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Li H, Zheng K, Xie M. A novel small deletion in CWC27 gene associated with CWC27-related spliceosomeopathy. Ophthalmic Genet 2024; 45:537-541. [PMID: 38956876 DOI: 10.1080/13816810.2024.2368791] [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: 09/21/2023] [Revised: 06/02/2024] [Accepted: 06/11/2024] [Indexed: 07/04/2024]
Abstract
BACKGROUND CWC27-related spliceosomeopathy is a rare autosomal recessive disorder with only 14 patients have been reported. It is characterized by retinal degeneration, short stature, skeletal anomalies, and neurological defects. We described the clinical features of a Chinese patient with CWC27-related spliceosomeopathy and identified the pathogenic variant. METHODS The affected subject underwent detailed ophthalmic examinations. Systemic abnormalities were assessed, including body height, craniofacial morphology, oral cavity, hands, feet, hair and skin. Genomic DNA was isolated from peripheral blood and sequenced by next-generation sequencing. Sanger sequencing was performed for validation and segregation. RESULTS The patient had poor vision, nyctalopia and nystagmus from childhood. Fundoscopy revealed extensive chorioretinal atrophy with numerous scattered greyish pigmentation. Severe circular areas of macular atrophy were observed. Optical coherent tomography showed reduced retinal thickness with nearly absent ellipsoid zone and retinal pigment epithelium. In addition, craniofacial abnormalities, short statue, brachydactyly, dental anomalies, cafe-au-lait spots, scant hair, absent eyebrows and thin eyelashes were documented. Genetic analysis revealed a novel homozygous novel small deletion c.1133delG(p.G378Efs*12) in CWC27 (NM_005869.2). CONCLUSIONS We present a patient with early-onset retinitis pigmentosa and marked syndromic features. A novel CWC27 pathogenic variant was identified. Our findings broaden the clinical and mutation spectrum of CWC27-related spliceosomeopathy, and could be helpful in diagnosis of this rare disease.
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Affiliation(s)
- Huajin Li
- Department of Ophthalmology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Kailing Zheng
- Department of Ophthalmology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Maosong Xie
- Department of Ophthalmology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
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2
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Keuthan CJ, Karma S, Zack DJ. Alternative RNA Splicing in the Retina: Insights and Perspectives. Cold Spring Harb Perspect Med 2023; 13:a041313. [PMID: 36690463 PMCID: PMC10547393 DOI: 10.1101/cshperspect.a041313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Alternative splicing is a fundamental and highly regulated post-transcriptional process that enhances transcriptome and proteome diversity. This process is particularly important in neuronal tissues, such as the retina, which exhibit some of the highest levels of differentially spliced genes in the body. Alternative splicing is regulated both temporally and spatially during neuronal development, can be cell-type-specific, and when altered can cause a number of pathologies, including retinal degeneration. Advancements in high-throughput sequencing technologies have facilitated investigations of the alternative splicing landscape of the retina in both healthy and disease states. Additionally, innovations in human stem cell engineering, specifically in the generation of 3D retinal organoids, which recapitulate many aspects of the in vivo retinal microenvironment, have aided studies of the role of alternative splicing in human retinal development and degeneration. Here we review these advances and discuss the ongoing development of strategies for the treatment of alternative splicing-related retinal disease.
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Affiliation(s)
- Casey J Keuthan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Sadik Karma
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Donald J Zack
- Departments of Ophthalmology, Wilmer Eye Institute, Neuroscience, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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3
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Bohnsack KE, Yi S, Venus S, Jankowsky E, Bohnsack MT. Cellular functions of eukaryotic RNA helicases and their links to human diseases. Nat Rev Mol Cell Biol 2023; 24:749-769. [PMID: 37474727 DOI: 10.1038/s41580-023-00628-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2023] [Indexed: 07/22/2023]
Abstract
RNA helicases are highly conserved proteins that use nucleoside triphosphates to bind or remodel RNA, RNA-protein complexes or both. RNA helicases are classified into the DEAD-box, DEAH/RHA, Ski2-like, Upf1-like and RIG-I families, and are the largest class of enzymes active in eukaryotic RNA metabolism - virtually all aspects of gene expression and its regulation involve RNA helicases. Mutation and dysregulation of these enzymes have been linked to a multitude of diseases, including cancer and neurological disorders. In this Review, we discuss the regulation and functional mechanisms of RNA helicases and their roles in eukaryotic RNA metabolism, including in transcription regulation, pre-mRNA splicing, ribosome assembly, translation and RNA decay. We highlight intriguing models that link helicase structure, mechanisms of function (such as local strand unwinding, translocation, winching, RNA clamping and displacing RNA-binding proteins) and biological roles, including emerging connections between RNA helicases and cellular condensates formed through liquid-liquid phase separation. We also discuss associations of RNA helicases with human diseases and recent efforts towards the design of small-molecule inhibitors of these pivotal regulators of eukaryotic gene expression.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
| | - Soon Yi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah Venus
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Moderna, Cambridge, MA, USA.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
- Göttingen Centre for Molecular Biosciences, University of Göttingen, Göttingen, Germany.
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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4
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Turner BRH, Mellor C, McElroy C, Bowen N, Gu W, Knill C, Itasaki N. Non-ubiquitous expression of core spliceosomal protein SmB/B' in chick and mouse embryos. Dev Dyn 2023; 252:276-293. [PMID: 36058892 PMCID: PMC10087933 DOI: 10.1002/dvdy.537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/02/2022] [Accepted: 08/25/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Although splicing is an integral part of the expression of many genes in our body, genetic syndromes with spliceosomal defects affect only specific tissues. To help understand the mechanism, we investigated the expression pattern of a core protein of the major spliceosome, SmB/B' (Small Nuclear Ribonucleoprotein Polypeptides B/B'), which is encoded by SNRPB. Loss-of-function mutations of SNRPB in humans cause cerebro-costo-mandibular syndrome (CCMS) characterized by rib gaps, micrognathia, cleft palate, and scoliosis. Our expression analysis focused on the affected structures as well as non-affected tissues, using chick and mouse embryos as model animals. RESULTS Embryos at young stages (gastrula) showed ubiquitous expression of SmB/B'. However, the level and pattern of expression became tissue-specific as differentiation proceeded. The regions relating to CCMS phenotypes such as cartilages of ribs and vertebrae and palatal mesenchyme express SmB/B' in the nucleus sporadically. However, cartilages that are not affected in CCMS also showed similar expressions. Another spliceosomal gene, SNRNP200, which mutations cause retinitis pigmentosa, was also prominently expressed in cartilages in addition to the retina. CONCLUSION The expression of SmB/B' is spatiotemporally regulated during embryogenesis despite the ubiquitous requirement of the spliceosome, however, the expression pattern is not strictly correlated with the phenotype presentation.
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Affiliation(s)
| | | | - Clara McElroy
- Faculty of Health Sciences, University of Bristol, Bristol, UK
| | - Natalie Bowen
- Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Wenjia Gu
- Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Chris Knill
- Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Nobue Itasaki
- Faculty of Health Sciences, University of Bristol, Bristol, UK
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5
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Rodríguez-Muñoz A, García-Bohórquez B, Udaondo P, Hervás-Ontiveros A, Salom D, Aller E, Jaijo T, García-García G, Millán J. CONCOMITANT MUTATIONS IN INHERITED RETINAL DYSTROPHIES: Why the Reproductive and Therapeutic Counseling Should Be Addressed Cautiously. Retina 2021; 41:1966-1975. [PMID: 33411470 DOI: 10.1097/iae.0000000000003103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
PURPOSE To highlight the challenge of correct reproductive and therapeutic counseling in complex pedigrees with different inherited retinal dystrophies (IRD). METHODS Two hundred eight patients diagnosed with nonsyndromic IRD underwent full ophthalmologic examination and molecular analysis using targeted next-generation sequencing. RESULTS Five families (4%) carried mutations in more than one gene that contribute to different IRD. Family fRPN-NB had a dominant mutation in SNRNP200, which was present in nine affected individuals and four unaffected, and a mutation in RP2 among 11 family members. Family fRPN-142 carried a mutation in RPGR that cosegregated with the disease in all affected individuals. In addition, the proband also harbored two disease-causing mutations in the genes BEST1 and SNRNP200. Family fRPN-169 beared compound heterozygous mutations in USH2A and a dominant mutation in RP1. Genetic testing of fRPN-194 determined compound heterozygous mutations in CNGA3 and a dominant mutation in PRPF8 only in the proband. Finally, fRPN-219 carried compound heterozygous mutations in the genes ABCA4 and TYR. CONCLUSION These findings reinforce the complexity of IRD and underscore the need for the combination of high-throughput genetic testing and clinical characterization. Because of these features, the reproductive and therapeutic counseling for IRD must be approached with caution.
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Affiliation(s)
- Ana Rodríguez-Muñoz
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
| | - Belén García-Bohórquez
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
| | - Patricia Udaondo
- Department of Ophthalmology, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Ana Hervás-Ontiveros
- Department of Ophthalmology, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - David Salom
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
- Department of Ophthalmology Hospital de Manises, Valencia, Spain; and
| | - Elena Aller
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
- Unit of Genetics, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Teresa Jaijo
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
- Unit of Genetics, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Gema García-García
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
| | - José Millán
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
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6
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Wood KA, Eadsforth MA, Newman WG, O'Keefe RT. The Role of the U5 snRNP in Genetic Disorders and Cancer. Front Genet 2021; 12:636620. [PMID: 33584830 PMCID: PMC7876476 DOI: 10.3389/fgene.2021.636620] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022] Open
Abstract
Pre-mRNA splicing is performed by the spliceosome, a dynamic macromolecular complex consisting of five small uridine-rich ribonucleoprotein complexes (the U1, U2, U4, U5, and U6 snRNPs) and numerous auxiliary splicing factors. A plethora of human disorders are caused by genetic variants affecting the function and/or expression of splicing factors, including the core snRNP proteins. Variants in the genes encoding proteins of the U5 snRNP cause two distinct and tissue-specific human disease phenotypes – variants in PRPF6, PRPF8, and SNRP200 are associated with retinitis pigmentosa (RP), while variants in EFTUD2 and TXNL4A cause the craniofacial disorders mandibulofacial dysostosis Guion-Almeida type (MFDGA) and Burn-McKeown syndrome (BMKS), respectively. Furthermore, recurrent somatic mutations or changes in the expression levels of a number of U5 snRNP proteins (PRPF6, PRPF8, EFTUD2, DDX23, and SNRNP40) have been associated with human cancers. How and why variants in ubiquitously expressed spliceosome proteins required for pre-mRNA splicing in all human cells result in tissue-restricted disease phenotypes is not clear. Additionally, why variants in different, yet interacting, proteins making up the same core spliceosome snRNP result in completely distinct disease outcomes – RP, craniofacial defects or cancer – is unclear. In this review, we define the roles of different U5 snRNP proteins in RP, craniofacial disorders and cancer, including how disease-associated genetic variants affect pre-mRNA splicing and the proposed disease mechanisms. We then propose potential hypotheses for how U5 snRNP variants cause tissue specificity resulting in the restricted and distinct human disorders.
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Affiliation(s)
- Katherine A Wood
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Megan A Eadsforth
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
| | - William G Newman
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Raymond T O'Keefe
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
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7
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Zhang T, Bai J, Zhang X, Zheng X, Lu N, Liang Z, Lin L, Chen Y. SNRNP200 Mutations Cause Autosomal Dominant Retinitis Pigmentosa. Front Med (Lausanne) 2020; 7:588991. [PMID: 33553197 PMCID: PMC7859630 DOI: 10.3389/fmed.2020.588991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/18/2020] [Indexed: 02/05/2023] Open
Abstract
The small nuclear ribonucleoprotein 200 kDa (SNRNP200) gene plays a key role in the maturation of pre-message RNA (pre-mRNA) splicing with the indication for the etiology of retinitis pigmentosa (RP). Gene recognition can facilitate the diagnosis of these patients for better clinical management, treatment and counseling. This study aimed to outline the causative mutation in a Chinese family and the pathogenic mechanism of this SNRNP200 mutation in RP. Eighteen individuals from the affected family underwent a complete ophthalmic examination. Whole exome sequencing (WES) was conducted to identify the pathogenic variant in the proband, which was then confirmed by Sanger sequencing. Expression of the SNRNP200 transcript in zebrafish was identified via whole mount in situ hybridization. Morpholino oligonucleotide (MO) and SNRNP200 wild and mutant mRNA were injected into zebrafish embryos followed by analyses of the systemic changes and retinal phenotypes using immunofluorescence. Heterozygous SNRNP200c.C6088T (p.Arg2030Cys) mutation was ascertained in two members of this family: the proband and his father (II-2). Overexpression of SNRNP200Arg2030Cys, but not SNRNP200WT caused systemic deformities in the wild-type zebrafish embryos with the retina primarily injured, and significantly increased death rates in the morphant embryos, in which the orthologous zebrafish SNRNP200 gene was blocked. In conclusion, this study reports a novel heterozygous SNRNP200c.C6088T mutation, which is evidenced to cause RP via a dominant-negative effect.
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Affiliation(s)
- Tao Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- The Clinical Research Center of the First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Jingshan Bai
- Department of Ophthalmology, The Second People's Hospital of Dongying, Dongying, China
- Department of Ophthalmology, The Dawang Hospital of Guangrao of Dongying, Dongying, China
| | - Xinyi Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- The Clinical Research Center of the First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Xiaowei Zheng
- Department of Ophthalmology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- The Clinical Research Center of the First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Nan Lu
- Department of Cardiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Zhongyin Liang
- Department of Bioinformatics, Berry Genomics Co., Ltd., Beijing, China
| | - Ling Lin
- The Clinical Research Center of the First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Department of Rheumatology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- *Correspondence: Ling Lin
| | - Yongsong Chen
- The Clinical Research Center of the First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Department of Endocrinology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Yongsong Chen
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8
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Gerth-Kahlert C, Koller S, Hanson JVM, Baehr L, Tiwari A, Kivrak-Pfiffner F, Bahr A, Berger W. Genotype-Phenotype Analysis of a Novel Recessive and a Recurrent Dominant SNRNP200 Variant Causing Retinitis Pigmentosa. Invest Ophthalmol Vis Sci 2019; 60:2822-2835. [PMID: 31260034 DOI: 10.1167/iovs.18-25643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To compare phenotype variability in retinitis pigmentosa patients with recessive and dominant mutations in the SNRNP200 gene. Methods In a retrospective study, patients of two unrelated families were identified: family A, five patients aged 36 to 77 years; family B, one patient aged 9 years and his asymptomatic parents and sister. All patients received a comprehensive eye examination with a detailed retinal functional and morphologic assessment. Genetic testing was performed by whole exome sequencing (WES) in the index patient from each family. Genes described to be involved in eye diseases (n > 450) were screened for rare variants and segregation analysis was performed. Results A known heterozygous missense variant (c.3260C>T, p.(Ser1087Leu)) in the SNRNP200 gene was identified in the index patient of family A while a novel homozygous missense mutation (c.1634G>A, p.(Arg545His)) was found in the index patient of family B. Nyctalopia and photophobia were reported by 6/6 and 2/6 patients, respectively. The phenotype associated with the dominant mutation was characterized by variable disease onset (early childhood to the sixth decade of life), disease severity (visual acuity of 20/20-20/200 in the seventh to eighth decade), and advanced rod-cone dysfunction. Characteristics of recessive disease included distinct fundus changes of dot-like hypopigmentation together with retinal atrophy and severe rod-cone dysfunction. Conclusions The phenotype characteristics in autosomal dominant and recessive SNRNP200 mutations show distinct features, with earlier severe disease in the recessive case and a variable disease expression in the dominant inheritance pattern.
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Affiliation(s)
| | - Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
| | - James V M Hanson
- Department of Ophthalmology, University Hospital Zurich, Zurich, Switzerland
| | - Luzy Baehr
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
| | - Amit Tiwari
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
| | - Fatma Kivrak-Pfiffner
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
| | - Angela Bahr
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University and ETH Zurich, Zurich, Switzerland
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9
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Yusuf IH, Birtel J, Shanks ME, Clouston P, Downes SM, Charbel Issa P, MacLaren RE. Clinical Characterization of Retinitis Pigmentosa Associated With Variants in SNRNP200. JAMA Ophthalmol 2019; 137:1295-1300. [PMID: 31486839 DOI: 10.1001/jamaophthalmol.2019.3298] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Importance SNRNP200 is a recently identified genetic cause of autosomal dominant retinitis pigmentosa (RP). However, the associated retinal phenotype is not well characterized. Objective To describe the retinal phenotype in patients with RP secondary to variants in SNRNP200. Design, Setting, and Participants This retrospective, case-series study was performed at 2 tertiary referral centers for inherited retinal diseases. Participants included 9 consecutive patients from 8 families with RP attributed to variants in SNRNP200. Data were collected from August 2017 to March 2018 and analyzed from May to July 2018. Main Outcomes and Measures Results of clinical evaluation, multimodal retinal imaging, and molecular genetic testing using targeted next-generation sequencing. Results Of the 9 patients included in the analysis (4 female and 5 male; mean [SD] age at presentation, 19 [15] years), each presented with nyctalopia, typically in the first 2 decades of life, although 2 patients experienced symptom onset in middle age. None had any consistent systemic features suggestive of syndromic RP. Retinal imaging studies and electroretinography findings were typical of a rod-predominant dystrophy with later involvement of cone photoreceptors. Phenotypic heterogeneity was typified by 4 unrelated patients with the common c.2041C>T SNRNP200 variant who demonstrated a variable age of disease onset (middle teenage years to the fourth decade of life). Disease progression was slow, with all but 1 patient maintaining visual acuity of better than 20/40 in the better-seeing eye in the fifth and sixth decades of life. Conclusions and Relevance These data suggest that variants in SNRNP200 result in nonsyndromic RP with a typical phenotype of a rod-predominant dystrophy. Significant phenotypic heterogeneity and nonpenetrance were noted within some affected families. Symptom onset was typically within the first 2 decades of life, with slow progression and well-preserved visual acuities into the fifth and sixth decades.
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Affiliation(s)
- Imran H Yusuf
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, Oxford University, John Radcliffe Hospital, Oxford, United Kingdom.,Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS (National Health Service) Foundation Trust, Oxford, United Kingdom
| | - Johannes Birtel
- Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Morag E Shanks
- Oxford Medical Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, The Churchill Hospital, Oxford, United Kingdom
| | - Penny Clouston
- Oxford Medical Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, The Churchill Hospital, Oxford, United Kingdom
| | - Susan M Downes
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, Oxford University, John Radcliffe Hospital, Oxford, United Kingdom.,Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS (National Health Service) Foundation Trust, Oxford, United Kingdom
| | - Peter Charbel Issa
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, Oxford University, John Radcliffe Hospital, Oxford, United Kingdom.,Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS (National Health Service) Foundation Trust, Oxford, United Kingdom.,Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Robert E MacLaren
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, Oxford University, John Radcliffe Hospital, Oxford, United Kingdom.,Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS (National Health Service) Foundation Trust, Oxford, United Kingdom
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10
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snRNP proteins in health and disease. Semin Cell Dev Biol 2017; 79:92-102. [PMID: 29037818 DOI: 10.1016/j.semcdb.2017.10.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/09/2017] [Accepted: 10/12/2017] [Indexed: 01/16/2023]
Abstract
Split gene architecture of most human genes requires removal of intervening sequences by mRNA splicing that occurs on large multiprotein complexes called spliceosomes. Mutations compromising several spliceosomal components have been recorded in degenerative syndromes and haematological neoplasia, thereby highlighting the importance of accurate splicing execution in homeostasis of assorted adult tissues. Moreover, insufficient splicing underlies defective development of craniofacial skeleton and upper extremities. This review summarizes recent advances in the understanding of splicing factor function deduced from cryo-EM structures. We combine these data with the characterization of splicing factors implicated in hereditary or somatic disorders, with a focus on potential functional consequences the mutations may elicit in spliceosome assembly and/or performance. Given aberrant splicing or perturbations in splicing efficiency substantially underpin disease pathogenesis, profound understanding of the mis-splicing principles may open new therapeutic vistas. In three major sections dedicated to retinal dystrophies, hereditary acrofacial syndromes, and haematological malignancies, we delineate the noticeable variety of conditions associated with dysfunctional splicing and accentuate recurrent patterns in splicing defects.
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11
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Genetic characterization and disease mechanism of retinitis pigmentosa; current scenario. 3 Biotech 2017; 7:251. [PMID: 28721681 DOI: 10.1007/s13205-017-0878-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 07/10/2017] [Indexed: 12/21/2022] Open
Abstract
Retinitis pigmentosa is a group of genetically transmitted disorders affecting 1 in 3000-8000 individual people worldwide ultimately affecting the quality of life. Retinitis pigmentosa is characterized as a heterogeneous genetic disorder which leads by progressive devolution of the retina leading to a progressive visual loss. It can occur in syndromic (with Usher syndrome and Bardet-Biedl syndrome) as well as non-syndromic nature. The mode of inheritance can be X-linked, autosomal dominant or autosomal recessive manner. To date 58 genes have been reported to associate with retinitis pigmentosa most of them are either expressed in photoreceptors or the retinal pigment epithelium. This review focuses on the disease mechanisms and genetics of retinitis pigmentosa. As retinitis pigmentosa is tremendously heterogeneous disorder expressing a multiplicity of mutations; different variations in the same gene might induce different disorders. In recent years, latest technologies including whole-exome sequencing contributing effectively to uncover the hidden genesis of retinitis pigmentosa by reporting new genetic mutations. In future, these advancements will help in better understanding the genotype-phenotype correlations of disease and likely to develop new therapies.
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12
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Van Cauwenbergh C, Coppieters F, Roels D, De Jaegere S, Flipts H, De Zaeytijd J, Walraedt S, Claes C, Fransen E, Van Camp G, Depasse F, Casteels I, de Ravel T, Leroy BP, De Baere E. Mutations in Splicing Factor Genes Are a Major Cause of Autosomal Dominant Retinitis Pigmentosa in Belgian Families. PLoS One 2017; 12:e0170038. [PMID: 28076437 PMCID: PMC5226823 DOI: 10.1371/journal.pone.0170038] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 12/27/2016] [Indexed: 12/14/2022] Open
Abstract
Purpose Autosomal dominant retinitis pigmentosa (adRP) is characterized by an extensive genetic heterogeneity, implicating 27 genes, which account for 50 to 70% of cases. Here 86 Belgian probands with possible adRP underwent genetic testing to unravel the molecular basis and to assess the contribution of the genes underlying their condition. Methods Mutation detection methods evolved over the past ten years, including mutation specific methods (APEX chip analysis), linkage analysis, gene panel analysis (Sanger sequencing, targeted next-generation sequencing or whole exome sequencing), high-resolution copy number screening (customized microarray-based comparative genomic hybridization). Identified variants were classified following American College of Medical Genetics and Genomics (ACMG) recommendations. Results Molecular genetic screening revealed mutations in 48/86 cases (56%). In total, 17 novel pathogenic mutations were identified: four missense mutations in RHO, five frameshift mutations in RP1, six mutations in genes encoding spliceosome components (SNRNP200, PRPF8, and PRPF31), one frameshift mutation in PRPH2, and one frameshift mutation in TOPORS. The proportion of RHO mutations in our cohort (14%) is higher than reported in a French adRP population (10.3%), but lower than reported elsewhere (16.5–30%). The prevalence of RP1 mutations (10.5%) is comparable to other populations (3.5%-10%). The mutation frequency in genes encoding splicing factors is unexpectedly high (altogether 19.8%), with PRPF31 the second most prevalent mutated gene (10.5%). PRPH2 mutations were found in 4.7% of the Belgian cohort. Two families (2.3%) have the recurrent NR2E3 mutation p.(Gly56Arg). The prevalence of the recurrent PROM1 mutation p.(Arg373Cys) was higher than anticipated (3.5%). Conclusions Overall, we identified mutations in 48 of 86 Belgian adRP cases (56%), with the highest prevalence in RHO (14%), RP1 (10.5%) and PRPF31 (10.5%). Finally, we expanded the molecular spectrum of PRPH2, PRPF8, RHO, RP1, SNRNP200, and TOPORS-associated adRP by the identification of 17 novel mutations.
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Affiliation(s)
- Caroline Van Cauwenbergh
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Frauke Coppieters
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Dimitri Roels
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Sarah De Jaegere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Helena Flipts
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
- Center for Human Genetics, University Hospitals Leuven, Louvain, Belgium
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Sophie Walraedt
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Charlotte Claes
- Center for Medical Genetics Antwerp, Antwerp University, Antwerp, Belgium
| | - Erik Fransen
- Center for Medical Genetics Antwerp, Antwerp University, Antwerp, Belgium
| | - Guy Van Camp
- Center for Medical Genetics Antwerp, Antwerp University, Antwerp, Belgium
| | - Fanny Depasse
- Department of Ophthalmology, Hôpital Erasme-ULB, Brussels, Belgium
| | - Ingele Casteels
- Department of Ophthalmology, University Hospitals Leuven, Louvain, Belgium
| | - Thomy de Ravel
- Center for Human Genetics, University Hospitals Leuven, Louvain, Belgium
| | - Bart P. Leroy
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
- Division of Ophthalmology & Center for Cellular & Molecular Therapy, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
- * E-mail:
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13
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Absmeier E, Santos KF, Wahl MC. Functions and regulation of the Brr2 RNA helicase during splicing. Cell Cycle 2016; 15:3362-3377. [PMID: 27792457 DOI: 10.1080/15384101.2016.1249549] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Pre-mRNA splicing entails the stepwise assembly of an inactive spliceosome, its catalytic activation, splicing catalysis and spliceosome disassembly. Transitions in this reaction cycle are accompanied by compositional and conformational rearrangements of the underlying RNA-protein interaction networks, which are driven and controlled by 8 conserved superfamily 2 RNA helicases. The Ski2-like helicase, Brr2, provides the key remodeling activity during spliceosome activation and is additionally implicated in the catalytic and disassembly phases of splicing, indicating that Brr2 needs to be tightly regulated during splicing. Recent structural and functional analyses have begun to unravel how Brr2 regulation is established via multiple layers of intra- and inter-molecular mechanisms. Brr2 has an unusual structure, including a long N-terminal region and a catalytically inactive C-terminal helicase cassette, which can auto-inhibit and auto-activate the enzyme, respectively. Both elements are essential, also serve as protein-protein interaction devices and the N-terminal region is required for stable Brr2 association with the tri-snRNP, tri-snRNP stability and retention of U5 and U6 snRNAs during spliceosome activation in vivo. Furthermore, a C-terminal region of the Prp8 protein, comprising consecutive RNase H-like and Jab1/MPN-like domains, can both up- and down-regulate Brr2 activity. Biochemical studies revealed an intricate cross-talk among the various cis- and trans-regulatory mechanisms. Comparison of isolated Brr2 to electron cryo-microscopic structures of yeast and human U4/U6•U5 tri-snRNPs and spliceosomes indicates how some of the regulatory elements exert their functions during splicing. The various modulatory mechanisms acting on Brr2 might be exploited to enhance splicing fidelity and to regulate alternative splicing.
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Affiliation(s)
- Eva Absmeier
- a Freie Universität Berlin, Laboratory of Structural Biochemistry , Berlin , Germany
| | - Karine F Santos
- a Freie Universität Berlin, Laboratory of Structural Biochemistry , Berlin , Germany
| | - Markus C Wahl
- a Freie Universität Berlin, Laboratory of Structural Biochemistry , Berlin , Germany.,b Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography , Berlin , Germany
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14
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Abstract
A majority of human genes contain non-coding intervening sequences – introns that must be precisely excised from the pre-mRNA molecule. This event requires the coordinated action of five major small nuclear ribonucleoprotein particles (snRNPs) along with additional non-snRNP splicing proteins. Introns must be removed with nucleotidal precision, since even a single nucleotide mistake would result in a reading frame shift and production of a non-functional protein. Numerous human inherited diseases are caused by mutations that affect splicing, including mutations in proteins which are directly involved in splicing catalysis. One of the most common hereditary diseases associated with mutations in core splicing proteins is retinitis pigmentosa (RP). So far, mutations in more than 70 genes have been connected to RP. While the majority of mutated genes are expressed specifically in the retina, eight target genes encode for ubiquitous core snRNP proteins (Prpf3, Prpf4, Prpf6, Prpf8, Prpf31, and SNRNP200/Brr2) and splicing factors (RP9 and DHX38). Why mutations in spliceosomal proteins, which are essential in nearly every cell in the body, causes a disease that displays such a tissue-specific phenotype is currently a mystery. In this review, we recapitulate snRNP functions, summarize the missense mutations which are found in spliceosomal proteins as well as their impact on protein functions and discuss specific models which may explain why the retina is sensitive to these mutations.
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Affiliation(s)
- Šárka Růžičková
- a Department of RNA Biology , Institute of Molecular Genetics AS CR , Prague , Czech Republic
| | - David Staněk
- a Department of RNA Biology , Institute of Molecular Genetics AS CR , Prague , Czech Republic
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15
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Ledoux S, Guthrie C. Retinitis Pigmentosa Mutations in Bad Response to Refrigeration 2 (Brr2) Impair ATPase and Helicase Activity. J Biol Chem 2016; 291:11954-65. [PMID: 27072132 DOI: 10.1074/jbc.m115.710848] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Indexed: 11/06/2022] Open
Abstract
Brr2 is an RNA-dependent ATPase required to unwind the U4/U6 snRNA duplex during spliceosome assembly. Mutations within the ratchet helix of the Brr2 RNA binding channel result in a form of degenerative human blindness known as retinitis pigmentosa (RP). The biochemical consequences of these mutations on Brr2's RNA binding, helicase, and ATPase activity have not yet been characterized. Therefore, we identified the largest construct of Brr2 that is soluble in vitro, which truncates the first 247 amino acids of the N terminus (Δ247-Brr2), to characterize the effects of the RP mutations on Brr2 activity. The Δ247-Brr2 RP mutants exhibit a gradient of severity of weakened RNA binding, reduced helicase activity, and reduced ATPase activity compared with wild type Δ247-Brr2. The globular C-terminal Jab1/Mpn1-like domain of Prp8 increases the ability of Δ247-Brr2 to bind the U4/U6 snRNA duplex at high pH and increases Δ247-Brr2's RNA-dependent ATPase activity and the extent of RNA unwinding. However, this domain of Prp8 does not differentially affect the Δ247-Brr2 RP mutants compared with the wild type Δ247-Brr2. When stimulated by Prp8, wild type Δ247-Brr2 is able to unwind long stable duplexes in vitro, and even the RP mutants capable of binding RNA with tight affinity are incapable of fully unwinding short duplex RNAs. Our data suggest that the RP mutations within the ratchet helix impair Brr2 translocation through RNA helices.
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Affiliation(s)
- Sarah Ledoux
- From the Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
| | - Christine Guthrie
- From the Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
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16
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Knocking Down Snrnp200 Initiates Demorphogenesis of Rod Photoreceptors in Zebrafish. J Ophthalmol 2015; 2015:816329. [PMID: 26137319 PMCID: PMC4469172 DOI: 10.1155/2015/816329] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/17/2014] [Accepted: 12/29/2014] [Indexed: 11/18/2022] Open
Abstract
Purpose. The small nuclear ribonucleoprotein 200 kDa (SNRNP200) gene is a fundamental component for precursor message RNA (pre-mRNA) splicing and has been implicated in the etiology of autosomal dominant retinitis pigmentosa (adRP). This study aims to determine the consequences of knocking down Snrnp200 in zebrafish. Methods. Expression of the Snrnp200 transcript in zebrafish was determined via whole mount in situ hybridization. Morpholino oligonucleotide (MO) aiming to knock down the expression of Snrnp200 was injected into zebrafish embryos, followed by analyses of aberrant splicing and expression of the U4/U6-U5 tri-small nuclear ribonucleoproteins (snRNPs) components and retina-specific transcripts. Systemic changes and retinal phenotypes were further characterized by histological study and immunofluorescence staining. Results. Snrnp200 was ubiquitously expressed in zebrafish. Knocking down Snrnp200 in zebrafish triggered aberrant splicing of the cbln1 gene, upregulation of other U4/U6-U5 tri-snRNP components, and downregulation of a panel of retina-specific transcripts. Systemic defects were found correlated with knockdown of Snrnp200 in zebrafish. Only demorphogenesis of rod photoreceptors was detected in the initial stage, mimicking the disease characteristics of RP. Conclusions. We conclude that knocking down Snrnp200 in zebrafish could alter regular splicing and expression of a panel of genes, which may eventually trigger rod defects.
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17
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Wickramasinghe VO, Gonzàlez-Porta M, Perera D, Bartolozzi AR, Sibley CR, Hallegger M, Ule J, Marioni JC, Venkitaraman AR. Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength. Genome Biol 2015; 16:201. [PMID: 26392272 PMCID: PMC4578845 DOI: 10.1186/s13059-015-0749-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/27/2015] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Sequential assembly of the human spliceosome on RNA transcripts regulates splicing across the human transcriptome. The core spliceosome component PRPF8 is essential for spliceosome assembly through its participation in ribonucleoprotein (RNP) complexes for splice-site recognition, branch-point formation and catalysis. PRPF8 deficiency is linked to human diseases like retinitis pigmentosa or myeloid neoplasia, but its genome-wide effects on constitutive and alternative splicing remain unclear. RESULTS Here, we show that alterations in RNA splicing patterns across the human transcriptome that occur in conditions of restricted cellular PRPF8 abundance are defined by the altered splicing of introns with weak 5' splice sites. iCLIP of spliceosome components reveals that PRPF8 depletion decreases RNP complex formation at most splice sites in exon-intron junctions throughout the genome. However, impaired splicing affects only a subset of human transcripts, enriched for mitotic cell cycle factors, leading to mitotic arrest. Preferentially retained introns and differentially used exons in the affected genes contain weak 5' splice sites, but are otherwise indistinguishable from adjacent spliced introns. Experimental enhancement of splice-site strength in mini-gene constructs overcomes the effects of PRPF8 depletion on the kinetics and fidelity of splicing during transcription. CONCLUSIONS Competition for PRPF8 availability alters the transcription-coupled splicing of RNAs in which weak 5' splice sites predominate, enabling diversification of human gene expression during biological processes like mitosis. Our findings exemplify the regulatory potential of changes in the core spliceosome machinery, which may be relevant to slow-onset human genetic diseases linked to PRPF8 deficiency.
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Affiliation(s)
- Vihandha O. Wickramasinghe
- The Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Box 197, Cambridge, CB2 0XZ UK
| | - Mar Gonzàlez-Porta
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - David Perera
- The Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Box 197, Cambridge, CB2 0XZ UK
| | - Arthur R. Bartolozzi
- The Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Box 197, Cambridge, CB2 0XZ UK
| | - Christopher R. Sibley
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG UK
| | - Martina Hallegger
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG UK
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG UK
| | - John C. Marioni
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ashok R. Venkitaraman
- The Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Box 197, Cambridge, CB2 0XZ UK
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18
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Benaglio P, San Jose PF, Avila-Fernandez A, Ascari G, Harper S, Manes G, Ayuso C, Hamel C, Berson EL, Rivolta C. Mutational screening of splicing factor genes in cases with autosomal dominant retinitis pigmentosa. Mol Vis 2014; 20:843-51. [PMID: 24959063 PMCID: PMC4063357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 06/16/2014] [Indexed: 11/04/2022] Open
Abstract
PURPOSE Mutations in genes encoding proteins from the tri-snRNP complex of the spliceosome account for more than 12% of cases of autosomal dominant retinitis pigmentosa (adRP). Although the exact mechanism by which splicing factor defects trigger photoreceptor death is not completely clear, their role in retinitis pigmentosa has been demonstrated by several genetic and functional studies. To test for possible novel associations between splicing factors and adRP, we screened four tri-snRNP splicing factor genes (EFTUD2, PRPF4, NHP2L1, and AAR2) as candidate disease genes. METHODS We screened up to 303 patients with adRP from Europe and North America who did not carry known RP mutations. Exon-PCR and Sanger methods were used to sequence the NHP2L1 and AAR2 genes, while the sequences of EFTUD2 and PRPF4 were obtained by using long-range PCRs spanning coding and non-coding regions followed by next-generation sequencing. RESULTS We detected novel missense changes in individual patients in the sequence of the genes PRPF4 and EFTUD2, but the role of these changes in relationship to disease could not be verified. In one other patient we identified a novel nucleotide substitution in the 5' untranslated region (UTR) of NHP2L1, which did not segregate with the disease in the family. CONCLUSIONS The absence of clearly pathogenic mutations in the candidate genes screened in our cohort suggests that EFTUD2, PRPF4, NHP2L1, and AAR2 are either not involved in adRP or are associated with the disease in rare instances, at least as observed in this study in patients of European and North American origin.
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Affiliation(s)
- Paola Benaglio
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Patricia Fernandez San Jose
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Almudena Avila-Fernandez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Giulia Ascari
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Shyana Harper
- The Berman-Gund Laboratory for the Study of Retinal Degenerations, Harvard Medical School, Massachusetts Eye and Ear, Boston, MA
| | - Gaël Manes
- INSERM U1051, Institut des Neurosciences de Montpellier, Hôpital Saint Eloi, Montpellier, France
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Christian Hamel
- INSERM U1051, Institut des Neurosciences de Montpellier, Hôpital Saint Eloi, Montpellier, France
| | - Eliot L. Berson
- The Berman-Gund Laboratory for the Study of Retinal Degenerations, Harvard Medical School, Massachusetts Eye and Ear, Boston, MA
| | - Carlo Rivolta
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
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19
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Chen X, Liu Y, Sheng X, Tam POS, Zhao K, Chen X, Rong W, Liu Y, Liu X, Pan X, Chen LJ, Zhao Q, Vollrath D, Pang CP, Zhao C. PRPF4 mutations cause autosomal dominant retinitis pigmentosa. Hum Mol Genet 2014; 23:2926-39. [PMID: 24419317 DOI: 10.1093/hmg/ddu005] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Retinitis pigmentosa (RP), a disease characterized by progressive loss of photoreceptors, exhibits significant genetic heterogeneity. Several genes associated with U4/U6-U5 triple small nuclear ribonucleoprotein (tri-snRNP) complex of the spliceosome have been implicated in autosomal dominant RP (adRP). HPrp4, encoded by PRPF4, regulates the stability of U4/U6 di-snRNP, which is essential for continuous splicing. Here, we identified two heterozygous variants in PRPF4, including c.-114_-97del in a simplex RP patient and c.C944T (p.Pro315Leu), which co-segregates with disease phenotype in a family with adRP. Both variants were absent in 400 unrelated controls. The c.-114_-97del, predicted to affect two transcription factor binding sites, was shown to down-regulate the promoter activity of PRPF4 by a luciferase assay, and was associated with a significant reduction of PRPF4 expression in the blood cells of the patient. In fibroblasts from an affected individual with the p.Pro315Leu variant, the expression levels of several tri-snRNP components, including PRPF4 itself, were up-regulated, with altered expression pattern of SC35, a spliceosome marker. The same alterations were also observed in cells over expressing hPrp4(Pro315Leu), suggesting that they arose as a compensatory response to a compromised splicing mechanism caused by hPrp4 dysfunction. Further, over expression of hPrp4(Pro315Leu), but not hPrp4(WT), triggered systemic deformities in wild-type zebrafish embryos with the retina primarily affected, and dramatically augmented death rates in morphant embryos, in which orthologous zebrafish prpf4 gene was silenced. We conclude that mutations of PRPF4 cause RP via haploinsufficiency and dominant-negative effects, and establish PRPF4 as a new U4/U6-U5 snRNP component associated with adRP.
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Affiliation(s)
- Xue Chen
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University and State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China
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20
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Cvačková Z, Matějů D, Staněk D. Retinitis Pigmentosa Mutations ofSNRNP200Enhance Cryptic Splice-Site Recognition. Hum Mutat 2013; 35:308-17. [DOI: 10.1002/humu.22481] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 11/05/2013] [Indexed: 12/16/2022]
Affiliation(s)
- Zuzana Cvačková
- Laboratory of RNA Biology; Institute of Molecular Genetics ASCR; Prague 142 20 Czech Republic
| | - Daniel Matějů
- Laboratory of RNA Biology; Institute of Molecular Genetics ASCR; Prague 142 20 Czech Republic
| | - David Staněk
- Laboratory of RNA Biology; Institute of Molecular Genetics ASCR; Prague 142 20 Czech Republic
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21
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Zhang X, Lai TYY, Chiang SWY, Tam POS, Liu DTL, Chan CKM, Pang CP, Zhao C, Chen LJ. Contribution of SNRNP200 sequence variations to retinitis pigmentosa. Eye (Lond) 2013; 27:1204-13. [PMID: 23887765 DOI: 10.1038/eye.2013.137] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 05/21/2013] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Mutations in the SNRNP200 gene have been reported to cause autosomal dominant retinitis pigmentosa (adRP). In this study, we evaluate the mutation profile of SNRNP200 in a cohort of southern Chinese RP patients. METHODS Twenty adRP patients from 11 families and 165 index patients with non-syndromic RP with mixed inheritance patterns were screened for mutations in the mutation hotspots of SNRNP200. These included exons 12-16, 22-32, and 38-45, which covered the two helicase ATP-binding domains in DEAD-box and two sec-63 domains. The targeted regions were amplified by polymerase chain reaction and analyzed by direct DNA sequencing, followed by in silico analyses. RESULTS Totally 26 variants were identified, 18 of which were novel. Three non-synonymous variants (p.C502R, p.R1779H and p.I698V) were found exclusively in patients. Two of them, p.C502R and p.R1779H, were each identified in one simplex RP patient, whereas p.I698V occurred in one patient with unknown inheritance pattern. All three residues are highly conserved in SNRNP200 orthologs. Nevertheless, only p.C502R and p.R1779H were predicted to affect protein function by in silico analyses, suggesting these two variants are likely to be disease-causing mutations. Notably, all mutations previously identified in other study populations were not detected in this study. CONCLUSIONS Our results reveal a distinct mutation profile of the SNRNP200 gene in a southern Chinese cohort of RP patients. The identification of two novel candidate mutations in two respective patients affirmed that SNRNP200 contributes to a proportion of overall RP.
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Affiliation(s)
- X Zhang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
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22
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Liu MM, Zack DJ. Alternative splicing and retinal degeneration. Clin Genet 2013; 84:142-9. [PMID: 23647439 DOI: 10.1111/cge.12181] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 04/30/2013] [Accepted: 04/30/2013] [Indexed: 12/27/2022]
Abstract
Alternative splicing is highly regulated in tissue-specific and development-specific patterns, and it has been estimated that 15% of disease-causing point mutations affect pre-mRNA splicing. In this review, we consider the cis-acting splice site and trans-acting splicing factor mutations that affect pre-mRNA splicing and contribute to retinal degeneration. Numerous splice site mutations have been identified in retinitis pigmentosa (RP) and various cone-rod dystrophies. Mutations in alternatively spliced retina-specific exons of the widely expressed RPGR and COL2A1 genes lead primarily to X-linked RP and ocular variants of Stickler syndrome, respectively. Furthermore, mutations in general pre-mRNA splicing factors, such as PRPF31, PRPF8, and PRPF3, predominantly cause autosomal dominant RP. These findings suggest an important role for pre-mRNA splicing in retinal homeostasis and the pathogenesis of retinal degenerative diseases. The development of novel therapeutic strategies to modulate aberrant splicing, including small molecule-based therapies, has the potential to lead to new treatments for retinal degenerative diseases.
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Affiliation(s)
- M M Liu
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
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Structural basis for functional cooperation between tandem helicase cassettes in Brr2-mediated remodeling of the spliceosome. Proc Natl Acad Sci U S A 2012; 109:17418-23. [PMID: 23045696 DOI: 10.1073/pnas.1208098109] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Assembly of a spliceosome, catalyzing precursor-messenger RNA splicing, involves multiple RNA-protein remodeling steps, driven by eight conserved DEXD/H-box RNA helicases. The 250-kDa Brr2 enzyme, which is essential for U4/U6 di-small nuclear ribonucleoprotein disruption during spliceosome catalytic activation and for spliceosome disassembly, is the only member of this group that is permanently associated with the spliceosome, thus requiring its faithful regulation. At the same time, Brr2 represents a unique subclass of superfamily 2 nucleic acid helicases, containing tandem helicase cassettes. Presently, the mechanistic and regulatory consequences of this unconventional architecture are unknown. Here we show that in human Brr2, two ring-like helicase cassettes intimately interact and functionally cooperate and how retinitis pigmentosa-linked Brr2 mutations interfere with the enzyme's function. Only the N-terminal cassette harbors ATPase and helicase activities in isolation. Comparison with other helicases and mutational analyses show how it threads single-stranded RNA, and structural features suggest how it can load onto an internal region of U4/U6 di-snRNA. Although the C-terminal cassette does not seem to engage RNA in the same fashion, it binds ATP and strongly stimulates the N-terminal helicase. Mutations at the cassette interface, in an intercassette linker or in the C-terminal ATP pocket, affect this cross-talk in diverse ways. Together, our results reveal the structural and functional interplay between two helicase cassettes in a tandem superfamily 2 enzyme and point to several sites through which Brr2 activity may be regulated.
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Liu T, Jin X, Zhang X, Yuan H, Cheng J, Lee J, Zhang B, Zhang M, Wu J, Wang L, Tian G, Wang W. A novel missense SNRNP200 mutation associated with autosomal dominant retinitis pigmentosa in a Chinese family. PLoS One 2012; 7:e45464. [PMID: 23029027 PMCID: PMC3446876 DOI: 10.1371/journal.pone.0045464] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Accepted: 08/22/2012] [Indexed: 11/18/2022] Open
Abstract
The SNRNP200 gene encodes hBrr2, a helicase essential for pre-mRNA splicing. Six mutations in SNRNP200 have recently been discovered to be associated with autosomal dominant retinitis pigmentosa (adRP). In this work, we analyzed a Chinese family with adRP and identified a novel missense mutation in SNRNP200. To identify the genetic defect in this family, exome of the proband was captured and sequencing analysis was performed to exclude known genetic defects and find possible pathogenic mutations. Subsequently, candidate mutations were validated in affected family members using Sanger sequencing. A novel missense mutation, c.2653C>G transition (p.Q885E), in exon 20 of SNRNP200 was identified. The mutation co-segregated with the disease phenotype over four generations and was absent in 100 normal unaffected individuals. This mutation occurs at highly conserved position in hBrr2 and is predicted to have a functional impact, suggesting that hBrr2-dependent small nuclear riboproteins (snRNPs) unwinding and spliceosome activation is important in the pathogenesis of some variants of RP.
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Affiliation(s)
- Tiecheng Liu
- Department of Ophthalmology, Chinese PLA General Hospital, Beijing, China
- Department of Ophthalmology, Hainan Branch of Chinese PLA General Hospital, Sanya, China
| | - Xin Jin
- Department of Ophthalmology, Chinese PLA General Hospital, Beijing, China
| | - Xuemin Zhang
- Department of Ophthalmology, Chinese PLA General Hospital, Beijing, China
| | - Huijun Yuan
- Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Jing Cheng
- Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Janet Lee
- Department of Ophthalmology and Shiley Eye Center, University of California San Diego, La Jolla, California, United States of America
| | - Baoquan Zhang
- Department of Ophthalmology, Chinese PLA General Hospital, Beijing, China
| | - Maonian Zhang
- Department of Ophthalmology, Chinese PLA General Hospital, Beijing, China
| | - Jing Wu
- Department of Science and Technology, BGI-Tianjin, Tianjin, China
| | - Lijuan Wang
- Department of Reproductive Health, BGI-Shenzhen, Shenzhen, China
| | - Geng Tian
- Department of Science and Technology, BGI-Tianjin, Tianjin, China
| | - Weifeng Wang
- Department of Gastroenterology and Hepatology, Hainan Branch of Chinese PLA General Hospital, Sanya, China
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25
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Chang S, Vaccarella L, Olatunji S, Cebulla C, Christoforidis J. Diagnostic challenges in retinitis pigmentosa: genotypic multiplicity and phenotypic variability. Curr Genomics 2012; 12:267-75. [PMID: 22131872 PMCID: PMC3131734 DOI: 10.2174/138920211795860116] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 04/06/2011] [Accepted: 04/15/2011] [Indexed: 12/03/2022] Open
Abstract
Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal disorders. Diagnosis can be challenging as more than 40 genes are known to cause non-syndromic RP and phenotypic expression can differ significantly resulting in variations in disease severity, age of onset, rate of progression, and clinical findings. We describe the clinical manifestations of RP, the more commonly known causative gene mutations, and the genotypic-phenotypic correlation of RP.
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Affiliation(s)
- Susie Chang
- Retina Division, Havener Eye Institute, The Ohio State University College of Medicine, Columbus, Ohio, USA
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26
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Tanackovic G, Ransijn A, Thibault P, Abou Elela S, Klinck R, Berson EL, Chabot B, Rivolta C. PRPF mutations are associated with generalized defects in spliceosome formation and pre-mRNA splicing in patients with retinitis pigmentosa. Hum Mol Genet 2011; 20:2116-30. [PMID: 21378395 PMCID: PMC3090192 DOI: 10.1093/hmg/ddr094] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 02/08/2011] [Accepted: 03/01/2011] [Indexed: 01/22/2023] Open
Abstract
Proteins PRPF31, PRPF3 and PRPF8 (RP-PRPFs) are ubiquitously expressed components of the spliceosome, a macromolecular complex that processes nearly all pre-mRNAs. Although these spliceosomal proteins are conserved in eukaryotes and are essential for survival, heterozygous mutations in human RP-PRPF genes lead to retinitis pigmentosa, a hereditary disease restricted to the eye. Using cells from patients with 10 different mutations, we show that all clinically relevant RP-PRPF defects affect the stoichiometry of spliceosomal small nuclear RNAs (snRNAs), the protein composition of tri-small nuclear ribonucleoproteins and the kinetics of spliceosome assembly. These mutations cause inefficient splicing in vitro and affect constitutive splicing ex-vivo by impairing the removal of at least 9% of endogenously expressed introns. Alternative splicing choices are also affected when RP-PRPF defects are present. Furthermore, we show that the steady-state levels of snRNAs and processed pre-mRNAs are highest in the retina, indicating a particularly elevated splicing activity. Our results suggest a role for PRPFs defects in the etiology of PRPF-linked retinitis pigmentosa, which appears to be a truly systemic splicing disease. Although these mutations cause widespread and important splicing defects, they are likely tolerated by the majority of human tissues but are critical for retinal cell survival.
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Affiliation(s)
- Goranka Tanackovic
- Department of Medical Genetics, University of Lausanne, Lausanne 1005, Switzerland
| | - Adriana Ransijn
- Department of Medical Genetics, University of Lausanne, Lausanne 1005, Switzerland
| | - Philippe Thibault
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Sherbrooke, Canada
| | - Sherif Abou Elela
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Sherbrooke, Canada
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, CanadaJ1H 5N4 and
| | - Roscoe Klinck
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Sherbrooke, Canada
| | - Eliot L. Berson
- The Berman-Gund Laboratory for the Study of Retinal Degenerations, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | - Benoit Chabot
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Sherbrooke, Canada
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, CanadaJ1H 5N4 and
| | - Carlo Rivolta
- Department of Medical Genetics, University of Lausanne, Lausanne 1005, Switzerland
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Tanackovic G, Ransijn A, Ayuso C, Harper S, Berson E, Rivolta C. A missense mutation in PRPF6 causes impairment of pre-mRNA splicing and autosomal-dominant retinitis pigmentosa. Am J Hum Genet 2011; 88:643-9. [PMID: 21549338 DOI: 10.1016/j.ajhg.2011.04.008] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 04/11/2011] [Accepted: 04/13/2011] [Indexed: 01/08/2023] Open
Abstract
Retinitis pigmentosa (RP) is an inherited form of retinal degeneration that leads to progressive visual-field constriction and blindness. Although the disease manifests only in the retina, mutations in ubiquitously expressed genes associated with the tri-snRNP complex of the spliceosome have been identified in patients with dominantly inherited RP. We screened for mutations in PRPF6 (NM_012469.3), a gene on chromosome 20q13.33 encoding an essential protein for tri-snRNP assembly and stability, in 188 unrelated patients with autosomal-dominant RP and identified a missense mutation, c.2185C>T (p.Arg729Trp). This change affected a residue that is conserved from humans to yeast and cosegregated with the disease in the family in which it was identified. Lymphoblasts derived from patients with this mutation showed abnormal localization of endogenous PRPF6 within the nucleus. Specifically, this protein accumulated in the Cajal bodies, indicating a possible impairment in the tri-snRNP assembly or recycling. Expression of GFP-tagged PRPF6 in HeLa cells showed that this phenomenon depended exclusively on the mutated form of the protein. Furthermore, analysis of endogenous transcripts in cells from patients revealed intron retention for pre-mRNA bearing specific splicing signals, according to the same pattern displayed by lymphoblasts with mutations in other PRPF genes. Our results identify PRPF6 as the sixth gene involved in pre-mRNA splicing and dominant RP, corroborating the hypothesis that deficiencies in the spliceosome play an important role in the molecular pathology of this disease.
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Yuan Y, Zhou X, Wang F, Yan M, Ding F. Evidence for a novel autosomal dominant retinitis pigmentosa linked to chromosome 1p22.1-q12 in a Chinese family. Curr Eye Res 2011; 36:154-67. [PMID: 21281067 DOI: 10.3109/02713683.2010.511393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE To identify the causative genetic locus in a Chinese autosomal dominant retinitis pigmentosa (adRP) family that contained seven affected members in three generations. METHODS After clinical diagnosis and exclusion of all mapped genes and loci, the SLINK program was used to simulate the maximum logarithm of the likelihood ratio (LOD) score for a linkage study in this small family. A genome-wide scan was performed using microsatellite markers at 10 cM intervals. Two-point and multipoint LOD scores were calculated, and haplotypes were constructed. RESULTS The H11 family clinical presentation included an early onset of night blindness, a progressive loss of the peripheral visual field, typical retinitis pigmentosa (RP) fundus changes, and a cataract complication. A maximum two-point LOD score of 2.54 (θ = 0) was found at markers D1S2739, D1S457, D1S187, D1S189, and D1S305, and multipoint linkage analysis yielded a maximum LOD score of 2.54 for marker D1S187. These LOD scores were the closest to the maximum simulated LOD score. Haplotype analysis revealed that this form of adRP segregates with a 38.25 cM region that spanned 50 Mb on chromosome 1p22.1-q12. CONCLUSIONS Although this locus overlaps the RP19 locus caused by mutations in ABCA4 and the RP32 locus, both are inherited in an autosomal recessive mode rather than the autosomal dominant mode of inheritance found in the H11 family. The identification of this potential new locus for adRP further confirms the high level of heterogeneity for RP.
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Affiliation(s)
- Yuan Yuan
- Center for Gene Diagnosis, Zhongnan Hospital, Wuhan University, Wuhan, China
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29
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Poulos MG, Batra R, Charizanis K, Swanson MS. Developments in RNA splicing and disease. Cold Spring Harb Perspect Biol 2011; 3:a000778. [PMID: 21084389 DOI: 10.1101/cshperspect.a000778] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Pre-mRNA processing, including 5'-end capping, splicing, editing, and polyadenylation, consists of a series of orchestrated and primarily cotranscriptional steps that ensure both the high fidelity and extreme diversity characteristic of eukaryotic gene expression. Alternative splicing and editing allow relatively small genomes to encode vast proteomic arrays while alternative 3'-end formation enables variations in mRNA localization, translation, and stability. Of course, this mechanistic complexity comes at a high price. Mutations in the myriad of RNA sequence elements that regulate mRNA biogenesis, as well as the trans-acting factors that act upon these sequences, underlie a number of human diseases. In this review, we focus on one of these key RNA processing steps, splicing, to highlight recent studies that describe both conventional and novel pathogenic mechanisms that underlie muscle and neurological diseases.
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Affiliation(s)
- Michael G Poulos
- Department of Molecular Genetics and Microbiology and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida 32611, USA
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30
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Brr2p RNA helicase with a split personality: insights into structure and function. Biochem Soc Trans 2010; 38:1105-9. [PMID: 20659012 DOI: 10.1042/bst0381105] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
RNA helicases are involved in many cellular processes. Pre-mRNA splicing requires eight different DExD/H-box RNA helicases, which facilitate spliceosome assembly and remodelling of the intricate network of RNA rearrangements that are central to the splicing process. Brr2p, one of the spliceosomal RNA helicases, stands out through its unusual domain architecture. In the present review we highlight the advances made by recent structural and biochemical studies that have important implications for the mechanism and regulation of Brr2p activity. We also discuss the involvement of human Brr2 in retinitis pigmentosa, a degenerative eye disease, and how its functions in splicing might connect to the molecular pathology of the disease.
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31
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Linder B, Dill H, Hirmer A, Brocher J, Lee GP, Mathavan S, Bolz HJ, Winkler C, Laggerbauer B, Fischer U. Systemic splicing factor deficiency causes tissue-specific defects: a zebrafish model for retinitis pigmentosa. Hum Mol Genet 2010; 20:368-77. [PMID: 21051334 DOI: 10.1093/hmg/ddq473] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Retinitis pigmentosa (RP) is a common hereditary eye disease that causes blindness due to a progressive loss of photoreceptors in the retina. RP can be elicited by mutations that affect the tri-snRNP subunit of the pre-mRNA splicing machinery, but how defects in this essential macromolecular complex transform into a photoreceptor-specific phenotype is unknown. We have modeled the disease in zebrafish by silencing the RP-associated splicing factor Prpf31 and observed detrimental effects on visual function and photoreceptor morphology. Despite reducing the level of a constitutive splicing factor, no general defects in gene expression were found. Instead, retinal genes were selectively affected, providing the first in vivo link between mutations in splicing factors and the RP phenotype. Silencing of Prpf4, a splicing factor hitherto unrelated to RP, evoked the same defects in vision, photoreceptor morphology and retinal gene expression. Hence, various routes affecting the tri-snRNP can elicit tissue-specific gene expression defects and lead to the RP phenotype.
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Affiliation(s)
- Bastian Linder
- Department of Biochemistry, University of Würzburg, Würzburg, Germany
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32
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Zhao C, Bellur DL, Lu S, Zhao F, Grassi MA, Bowne SJ, Sullivan LS, Daiger SP, Chen LJ, Pang CP, Zhao K, Staley JP, Larsson C. Autosomal-dominant retinitis pigmentosa caused by a mutation in SNRNP200, a gene required for unwinding of U4/U6 snRNAs. Am J Hum Genet 2009; 85:617-27. [PMID: 19878916 DOI: 10.1016/j.ajhg.2009.09.020] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 09/19/2009] [Accepted: 09/30/2009] [Indexed: 01/20/2023] Open
Abstract
Mutations in genes associated with the U4/U6-U5 small nuclear ribonucleoprotein (snRNP) complex of the spliceosome are implicated in autosomal-dominant retinitis pigmentosa (adRP), a group of progressive retinal degenerative disorders leading to visual impairment, loss of visual field, and even blindness. We recently assigned a locus (RP33) for adRP to 2cen-q12.1, a region that harbors the SNRNP200 gene encoding hBrr2, another U4/U6-U5 snRNP component that is required for unwinding of U4/U6 snRNAs during spliceosome activation and for disassembly of the spliceosome. Here, we report the identification of a missense mutation, c.3260C>T (p.S1087L), in exon 25 of the SNRNP200 gene in an RP33-linked family. The c.3260C>T substitution showed complete cosegregation with the retinitis pigmentosa (RP) phenotype over four generations, but was absent in a panel of 400 controls. The p.S1087L mutation and p.R1090L, another adRP-associated allele, reside in the "ratchet" helix of the first of two Sec63 domains implicated in the directionality and processivity of nucleic acid unwinding. Indeed, marked defects in U4/U6 unwinding, but not U4/U6-U5 snRNP assembly, were observed in budding yeast for the analogous mutations (N1104L and R1107L) of the corresponding Brr2p residues. The linkage of hBrr2 to adRP suggests that the mechanism of pathogenesis for splicing-factor-related RP may fundamentally derive from a defect in hBrr2-dependent RNA unwinding and a consequent defect in spliceosome activation.
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