Spirin PV, Prasolov VS, Zubkova NA, Petryaikina EE, Tyul’pakov AN, Rubtsov PM. Functional characterization of two novel splicing mutations of glucokinase gene associated with maturity-onset diabetes of the young type 2 (MODY2). Mol Biol 2014. [DOI: 10.1134/s0026893314020071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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Grodecká L, Lockerová P, Ravčuková B, Buratti E, Baralle FE, Dušek L, Freiberger T. Exon first nucleotide mutations in splicing: evaluation of in silico prediction tools. PLoS One 2014; 9:e89570. [PMID: 24586880 PMCID: PMC3931810 DOI: 10.1371/journal.pone.0089570] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/21/2014] [Indexed: 12/20/2022] Open
Abstract
Mutations in the first nucleotide of exons (E+1) mostly affect pre-mRNA splicing when found in AG-dependent 3′ splice sites, whereas AG-independent splice sites are more resistant. The AG-dependency, however, may be difficult to assess just from primary sequence data as it depends on the quality of the polypyrimidine tract. For this reason, in silico prediction tools are commonly used to score 3′ splice sites. In this study, we have assessed the ability of sequence features and in silico prediction tools to discriminate between the splicing-affecting and non-affecting E+1 variants. For this purpose, we newly tested 16 substitutions in vitro and derived other variants from literature. Surprisingly, we found that in the presence of the substituting nucleotide, the quality of the polypyrimidine tract alone was not conclusive about its splicing fate. Rather, it was the identity of the substituting nucleotide that markedly influenced it. Among the computational tools tested, the best performance was achieved using the Maximum Entropy Model and Position-Specific Scoring Matrix. As a result of this study, we have now established preliminary discriminative cut-off values showing sensitivity up to 95% and specificity up to 90%. This is expected to improve our ability to detect splicing-affecting variants in a clinical genetic setting.
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Affiliation(s)
- Lucie Grodecká
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pavla Lockerová
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Barbora Ravčuková
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | - Ladislav Dušek
- Institute of Biostatistics and Analyses, Masaryk University, Brno, Czech Republic
| | - Tomáš Freiberger
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Institute of Clinical Immunology and Allergology, St. Anne’s University Hospital and Masaryk University, Brno, Czech Republic
- * E-mail:
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35
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Caridi G, Dagnino M, Erdeve O, Di Duca M, Yildiz D, Alan S, Atasay B, Arsan S, Campagnoli M, Galliano M, Minchiotti L. Congenital analbuminemia caused by a novel aberrant splicing in the albumin gene. Biochem Med (Zagreb) 2014; 24:151-8. [PMID: 24627724 PMCID: PMC3936982 DOI: 10.11613/bm.2014.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 12/10/2013] [Indexed: 12/25/2022] Open
Abstract
Introduction: Congenital analbuminemia is a rare autosomal recessive disorder manifested by the presence of a very low amount of circulating serum albumin. It is an allelic heterogeneous defect, caused by variety of mutations within the albumin gene in homozygous or compound heterozygous state. Herein we report the clinical and molecular characterization of a new case of congenital analbuminemia diagnosed in a female newborn of consanguineous (first degree cousins) parents from Ankara, Turkey, who presented with a low albumin concentration (< 8 g/L) and severe clinical symptoms. Materials and methods: The albumin gene of the index case was screened by single-strand conformation polymorphism, heteroduplex analysis, and direct DNA sequencing. The effect of the splicing mutation was evaluated by examining the cDNA obtained by reverse transcriptase - polymerase chain reaction (RT-PCR) from the albumin mRNA extracted from proband’s leukocytes. Results: DNA sequencing revealed that the proband is homozygous, and both parents are heterozygous, for a novel G>A transition at position c.1652+1, the first base of intron 12, which inactivates the strongly conserved GT dinucleotide at the 5′ splice site consensus sequence of this intron. The splicing defect results in the complete skipping of the preceding exon (exon 12) and in a frame-shift within exon 13 with a premature stop codon after the translation of three mutant amino acid residues. Conclusions: Our results confirm the clinical diagnosis of congenital analbuminemia in the proband and the inheritance of the trait and contribute to shed light on the molecular genetics of analbuminemia.
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Affiliation(s)
- Gianluca Caridi
- Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini IRCCS, Genova, Italy
| | - Monica Dagnino
- Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini IRCCS, Genova, Italy
| | - Omer Erdeve
- Ankara University School of Medicine, Department of Pediatrics, Division of Neonatology, Ankara, Turkey
| | - Marco Di Duca
- Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini IRCCS, Genova, Italy
| | - Duran Yildiz
- Ankara University School of Medicine, Department of Pediatrics, Division of Neonatology, Ankara, Turkey
| | - Serdar Alan
- Ankara University School of Medicine, Department of Pediatrics, Division of Neonatology, Ankara, Turkey
| | - Begum Atasay
- Ankara University School of Medicine, Department of Pediatrics, Division of Neonatology, Ankara, Turkey
| | - Saadet Arsan
- Ankara University School of Medicine, Department of Pediatrics, Division of Neonatology, Ankara, Turkey
| | | | - Monica Galliano
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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36
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The thermodynamic patterns of eukaryotic genes suggest a mechanism for intron-exon recognition. Nat Commun 2013; 4:2101. [PMID: 23817463 DOI: 10.1038/ncomms3101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/03/2013] [Indexed: 12/11/2022] Open
Abstract
The essential cis- and trans-acting elements required for RNA splicing have been defined, however, the detailed molecular mechanisms underlying intron-exon recognition are still unclear. Here we demonstrate that the ratio between stability of mRNA/DNA and DNA/DNA duplexes near 3'-spice sites is a characteristic feature that can contribute to intron-exon differentiation. Remarkably, throughout all transcripts, the most unstable mRNA/DNA duplexes, compared with the corresponding DNA/DNA duplexes, are situated upstream of the 3'-splice sites and include the polypyrimidine tracts. This characteristic instability is less pronounced in weak alternative splice sites and disease-associated cryptic 3'-splice sites. Our results suggest that this thermodynamic pattern can prevent the re-annealing of mRNA to the DNA template behind the RNA polymerase to ensure access of the splicing machinery to the polypyrimidine tract and the branch point. In support of this mechanism, we demonstrate that RNA/DNA duplex formation at this region prevents pre-spliceosome A complex assembly.
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37
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Geahlen JH, Lapid C, Thorell K, Nikolskiy I, Huh WJ, Oates EL, Lennerz JKM, Tian X, Weis VG, Khurana SS, Lundin SB, Templeton AR, Mills JC. Evolution of the human gastrokine locus and confounding factors regarding the pseudogenicity of GKN3. Physiol Genomics 2013; 45:667-83. [PMID: 23715263 DOI: 10.1152/physiolgenomics.00169.2012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
In a screen for genes expressed specifically in gastric mucous neck cells, we identified GKN3, the recently discovered third member of the gastrokine family. We present confirmatory mouse data and novel porcine data showing that mouse GKN3 expression is confined to mucous cells of the corpus neck and antrum base and is prominently expressed in metaplastic lesions. GKN3 was proposed originally to be expressed in some human populations and a pseudogene in others. To investigate that hypothesis, we studied human GKN3 evolution in the context of its paralogous genomic neighbors, GKN1 and GKN2. Haplotype analysis revealed that GKN3 mimics GKN2 in patterns of exonic SNP allocation, whereas GKN1 appeared to be more stringently selected. GKN3 showed signatures of both directional selection and population based selective sweeps in humans. One such selective sweep includes SNP rs10187256, originally identified as an ancestral tryptophan to premature STOP codon mutation. The derived (nonancestral) allele went to fixation in Asia. We show that another SNP, rs75578132, identified 5 bp downstream of rs10187256, exhibits a second selective sweep in almost all Europeans, some Latinos, and some Africans, possibly resulting from a reintroduction of European genes during African colonization. Finally, we identify a mutation that would destroy the splice donor site in the putative exon3-intron3 boundary, which occurs in all human genomes examined to date. Our results highlight a stomach-specific human genetic locus, which has undergone various selective sweeps across European, Asian, and African populations and thus reflects geographic and ethnic patterns in genome evolution.
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Affiliation(s)
- Jessica H Geahlen
- Division of Gastroenterology, Department of Medicine, School of Medicine, Washington University, St. Louis, Missouri 63110, USA
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Kurmangaliyev YZ, Sutormin RA, Naumenko SA, Bazykin GA, Gelfand MS. Functional implications of splicing polymorphisms in the human genome. Hum Mol Genet 2013; 22:3449-59. [PMID: 23640990 DOI: 10.1093/hmg/ddt200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Proper splicing is often crucial for gene functioning and its disruption may be strongly deleterious. Nevertheless, even the essential for splicing canonical dinucleotides of the splice sites are often polymorphic. Here, we use data from The 1000 Genomes Project to study single-nucleotide polymorphisms (SNPs) in the canonical dinucleotides. Splice sites carrying SNPs are enriched in weakly expressed genes and in rarely used alternative splice sites. Genes with disrupted splice sites tend to have low selective constraint, and the splice sites disrupted by SNPs are less likely to be conserved in mouse. Furthermore, SNPs are enriched in splice sites whose effects on gene function are minor: splice sites located outside of protein-coding regions, in shorter exons, closer to the 3'-ends of proteins, and outside of functional protein domains. Most of these effects are more pronounced for high-frequency SNPs. Despite these trends, many of the polymorphic sites may still substantially affect the function of the corresponding genes. A number of the observed splice site-disrupting SNPs, including several high-frequency ones, were found among mutations described in OMIM.
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Affiliation(s)
- Yerbol Z Kurmangaliyev
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow 127994, Russia
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39
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Minchiotti L, Galliano M, Caridi G, Kragh-Hansen U, Peters T. Congenital analbuminaemia: molecular defects and biochemical and clinical aspects. Biochim Biophys Acta Gen Subj 2013; 1830:5494-502. [PMID: 23612153 DOI: 10.1016/j.bbagen.2013.04.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 04/11/2013] [Accepted: 04/15/2013] [Indexed: 12/25/2022]
Abstract
BACKGROUND DNA and mRNA sequencing of the coding regions of the human albumin gene (ALB) and of its intron/exon junctions has revealed twenty-one different molecular defects causing congenital analbuminaemia (CAA). SCOPE OF REVIEW To describe the mutations in molecular terms and to present the current knowledge about the most important biochemical and clinical effects of CAA. MAJOR CONCLUSIONS CAA is rare, but its frequency seems to be significantly higher in restricted and minimally admixed populations. The condition affects especially the lipid metabolism but apart from a possible increased risk for atherosclerotic complications, it is generally associated with mild clinical symptoms in adults. By contrast, several reports indicate that analbuminaemic individuals may be at risk during the perinatal and childhood periods, in which they seem to show increased morbidity and mortality. The twenty-one causative defects include seven nonsense mutations, seven changes affecting splicing, five frame-shift/deletions, one frame-shift/insertion and one mutation in the start codon. These results indicate that the trait is an allelic heterogeneous disorder caused by homozygous (nineteen cases) or compound heterozygous (single case) inheritance of defects. Most mutations are unique, but one, named Kayseri, is responsible for about half of the known cases. GENERAL SIGNIFICANCE Study of the defects in the ALB resulting in CAA allows the identification of "hot spot" regions and contributes to understanding the molecular mechanism underlying the trait. Such studies could also give molecular information about different aspects of ALB regulation and shed light on the regulatory mechanisms involved in the synthesis of the protein. This article is part of a Special Issue entitled Serum Albumin.
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Affiliation(s)
- Lorenzo Minchiotti
- Department of Molecular Medicine, University of Pavia, I-27100 Pavia, Italy.
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Zarnack K, König J, Tajnik M, Martincorena I, Eustermann S, Stévant I, Reyes A, Anders S, Luscombe N, Ule J. Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell 2013; 152:453-66. [PMID: 23374342 PMCID: PMC3629564 DOI: 10.1016/j.cell.2012.12.023] [Citation(s) in RCA: 336] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 09/22/2012] [Accepted: 12/12/2012] [Indexed: 11/26/2022]
Abstract
There are ~650,000 Alu elements in transcribed regions of the human genome. These elements contain cryptic splice sites, so they are in constant danger of aberrant incorporation into mature transcripts. Despite posing a major threat to transcriptome integrity, little is known about the molecular mechanisms preventing their inclusion. Here, we present a mechanism for protecting the human transcriptome from the aberrant exonization of transposable elements. Quantitative iCLIP data show that the RNA-binding protein hnRNP C competes with the splicing factor U2AF65 at many genuine and cryptic splice sites. Loss of hnRNP C leads to formation of previously suppressed Alu exons, which severely disrupt transcript function. Minigene experiments explain disease-associated mutations in Alu elements that hamper hnRNP C binding. Thus, by preventing U2AF65 binding to Alu elements, hnRNP C plays a critical role as a genome-wide sentinel protecting the transcriptome. The findings have important implications for human evolution and disease.
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Affiliation(s)
- Kathi Zarnack
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Julian König
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Mojca Tajnik
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1104 Ljubljana, Slovenia
| | - Iñigo Martincorena
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Isabelle Stévant
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alejandro Reyes
- EMBL, Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Simon Anders
- EMBL, Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Nicholas M. Luscombe
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- UCL Genetics Institute, Department of Genetics, Environment and Evolution, University College London, Gower Street, London WC1E 6BT, UK
- Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
- Okinawa Institute for Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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Radic CP, Rossetti LC, Abelleyro MM, Candela M, Pérez Bianco R, de Tezanos Pinto M, Larripa IB, Goodeve A, De Brasi CD. Assessment of the F9 genotype-specific FIX inhibitor risks and characterisation of 10 novel severe F9 defects in the first molecular series of Argentinian patients with haemophilia B. Thromb Haemost 2012; 109:24-33. [PMID: 23093250 DOI: 10.1160/th12-05-0302] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 09/13/2012] [Indexed: 11/05/2022]
Abstract
In haemophilia B (HB) (factor IX [FIX] deficiency), F9 genotype largely determines clinical phenotype. Aimed to characterise Argentinian families with HB, this study presents F9 genotype frequencies and their specific FIX inhibitor risk and 10 novel F9 mutations. Ninety-one DNA samples from HB patients and relatives were subjected to a new scheme: a primary screen for large deletions, a secondary screen for point mutations using conformation sensitive gel electrophoresis, DNA-sequencing and bioinformatic analysis. Our unbiased HB population (N=52) (77% with severe, 11.5% moderate and 11.5% mild HB) showed 32 missense (61.5%), including three novel mutations predicting specific structural/functional defects in silico , seven nonsense (13.5%) (one novel), five large deletions, four splice including three novel mutations affecting predicted splicing scores, three indels (two novel) and one Leiden mutation. Our comprehensive HB population included five patients with long-lasting FIX inhibitors: three nonsense (p.E35* (novel), p.R75*, p.W240*) and two entire- F9 deletions. Another patient with an indel (p.A26Rfs*14) developed transient inhibitors. A case-control analysis, based on our global prevalence of 3.05% for developing inhibitors in HB revealed that missense mutations were associated with a low risk odds ratio (OR) of 0.05 and a prevalence of 0.39%, whereas nonsense and entire- F9 deletions had significantly higher risks (OR 11.0 and 32.7) and prevalence (14.3% and 44.5%, respectively). Our cost-effective practical approach enabled identification of the causative mutation in all 55 Argentine families with HB, analysis of the molecular pathology of novel F9 defects and determination of mutation-associated FIX inhibitor risks.
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Affiliation(s)
- Claudia Pamela Radic
- Molecular Genetics of Haemophilia Laboratory, Instituto de Medicina Experimental IMEX, CONICET-Academia Nacional de Medicina, Pacheco de Melo 3081, Ciudad de Buenos Aires 1425, Argentina.
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Kameyama T, Suzuki H, Mayeda A. Re-splicing of mature mRNA in cancer cells promotes activation of distant weak alternative splice sites. Nucleic Acids Res 2012; 40:7896-906. [PMID: 22675076 PMCID: PMC3439910 DOI: 10.1093/nar/gks520] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Transcripts of the human tumor susceptibility gene 101 (TSG101) are aberrantly spliced in many cancers. A major aberrant splicing event on the TSG101 pre-mRNA involves joining of distant alternative 5′ and 3′ splice sites within exon 2 and exon 9, respectively, resulting in the extensive elimination of the mRNA. The estimated strengths of the alternative splice sites are much lower than those of authentic splice sites. We observed that the equivalent aberrant mRNA could be generated from an intron-less TSG101 gene expressed ectopically in breast cancer cells. Remarkably, we identified a pathway-specific endogenous lariat RNA consisting solely of exonic sequences, predicted to be generated by a re-splicing between exon 2 and exon 9 on the spliced mRNA. Our results provide evidence for a two-step splicing pathway in which the initial constitutive splicing removes all 14 authentic splice sites, thereby bringing the weak alternative splice sites into close proximity. We also demonstrate that aberrant multiple-exon skipping of the fragile histidine triad (FHIT) pre-mRNA in cancer cells occurs via re-splicing of spliced FHIT mRNA. The re-splicing of mature mRNA can potentially generate mutation-independent diversity in cancer transcriptomes. Conversely, a mechanism may exist in normal cells to prevent potentially deleterious mRNA re-splicing events.
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Affiliation(s)
- Toshiki Kameyama
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
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De Conti L, Skoko N, Buratti E, Baralle M. Complexities of 5'splice site definition: implications in clinical analyses. RNA Biol 2012; 9:911-23. [PMID: 22617876 DOI: 10.4161/rna.20386] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
In higher eukaryotes, the 5' splice site (5'ss) is initially recognized through an RNA-RNA interaction by U1 small nuclear ribonucleoprotein (U1 snRNP). This event represents one of the key steps in initial spliceosomal assembly and many disease-associated mutations in humans often disrupt this process. Beside base pair complementarity, 5'ss recognition can also be modified by additional factors such as RNA secondary structures or the specific binding of other nuclear proteins. In this work, we have focused on investigating a few examples of changes detected within the 5'ss in patients, that would not be immediately considered "disease causing mutations". We show that the splicing outcome of very similar mutations can be very different due to variations in trans-acting factor(s) interactions and specific context influences. Using several NF1 donor sites and SELEX approaches as experimental models, we have examined the binding properties of particular sequence motifs such as GGGU found in donor sites, and how the sequence context can change their interaction with hnRNPs such as H/F and A1/A2. Our results clearly show that even minor differences in local nucleotide context can differentially affect the binding ability of these factors to the GGGU core. Finally, using a previously identified mutation in KCNH2 that resulted in intron retention we show how very similar 5'ss mutations found in patients can have a very different splicing outcome due to the neighbouring sequence context, thus highlighting the general need to approach splicing problems with suitable experimental approaches.
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Affiliation(s)
- Laura De Conti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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Caridi G, Dagnino M, Di Duca M, Pinto H, Espinheira MDC, Guerra A, Fernandes S, Campagnoli M, Galliano M, Minchiotti L. A novel splicing mutation causes analbuminemia in a Portuguese boy. Mol Genet Metab 2012; 105:479-83. [PMID: 22227324 DOI: 10.1016/j.ymgme.2011.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 12/12/2011] [Accepted: 12/12/2011] [Indexed: 12/25/2022]
Abstract
Analbuminemia is a rare autosomal recessive disorder manifested by the absence or severe reduction of circulating serum albumin in homozygous or compound heterozygous subjects. It is an allelic heterogeneous defect, caused by a variety of mutations within the albumin gene. The analbuminemic condition was suspected in a Portuguese boy who presented with low albumin level (about 3.8 g/L) and a significant hypercholesterolemia, but with no clinical findings. The albumin gene was screened by single strand conformational polymorphism and heteroduplex analysis and submitted to direct DNA sequencing. The proband was found to be homozygous for a previously unreported G>A change at position c.1289+1, the first base of intron 10, which inactivates the strongly conserved GT dinucleotide at the 5' splice site consensus sequence of the intron. The effect of this mutation was evaluated by examining the cDNA obtained by RT-PCR from the albumin mRNA extracted from proband's leukocytes. The splicing defect results in the skipping of the preceding exon. The subsequent reading frame-shift in exon 11 produces a premature stop codon located 33 codons downstream the 5' end of the exon. This extensive cDNA alteration is responsible for the analbuminemic trait. Both parents were found to be heterozygous for the same mutation. DNA and cDNA sequence analysis established the diagnosis of congenital analbuminemia in the proband. The effects of the so far identified splice-site mutations in the albumin gene are discussed.
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Affiliation(s)
- Gianluca Caridi
- Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini IRCCS, Genova, Italy.
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Abstract
Defects at the level of pre-mRNA splicing represent a common source of disease mutations in almost all known diseases with a genetic aetiology. In general, it is commonly accepted that 15% of all pathogenic mutations are caused by splicing defects. However, this is probably a conservative estimate since clinical practice has only recently begun to routinely assess for this types of abnormalities. Therefore, it is expected that many currently unclassified or apparently harmless genetic variants will really turn out to be splicing-affecting defects. It is also well known that some genes are more susceptible than others to alterations in their splicing processes. Among these genes, one of the most representative is the NF-1 gene. In this gene, almost 50% of all reported disease-causing mutations can be directly attributed to alterations of the pre-mRNA process. In this chapter, we review the splicing process of the NF-1 gene and the most commonly used methods to identify splicing alterations. In particular, we provide practical notes on how to perform this analysis to maximize the chance of correctly identifying aberrant pre-mRNA splicing events in this gene.
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46
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Wang J, Zhang J, Li K, Zhao W, Cui Q. SpliceDisease database: linking RNA splicing and disease. Nucleic Acids Res 2011; 40:D1055-9. [PMID: 22139928 PMCID: PMC3245055 DOI: 10.1093/nar/gkr1171] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
RNA splicing is an important aspect of gene regulation in many organisms. Splicing of RNA is regulated by complicated mechanisms involving numerous RNA-binding proteins and the intricate network of interactions among them. Mutations in cis-acting splicing elements or its regulatory proteins have been shown to be involved in human diseases. Defects in pre-mRNA splicing process have emerged as a common disease-causing mechanism. Therefore, a database integrating RNA splicing and disease associations would be helpful for understanding not only the RNA splicing but also its contribution to disease. In SpliceDisease database, we manually curated 2337 splicing mutation disease entries involving 303 genes and 370 diseases, which have been supported experimentally in 898 publications. The SpliceDisease database provides information including the change of the nucleotide in the sequence, the location of the mutation on the gene, the reference Pubmed ID and detailed description for the relationship among gene mutations, splicing defects and diseases. We standardized the names of the diseases and genes and provided links for these genes to NCBI and UCSC genome browser for further annotation and genomic sequences. For the location of the mutation, we give direct links of the entry to the respective position/region in the genome browser. The users can freely browse, search and download the data in SpliceDisease at http://cmbi.bjmu.edu.cn/sdisease.
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Affiliation(s)
- Juan Wang
- Department of Biomedical Informatics, Peking University Health Science Center, MOE Key Laboratory of Molecular Cardiology, Peking University, Beijing 100191, China.
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Rubtsov PM, Igudin EL, Pichugina MY, Spirin PV, Prassolov VS, Tyul’pakov AN. Characterization of a new splicing mutation in the steroid 21-hydroxylase gene. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:815-20. [DOI: 10.1134/s1068162011060124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Kralovicova J, Hwang G, Asplund AC, Churbanov A, Smith CIE, Vorechovsky I. Compensatory signals associated with the activation of human GC 5' splice sites. Nucleic Acids Res 2011; 39:7077-91. [PMID: 21609956 PMCID: PMC3167603 DOI: 10.1093/nar/gkr306] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
GC 5′ splice sites (5′ss) are present in ∼1% of human introns, but factors promoting their efficient selection are poorly understood. Here, we describe a case of X-linked agammaglobulinemia resulting from a GC 5′ss activated by a mutation in BTK intron 3. This GC 5′ss was intrinsically weak, yet it was selected in >90% primary transcripts in the presence of a strong and intact natural GT counterpart. We show that efficient selection of this GC 5′ss required a high density of GAA/CAA-containing splicing enhancers in the exonized segment and was promoted by SR proteins 9G8, Tra2β and SC35. The GC 5′ss was efficiently inhibited by splice-switching oligonucleotides targeting either the GC 5′ss itself or the enhancer. Comprehensive analysis of natural GC-AG introns and previously reported pathogenic GC 5′ss showed that their efficient activation was facilitated by higher densities of splicing enhancers and lower densities of silencers than their GT 5′ss equivalents. Removal of the GC-AG introns was promoted to a minor extent by the splice-site strength of adjacent exons and inhibited by flanking Alu repeats, with the first downstream Alus located on average at a longer distance from the GC 5′ss than other transposable elements. These results provide new insights into the splicing code that governs selection of noncanonical splice sites.
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Affiliation(s)
- Jana Kralovicova
- University of Southampton School of Medicine, Division of Human Genetics, Southampton SO16 6YD, UK
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49
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Betz B, Theiss S, Aktas M, Konermann C, Goecke TO, Möslein G, Schaal H, Royer-Pokora B. Comparative in silico analyses and experimental validation of novel splice site and missense mutations in the genes MLH1 and MSH2. J Cancer Res Clin Oncol 2011; 136:123-34. [PMID: 19669161 DOI: 10.1007/s00432-009-0643-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Accepted: 07/17/2009] [Indexed: 12/24/2022]
Abstract
Hereditary non-polyposis colorectal cancer, an autosomal dominant predisposition to colorectal cancer and other malignancies, is caused by inactivating mutations of DNA mismatch repair genes, mainly MLH1 and MSH2. Missense mutations affect protein structure or function, but may also cause aberrant splicing, if located within splice sites (ss) or cis-acting sequences of splicing regulatory proteins, i.e., exonic splicing enhancers or exonic splicing silencers. Despite significant progress of ss scoring algorithms, the prediction for the impact of mutations on splicing is still unsatisfactory. For this study, we assessed ten ss and nine missense mutations outside ss in MLH1 and MSH2, including eleven newly identified mutations, and experimentally analyzed their effect at the RNA level. We additionally tested and compared the reliability of several web-based programs for the prediction of splicing outcome for these mutations.
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Affiliation(s)
- Beate Betz
- Institut fuer Humangenetik, Universitaetsklinikum Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
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Fu Y, Masuda A, Ito M, Shinmi J, Ohno K. AG-dependent 3'-splice sites are predisposed to aberrant splicing due to a mutation at the first nucleotide of an exon. Nucleic Acids Res 2011; 39:4396-404. [PMID: 21288883 PMCID: PMC3105431 DOI: 10.1093/nar/gkr026] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In pre-mRNA splicing, a conserved AG/G at the 3′-splice site is recognized by U2AF35. A disease-causing mutation abrogating the G nucleotide at the first position of an exon (E+1) causes exon skipping in GH1, FECH and EYA1, but not in LPL or HEXA. Knockdown of U2AF35 enhanced exon skipping in GH1 and FECH. RNA-EMSA revealed that wild-type FECH requires U2AF35 but wild-type LPL does not. A series of artificial mutations in the polypyrimidine tracts of GH1, FECH, EYA1, LPL and HEXA disclosed that a stretch of at least 10–15 pyrimidines is required to ensure normal splicing in the presence of a mutation at E+1. Analysis of nine other disease-causing mutations at E+1 detected five splicing mutations. Our studies suggest that a mutation at the AG-dependent 3′-splice site that requires U2AF35 for spliceosome assembly causes exon skipping, whereas one at the AG-independent 3′-splice site that does not require U2AF35 gives rise to normal splicing. The AG-dependence of the 3′-splice site that we analyzed in disease-causing mutations at E+1 potentially helps identify yet unrecognized splicing mutations at E+1.
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Affiliation(s)
- Yuan Fu
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-8550, Japan
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