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Su Y, Wu J, Chen W, Shan J, Chen D, Zhu G, Ge S, Liu Y. Spliceosomal snRNAs, the Essential Players in pre-mRNA Processing in Eukaryotic Nucleus: From Biogenesis to Functions and Spatiotemporal Characteristics. Adv Biol (Weinh) 2024; 8:e2400006. [PMID: 38797893 DOI: 10.1002/adbi.202400006] [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: 01/03/2024] [Revised: 04/30/2024] [Indexed: 05/29/2024]
Abstract
Spliceosomal small nuclear RNAs (snRNAs) are a fundamental class of non-coding small RNAs abundant in the nucleoplasm of eukaryotic cells, playing a crucial role in splicing precursor messenger RNAs (pre-mRNAs). They are transcribed by DNA-dependent RNA polymerase II (Pol II) or III (Pol III), and undergo subsequent processing and 3' end cleavage to become mature snRNAs. Numerous protein factors are involved in the transcription initiation, elongation, termination, splicing, cellular localization, and terminal modification processes of snRNAs. The transcription and processing of snRNAs are regulated spatiotemporally by various mechanisms, and the homeostatic balance of snRNAs within cells is of great significance for the growth and development of organisms. snRNAs assemble with specific accessory proteins to form small nuclear ribonucleoprotein particles (snRNPs) that are the basal components of spliceosomes responsible for pre-mRNA maturation. This article provides an overview of the biological functions, biosynthesis, terminal structure, and tissue-specific regulation of snRNAs.
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Affiliation(s)
- Yuan Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Jiaming Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Wei Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Junling Shan
- Department of basic medicine, Guangxi Medical University of Nursing College, Nanning, Guangxi, 530021, China
| | - Dan Chen
- Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, Guangxi, 530011, China
| | - Guangyu Zhu
- Guangxi Medical University Hospital of Stomatology, Nanning, Guangxi, 530021, China
| | - Shengchao Ge
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Yunfeng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
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2
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Kurzawa-Akanbi M, Tzoumas N, Corral-Serrano JC, Guarascio R, Steel DH, Cheetham ME, Armstrong L, Lako M. Pluripotent stem cell-derived models of retinal disease: Elucidating pathogenesis, evaluating novel treatments, and estimating toxicity. Prog Retin Eye Res 2024; 100:101248. [PMID: 38369182 DOI: 10.1016/j.preteyeres.2024.101248] [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: 12/07/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
Blindness poses a growing global challenge, with approximately 26% of cases attributed to degenerative retinal diseases. While gene therapy, optogenetic tools, photosensitive switches, and retinal prostheses offer hope for vision restoration, these high-cost therapies will benefit few patients. Understanding retinal diseases is therefore key to advance effective treatments, requiring in vitro models replicating pathology and allowing quantitative assessments for drug discovery. Pluripotent stem cells (PSCs) provide a unique solution given their limitless supply and ability to differentiate into light-responsive retinal tissues encompassing all cell types. This review focuses on the history and current state of photoreceptor and retinal pigment epithelium (RPE) cell generation from PSCs. We explore the applications of this technology in disease modelling, experimental therapy testing, biomarker identification, and toxicity studies. We consider challenges in scalability, standardisation, and reproducibility, and stress the importance of incorporating vasculature and immune cells into retinal organoids. We advocate for high-throughput automation in data acquisition and analyses and underscore the value of advanced micro-physiological systems that fully capture the interactions between the neural retina, RPE, and choriocapillaris.
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3
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Lv Y, Li J, Yu S, Zhang Y, Hu H, Sun K, Jia D, Han Y, Tu J, Huang Y, Liu X, Zhang X, Gao P, Chen X, Shaw Williams MT, Tang Z, Shu X, Liu M, Ren X. The splicing factor Prpf31 is required for hematopoietic stem and progenitor cell expansion during zebrafish embryogenesis. J Biol Chem 2024; 300:105772. [PMID: 38382674 PMCID: PMC10959673 DOI: 10.1016/j.jbc.2024.105772] [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: 08/20/2023] [Revised: 01/17/2024] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
Pre-mRNA splicing is a precise regulated process and is crucial for system development and homeostasis maintenance. Mutations in spliceosomal components have been found in various hematopoietic malignancies (HMs) and have been considered as oncogenic derivers of HMs. However, the role of spliceosomal components in normal and malignant hematopoiesis remains largely unknown. Pre-mRNA processing factor 31 (PRPF31) is a constitutive spliceosomal component, which mutations are associated with autosomal dominant retinitis pigmentosa. PRPF31 was found to be mutated in several HMs, but the function of PRPF31 in normal hematopoiesis has not been explored. In our previous study, we generated a prpf31 knockout (KO) zebrafish line and reported that Prpf31 regulates the survival and differentiation of retinal progenitor cells by modulating the alternative splicing of genes involved in mitosis and DNA repair. In this study, by using the prpf31 KO zebrafish line, we discovered that prpf31 KO zebrafish exhibited severe defects in hematopoietic stem and progenitor cell (HSPC) expansion and its sequentially differentiated lineages. Immunofluorescence results showed that Prpf31-deficient HSPCs underwent malformed mitosis and M phase arrest during HSPC expansion. Transcriptome analysis and experimental validations revealed that Prpf31 deficiency extensively perturbed the alternative splicing of mitosis-related genes. Collectively, our findings elucidate a previously undescribed role for Prpf31 in HSPC expansion, through regulating the alternative splicing of mitosis-related genes.
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Affiliation(s)
- Yuexia Lv
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Department of Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jingzhen Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Research Center for Biochemistry and Molecular Biology, Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, China
| | - Shanshan Yu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Institute of Visual Neuroscience and Stem Cell Engineering, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Yangjun Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hualei Hu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Kui Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Danna Jia
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yunqiao Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jiayi Tu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiliang Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xianghan Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Pan Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiang Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mark Thomas Shaw Williams
- Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xinhua Shu
- Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Xiang Ren
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
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Aweidah H, Xi Z, Sahel JA, Byrne LC. PRPF31-retinitis pigmentosa: Challenges and opportunities for clinical translation. Vision Res 2023; 213:108315. [PMID: 37714045 PMCID: PMC10872823 DOI: 10.1016/j.visres.2023.108315] [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: 04/30/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/17/2023]
Abstract
Mutations in pre-mRNA processing factor 31 cause autosomal dominant retinitis pigmentosa (PRPF31-RP), for which there is currently no efficient treatment, making this disease a prime target for the development of novel therapeutic strategies. PRPF31-RP exhibits incomplete penetrance due to haploinsufficiency, in which reduced levels of gene expression from the mutated allele result in disease. A variety of model systems have been used in the investigation of disease etiology and therapy development. In this review, we discuss recent advances in both in vivo and in vitro model systems, evaluating their advantages and limitations in the context of therapy development for PRPF31-RP. Additionally, we describe the latest approaches for treatment, including AAV-mediated gene augmentation, genome editing, and late-stage therapies such as optogenetics, cell transplantation, and retinal prostheses.
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Affiliation(s)
- Hamzah Aweidah
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhouhuan Xi
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Ophthalmology, Eye Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - José-Alain Sahel
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Leah C Byrne
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA.
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Watson A, Lako M. Retinal organoids provide unique insights into molecular signatures of inherited retinal disease throughout retinogenesis. J Anat 2023; 243:186-203. [PMID: 36177499 PMCID: PMC10335378 DOI: 10.1111/joa.13768] [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: 06/17/2022] [Revised: 09/06/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022] Open
Abstract
The demand for induced pluripotent stem cells (iPSC)-derived retinal organoid and retinal pigment epithelium (RPE) models for the modelling of inherited retinopathies has increased significantly in the last decade. These models are comparable with foetal retinas up until the later stages of retinogenesis, expressing all of the key neuronal markers necessary for retinal function. These models have proven to be invaluable in the understanding of retinogenesis, particular in the context of patient-specific diseases. Inherited retinopathies are infamously described as clinically and phenotypically heterogeneous, such that developing gene/mutation-specific animal models in each instance of retinal disease is not financially or ethically feasible. Further to this, many animal models are insufficient in the study of disease pathogenesis due to anatomical differences and failure to recapitulate human disease phenotypes. In contrast, iPSC-derived retinal models provide a high throughput platform which is physiologically relevant for studying human health and disease. They also serve as a platform for drug screening, gene therapy approaches and in vitro toxicology of novel therapeutics in pre-clinical studies. One unique characteristic of stem cell-derived retinal models is the ability to mimic in vivo retinogenesis, providing unparalleled insights into the effects of pathogenic mutations in cells of the developing retina, in a highly accessible way. This review aims to give the reader an overview of iPSC-derived retinal organoids and/or RPE in the context of disease modelling of several inherited retinopathies including Retinitis Pigmentosa, Stargardt disease and Retinoblastoma. We describe the ability of each model to recapitulate in vivo disease phenotypes, validate previous findings from animal models and identify novel pathomechanisms that underpin individual IRDs.
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Affiliation(s)
- Avril Watson
- Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Majlinda Lako
- Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
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Gene augmentation prevents retinal degeneration in a CRISPR/Cas9-based mouse model of PRPF31 retinitis pigmentosa. Nat Commun 2022; 13:7695. [PMID: 36509783 PMCID: PMC9744804 DOI: 10.1038/s41467-022-35361-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
Mutations in PRPF31 cause autosomal dominant retinitis pigmentosa, an untreatable form of blindness. Gene therapy is a promising treatment for PRPF31-retinitis pigmentosa, however, there are currently no suitable animal models in which to develop AAV-mediated gene augmentation. Here we establish Prpf31 mutant mouse models using AAV-mediated CRISPR/Cas9 knockout, and characterize the resulting retinal degeneration phenotype. Mouse models with early-onset morphological and functional impairments like those in patients were established, providing new platforms in which to investigate pathogenetic mechanisms and develop therapeutic methods. AAV-mediated PRPF31 gene augmentation restored the retinal structure and function in a rapidly degenerating mouse model, demonstrating the first in vivo proof-of-concept for AAV-mediated gene therapy to treat PRPF31-retinitis pigmentosa. AAV-CRISPR/Cas9-PRPF31 knockout constructs also mediated efficient PRPF31 knockout in human and non-human primate retinal explants, laying a foundation for establishing non-human primate models using the method developed here.
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Impact of Alternative Splicing Variants on Liver Cancer Biology. Cancers (Basel) 2021; 14:cancers14010018. [PMID: 35008179 PMCID: PMC8750444 DOI: 10.3390/cancers14010018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Among the top ten deadly solid tumors are the two most frequent liver cancers, hepatocellular carcinoma, and intrahepatic cholangiocarcinoma, whose development and malignancy are favored by multifactorial conditions, which include aberrant maturation of pre-mRNA due to abnormalities in either the machinery involved in the splicing, i.e., the spliceosome and associated factors, or the nucleotide sequences of essential sites for the exon recognition process. As a consequence of cancer-associated aberrant splicing in hepatocytes- and cholangiocytes-derived cancer cells, abnormal proteins are synthesized. They contribute to the dysregulated proliferation and eventually transformation of these cells to phenotypes with enhanced invasiveness, migration, and multidrug resistance, which contributes to the poor prognosis that characterizes these liver cancers. Abstract The two most frequent primary cancers affecting the liver, whose incidence is growing worldwide, are hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA), which are among the five most lethal solid tumors with meager 5-year survival rates. The common difficulty in most cases to reach an early diagnosis, the aggressive invasiveness of both tumors, and the lack of favorable response to pharmacotherapy, either classical chemotherapy or modern targeted therapy, account for the poor outcome of these patients. Alternative splicing (AS) during pre-mRNA maturation results in changes that might affect proteins involved in different aspects of cancer biology, such as cell cycle dysregulation, cytoskeleton disorganization, migration, and adhesion, which favors carcinogenesis, tumor promotion, and progression, allowing cancer cells to escape from pharmacological treatments. Reasons accounting for cancer-associated aberrant splicing include mutations that create or disrupt splicing sites or splicing enhancers or silencers, abnormal expression of splicing factors, and impaired signaling pathways affecting the activity of the splicing machinery. Here we have reviewed the available information regarding the impact of AS on liver carcinogenesis and the development of malignant characteristics of HCC and iCCA, whose understanding is required to develop novel therapeutical approaches aimed at manipulating the phenotype of cancer cells.
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Impact of alternative splicing on mechanisms of resistance to anticancer drugs. Biochem Pharmacol 2021; 193:114810. [PMID: 34673012 DOI: 10.1016/j.bcp.2021.114810] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/15/2022]
Abstract
A shared characteristic of many tumors is the lack of response to anticancer drugs. Multiple mechanisms of pharmacoresistance (MPRs) are involved in permitting cancer cells to overcome the effect of these agents. Pharmacoresistance can be primary (intrinsic) or secondary (acquired), i.e., triggered or enhanced in response to the treatment. Moreover, MPRs usually result in the lack of sensitivity to several agents, which accounts for diverse multidrug-resistant (MDR) phenotypes. MPRs are based on the dynamic expression of more than one hundred genes, constituting the so-called resistome. Alternative splicing (AS) during pre-mRNA maturation results in changes affecting proteins involved in the resistome. The resulting splicing variants (SVs) reduce the efficacy of anticancer drugs by lowering the intracellular levels of active agents, altering molecular targets, enhancing both DNA repair ability and defensive mechanism of tumors, inducing changes in the balance between pro-survival and pro-apoptosis signals, modifying interactions with the tumor microenvironment, and favoring malignant phenotypic transitions. Reasons accounting for cancer-associated aberrant splicing include mutations that create or disrupt splicing sites or splicing enhancers or silencers, abnormal expression of splicing factors, and impaired signaling pathways affecting the activity of the splicing machinery. Here we have reviewed the impact of AS on MPR in cancer cells.
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Determinants of Disease Penetrance in PRPF31-Associated Retinopathy. Genes (Basel) 2021; 12:genes12101542. [PMID: 34680937 PMCID: PMC8535263 DOI: 10.3390/genes12101542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 11/17/2022] Open
Abstract
Retinitis pigmentosa 11 (RP11) is caused by dominant mutations in PRPF31, however a significant proportion of mutation carriers do not develop retinopathy. Here, we investigated the relationship between CNOT3 polymorphism, MSR1 repeat copy number and disease penetrance in RP11 patients and non-penetrant carriers (NPCs). We further characterized PRPF31 and CNOT3 expression in fibroblasts from eight RP11 patients and one NPC from a family carrying the c.1205C>T variant. Retinal organoids (ROs) and retinal pigment epithelium (RPE) were differentiated from induced pluripotent stem cells derived from RP11 patients, an NPC and a control subject. All RP11 patients were homozygous for the 3-copy MSR1 repeat in the PRPF31 promoter, while 3/5 NPCs carried a 4-copy MSR1 repeat. The CNOT3 rs4806718 genotype did not correlate with disease penetrance. PRFP31 expression declined with age in adult cadaveric retina. PRPF31 and CNOT3 expression was reduced in RP11 fibroblasts, RO and RPE compared with controls. Both RP11 and NPC RPE displayed shortened primary cilia compared with controls, however a subpopulation of cells with normal cilia lengths was present in NPC RPE monolayers. Our results indicate that RP11 non-penetrance is associated with the inheritance of a 4-copy MSR1 repeat, but not with CNOT3 polymorphisms.
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Yang C, Georgiou M, Atkinson R, Collin J, Al-Aama J, Nagaraja-Grellscheid S, Johnson C, Ali R, Armstrong L, Mozaffari-Jovin S, Lako M. Pre-mRNA Processing Factors and Retinitis Pigmentosa: RNA Splicing and Beyond. Front Cell Dev Biol 2021; 9:700276. [PMID: 34395430 PMCID: PMC8355544 DOI: 10.3389/fcell.2021.700276] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
Retinitis pigmentosa (RP) is the most common inherited retinal disease characterized by progressive degeneration of photoreceptors and/or retinal pigment epithelium that eventually results in blindness. Mutations in pre-mRNA processing factors (PRPF3, 4, 6, 8, 31, SNRNP200, and RP9) have been linked to 15–20% of autosomal dominant RP (adRP) cases. Current evidence indicates that PRPF mutations cause retinal specific global spliceosome dysregulation, leading to mis-splicing of numerous genes that are involved in a variety of retina-specific functions and/or general biological processes, including phototransduction, retinol metabolism, photoreceptor disk morphogenesis, retinal cell polarity, ciliogenesis, cytoskeleton and tight junction organization, waste disposal, inflammation, and apoptosis. Importantly, additional PRPF functions beyond RNA splicing have been documented recently, suggesting a more complex mechanism underlying PRPF-RPs driven disease pathogenesis. The current review focuses on the key RP-PRPF genes, depicting the current understanding of their roles in RNA splicing, impact of their mutations on retinal cell’s transcriptome and phenome, discussed in the context of model species including yeast, zebrafish, and mice. Importantly, information on PRPF functions beyond RNA splicing are discussed, aiming at a holistic investigation of PRPF-RP pathogenesis. Finally, work performed in human patient-specific lab models and developing gene and cell-based replacement therapies for the treatment of PRPF-RPs are thoroughly discussed to allow the reader to get a deeper understanding of the disease mechanisms, which we believe will facilitate the establishment of novel and better therapeutic strategies for PRPF-RP patients.
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Affiliation(s)
- Chunbo Yang
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Maria Georgiou
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Robert Atkinson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jumana Al-Aama
- Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Colin Johnson
- Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
| | - Robin Ali
- King's College London, London, United Kingdom
| | - Lyle Armstrong
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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11
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Maxwell DW, O'Keefe RT, Roy S, Hentges KE. The role of splicing factors in retinitis pigmentosa: links to cilia. Biochem Soc Trans 2021; 49:1221-1231. [PMID: 34060618 DOI: 10.1042/bst20200798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 01/27/2023]
Abstract
Cilia are critical to numerous biological functions, both in development and everyday homeostatic processes. Diseases arising from genetic mutations that cause cilia dysfunction are termed ciliopathies. Several ubiquitously expressed splicing factors have been implicated in the condition Retinitis Pigmentosa (RP), a group of diseases characterised by the progressive degeneration of the retina. In many types of RP the disease affects the modified primary cilium of the photoreceptor cells and thus, these types of RP are considered ciliopathies. Here, we discuss sequence variants found within a number of these splicing factors, the resulting phenotypes, and the mechanisms underpinning disease pathology. Additionally, we discuss recent evidence investigating why RP patients with mutations in globally expressed splicing factors present with retina-specific phenotypes.
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Affiliation(s)
- Dale W Maxwell
- Division of Evolution and Genome Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, U.K
- Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Raymond T O'Keefe
- Division of Evolution and Genome Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, U.K
| | - Sudipto Roy
- Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
- Department of Pediatrics, National University of Singapore, 1E Kent Ridge Road, Singapore 119228, Singapore
| | - Kathryn E Hentges
- Division of Evolution and Genome Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, U.K
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12
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Yildirim A, Mozaffari-Jovin S, Wallisch AK, Schäfer J, Ludwig SEJ, Urlaub H, Lührmann R, Wolfrum U. SANS (USH1G) regulates pre-mRNA splicing by mediating the intra-nuclear transfer of tri-snRNP complexes. Nucleic Acids Res 2021; 49:5845-5866. [PMID: 34023904 PMCID: PMC8191790 DOI: 10.1093/nar/gkab386] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/22/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Splicing is catalyzed by the spliceosome, a compositionally dynamic complex assembled stepwise on pre-mRNA. We reveal links between splicing machinery components and the intrinsically disordered ciliopathy protein SANS. Pathogenic mutations in SANS/USH1G lead to Usher syndrome—the most common cause of deaf-blindness. Previously, SANS was shown to function only in the cytosol and primary cilia. Here, we have uncovered molecular links between SANS and pre-mRNA splicing catalyzed by the spliceosome in the nucleus. We show that SANS is found in Cajal bodies and nuclear speckles, where it interacts with components of spliceosomal sub-complexes such as SF3B1 and the large splicing cofactor SON but also with PRPFs and snRNAs related to the tri-snRNP complex. SANS is required for the transfer of tri-snRNPs between Cajal bodies and nuclear speckles for spliceosome assembly and may also participate in snRNP recycling back to Cajal bodies. SANS depletion alters the kinetics of spliceosome assembly, leading to accumulation of complex A. SANS deficiency and USH1G pathogenic mutations affects splicing of genes related to cell proliferation and human Usher syndrome. Thus, we provide the first evidence that splicing dysregulation may participate in the pathophysiology of Usher syndrome.
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Affiliation(s)
- Adem Yildirim
- Molecular Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Germany
| | - Sina Mozaffari-Jovin
- Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany.,Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
| | - Ann-Kathrin Wallisch
- Molecular Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Germany
| | - Jessica Schäfer
- Molecular Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Germany
| | - Sebastian E J Ludwig
- Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany.,Bioanalytics, Department of Clinical Chemistry, University Medical Center Goettingen, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
| | - Uwe Wolfrum
- Molecular Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Germany
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13
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TSSC4 is a component of U5 snRNP that promotes tri-snRNP formation. Nat Commun 2021; 12:3646. [PMID: 34131137 PMCID: PMC8206348 DOI: 10.1038/s41467-021-23934-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 05/19/2021] [Indexed: 11/29/2022] Open
Abstract
U5 snRNP is a complex particle essential for RNA splicing. U5 snRNPs undergo intricate biogenesis that ensures that only a fully mature particle assembles into a splicing competent U4/U6•U5 tri-snRNP and enters the splicing reaction. During splicing, U5 snRNP is substantially rearranged and leaves as a U5/PRPF19 post-splicing particle, which requires re-generation before the next round of splicing. Here, we show that a previously uncharacterized protein TSSC4 is a component of U5 snRNP that promotes tri-snRNP formation. We provide evidence that TSSC4 associates with U5 snRNP chaperones, U5 snRNP and the U5/PRPF19 particle. Specifically, TSSC4 interacts with U5-specific proteins PRPF8, EFTUD2 and SNRNP200. We also identified TSSC4 domains critical for the interaction with U5 snRNP and the PRPF19 complex, as well as for TSSC4 function in tri-snRNP assembly. TSSC4 emerges as a specific chaperone that acts in U5 snRNP de novo biogenesis as well as post-splicing recycling. The correct assembly and recycling of the multicomponent spliceosome remains largely elusive. Here, the authors show that a previously uncharacterized protein TSSC4 associates with de novo formed spliceosomal U5 snRNP as well as with a post-splicing U5-PRPF19 particle, and that TSSC4 is important for assembly of the splicing competent tri-snRNP.
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14
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Li J, Liu F, Lv Y, Sun K, Zhao Y, Reilly J, Zhang Y, Tu J, Yu S, Liu X, Qin Y, Huang Y, Gao P, Jia D, Chen X, Han Y, Shu X, Luo D, Tang Z, Liu M. Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing. Nucleic Acids Res 2021; 49:2027-2043. [PMID: 33476374 PMCID: PMC7913766 DOI: 10.1093/nar/gkab003] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 01/01/2021] [Accepted: 01/05/2021] [Indexed: 12/23/2022] Open
Abstract
Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis, especially in neural tissues. Mutations in pre-mRNAs processing factor 31 (PRPF31) cause autosomal dominant retinitis pigmentosa, a progressive retinal degeneration disease. The transcriptome-wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here, we showed that the differentiation and viability of retinal progenitor cells (RPCs) are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level, significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild-type human PRPF31 rather than the disease-associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak 5′ splicing site. Moreover, genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events, which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis.
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Affiliation(s)
- Jingzhen Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Fei Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yuexia Lv
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Kui Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yuntong Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Science, Wuhan 430072, PR China
| | - Jamas Reilly
- Department of Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, Scotland, UK
| | - Yangjun Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Jiayi Tu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Shanshan Yu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Xiliang Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yayun Qin
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Pan Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Danna Jia
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Xiang Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yunqiao Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Xinhua Shu
- Department of Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, Scotland, UK
| | - Daji Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Science, Wuhan 430072, PR China
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
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15
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Ka HI, Lee S, Han S, Jeong AL, Park JY, Joo HJ, Soh SJ, Park D, Yang Y. Deubiquitinase USP47-stabilized splicing factor IK regulates the splicing of ATM pre-mRNA. Cell Death Discov 2020; 6:34. [PMID: 32377397 PMCID: PMC7198525 DOI: 10.1038/s41420-020-0268-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/24/2020] [Accepted: 04/21/2020] [Indexed: 12/30/2022] Open
Abstract
IK depletion leads to an aberrant mitotic entry because of chromosomal misalignment through the enhancement of Aurora B activity at the interphase. Here, we demonstrate that IK, a spliceosomal component, plays a crucial role in the proper splicing of the ATM pre-mRNA among other genes related with the DNA Damage Response (DDR). Intron 1 in the ATM pre-mRNA, having lengths <200 bp, was not spliced in the IK-depleted cells and led to a deficiency of the ATM protein. Subsequently, the IK depletion-induced ATM protein deficiency impaired the ability to repair the damaged DNA. Because the absence of SMU1 results in IK degradation, the mechanism underlying IK degradation was exploited. IK was ubiquitinated in the absence of SMU1 and then subjected to proteolysis through the 26S proteasome. To prevent the proteolytic degradation of IK, a deubiquitinating enzyme, USP47, directly interacted with IK and stabilized it through deubiquitination. Collectively, our results suggest that IK is required for proper splicing of the ATM pre-mRNA and USP47 contributes toward the stabilization of IK.
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Affiliation(s)
- Hye In Ka
- Department of Biological Sciences, Sookmyung Women’s University, Seoul, 04310 Korea
| | - Sunyi Lee
- Drug Evaluation Group, R&D Center CJ HealthCare, Icheon, 04551 Korea
| | - Sora Han
- Research Institute of Women’s Health, Sookmyung Women’s University, Seoul, 04310 Korea
| | - Ae Lee Jeong
- New Drug Development Center, Osong Medical Innovation Foundation, Osong, 28160 Korea
| | - Ji Young Park
- Department of Biological Sciences, Sookmyung Women’s University, Seoul, 04310 Korea
| | - Hyun Jeong Joo
- Department of Biological Sciences, Sookmyung Women’s University, Seoul, 04310 Korea
| | - Su Jung Soh
- Department of Biological Sciences, Sookmyung Women’s University, Seoul, 04310 Korea
| | - Doyeon Park
- Department of Biological Sciences, Sookmyung Women’s University, Seoul, 04310 Korea
| | - Young Yang
- Department of Biological Sciences, Sookmyung Women’s University, Seoul, 04310 Korea
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16
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Hamieh A, Nandrot EF. Retinal Pigment Epithelial Cells: The Unveiled Component in the Etiology of Prpf Splicing Factor-Associated Retinitis Pigmentosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1185:227-231. [PMID: 31884616 DOI: 10.1007/978-3-030-27378-1_37] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pre-mRNA splicing is a critical step in RNA processing in all eukaryotic cells. It consists of introns removal and requires the assembly of a large RNA-protein complex called the spliceosome. This complex of small nuclear ribonucleoproteins is associated with accessory proteins from the pre-mRNA processing factor (PRPF) family. Mutations in different splicing factor-encoding genes were identified in retinitis pigmentosa (RP) patients. A surprising feature of these ubiquitous factors is that the outcome of their alteration is restricted to the retina. Because of their high metabolic demand, most studies focused on photoreceptors dysfunction and associated degeneration. However, cells from the retinal pigment epithelium (RPE) are also crucial to maintaining retinal homeostasis and photoreceptor function. Moreover, mutations in RPE-specific genes are associated with some RP cases. Indeed, we identified major RPE defects in Prpf31-mutant mice: circadian rhythms of both photoreceptor outer segments (POS) phagocytosis and retinal adhesion were attenuated or lost, leading to ultrastructural anomalies and vacuoles. Taken together, our published and ongoing data suggest that (1) similar molecular events take place in human and mouse cells and (2) these functional defects generate various stress processes.
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Affiliation(s)
- Abdallah Hamieh
- Therapeutics Department, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Emeline F Nandrot
- Therapeutics Department, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.
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17
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Mutation spectrum of PRPF31, genotype-phenotype correlation in retinitis pigmentosa, and opportunities for therapy. Exp Eye Res 2020; 192:107950. [PMID: 32014492 PMCID: PMC7065041 DOI: 10.1016/j.exer.2020.107950] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/13/2020] [Accepted: 01/27/2020] [Indexed: 12/11/2022]
Abstract
Pathogenic variants in pre-messenger RNA (pre-mRNA) splicing factor 31, PRPF31, are the second most common genetic cause of autosomal dominant retinitis pigmentosa (adRP) in most populations. This remains a completely untreatable and incurable form of blindness, and it can be difficult to predict the clinical course of disease. In order to design appropriate targeted therapies, a thorough understanding of the genetics and molecular mechanism of this disease is required. Here, we present the structure of the PRPF31 gene and PRPF31 protein, current understanding of PRPF31 protein function and the full spectrum of all reported clinically relevant variants in PRPF31. We delineate the correlation between specific PRPF31 genotype and RP phenotype, suggesting that, except in cases of complete gene deletion or large-scale deletions, dominant negative effects contribute to phenotype as well as haploinsufficiency. This has important impacts on design of targeted therapies, particularly the feasibility of gene augmentation as a broad approach for treatment of PRPF31-associated RP. We discuss other opportunities for therapy, including antisense oligonucleotide therapy and gene-independent approaches and offer future perspectives on treatment of this form of RP. PRPF31 is the second most common cause of autosomal dominant retinitis pigmentosa and a potential target for gene therapy. We present all reported pathogenic variants in PRPF31 as a resource for clinicians, diagnostic genetics labs, and researchers. Genotype-phenotype correlations suggest that, dominant negative effects contribute to disease in addition to haploinsufficiency. This finding has important impacts on the suitability of gene augmentation approaches across all mutation types. This finding may aid prognosis of disease in PRPF31-associated RP patients.
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18
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Valdés-Sánchez L, Calado SM, de la Cerda B, Aramburu A, García-Delgado AB, Massalini S, Montero-Sánchez A, Bhatia V, Rodríguez-Bocanegra E, Diez-Lloret A, Rodríguez-Martínez D, Chakarova C, Bhattacharya SS, Díaz-Corrales FJ. Retinal pigment epithelium degeneration caused by aggregation of PRPF31 and the role of HSP70 family of proteins. Mol Med 2019; 26:1. [PMID: 31892304 PMCID: PMC6938640 DOI: 10.1186/s10020-019-0124-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 12/05/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Mutations in pre-mRNA splicing factor PRPF31 can lead to retinitis pigmentosa (RP). Although the exact disease mechanism remains unknown, it has been hypothesized that haploinsufficiency might be involved in the pathophysiology of the disease. METHODS In this study, we have analyzed a mouse model containing the p.A216P mutation in Prpf31 gene. RESULTS We found that mutant Prpf31 protein produces cytoplasmic aggregates in the retinal pigment epithelium and decreasing the protein levels of this splicing factor in the nucleus. Additionally, normal protein was recruited in insoluble aggregates when the mutant protein was overexpressed in vitro. In response to protein aggregation, Hspa4l is overexpressed. This member of the HSP70 family of chaperones might contribute to the correct folding and solubilization of the mutant protein, allowing its translocation to the nucleus. CONCLUSIONS Our data suggests that a mechanism haploinsufficiency and dominant-negative is involved in retinal degeneration due to mutations in PRPF31. HSP70 over-expression might be a new therapeutic target for the treatment of retinal degeneration due to PRPF31 mutations.
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Affiliation(s)
- Lourdes Valdés-Sánchez
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
| | - Sofia M Calado
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
- Present Address: Center for Biomedical Research (CBMR), University of Algarve, 8800-139, Faro, Portugal
| | - Berta de la Cerda
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
| | - Ana Aramburu
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
- Present Address: Clinique de l'Oeil, Avenue Bois de la Chapelle 15, 1213, Onex, Switzerland
| | - Ana Belén García-Delgado
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
| | - Simone Massalini
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
- Present Address: Center for Molecular and Cellular Bioengineering (CMCB) DFG-Research Center for Regenerative Therapies Dresden (CRTD) Cluster of Excellence, Technische Universität Dresden, Fetscherstraße, 105 01307, Dresden, Germany
| | - Adoración Montero-Sánchez
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
| | - Vaibhav Bhatia
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
| | - Eduardo Rodríguez-Bocanegra
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
- Present Address: Universitätsklinikum Tübingen, Forschungsinstitut für Augenheilkunde, Elfriede-Aulhorn-Str. 7, 72076, Tübingen, Germany
| | - Andrea Diez-Lloret
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
| | - Daniel Rodríguez-Martínez
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
| | - Christina Chakarova
- Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK
| | - Shom S Bhattacharya
- Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK.
| | - Francisco J Díaz-Corrales
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain.
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19
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Hirata CL, Ito S, Masutani H. Thioredoxin interacting protein (Txnip) forms redox sensitive high molecular weight nucleoprotein complexes. Arch Biochem Biophys 2019; 677:108159. [DOI: 10.1016/j.abb.2019.108159] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/11/2019] [Accepted: 10/16/2019] [Indexed: 10/25/2022]
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20
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Keiper S, Papasaikas P, Will CL, Valcárcel J, Girard C, Lührmann R. Smu1 and RED are required for activation of spliceosomal B complexes assembled on short introns. Nat Commun 2019; 10:3639. [PMID: 31409787 PMCID: PMC6692369 DOI: 10.1038/s41467-019-11293-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 07/01/2019] [Indexed: 12/02/2022] Open
Abstract
Human pre-catalytic spliceosomes contain several proteins that associate transiently just prior to spliceosome activation and are absent in yeast, suggesting that this critical step is more complex in higher eukaryotes. We demonstrate via RNAi coupled with RNA-Seq that two of these human-specific proteins, Smu1 and RED, function both as alternative splicing regulators and as general splicing factors and are required predominantly for efficient splicing of short introns. In vitro splicing assays reveal that Smu1 and RED promote spliceosome activation, and are essential for this step when the distance between the pre-mRNA’s 5′ splice site (SS) and branch site (BS) is sufficiently short. This Smu1-RED requirement can be bypassed when the 5′ and 3′ regions of short introns are physically separated. Our observations suggest that Smu1 and RED relieve physical constraints arising from a short 5′SS-BS distance, thereby enabling spliceosomes to overcome structural challenges associated with the splicing of short introns. Human spliceosome components Smu1 and RED regulate alternative splicing. Here the authors show that Smu1 and RED are also required for constitutive splicing of short introns.
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Affiliation(s)
- Sandra Keiper
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Panagiotis Papasaikas
- Centre de Regulació Genòmica, The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Dr. Aiguader 88, 08003, Barcelona, Spain.,Friedrich Miescher Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058, Basel, Switzerland.,Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Juan Valcárcel
- Centre de Regulació Genòmica, The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Dr. Aiguader 88, 08003, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys, 08010, Barcelona, Spain
| | - Cyrille Girard
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
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21
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A bioinformatic analysis identifies circadian expression of splicing factors and time-dependent alternative splicing events in the HD-MY-Z cell line. Sci Rep 2019; 9:11062. [PMID: 31363108 PMCID: PMC6667479 DOI: 10.1038/s41598-019-47343-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
The circadian clock regulates key cellular processes and its dysregulation is associated to several pathologies including cancer. Although the transcriptional regulation of gene expression by the clock machinery is well described, the role of the clock in the regulation of post-transcriptional processes, including splicing, remains poorly understood. In the present work, we investigated the putative interplay between the circadian clock and splicing in a cancer context. For this, we applied a computational pipeline to identify oscillating genes and alternatively spliced transcripts in time-course high-throughput data sets from normal cells and tissues, and cancer cell lines. We investigated the temporal phenotype of clock-controlled genes and splicing factors, and evaluated their impact in alternative splice patterns in the Hodgkin Lymphoma cell line HD-MY-Z. Our data points to a connection between clock-controlled genes and splicing factors, which correlates with temporal alternative splicing in several genes in the HD-MY-Z cell line. These include the genes DPYD, SS18, VIPR1 and IRF4, involved in metabolism, cell cycle, apoptosis and proliferation. Our results highlight a role for the clock as a temporal regulator of alternative splicing, which may impact malignancy in this cellular model.
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22
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Li X, Fan Z, Yan M, Qu J, Xu JR, Jin Q. Spontaneous mutations in FgSAD1 suppress the growth defect of the Fgprp4 mutant by affecting tri-snRNP stability and its docking in Fusarium graminearum. Environ Microbiol 2019; 21:4488-4503. [PMID: 31291045 DOI: 10.1111/1462-2920.14736] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 12/27/2022]
Abstract
FgPrp4, the only kinase in the spliceosome, is not essential for viability, but is important for splicing efficiency in Fusarium graminearum. The Fgprp4 deletion mutant had severe growth defects but often produced spontaneous suppressors with faster growth rate. To better understand the suppression mechanism, we identified and characterized spontaneous mutations in the tri-snRNP-specific protein, FgSad1, which suppressed the growth defects of Fgprp4. The L512P mutation was verified for its suppressive effects on Fgprp4, suggesting that mutations in FgSad1 may have effects involving FgPrp4 phosphorylation on FgSad1. Phosphoproteomics analysis showed that FgSad1 may not be the direct substrate of FgPrp4 kinase. Furthermore, truncation analysis showed that the N-terminal, extra RS-rich region of FgSad1 is critical for its function and is post-translationally modified. The P258S or S269P mutations in FgSad1 increased its interactions with the U5 protein FgPrp8 and the U4/U6 protein FgPrp31, which may result in tri-snRNP stabilization. Additionally, the D76N mutation increased the association of FgSad1 with the U2 snRNP. These data indicate that suppressor mutations in FgSad1 increase the stability of the tri-snRNP and/or the affinity of FgSad1 with U2 snRNP and therefore potentially facilitate the docking of tri-snRNP into the spliceosome.
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Affiliation(s)
- Xiaoping Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhili Fan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ming Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jia Qu
- Microbial Resource Center, Microbiology Institute of Shaanxi, Xi'an, Shaanxi, 710043, China
| | - Jin-Rong Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Qiaojun Jin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
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23
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Wheway G, Nazlamova L, Meshad N, Hunt S, Jackson N, Churchill A. A Combined in silico, in vitro and Clinical Approach to Characterize Novel Pathogenic Missense Variants in PRPF31 in Retinitis Pigmentosa. Front Genet 2019; 10:248. [PMID: 30967900 PMCID: PMC6438860 DOI: 10.3389/fgene.2019.00248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/05/2019] [Indexed: 11/30/2022] Open
Abstract
At least six different proteins of the spliceosome, including PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, and SNRNP200, are mutated in autosomal dominant retinitis pigmentosa (adRP). These proteins have recently been shown to localize to the base of the connecting cilium of the retinal photoreceptor cells, elucidating this form of RP as a retinal ciliopathy. In the case of loss-of-function variants in these genes, pathogenicity can easily be ascribed. In the case of missense variants, this is more challenging. Furthermore, the exact molecular mechanism of disease in this form of RP remains poorly understood. In this paper we take advantage of the recently published cryo EM-resolved structure of the entire human spliceosome, to predict the effect of a novel missense variant in one component of the spliceosome; PRPF31, found in a patient attending the genetics eye clinic at Bristol Eye Hospital. Monoallelic variants in PRPF31 are a common cause of autosomal dominant retinitis pigmentosa (adRP) with incomplete penetrance. We use in vitro studies to confirm pathogenicity of this novel variant PRPF31 c.341T > A, p.Ile114Asn. This work demonstrates how in silico modeling of structural effects of missense variants on cryo-EM resolved protein complexes can contribute to predicting pathogenicity of novel variants, in combination with in vitro and clinical studies. It is currently a considerable challenge to assign pathogenic status to missense variants in these proteins.
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Affiliation(s)
- Gabrielle Wheway
- Centre for Research in Biosciences, University of the West of England, Bristol, United Kingdom
| | - Liliya Nazlamova
- Centre for Research in Biosciences, University of the West of England, Bristol, United Kingdom
| | - Nervine Meshad
- Bristol Eye Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Samantha Hunt
- Bristol Eye Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Nicola Jackson
- Clinical Genetics Service, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Amanda Churchill
- Bristol Eye Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
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Lu J, Shu R, Zhu Y. Dysregulation and Dislocation of SFPQ Disturbed DNA Organization in Alzheimer's Disease and Frontotemporal Dementia. J Alzheimers Dis 2019; 61:1311-1321. [PMID: 29376859 DOI: 10.3233/jad-170659] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
SFPQ (Splicing factor proline- and glutamine-rich) is a DNA and RNA binding protein involved in transcription, pre-mRNA splicing, and DNA damage repair. SFPQ was found dysregulated in a few tauopathies such as Alzheimer's disease (AD) and frontotemporal dementia (FTD). In addition, knock-down of SFPQ induced FTD-like behavior in mouse. To confirm the role of SFPQ in AD and FTD, we analyzed the brain sections from the AD and FTD brain samples with SFPQ upregulation and dislocation. Specifically, we observed SFPQ dislocated to the cytoplasm and nuclear envelopes, and DNA structures and organizations were associated with these dislocation phenotypes in AD and FTD brains. Consistently, we also found decreased DAPI intensities and smaller chromocenters associated with SFPQ dislocation in nerural-2a (N2a) cells. As the upregulation and hyperphosphorylation of tau protein is a hallmark of AD and FTD, our study sought to investigate potential interactions between tau and SFPQ by co-transfection and co-immunoprecipitation assays in N2a cells. SFPQ dislocation was found enhanced with tau co-transfection and tau co-transfection further resulted in extended DNA disorganization in N2a cells. Overall, our results indicate that dysregulation and dislocation of SFPQ and subsequent DNA disorganization might be a novel pathway in the progression of AD and FTD.
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Affiliation(s)
- Jing Lu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia.,Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Runzhe Shu
- Hudson Institute of Medical Research, Monash University, Melbourne, Australia
| | - Yan Zhu
- Biomedicine Discovery Institute, Monash University, Melbourne, Australia
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Xie D, Peng K, Yi Q, Liu W, Yang Y, Sun K, Zhu X, Lu F. Targeted Next Generation Sequencing Revealed Novel PRPF31 Mutations in Autosomal Dominant Retinitis Pigmentosa. Genet Test Mol Biomarkers 2018; 22:425-432. [PMID: 29957067 DOI: 10.1089/gtmb.2018.0036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Retinitis pigmentosa (RP) is a rare type of inherited retinal dystrophy that can result in progressive vision loss. Molecular diagnosis of RP is challenging due to phenotypic and genotypic heterogeneities. AIMS This study aimed to identify the pathogenic mutations in two Chinese families with autosomal dominant RP (adRP) and in a patient with sporadic RP. MATERIALS AND METHODS Peripheral blood DNA samples were obtained from the participants. Targeted next generation sequencing (NGS) was applied to identify mutations in these patients. For pathogenic mutation analyses, stringent NGS data analyses and segregation analyses were applied. Primers were designed to validate the identified mutations by Sanger sequencing analyses. RESULTS A novel heterozygous insertion frameshift mutation c.1226_1227insA, p.T410Dfs*65, and a novel heterozygous stopgain mutation c.1015C>T, p.Q339* were identified in PRPF31. A known c.527 + 3A>G splicing mutation was identified in one of the adRP-074 families. All mutations were found to co-segregate with the disease, and none of these mutations were detected in 500 control samples. CONCLUSIONS Our data identified two new autosomal dominant mutations in PRPF31, expanding the mutational spectrum of this gene.
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Affiliation(s)
- Dan Xie
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China .,2 Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China
| | - Kun Peng
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China .,2 Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China
| | - Qian Yi
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China .,2 Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China
| | - Wenjinag Liu
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China
| | - Yeming Yang
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China
| | - Kuanxiang Sun
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China
| | - Xianjun Zhu
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China .,2 Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China .,3 Institute of Laboratory Animal Sciences, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China
| | - Fang Lu
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China .,2 Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China
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Phosphorylation by Prp4 kinase releases the self-inhibition of FgPrp31 in Fusarium graminearum. Curr Genet 2018; 64:1261-1274. [PMID: 29671102 DOI: 10.1007/s00294-018-0838-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/04/2018] [Accepted: 04/11/2018] [Indexed: 02/06/2023]
Abstract
Prp31 is one of the key tri-snRNP components essential for pre-mRNA splicing although its exact molecular function is not well studied. In a previous study, suppressor mutations were identified in the PRP31 ortholog in two spontaneous suppressors of Fgprp4 mutant deleted of the only kinase of the spliceosome in Fusarium graminearum. To further characterize the function of FgPrp31 and its relationship with FgPrp4 kinase, in this study we identified additional suppressor mutations in FgPrp31 and determined the suppressive effects of selected mutations. In total, 28 of the 35 suppressors had missense or nonsense mutations in the C terminus 465-594 aa (CT130) region of FgPrp31. The other 7 had missense or deletion mutations in the 7-64 aa region. The nonsense mutation at R464 in FgPRP31 resulted in the truncation of CT130 that contains all the putative Prp4 kinase-phosphorylation sites reported in humans, and partially rescued intron splicing defects of Fgprp4. The CT130 of FgPrp31 displayed self-inhibitory interaction with the N-terminal 1-463 (N463) region, which was reduced or abolished by the L532P, D534G, or G529D mutation in yeast two-hybrid assays. The N463 region, but not full-length FgPrp31, interacted with the N-terminal region of FgBrr2, one main U5 snRNP protein. The L532P mutation in FgPrp31 increased its interaction with FgBrr2. In contrast, suppressor mutations in FgPrp31 reduced its interaction with FgPrp6, another key component of tri-snRNP. Furthermore, we showed that FgPrp31 was phosphorylated by FgPrp4 in vivo. Site-directed mutagenesis analysis showed that phosphorylation at multiple sites in FgPrp31 is necessary to suppress Fgprp4, and S520 and S521 are important FgPrp4-phosphorylation sites. Overall, these results indicated that phosphorylation by FgPrp4 at multiple sites may release the self-inhibitory binding of FgPrp31 and affect its interaction with other components of tri-snRNP during spliceosome activation.
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Long-term clinical course of 2 Japanese patients with PRPF31-related retinitis pigmentosa. Jpn J Ophthalmol 2018; 62:186-193. [PMID: 29305715 DOI: 10.1007/s10384-017-0560-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022]
Abstract
PURPOSE To assess the long-term clinical course of 2 patients with PRPF31-related retinitis pigmentosa (RP). PATIENTS AND METHODS We clinically examined 2 unrelated patients with RP and collected peripheral blood samples from them. Ophthalmic examinations, including best-corrected visual acuity measurements, Goldmann perimetry, full-field electroretinography, fundus autofluorescence imaging, and optical coherence tomography, were also performed. The visual acuity and visual field were continuously monitored. To identify the causative mutations, 74 genes known to cause RP or Leber congenital amaurosis were examined via targeted next-generation sequencing. RESULTS The clinical courses of both patients were similar. The onset of nyctalopia occurred in the first decade. Fundus examination showed typical RP. Although the patients' visual acuity was relatively preserved even into the fourth decade, the visual field area exhibited rapid deterioration in the mid-teens, with severe concentric constriction in the third decade. Mutation analysis revealed PRPF31 mutations as the cause for autosomal dominant RP in both patients. CONCLUSIONS To the best of our knowledge, few reports of long-term observations pertaining to patients with PRPF31-related RP have been published. The findings reported herein, especially those relating to the progressive degeneration of the visual field, may ultimately play a role in the provision of high-quality counseling for patients with this condition.
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28
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Minor spliceosome and disease. Semin Cell Dev Biol 2017; 79:103-112. [PMID: 28965864 DOI: 10.1016/j.semcdb.2017.09.036] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/21/2017] [Accepted: 09/27/2017] [Indexed: 01/09/2023]
Abstract
The U12-dependent (minor) spliceosome excises a rare group of introns that are characterized by a highly conserved 5' splice site and branch point sequence. Several new congenital or somatic diseases have recently been associated with mutations in components of the minor spliceosome. A common theme in these diseases is the detection of elevated levels of transcripts containing U12-type introns, of which a subset is associated with other splicing defects. Here we review the present understanding of minor spliceosome diseases, particularly those associated with the specific components of the minor spliceosome. We also present a model for interpreting the molecular-level consequences of the different diseases.
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Abstract
Much evidence is now accumulating that, in addition to their general role in splicing, the components of the core splicing machinery have extensive regulatory potential. In particular, recent evidence has demonstrated that de-regulation of these factors cause the highest extent of alternative splicing changes compared to de-regulation of the classical splicing regulators. This lack of a general inhibition of splicing resonates the differential splicing effects observed in different disease pathologies associated with specific mutations targeting core spliceosomal components. In this review we will summarize what is currently known regarding the involvement of core spliceosomal U-snRNP complexes in perturbed tissue development and human diseases and argue for the existence of a compensatory mechanism enabling cells to cope with drastic perturbations in core splicing components. This system maintains the correct balance of spliceosomal snRNPs through differential expression of variant (v)U-snRNPs.
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Affiliation(s)
- Pilar Vazquez-Arango
- a Nuffield Department of Obstetrics and Gynaecology, Level 3 , Women's Centre, John Radcliffe Hospital , Oxford , England
| | - Dawn O'Reilly
- b Sir William Dunn School of pathology , University of Oxford , South Parks Road, Oxford , England
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30
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Rose AM, Luo R, Radia UK, Bhattacharya SS. Gene of the month: PRPF31. J Clin Pathol 2017; 70:729-732. [PMID: 28663330 DOI: 10.1136/jclinpath-2016-203971] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 06/01/2017] [Indexed: 11/04/2022]
Abstract
Pre-mRNA splicing is an essential process in eukaryotic cells where the transcribed intronic sequences are removed, prior to translation into protein. PRPF31 is a ubiquitously expressed splicing factor, which aids in the assembly of the macromolecular spliceosome. Mutations in PRPF31 cause autosomal dominant retinitis pigmentosa (adRP), a form of retinal degeneration that causes progressive visual impairment. Interestingly, mutations in PRPF31 are non-penetrant, with some mutation carriers being phenotypically unaffected. In this review, the gene organisation, protein structure and biological function of PRPF31 are discussed, and the mechanisms of non-penetrance in PRPF31-associated adRP are discussed.
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Affiliation(s)
- Anna M Rose
- Department of Genetics, UCL Institute of Ophthalmology, London, UK.,Department of Medicine, Imperial College, London, UK
| | - Rong Luo
- Department of Medicine, Imperial College, London, UK
| | - Utsav K Radia
- Department of Medicine, Imperial College, London, UK
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31
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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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Kinoshita W, Ogura N, Watashi K, Wakita T. Host factor PRPF31 is involved in cccDNA production in HBV-replicating cells. Biochem Biophys Res Commun 2016; 482:638-644. [PMID: 27864147 DOI: 10.1016/j.bbrc.2016.11.085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 11/15/2016] [Indexed: 02/07/2023]
Abstract
Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) plays a central role in chronic HBV infection and replication, and is an important factor for HBV surface antigen loss indicating the endpoint of HBV treatment. However, there is a known problem that current anti-HBV drugs, including interferons and nucleos(t)ide analogues, reduce HBV replication but have a little or no effect on reducing cccDNA. Therefore, the development of new therapeutic agents is necessary to eradicate cccDNA. In this study, we identified pre-mRNA processing factor 31 (PRPF31) by siRNA screening as a factor associated with cccDNA. PRPF31 knockdown by siRNA decreased cccDNA formation without serious cytotoxicity. In rescue experiments, expression of siRNA-resistant PRPF31 recovered cccDNA formation. PRPF31 knockdown did not affect HBV core protein and HBV core DNA levels in HBV-replicating cells. Chromatin immunoprecipitation and immunoprecipitation assays revealed an association between PRPF31 and cccDNA. Furthermore, co-overexpression of PRPF31 and HBx enhanced cccDNA formation in HepAD38 cells. Taken together, the present findings suggest that the interaction between PRPF31 and HBx may be a novel target for anti-HBV treatment.
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Affiliation(s)
- Wataru Kinoshita
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, Japan.
| | - Naoki Ogura
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, Japan.
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
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Abstract
Spliceosomal snRNPs are complex particles that proceed through a fascinating maturation pathway. Several steps of this pathway are closely linked to nuclear non-membrane structures called Cajal bodies. In this review, I summarize the last 20 y of research in this field. I primarily focus on snRNP biogenesis, specifically on the steps that involve Cajal bodies. I also evaluate the contribution of the Cajal body in snRNP quality control and discuss the role of snRNPs in Cajal body formation.
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Affiliation(s)
- David Staněk
- a Institute of Molecular Genetics, Czech Academy of Sciences , Prague , Czech Republic
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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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Rose AM, Bhattacharya SS. Variant haploinsufficiency and phenotypic non-penetrance in PRPF31-associated retinitis pigmentosa. Clin Genet 2016; 90:118-26. [PMID: 26853529 DOI: 10.1111/cge.12758] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 11/30/2022]
Abstract
Retinitis pigmentosa (RP) is a genetically heterogenous group of inherited disorders, characterized by death of the retinal photoreceptor cells, leading to progressive visual impairment. One form of RP is caused by mutations in the ubiquitously expressed splicing factor, PRPF31, this form being known as RP11. An intriguing feature of RP11 is the presence of non-penetrance, which has been observed in the majority of PRPF31 mutation-carrying families. In contrast to variable expressivity, which is highly pervasive, true non-penetrance is a very rare phenomenon in Mendelian disorders. In this article, the molecular mechanisms underlying phenotypic non-penetrance in RP11 are explored. It is an elegant example of how our understanding of monogenic disorders has evolved from studying only the disease gene, to considering a mutation on the genetic background of the individual - the logical evolution in this genomic era.
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Affiliation(s)
- A M Rose
- Department of Genetics, UCL Institute of Ophthalmology, London, UK
| | - S S Bhattacharya
- Department of Genetics, UCL Institute of Ophthalmology, London, UK
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36
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Rose AM, Shah AZ, Venturini G, Krishna A, Chakravarti A, Rivolta C, Bhattacharya SS. Transcriptional regulation of PRPF31 gene expression by MSR1 repeat elements causes incomplete penetrance in retinitis pigmentosa. Sci Rep 2016; 6:19450. [PMID: 26781568 PMCID: PMC4725990 DOI: 10.1038/srep19450] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/14/2015] [Indexed: 11/26/2022] Open
Abstract
PRPF31-associated retinitis pigmentosa presents a fascinating enigma: some mutation carriers are blind, while others are asymptomatic. We identify the major molecular cause of this incomplete penetrance through three cardinal features: (1) there is population variation in the number (3 or 4) of a minisatellite repeat element (MSR1) adjacent to the PRPF31 core promoter; (2) in vitro, 3-copies of the MSR1 element can repress gene transcription by 50 to 115-fold; (3) the higher-expressing 4-copy allele is not observed among symptomatic PRPF31 mutation carriers and correlates with the rate of asymptomatic carriers in different populations. Thus, a linked transcriptional modifier decreases PRPF31 gene expression that leads to haploinsufficiency. This result, taken with other identified risk alleles, allows precise genetic counseling for the first time. We also demonstrate that across the human genome, the presence of MSR1 repeats in the promoters or first introns of genes is associated with greater population variability in gene expression indicating that copy number variation of MSR1s is a generic controller of gene expression and promises to provide new insights into our understanding of gene expression regulation.
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Affiliation(s)
- Anna M. Rose
- UCL Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
| | - Amna Z. Shah
- UCL Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
| | - Giulia Venturini
- Department of Medical Genetics, University of Lausanne, 1005 Lausanne, Switzerland
| | - Abhay Krishna
- Department of Cell Therapy and Regenerative Medicine, CABIMER, 41092 Seville, Spain
| | - Aravinda Chakravarti
- Johns Hopkins University School of Medicine, Institute of Genetic Medicine, 733 N. Broadway MRB 579 Baltimore, MD 21287, USA
| | - Carlo Rivolta
- Department of Medical Genetics, University of Lausanne, 1005 Lausanne, Switzerland
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Bizarro J, Dodré M, Huttin A, Charpentier B, Schlotter F, Branlant C, Verheggen C, Massenet S, Bertrand E. NUFIP and the HSP90/R2TP chaperone bind the SMN complex and facilitate assembly of U4-specific proteins. Nucleic Acids Res 2015; 43:8973-89. [PMID: 26275778 PMCID: PMC4605303 DOI: 10.1093/nar/gkv809] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/27/2015] [Indexed: 12/17/2022] Open
Abstract
The Sm proteins are loaded on snRNAs by the SMN complex, but how snRNP-specific proteins are assembled remains poorly characterized. U4 snRNP and box C/D snoRNPs have structural similarities. They both contain the 15.5K and proteins with NOP domains (PRP31 for U4, NOP56/58 for snoRNPs). Biogenesis of box C/D snoRNPs involves NUFIP and the HSP90/R2TP chaperone system and here, we explore the function of this machinery in U4 RNP assembly. We show that yeast Prp31 interacts with several components of the NUFIP/R2TP machinery, and that these interactions are separable from each other. In human cells, PRP31 mutants that fail to stably associate with U4 snRNA still interact with components of the NUFIP/R2TP system, indicating that these interactions precede binding of PRP31 to U4 snRNA. Knock-down of NUFIP leads to mislocalization of PRP31 and decreased association with U4. Moreover, NUFIP is associated with the SMN complex through direct interactions with Gemin3 and Gemin6. Altogether, our data suggest a model in which the NUFIP/R2TP system is connected with the SMN complex and facilitates assembly of U4 snRNP-specific proteins.
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Affiliation(s)
- Jonathan Bizarro
- Equipe labélisée Ligue contre le Cancer, Institut de Génétique Moléculaire de Montpellier, IGMM-UMR 5535 du CNRS-Université de Montpellier, 1919, route de Mende, 34293 Montpellier Cedex 5, France
| | - Maxime Dodré
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Alexandra Huttin
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Bruno Charpentier
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Florence Schlotter
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Christiane Branlant
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Céline Verheggen
- Equipe labélisée Ligue contre le Cancer, Institut de Génétique Moléculaire de Montpellier, IGMM-UMR 5535 du CNRS-Université de Montpellier, 1919, route de Mende, 34293 Montpellier Cedex 5, France
| | - Séverine Massenet
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Edouard Bertrand
- Equipe labélisée Ligue contre le Cancer, Institut de Génétique Moléculaire de Montpellier, IGMM-UMR 5535 du CNRS-Université de Montpellier, 1919, route de Mende, 34293 Montpellier Cedex 5, France
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Du JL, Zhang SW, Huang HW, Cai T, Li L, Chen S, He XJ. The Splicing Factor PRP31 Is Involved in Transcriptional Gene Silencing and Stress Response in Arabidopsis. MOLECULAR PLANT 2015; 8:1053-68. [PMID: 25684655 DOI: 10.1016/j.molp.2015.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 01/11/2015] [Accepted: 02/05/2015] [Indexed: 05/10/2023]
Abstract
Although DNA methylation is known to play an important role in the silencing of transposable elements (TEs) and introduced transgenes, the mechanisms that generate DNA methylation-independent transcriptional silencing are poorly understood. Previous studies suggest that RNA-directed DNA methylation (RdDM) is required for the silencing of the RD29A-LUC transgene in the Arabidopsis ros1 mutant background with defective DNA demethylase. Loss of function of ARGONAUTE 4 (AGO4) gene, which encodes a core RdDM component, partially released the silencing of RD29A-LUC in the ros1/ago4 double mutant plants. A forward genetic screen was performed to identify the mutants with elevated RD29A-LUC transgene expression in the ros1/ago4 mutant background. We identified a mutation in the homologous gene of PRP31, which encodes a conserved pre-mRNA splicing factor that regulates the formation of the U4/U6.U5 snRNP complex in fungi and animals. We previously demonstrated that the splicing factors ZOP1 and STA1 contribute to transcriptional gene silencing. Here, we reveal that Arabidopsis PRP31 associates with ZOP1, STA1, and several other splicing-related proteins, suggesting that these splicing factors are both physically and functionally connected. We show that Arabidopsis PRP31 participates in transcriptional gene silencing. Moreover, we report that PRP31, STA1, and ZOP1 are required for development and stress response. Under cold stress, PRP31 is not only necessary for pre-mRNA splicing but also for regulation of cold-responsive gene expression. Our results suggest that the splicing machinery has multiple functions including pre-mRNA splicing, gene regulation, transcriptional gene silencing, and stress response.
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Affiliation(s)
- Jin-Lu Du
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Su-Wei Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Huan-Wei Huang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Tao Cai
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing 102206, China.
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Makarova OV, Makarov EM. The 35S U5 snRNP Is Generated from the Activated Spliceosome during In vitro Splicing. PLoS One 2015; 10:e0128430. [PMID: 26020933 PMCID: PMC4447412 DOI: 10.1371/journal.pone.0128430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/27/2015] [Indexed: 11/18/2022] Open
Abstract
Primary gene transcripts of eukaryotes contain introns, which are removed during processing by splicing machinery. Biochemical studies In vitro have identified a specific pathway in which introns are recognised and spliced out. This occurs by progressive formation of spliceosomal complexes designated as E, A, B, and C. The composition and structure of these spliceosomal conformations have been characterised in many detail. In contrast, transitions between the complexes and the intermediates of these reactions are currently less clear. We have previously isolated a novel 35S U5 snRNP from HeLa nuclear extracts. The protein composition of this particle differed from the canonical 20S U5 snRNPs but was remarkably similar to the activated B* spliceosomes. Based on this observation we have proposed a hypothesis that 35S U5 snRNPs represent a dissociation product of the spliceosome after both transesterification reactions are completed. Here we provide experimental evidence that 35S U5 snRNPs are generated from the activated B* spliceosomes during In vitro splicing.
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Affiliation(s)
- Olga V. Makarova
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen D-, Germany
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
| | - Evgeny M. Makarov
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen D-, Germany
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
- * E-mail:
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SART3-Dependent Accumulation of Incomplete Spliceosomal snRNPs in Cajal Bodies. Cell Rep 2015; 10:429-440. [PMID: 25600876 DOI: 10.1016/j.celrep.2014.12.030] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/18/2014] [Accepted: 12/13/2014] [Indexed: 12/16/2022] Open
Abstract
Cajal bodies (CBs) are evolutionarily conserved nuclear structures involved in the metabolism of spliceosomal small nuclear ribonucleoprotein particles (snRNPs). CBs are not present in all cell types, and the trigger for their formation is not yet known. Here, we depleted cells of factors required for the final steps of snRNP assembly and assayed for the presence of stalled intermediates in CBs. We show that depletion induces formation of CBs in cells that normally lack these nuclear compartments, suggesting that CB nucleation is triggered by an imbalance in snRNP assembly. Accumulation of stalled intermediates in CBs depends on the di-snRNP assembly factor SART3. SART3 is required for both the induction of CB formation as well as the tethering of incomplete snRNPs to coilin, the CB scaffolding protein. We propose a model wherein SART3 monitors tri-snRNP assembly and sequesters incomplete particles in CBs, thereby allowing cells to maintain a homeostatic balance of mature snRNPs in the nucleoplasm.
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Feng JM, Tian HF, Wen JF. Origin and evolution of the eukaryotic SSU processome revealed by a comprehensive genomic analysis and implications for the origin of the nucleolus. Genome Biol Evol 2014; 5:2255-67. [PMID: 24214024 PMCID: PMC3879963 DOI: 10.1093/gbe/evt173] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
As a nucleolar complex for small-subunit (SSU) ribosomal RNA processing, SSU processome
has been extensively studied mainly in Saccharomyces cerevisiae but not
in diverse organisms, leaving open the question of whether it is a ubiquitous mechanism
across eukaryotes and how it evolved in the course of the evolution of eukaryotes.
Genome-wide survey and identification of SSU processome components showed that the
majority of all 77 yeast SSU processome proteins possess homologs in almost all of the
main eukaryotic lineages, and 14 of them have homologs in archaea but few in bacteria,
suggesting that the complex is ubiquitous in eukaryotes, and its evolutionary history
began with abundant protein homologs being present in archaea and then a fairly complete
form of the complex emerged in the last eukaryotic common ancestor (LECA). Phylogenetic
analysis indicated that ancient gene duplication and functional divergence of the protein
components of the complex occurred frequently during the evolutionary origin of the LECA
from prokaryotes. We found that such duplications not only increased the complex’s
components but also produced some new functional proteins involved in other nucleolar
functions, such as ribosome biogenesis and even some nonnucleolar (but nuclear) proteins
participating in pre-mRNA splicing, implying the evolutionary emergence of the subnuclear
compartment—the nucleolus—has occurred in the LECA. Therefore, the LECA
harbored not only complicated SSU processomes but also a nucleolus. Our analysis also
revealed that gene duplication, innovation, and loss, caused further divergence of the
complex during the divergence of eukaryotes.
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Affiliation(s)
- Jin-Mei Feng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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Jafarifar F, Dietrich RC, Hiznay JM, Padgett RA. Biochemical defects in minor spliceosome function in the developmental disorder MOPD I. RNA (NEW YORK, N.Y.) 2014; 20:1078-89. [PMID: 24865609 PMCID: PMC4114687 DOI: 10.1261/rna.045187.114] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Biallelic mutations of the human RNU4ATAC gene, which codes for the minor spliceosomal U4atac snRNA, cause the developmental disorder, MOPD I/TALS. To date, nine separate mutations in RNU4ATAC have been identified in MOPD I patients. Evidence suggests that all of these mutations lead to abrogation of U4atac snRNA function and impaired minor intron splicing. However, the molecular basis of these effects is unknown. Here, we use a variety of in vitro and in vivo assays to address this question. We find that only one mutation, 124G>A, leads to significantly reduced expression of U4atac snRNA, whereas four mutations, 30G>A, 50G>A, 50G>C and 51G>A, show impaired binding of essential protein components of the U4atac/U6atac di-snRNP in vitro and in vivo. Analysis of MOPD I patient fibroblasts and iPS cells homozygous for the most common mutation, 51G>A, shows reduced levels of the U4atac/U6atac.U5 tri-snRNP complex as determined by glycerol gradient sedimentation and immunoprecipitation. In this report, we establish a mechanistic basis for MOPD I disease and show that the inefficient splicing of genes containing U12-dependent introns in patient cells is due to defects in minor tri-snRNP formation, and the MOPD I-associated RNU4ATAC mutations can affect multiple facets of minor snRNA function.
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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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Pan X, Chen X, Liu X, Gao X, Kang X, Xu Q, Chen X, Zhao K, Zhang X, Chu Q, Wang X, Zhao C. Mutation analysis of pre-mRNA splicing genes in Chinese families with retinitis pigmentosa. Mol Vis 2014; 20:770-9. [PMID: 24940031 PMCID: PMC4043610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 05/30/2014] [Indexed: 10/24/2022] Open
Abstract
PURPOSE Seven genes involved in precursor mRNA (pre-mRNA) splicing have been implicated in autosomal dominant retinitis pigmentosa (adRP). We sought to detect mutations in all seven genes in Chinese families with RP, to characterize the relevant phenotypes, and to evaluate the prevalence of mutations in splicing genes in patients with adRP. METHODS Six unrelated families from our adRP cohort (42 families) and two additional families with RP with uncertain inheritance mode were clinically characterized in the present study. Targeted sequence capture with next-generation massively parallel sequencing (NGS) was performed to screen mutations in 189 genes including all seven pre-mRNA splicing genes associated with adRP. Variants detected with NGS were filtered with bioinformatics analyses, validated with Sanger sequencing, and prioritized with pathogenicity analysis. RESULTS Mutations in pre-mRNA splicing genes were identified in three individual families including one novel frameshift mutation in PRPF31 (p.Leu366fs*1) and two known mutations in SNRNP200 (p.Arg681His and p.Ser1087Leu). The patients carrying SNRNP200 p.R681H showed rapid disease progression, and the family carrying p.S1087L presented earlier onset ages and more severe phenotypes compared to another previously reported family with p.S1087L. In five other families, we identified mutations in other RP-related genes, including RP1 p. Ser781* (novel), RP2 p.Gln65* (novel) and p.Ile137del (novel), IMPDH1 p.Asp311Asn (recurrent), and RHO p.Pro347Leu (recurrent). CONCLUSIONS Mutations in splicing genes identified in the present and our previous study account for 9.5% in our adRP cohort, indicating the important role of pre-mRNA splicing deficiency in the etiology of adRP. Mutations in the same splicing gene, or even the same mutation, could correlate with different phenotypic severities, complicating the genotype-phenotype correlation and clinical prognosis.
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Affiliation(s)
- Xinyuan Pan
- Department of Ophthalmology of the First Affiliated Hospital and State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Xue Chen
- Department of Ophthalmology of the First Affiliated Hospital and State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Xiaoxing Liu
- Department of Ophthalmology of the First Affiliated Hospital and State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Xiang Gao
- Department of Ophthalmology, Jiaozuo Health College, Henan, China
| | - Xiaoli Kang
- Department of Ophthalmology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qihua Xu
- Department of Ophthalmology of the First Affiliated Hospital and State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Xuejuan Chen
- Department of Ophthalmology of the First Affiliated Hospital and State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Kanxing Zhao
- Tianjin Medical University, Tianjin Eye Hospital, Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin, China
| | - Xiumei Zhang
- Department of Ophthalmology, Jiaozuo Health College, Henan, China
| | - Qiaomei Chu
- Department of Ophthalmology, Liqun Hospital, Shanghai, China
| | - Xiuying Wang
- Department of Ophthalmology of the First Affiliated Hospital and State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Chen Zhao
- Department of Ophthalmology of the First Affiliated Hospital and State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
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Mozaffari-Jovin S, Wandersleben T, Santos KF, Will CL, Lührmann R, Wahl MC. Novel regulatory principles of the spliceosomal Brr2 RNA helicase and links to retinal disease in humans. RNA Biol 2014; 11:298-312. [PMID: 24643059 DOI: 10.4161/rna.28353] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
For each round of pre-mRNA splicing, a spliceosome is assembled anew on its substrate. RNA-protein remodeling events required for spliceosome assembly, splicing catalysis, and spliceosome disassembly are driven and controlled by a conserved group of ATPases/RNA helicases. The activities of most of these enzymes are timed by their recruitment to the spliceosome. The Brr2 enzyme, however, which mediates spliceosome catalytic activation, is a stable subunit of the spliceosome, and thus, requires special regulation. Recent structural and functional studies have revealed diverse mechanisms whereby an RNaseH-like and a Jab1/MPN-like domain of the Prp8 protein regulate Brr2 activity during splicing both positively and negatively. Reversible Brr2 inhibition might in part be achieved via an intrinsically unstructured element of the Prp8 Jab1/MPN domain, a concept widespread in biological systems. Mutations leading to changes in the Prp8 Jab1/MPN domain, which are linked to a severe form of retinitis pigmentosa, disrupt Jab1/MPN-mediated regulation of Brr2.
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Affiliation(s)
- Sina Mozaffari-Jovin
- Dept. of Cellular Biochemistry; Max Planck Institute for Biophysical Chemistry; Am Fassberg 11; Göttingen, Germany
| | - Traudy Wandersleben
- Laboratory of Structural Biochemistry; Freie Universität Berlin; Takustr. 6; Berlin, Germany
| | - Karine F Santos
- Laboratory of Structural Biochemistry; Freie Universität Berlin; Takustr. 6; Berlin, Germany
| | - Cindy L Will
- Dept. of Cellular Biochemistry; Max Planck Institute for Biophysical Chemistry; Am Fassberg 11; Göttingen, Germany
| | - Reinhard Lührmann
- Dept. of Cellular Biochemistry; Max Planck Institute for Biophysical Chemistry; Am Fassberg 11; Göttingen, Germany
| | - Markus C Wahl
- Laboratory of Structural Biochemistry; Freie Universität Berlin; Takustr. 6; Berlin, Germany
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Lu F, Huang L, Lei C, Sha G, Zheng H, Liu X, Yang J, Shi Y, Lin Y, Gong B, Zhu X, Ma S, Qiao L, Lin H, Cheng J, Yang Z. A novel PRPF31 mutation in a large Chinese family with autosomal dominant retinitis pigmentosa and macular degeneration. PLoS One 2013; 8:e78274. [PMID: 24244300 PMCID: PMC3823919 DOI: 10.1371/journal.pone.0078274] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 09/10/2013] [Indexed: 11/19/2022] Open
Abstract
Purpose This study was intended to identify the disease causing genes in a large Chinese family with autosomal dominant retinitis pigmentosa and macular degeneration. Methods A genome scan analysis was conducted in this family for disease gene preliminary mapping. Snapshot analysis of selected SNPs for two-point LOD score analysis for candidate gene filter. Candidate gene PRPF31 whole exons' sequencing was executed to identify mutations. Results A novel nonsense mutation caused by an insertion was found in PRPF31 gene. All the 19 RP patients in 1085 family are carrying this heterozygous nonsense mutation. The nonsense mutation is in PRPF31 gene exon9 at chr19:54629961-54629961, inserting nucleotide “A” that generates the coding protein frame shift from p.307 and early termination at p.322 in the snoRNA binding domain (NOP domain). Conclusion This report is the first to associate PRPF31 gene's nonsense mutation and adRP and JMD. Our findings revealed that PRPF31 can lead to different clinical phenotypes in the same family, resulting either in adRP or syndrome of adRP and JMD. We believe our identification of the novel “A” insertion mutation in exon9 at chr19:54629961-54629961 in PRPF31 can provide further genetic evidence for clinical test for adRP and JMD.
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Affiliation(s)
- Fang Lu
- Center for Human Molecular Biology & Genetics, The Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Sichuan Translational Research Hospital, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Lulin Huang
- Center for Human Molecular Biology & Genetics, The Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Sichuan Translational Research Hospital, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Chuntao Lei
- Department of Ophthalmology, Sichuan Academy of Medical Sciences Affiliated Hospital and Sichuan Provincial People's Hospital, Sichuan, China
| | - Guiquan Sha
- Dechang County Hospital of Traditional Chinese Medicine, Liangshan Autonomous Prefecture, Sichuan, China
| | - Hong Zheng
- Center for Human Molecular Biology & Genetics, The Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Sichuan Translational Research Hospital, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Xiaoqi Liu
- Center for Human Molecular Biology & Genetics, The Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Sichuan Translational Research Hospital, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Jiyun Yang
- Center for Human Molecular Biology & Genetics, The Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Sichuan Translational Research Hospital, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Yi Shi
- Center for Human Molecular Biology & Genetics, The Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Sichuan Translational Research Hospital, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Ying Lin
- Center for Human Molecular Biology & Genetics, The Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Sichuan Translational Research Hospital, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Bo Gong
- Center for Human Molecular Biology & Genetics, The Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Sichuan Translational Research Hospital, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Xianjun Zhu
- Center for Human Molecular Biology & Genetics, The Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Sichuan Translational Research Hospital, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Shi Ma
- Center for Human Molecular Biology & Genetics, The Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Sichuan Translational Research Hospital, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Lifeng Qiao
- Department of Ophthalmology, Sichuan Academy of Medical Sciences Affiliated Hospital and Sichuan Provincial People's Hospital, Sichuan, China
| | - He Lin
- Center for Human Molecular Biology & Genetics, The Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Sichuan Translational Research Hospital, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Jing Cheng
- Center for Human Molecular Biology & Genetics, The Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Sichuan Translational Research Hospital, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Zhenglin Yang
- Center for Human Molecular Biology & Genetics, The Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
- Sichuan Translational Research Hospital, Chinese Academy of Sciences, Chengdu, Sichuan, China
- * E-mail:
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47
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Rose AM, Shah AZ, Venturini G, Rivolta C, Rose GE, Bhattacharya SS. Dominant PRPF31 mutations are hypostatic to a recessive CNOT3 polymorphism in retinitis pigmentosa: a novel phenomenon of "linked trans-acting epistasis". Ann Hum Genet 2013; 78:62-71. [PMID: 24116917 PMCID: PMC4240469 DOI: 10.1111/ahg.12042] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 09/01/2013] [Indexed: 12/31/2022]
Abstract
Mutations in PRPF31 are responsible for autosomal dominant retinitis pigmentosa (adRP, RP11 form) and affected families show nonpenetrance. Differential expression of the wildtype PRPF31 allele is responsible for this phenomenon: coinheritance of a mutation and a higher expressing wildtype allele provide protection against development of disease. It has been suggested that a major modulating factor lies in close proximity to the wildtype PRPF31 gene on Chromosome 19, implying that a cis-acting factor directly alters PRPF31 expression. Variable expression of CNOT3 is one determinant of PRPF31 expression. This study explored the relationship between CNOT3 (a trans-acting factor) and its paradoxical cis-acting nature in relation to RP11. Linkage analysis on Chromosome 19 was performed in mutation-carrying families, and the inheritance of the wildtype PRPF31 allele in symptomatic–asymptomatic sibships was assessed—confirming that differential inheritance of wildtype chromosome 19q13 determines the clinical phenotype (P < 2.6 × 10−7). A theoretical model was constructed that explains the apparent conflict between the linkage data and the recent demonstration that a trans-acting factor (CNOT3) is a major nonpenetrance factor: we propose that this apparently cis-acting effect arises due to the intimate linkage of CNOT3 and PRPF31 on Chromosome 19q13—a novel mechanism that we have termed “linked trans-acting epistasis.”
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Affiliation(s)
- Anna M Rose
- Department of Genetics, UCL Institute of Ophthalmology, London, United Kingdom
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48
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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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49
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Ehsani A, Alluin JV, Rossi JJ. Cell cycle abnormalities associated with differential perturbations of the human U5 snRNP associated U5-200kD RNA helicase. PLoS One 2013; 8:e62125. [PMID: 23637979 PMCID: PMC3639242 DOI: 10.1371/journal.pone.0062125] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 03/19/2013] [Indexed: 12/04/2022] Open
Abstract
Splicing of pre-messenger RNAs into functional messages requires a concerted assembly of proteins and small RNAs that identify the splice junctions and facilitate cleavage of exon-intron boundaries and ligation of exons. One of the key steps in the splicing reaction is the recruitment of a tri-snRNP harboring the U5/U4/U6 snRNPs. The U5 snRNP is also required for both steps of splicing and exon-exon joining. One of the key components of the tri-snRNP is the U5 200kd helicase. The human U5-200kD gene isolated from Hela cells encodes a 200 kDa protein with putative RNA helicase function. Surprisingly, little is known about the functional role of this protein in humans. Therefore, we have investigated the role of the U5-200kD RNA helicase in mammalian cell culture. We created and expressed a dominant negative domain I mutant of the RNA helicase in HEK293 cells and used RNAi to downregulate expression of the endogenous protein. Transient and stable expression of the domain I mutant U5-200kD protein using an ecdysone-inducible system and transient expression of an anti-U5-200kD short hairpin RNA (shRNA) resulted in differential splicing and growth defects in the 293/EcR cells. Cell cycle analysis of the dominant negative clones revealed delayed exit from the G2/M phase of the cell cycle due to a mild splicing defect. In contrast to the domain I dominant negative mutant expressing cells, transient expression of an anti-U5-200kD shRNA resulted in a pronounced S phase arrest and a minute splicing defect. Collectively, this work demonstrates for the first time establishment of differential human cell culture splicing and cell cycle defect models due to perturbed levels of an essential core splicing factor.
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Affiliation(s)
- Ali Ehsani
- Department of Molecular and Cellular Biology, and Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California, United States of America
| | - Jessica V. Alluin
- Department of Molecular and Cellular Biology, and Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California, United States of America
| | - John J. Rossi
- Department of Molecular and Cellular Biology, and Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California, United States of America
- * E-mail:
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50
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Ahmed S, Holt M, Riedel D, Jahn R. Small-scale isolation of synaptic vesicles from mammalian brain. Nat Protoc 2013; 8:998-1009. [PMID: 23619891 DOI: 10.1038/nprot.2013.053] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Synaptic vesicles (SVs) are essential organelles that participate in the release of neurotransmitters from a neuron. Biochemical analysis of purified SVs was instrumental in the identification of proteins involved in exocytotic membrane fusion and neurotransmitter uptake. Although numerous protocols have been published detailing the isolation of SVs from the brain, those that give the highest-purity vesicles often have low yields. Here we describe a protocol for the small-scale isolation of SVs from mouse and rat brain. The procedure relies on standard fractionation techniques, including differential centrifugation, rate-zonal centrifugation and size-exclusion chromatography, but it has been optimized for minimal vesicle loss while maintaining a high degree of purity. The protocol can be completed in less than 1 d and allows the recovery of ∼150 μg of vesicle protein from a single mouse brain, thus allowing vesicle isolation from transgenic mice.
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Affiliation(s)
- Saheeb Ahmed
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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