1
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Jiang T, Wang L, Tang L, Zeb A, Hou Y. Identification of two short peptide motifs from serine/arginine-rich protein ribonucleic acid recognition motif-1 domain acting as splicing regulators. PeerJ 2023; 11:e16103. [PMID: 37744237 PMCID: PMC10512959 DOI: 10.7717/peerj.16103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023] Open
Abstract
Background Serine/arginine-rich (SR) proteins regulate pre-mRNA splicing. However, structurally similar proteins often behave differently in splicing regulation and the underlying mechanisms are largely unknown. Here, using SMN1/2 minigenes we extensively analyzed four SR proteins, SRSF1/5/6/9. Methods In this study, the effects of these proteins on SMN1/2 exon 7 splicing when tethered at either intron 6 or 7 were evaluated using an MS2-tethering assay. Deletion analysis in four SR proteins and co-overexpression analysis were performed. Results Splicing outcomes varied among all four SR proteins, SRSF1 and SRSF5 function the same at the two sites, acting as repressor and stimulator, respectively; while SRSF6 and SRSF9 promote exon 7 inclusion at only one site. Further, the key domains of each SR proteins were investigated, which identified a potent inhibitory nonapeptide in the C-terminus of SRSF1/9 ribonucleic acid recognition motif-1 (RRM1) and a potent stimulatory heptapeptide at the N-terminus of SRSF5/6 RRM1. Conclusion The insight of the four SR proteins and their domains in affecting SMN gene splicing brings a new perspective on the modes of action of SR proteins; and the functional peptides obtained here offers new ideas for developing splice switching-related therapies.
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Affiliation(s)
- Tao Jiang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
- Department of Rehabilitation, Southwest Hospital, Third Military Medical University Army Medical University, Chongqing, China
| | - Li Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Liang Tang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Azhar Zeb
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
| | - Yanjun Hou
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China
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2
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Zhang X, Wang Z, Xu Q, Chen Y, Liu W, Zhong T, Li H, Quan C, Zhang L, Cui CP. Splicing factor Srsf5 deletion disrupts alternative splicing and causes noncompaction of ventricular myocardium. iScience 2021; 24:103097. [PMID: 34622152 PMCID: PMC8482499 DOI: 10.1016/j.isci.2021.103097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/17/2021] [Accepted: 09/06/2021] [Indexed: 11/21/2022] Open
Abstract
The serine/arginine-rich (SR) family of splicing factors plays important roles in mRNA splicing activation, repression, export, stabilization, and translation. SR-splicing factor 5 (SRSF5) is a glucose-inducible protein that promotes tumor cell growth. However, the functional role of SRSF5 in tissue development and disease remains unknown. Here, Srsf5 knockout (Srsf5−/−) mice were generated using CRISPR-Cas9. Mutant mice were perinatally lethal and exhibited cardiac dysfunction with noncompaction of the ventricular myocardium. The left ventricular internal diameter and volume were increased in Srsf5−/− mice during systole. Null mice had abnormal electrocardiogram patterns, indicative of a light atrioventricular block. Mechanistically, Srsf5 promoted the alternative splicing of Myom1 (myomesin-1), a protein that crosslinks myosin filaments to the sarcomeric M-line. The switch between embryonic and adult isoforms of Myom1 could not be completed in Srsf5-deficient heart. These findings indicate that Srsf5-regulated alternative splicing plays a critical role during heart development. Systemic loss of Srsf5 causes perinatal lethality in mice Srsf5 deficiency leads to cardiac dysfunction Alternative splicing of Myom1 in the heart around birth is regulated by Srsf5
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Affiliation(s)
- Xiaoli Zhang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun, Jilin 130021, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 27 Taiping Road, Beijing 100850, China
| | - Ze Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 27 Taiping Road, Beijing 100850, China
| | - Qing Xu
- Core Facilities Centre, Capital Medical University, Beijing 100069, China
| | - Yuhan Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 27 Taiping Road, Beijing 100850, China
| | - Wen Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 27 Taiping Road, Beijing 100850, China
| | - Tong Zhong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 27 Taiping Road, Beijing 100850, China
| | - Hongchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 27 Taiping Road, Beijing 100850, China
| | - Chengshi Quan
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun, Jilin 130021, China
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 27 Taiping Road, Beijing 100850, China
| | - Chun-Ping Cui
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 27 Taiping Road, Beijing 100850, China
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3
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Shibata S, Ajiro M, Hagiwara M. Mechanism-Based Personalized Medicine for Cystic Fibrosis by Suppressing Pseudo Exon Inclusion. Cell Chem Biol 2020; 27:1472-1482.e6. [DOI: 10.1016/j.chembiol.2020.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/29/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022]
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4
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Li JJ, Lin X, Tang C, Lu YQ, Hu X, Zuo E, Li H, Ying W, Sun Y, Lai LL, Chen HZ, Guo XX, Zhang QJ, Wu S, Zhou C, Shen X, Wang Q, Lin MT, Ma LX, Wang N, Krainer AR, Shi L, Yang H, Chen WJ. Disruption of splicing-regulatory elements using CRISPR/Cas9 to rescue spinal muscular atrophy in human iPSCs and mice. Natl Sci Rev 2019; 7:92-101. [PMID: 34691481 PMCID: PMC8446915 DOI: 10.1093/nsr/nwz131] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/27/2019] [Accepted: 08/28/2019] [Indexed: 12/22/2022] Open
Abstract
We here report a genome-editing strategy to correct spinal muscular atrophy (SMA). Rather
than directly targeting the pathogenic exonic mutations, our strategy employed Cas9 and
guide-sgRNA for the targeted disruption of intronic splicing-regulatory elements. We
disrupted intronic splicing silencers (ISSs, including ISS-N1 and ISS + 100) of survival
motor neuron (SMN) 2, a key modifier gene of SMA, to enhance exon 7 inclusion and
full-length SMN expression in SMA iPSCs. Survival of splicing-corrected iPSC-derived motor
neurons was rescued with SMN restoration. Furthermore, co-injection of Cas9 mRNA from
Streptococcus pyogenes (SpCas9) or Cas9 from Staphylococcus
aureus (SaCas9) alongside their corresponding sgRNAs targeting ISS-N1 into
zygotes rescued 56% and 100% of severe SMA transgenic mice
(Smn−/−, SMN2tg/−). The median
survival of the resulting mice was extended to >400 days. Collectively, our study
provides proof-of-principle for a new strategy to therapeutically intervene in SMA and
other RNA-splicing-related diseases.
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Affiliation(s)
- Jin-Jing Li
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China.,Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Xiang Lin
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China.,Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Cheng Tang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ying-Qian Lu
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Xinde Hu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Erwei Zuo
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - He Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenqin Ying
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yidi Sun
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lu-Lu Lai
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Hai-Zhu Chen
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Xin-Xin Guo
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Qi-Jie Zhang
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China.,Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Shuang Wu
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Changyang Zhou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaowen Shen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qifang Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Min-Ting Lin
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China.,Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Li-Xiang Ma
- Department of Anatomy, Histology & Embryology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ning Wang
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China.,Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Linyu Shi
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wan-Jin Chen
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China.,Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
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5
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Maule G, Casini A, Montagna C, Ramalho AS, De Boeck K, Debyser Z, Carlon MS, Petris G, Cereseto A. Allele specific repair of splicing mutations in cystic fibrosis through AsCas12a genome editing. Nat Commun 2019; 10:3556. [PMID: 31391465 PMCID: PMC6685978 DOI: 10.1038/s41467-019-11454-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 07/05/2019] [Indexed: 12/19/2022] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the CFTR gene. The 3272-26A>G and 3849+10kbC>T CFTR mutations alter the correct splicing of the CFTR gene, generating new acceptor and donor splice sites respectively. Here we develop a genome editing approach to permanently correct these genetic defects, using a single crRNA and the Acidaminococcus sp. BV3L6, AsCas12a. This genetic repair strategy is highly precise, showing very strong discrimination between the wild-type and mutant sequence and a complete absence of detectable off-targets. The efficacy of this gene correction strategy is verified in intestinal organoids and airway epithelial cells derived from CF patients carrying the 3272-26A>G or 3849+10kbC>T mutations, showing efficient repair and complete functional recovery of the CFTR channel. These results demonstrate that allele-specific genome editing with AsCas12a can correct aberrant CFTR splicing mutations, paving the way for a permanent splicing correction in genetic diseases.
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Affiliation(s)
- Giulia Maule
- Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Antonio Casini
- Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Claudia Montagna
- Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Anabela S Ramalho
- Department of Development and Regeneration, CF Centre, Woman and Child, KU Leuven, Herestraat 49, Leuven, 3000, Belgium
| | - Kris De Boeck
- Department of Development and Regeneration, CF Centre, Woman and Child, KU Leuven, Herestraat 49, Leuven, 3000, Belgium
- Pediatric Pulmonology, Department of Pediatrics, University Hospital Leuven, Herestraat 49, Leuven, 3000, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Drug Discovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Leuven, 3000, Belgium
| | - Marianne S Carlon
- Laboratory for Molecular Virology and Drug Discovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Leuven, 3000, Belgium.
| | - Gianluca Petris
- Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy.
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Anna Cereseto
- Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy.
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6
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Activation of Cryptic 3' Splice-Sites by SRSF2 Contributes to Cassette Exon Skipping. Cells 2019; 8:cells8070696. [PMID: 31295920 PMCID: PMC6678912 DOI: 10.3390/cells8070696] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/05/2019] [Accepted: 07/09/2019] [Indexed: 11/21/2022] Open
Abstract
Here we show that the serine/arginine rich splicing factor 2 (SRSF2) promotes cryptic 3′ splice-site (3′AG′) usage during cassette exon exclusion in survival of motor neuron (SMN2) minigenes. Deletion of the 3′AG′ (3′AG′1), its associated branch point (BP′) and polypyrimidine tract (PPT′) sequences directs SRSF2 to promote a second 3′AG′ (3′AG′2) with less conserved associated region for intron splicing. Furthermore, deletion of both 3′AG′1 and 3′AG′2 and their associated sequences triggered usage of a third 3′AG′3 that has very weak associated sequences. Interestingly, when intron splicing was directed to the 3′AG′ cryptic splice-sites, intron splicing from the canonical 3′AG splice-site was reduced along with a decrease in cassette exon inclusion. Moreover, multiple SRSF2 binding sites within the intron are responsible for 3′AG′ activation. We conclude that SRSF2 facilitates exon exclusion by activating a cryptic 3′AG′ and inhibiting downstream intron splicing.
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7
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Krchňáková Z, Thakur PK, Krausová M, Bieberstein N, Haberman N, Müller-McNicoll M, Staněk D. Splicing of long non-coding RNAs primarily depends on polypyrimidine tract and 5' splice-site sequences due to weak interactions with SR proteins. Nucleic Acids Res 2019; 47:911-928. [PMID: 30445574 PMCID: PMC6344860 DOI: 10.1093/nar/gky1147] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/26/2018] [Accepted: 10/30/2018] [Indexed: 12/20/2022] Open
Abstract
Many nascent long non-coding RNAs (lncRNAs) undergo the same maturation steps as pre-mRNAs of protein-coding genes (PCGs), but they are often poorly spliced. To identify the underlying mechanisms for this phenomenon, we searched for putative splicing inhibitory sequences using the ncRNA-a2 as a model. Genome-wide analyses of intergenic lncRNAs (lincRNAs) revealed that lincRNA splicing efficiency positively correlates with 5'ss strength while no such correlation was identified for PCGs. In addition, efficiently spliced lincRNAs have higher thymidine content in the polypyrimidine tract (PPT) compared to efficiently spliced PCGs. Using model lincRNAs, we provide experimental evidence that strengthening the 5'ss and increasing the T content in PPT significantly enhances lincRNA splicing. We further showed that lincRNA exons contain less putative binding sites for SR proteins. To map binding of SR proteins to lincRNAs, we performed iCLIP with SRSF2, SRSF5 and SRSF6 and analyzed eCLIP data for SRSF1, SRSF7 and SRSF9. All examined SR proteins bind lincRNA exons to a much lower extent than expression-matched PCGs. We propose that lincRNAs lack the cooperative interaction network that enhances splicing, which renders their splicing outcome more dependent on the optimality of splice sites.
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Affiliation(s)
- Zuzana Krchňáková
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Prasoon Kumar Thakur
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Michaela Krausová
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Nicole Bieberstein
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Nejc Haberman
- Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, UK
| | | | - David Staněk
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
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8
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Carvill GL, Engel KL, Ramamurthy A, Cochran JN, Roovers J, Stamberger H, Lim N, Schneider AL, Hollingsworth G, Holder DH, Regan BM, Lawlor J, Lagae L, Ceulemans B, Bebin EM, Nguyen J, Barsh GS, Weckhuysen S, Meisler M, Berkovic SF, De Jonghe P, Scheffer IE, Myers RM, Cooper GM, Mefford HC, Striano P, Zara F, Helbig I, Møller RS, von Spiczak S, Muhle H, Caglayan H, Sterbova K, Craiu D, Hoffman D, Lehesjoki AE, Selmer K, Depienne C, Lemke J, Marini C, Guerrini R, Neubauer B, Talvik T, Leguern E, de Jonghe P, Weckhuysen S. Aberrant Inclusion of a Poison Exon Causes Dravet Syndrome and Related SCN1A-Associated Genetic Epilepsies. Am J Hum Genet 2018; 103:1022-1029. [PMID: 30526861 DOI: 10.1016/j.ajhg.2018.10.023] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/25/2018] [Indexed: 12/30/2022] Open
Abstract
Developmental and epileptic encephalopathies (DEEs) are a group of severe epilepsies characterized by refractory seizures and developmental impairment. Sequencing approaches have identified causal genetic variants in only about 50% of individuals with DEEs.1-3 This suggests that unknown genetic etiologies exist, potentially in the ∼98% of human genomes not covered by exome sequencing (ES). Here we describe seven likely pathogenic variants in regions outside of the annotated coding exons of the most frequently implicated epilepsy gene, SCN1A, encoding the alpha-1 sodium channel subunit. We provide evidence that five of these variants promote inclusion of a "poison" exon that leads to reduced amounts of full-length SCN1A protein. This mechanism is likely to be broadly relevant to human disease; transcriptome studies have revealed hundreds of poison exons,4,5 including some present within genes encoding other sodium channels and in genes involved in neurodevelopment more broadly.6 Future research on the mechanisms that govern neuronal-specific splicing behavior might allow researchers to co-opt this system for RNA therapeutics.
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9
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Fratta P, Sivakumar P, Humphrey J, Lo K, Ricketts T, Oliveira H, Brito-Armas JM, Kalmar B, Ule A, Yu Y, Birsa N, Bodo C, Collins T, Conicella AE, Mejia Maza A, Marrero-Gagliardi A, Stewart M, Mianne J, Corrochano S, Emmett W, Codner G, Groves M, Fukumura R, Gondo Y, Lythgoe M, Pauws E, Peskett E, Stanier P, Teboul L, Hallegger M, Calvo A, Chiò A, Isaacs AM, Fawzi NL, Wang E, Housman DE, Baralle F, Greensmith L, Buratti E, Plagnol V, Fisher EM, Acevedo-Arozena A. Mice with endogenous TDP-43 mutations exhibit gain of splicing function and characteristics of amyotrophic lateral sclerosis. EMBO J 2018; 37:embj.201798684. [PMID: 29764981 PMCID: PMC5983119 DOI: 10.15252/embj.201798684] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/15/2018] [Accepted: 03/22/2018] [Indexed: 12/11/2022] Open
Abstract
TDP‐43 (encoded by the gene TARDBP) is an RNA binding protein central to the pathogenesis of amyotrophic lateral sclerosis (ALS). However, how TARDBP mutations trigger pathogenesis remains unknown. Here, we use novel mouse mutants carrying point mutations in endogenous Tardbp to dissect TDP‐43 function at physiological levels both in vitro and in vivo. Interestingly, we find that mutations within the C‐terminal domain of TDP‐43 lead to a gain of splicing function. Using two different strains, we are able to separate TDP‐43 loss‐ and gain‐of‐function effects. TDP‐43 gain‐of‐function effects in these mice reveal a novel category of splicing events controlled by TDP‐43, referred to as “skiptic” exons, in which skipping of constitutive exons causes changes in gene expression. In vivo, this gain‐of‐function mutation in endogenous Tardbp causes an adult‐onset neuromuscular phenotype accompanied by motor neuron loss and neurodegenerative changes. Furthermore, we have validated the splicing gain‐of‐function and skiptic exons in ALS patient‐derived cells. Our findings provide a novel pathogenic mechanism and highlight how TDP‐43 gain of function and loss of function affect RNA processing differently, suggesting they may act at different disease stages.
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Affiliation(s)
- Pietro Fratta
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Prasanth Sivakumar
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Jack Humphrey
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK.,UCL Genetics Institute, London, UK
| | - Kitty Lo
- UCL Genetics Institute, London, UK
| | | | | | - Jose M Brito-Armas
- Unidad de Investigación, Hospital Universitario de Canarias, Fundación Canaria de Investigación Sanitaria and Instituto de Tecnologías Biomédicas (CIBICAN), La Laguna, Spain
| | - Bernadett Kalmar
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Agnieszka Ule
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Yichao Yu
- UCL Centre for Advanced Biomedical Imaging, University College London, London, UK
| | - Nicol Birsa
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Cristian Bodo
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Toby Collins
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Alexander E Conicella
- Graduate Program in Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Alan Mejia Maza
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Alessandro Marrero-Gagliardi
- Unidad de Investigación, Hospital Universitario de Canarias, Fundación Canaria de Investigación Sanitaria and Instituto de Tecnologías Biomédicas (CIBICAN), La Laguna, Spain
| | | | | | | | | | | | - Michael Groves
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Ryutaro Fukumura
- Mutagenesis and Genomics Team, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Yoichi Gondo
- Mutagenesis and Genomics Team, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Mark Lythgoe
- UCL Centre for Advanced Biomedical Imaging, University College London, London, UK
| | | | | | | | | | | | - Andrea Calvo
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
| | - Adriano Chiò
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
| | - Adrian M Isaacs
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK.,UK Dementia Research Institute at UCL, UCL Institute of Neurology, London, UK
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology & Biotechnology, Brown University, Providence, RI, USA
| | - Eric Wang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David E Housman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Francisco Baralle
- International Center for Genomic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Linda Greensmith
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Emanuele Buratti
- International Center for Genomic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | | | - Elizabeth Mc Fisher
- UCL Institute of Neurology, and MRC Centre for Neuromuscular Disease, London, UK
| | - Abraham Acevedo-Arozena
- MRC Mammalian Genetics Unit, Harwell, UK .,Unidad de Investigación, Hospital Universitario de Canarias, Fundación Canaria de Investigación Sanitaria and Instituto de Tecnologías Biomédicas (CIBICAN), La Laguna, Spain
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10
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Moon H, Cho S, Loh TJ, Jang HN, Liu Y, Choi N, Oh J, Ha J, Zhou J, Cho S, Kim DE, Ye MB, Zheng X, Shen H. SRSF2 directly inhibits intron splicing to suppresses cassette exon inclusion. BMB Rep 2018; 50:423-428. [PMID: 28712387 PMCID: PMC5595172 DOI: 10.5483/bmbrep.2017.50.8.103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Indexed: 12/30/2022] Open
Abstract
SRSF2, a Serine-Arginine rich (SR) protein, is a splicing activator that mediates exon inclusion and exclusion events equally well. Here we show SRSF2 directly suppresses intron splicing to suppress cassette exon inclusion in SMN pre-mRNA. Through a serial mutagenesis, we demonstrate that a 10 nt RNA sequence surrounding the branch-point (BP), is important for SRSF2-mediated inhibition of cassette exon inclusion through directly interacting with SRSF2. We conclude that SRSF2 inhibits intron splicing to promote exon exclusion.
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Affiliation(s)
- Heegyum Moon
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Sunghee Cho
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Tiing Jen Loh
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Ha Na Jang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Yongchao Liu
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Namjeong Choi
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jagyeong Oh
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jiyeon Ha
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jianhua Zhou
- JiangSu Key Laboratory of Neuroregeneration, Nantong University, Nantong 226019, China
| | - Sungchan Cho
- Bio-Therapeutics Research Institute, Korea Research Institute of Bioscience and Biotechnology, Chungbuk 28116, Korea
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Michael B Ye
- Division of Liberal Arts and Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Xuexiu Zheng
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Haihong Shen
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
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11
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Perez-Marques F, Simpson P, Yan K, Quasney MW, Halligan N, Merchant D, Dahmer MK. Association of polymorphisms in genes of factors involved in regulation of splicing of cystic fibrosis transmembrane conductance regulator mRNA with acute respiratory distress syndrome in children with pneumonia. Crit Care 2016; 20:281. [PMID: 27596159 PMCID: PMC5011993 DOI: 10.1186/s13054-016-1454-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 08/15/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Previous work has demonstrated a strong association between lung injury in African American children with pneumonia and a polymorphic (TG)mTn region in cystic fibrosis transmembrane conductance (CFTR) involved in the generation of a nonfunctional CFTR protein lacking exon 9. A number of splicing factors that regulate the inclusion/exclusion of exon 9 have been identified. The objective of this study was to determine whether genetic variants in these splicing factors were associated with acute respiratory distress syndrome (ARDS) in children with pneumonia. METHODS This is a prospective cohort genetic association study of lung injury in African American and non-Hispanic Caucasian children with community-acquired pneumonia evaluated in the emergency department or admitted to the hospital. Linkage-disequilibrium-tag single nucleotide polymorphisms (LD-tag SNPs) in genes of the following splicing factors (followed by gene name) involved in exon 9 skipping PTB1 (PTBP1), SRp40 (SFRS1), SR2/ASF (SFRS5), TDP-43 (TARDBP), TIA-1 (TIA1), and U2AF(65) (U2AF2) were genotyped. SNPs in the gene of the splicing factor CELF2 (CELF2) were selected by conservation score. Multivariable analysis was used to examine association between genotypes and ARDS. RESULTS The African American cohort (n = 474) had 29 children with ARDS and the non-Hispanic Caucasian cohort (n = 304) had 32 children with ARDS. In the African American group multivariable analysis indicated that three variants in CELF2, rs7068124 (p = 0.004), rs3814634 (p = 0.032) and rs10905928 (p = 0.044), and two in TIA1, rs2592178 (p = 0.005) and rs13402990 (p = 0.018) were independently associated with ARDS. In the non-Hispanic Caucasian group, a single variant in CELF2, rs2277212 (p = 0.014), was associated with increased risk of developing ARDS. CONCLUSIONS The data indicate that SNPs in CELF2 may be associated with the risk of developing ARDS in both African American and non-Hispanic Caucasian children with pneumonia and suggest that the potential role of the splicing factor CELF2 in ARDS should be explored further.
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Affiliation(s)
| | - Pippa Simpson
- Section of Quantitative Health Sciences, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI USA
- Children’s Research Institute, Medical College of Wisconsin, Milwaukee, WI USA
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI USA
| | - Ke Yan
- Section of Quantitative Health Sciences, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI USA
- Children’s Research Institute, Medical College of Wisconsin, Milwaukee, WI USA
| | - Michael W. Quasney
- Division of Pediatric Critical Care, Department of Pediatrics and Communicable Diseases, University of Michigan, 1500 East Medical Center Dr, SPC 5243, Ann Arbor, MI 48109-5243 USA
| | - Nadine Halligan
- Division of Pediatric Critical Care, Department of Pediatrics and Communicable Diseases, University of Michigan, 1500 East Medical Center Dr, SPC 5243, Ann Arbor, MI 48109-5243 USA
| | - Daniel Merchant
- Section of Critical Care Medicine, Medical College of Wisconsin, Milwaukee, WI USA
- Children’s Research Institute, Medical College of Wisconsin, Milwaukee, WI USA
| | - Mary K. Dahmer
- Division of Pediatric Critical Care, Department of Pediatrics and Communicable Diseases, University of Michigan, 1500 East Medical Center Dr, SPC 5243, Ann Arbor, MI 48109-5243 USA
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12
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Xiao W, Adhikari S, Dahal U, Chen YS, Hao YJ, Sun BF, Sun HY, Li A, Ping XL, Lai WY, Wang X, Ma HL, Huang CM, Yang Y, Huang N, Jiang GB, Wang HL, Zhou Q, Wang XJ, Zhao YL, Yang YG. Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing. Mol Cell 2016; 61:507-519. [DOI: 10.1016/j.molcel.2016.01.012] [Citation(s) in RCA: 818] [Impact Index Per Article: 102.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/18/2015] [Accepted: 01/05/2016] [Indexed: 10/22/2022]
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13
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Tajnik M, Vigilante A, Braun S, Hänel H, Luscombe NM, Ule J, Zarnack K, König J. Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends. Nucleic Acids Res 2015; 43:10492-505. [PMID: 26400176 PMCID: PMC4666398 DOI: 10.1093/nar/gkv956] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 09/09/2015] [Accepted: 09/10/2015] [Indexed: 11/14/2022] Open
Abstract
The 3' untranslated regions (3' UTRs) of transcripts serve as important hubs for posttranscriptional gene expression regulation. Here, we find that the exonisation of intergenic Alu elements introduced new terminal exons and polyadenylation sites during human genome evolution. While Alu exonisation from introns has been described previously, we shed light on a novel mechanism to create alternative 3' UTRs, thereby opening opportunities for differential posttranscriptional regulation. On the mechanistic level, we show that intergenic Alu exonisation can compete both with alternative splicing and polyadenylation in the upstream gene. Notably, the Alu-derived isoforms are often expressed in a tissue-specific manner, and the Alu-derived 3' UTRs can alter mRNA stability. In summary, we demonstrate that intergenic elements can affect processing of preceding genes, and elucidate how intergenic Alu exonisation can contribute to tissue-specific posttranscriptional regulation by expanding the repertoire of 3' UTRs.
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Affiliation(s)
- Mojca Tajnik
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
| | - Alessandra Vigilante
- UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Simon Braun
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Heike Hänel
- Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Nicholas M Luscombe
- UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK Okinawa Institute of Science & Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Kathi Zarnack
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Julian König
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, Germany Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
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14
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Sohail M, Xie J. Diverse regulation of 3' splice site usage. Cell Mol Life Sci 2015; 72:4771-93. [PMID: 26370726 PMCID: PMC11113787 DOI: 10.1007/s00018-015-2037-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/12/2015] [Accepted: 09/03/2015] [Indexed: 01/13/2023]
Abstract
The regulation of splice site (SS) usage is important for alternative pre-mRNA splicing and thus proper expression of protein isoforms in cells; its disruption causes diseases. In recent years, an increasing number of novel regulatory elements have been found within or nearby the 3'SS in mammalian genes. The diverse elements recruit a repertoire of trans-acting factors or form secondary structures to regulate 3'SS usage, mostly at the early steps of spliceosome assembly. Their mechanisms of action mainly include: (1) competition between the factors for RNA elements, (2) steric hindrance between the factors, (3) direct interaction between the factors, (4) competition between two splice sites, or (5) local RNA secondary structures or longer range loops, according to the mode of protein/RNA interactions. Beyond the 3'SS, chromatin remodeling/transcription, posttranslational modifications of trans-acting factors and upstream signaling provide further layers of regulation. Evolutionarily, some of the 3'SS elements seem to have emerged in mammalian ancestors. Moreover, other possibilities of regulation such as that by non-coding RNA remain to be explored. It is thus likely that there are more diverse elements/factors and mechanisms that influence the choice of an intron end. The diverse regulation likely contributes to a more complex but refined transcriptome and proteome in mammals.
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Affiliation(s)
- Muhammad Sohail
- Department of Physiology and Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
| | - Jiuyong Xie
- Department of Physiology and Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
- Department of Biochemistry and Medical Genetics, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
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15
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Comiskey DF, Jacob AG, Singh RK, Tapia-Santos AS, Chandler DS. Splicing factor SRSF1 negatively regulates alternative splicing of MDM2 under damage. Nucleic Acids Res 2015; 43:4202-18. [PMID: 25845590 PMCID: PMC4417157 DOI: 10.1093/nar/gkv223] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 03/04/2015] [Indexed: 12/21/2022] Open
Abstract
Genotoxic stress induces alternative splicing of the oncogene MDM2 generating MDM2-ALT1, an isoform attributed with tumorigenic properties. However, the mechanisms underlying this event remain unclear. Here we explore MDM2 splicing regulation by utilizing a novel minigene that mimics endogenous MDM2 splicing in response to UV and cisplatinum-induced DNA damage. We report that exon 11 is necessary and sufficient for the damage-specific alternative splicing of the MDM2 minigene and that the splicing factor SRSF1 binds exon 11 at evolutionarily conserved sites. Interestingly, mutations disrupting this interaction proved sufficient to abolish the stress-induced alternative splicing of the MDM2 minigene. Furthermore, SRSF1 overexpression promoted exclusion of exon 11, while its siRNA-mediated knockdown prevented the stress-induced alternative splicing of endogenous MDM2. Additionally, we observed elevated SRSF1 levels under stress and in tumors correlating with the expression of MDM2-ALT1. Notably, we demonstrate that MDM2-ALT1 splicing can be blocked by targeting SRSF1 sites on exon 11 using antisense oligonucleotides. These results present conclusive evidence supporting a negative role for SRSF1 in MDM2 alternative splicing. Importantly, we define for the first time, a clear-cut mechanism for the regulation of damage-induced MDM2 splicing and present potential strategies for manipulating MDM2 expression via splicing modulation.
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Affiliation(s)
- Daniel F Comiskey
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital, 700 Childrens Drive WA5023, Columbus, OH 43205, USA
| | - Aishwarya G Jacob
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital, 700 Childrens Drive WA5023, Columbus, OH 43205, USA
| | - Ravi K Singh
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital, 700 Childrens Drive WA5023, Columbus, OH 43205, USA
| | - Aixa S Tapia-Santos
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital, 700 Childrens Drive WA5023, Columbus, OH 43205, USA
| | - Dawn S Chandler
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital, 700 Childrens Drive WA5023, Columbus, OH 43205, USA
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16
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Abstract
Sequence-specific RNA-binding proteins (RBPs) bind to pre-mRNA to control alternative splicing, but it is not yet possible to read the 'splicing code' that dictates splicing regulation on the basis of genome sequence. Each alternative splicing event is controlled by multiple RBPs, the combined action of which creates a distribution of alternatively spliced products in a given cell type. As each cell type expresses a distinct array of RBPs, the interpretation of regulatory information on a given RNA target is exceedingly dependent on the cell type. RBPs also control each other's functions at many levels, including by mutual modulation of their binding activities on specific regulatory RNA elements. In this Review, we describe some of the emerging rules that govern the highly context-dependent and combinatorial nature of alternative splicing regulation.
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Affiliation(s)
- Xiang-Dong Fu
- Department of Cellular and Molecular Medicine and Institute for Genomic, Medicine, University of California San Diego, La Jolla, California 92093–0651, USA
| | - Manuel Ares
- Center for Molecular Biology of RNA, and Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
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17
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Liu S, Cheng C. Alternative RNA splicing and cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2013; 4:547-66. [PMID: 23765697 PMCID: PMC4426271 DOI: 10.1002/wrna.1178] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Revised: 05/10/2013] [Accepted: 05/11/2013] [Indexed: 01/04/2023]
Abstract
Alternative splicing of pre-messenger RNA (mRNA) is a fundamental mechanism by which a gene can give rise to multiple distinct mRNA transcripts, yielding protein isoforms with different, even opposing, functions. With the recognition that alternative splicing occurs in nearly all human genes, its relationship with cancer-associated pathways has emerged as a rapidly growing field. In this review, we summarize recent findings that have implicated the critical role of alternative splicing in cancer and discuss current understandings of the mechanisms underlying dysregulated alternative splicing in cancer cells.
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Affiliation(s)
- Sali Liu
- Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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18
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Cléry A, Sinha R, Anczuków O, Corrionero A, Moursy A, Daubner GM, Valcárcel J, Krainer AR, Allain FHT. Isolated pseudo-RNA-recognition motifs of SR proteins can regulate splicing using a noncanonical mode of RNA recognition. Proc Natl Acad Sci U S A 2013; 110:E2802-11. [PMID: 23836656 PMCID: PMC3725064 DOI: 10.1073/pnas.1303445110] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Serine/arginine (SR) proteins, one of the major families of alternative-splicing regulators in Eukarya, have two types of RNA-recognition motifs (RRMs): a canonical RRM and a pseudo-RRM. Although pseudo-RRMs are crucial for activity of SR proteins, their mode of action was unknown. By solving the structure of the human SRSF1 pseudo-RRM bound to RNA, we discovered a very unusual and sequence-specific RNA-binding mode that is centered on one α-helix and does not involve the β-sheet surface, which typically mediates RNA binding by RRMs. Remarkably, this mode of binding is conserved in all pseudo-RRMs tested. Furthermore, the isolated pseudo-RRM is sufficient to regulate splicing of about half of the SRSF1 target genes tested, and the bound α-helix is a pivotal element for this function. Our results strongly suggest that SR proteins with a pseudo-RRM frequently regulate splicing by competing with, rather than recruiting, spliceosome components, using solely this unusual RRM.
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Affiliation(s)
- Antoine Cléry
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Rahul Sinha
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Olga Anczuków
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Anna Corrionero
- Institució Catalana de Recerca i Estudis Avançats, Universitat Pompeu Fabra 08003 Barcelona, Spain; and
- Centre de Regulació Genòmica, 08003 Barcelona, Spain
| | - Ahmed Moursy
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Gerrit M. Daubner
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Juan Valcárcel
- Institució Catalana de Recerca i Estudis Avançats, Universitat Pompeu Fabra 08003 Barcelona, Spain; and
- Centre de Regulació Genòmica, 08003 Barcelona, Spain
| | | | - Frédéric H.-T. Allain
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
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19
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Wang S, Wagner EJ, Mattox W. Half pint/Puf68 is required for negative regulation of splicing by the SR splicing factor Transformer2. RNA Biol 2013; 10:1396-406. [PMID: 23880637 DOI: 10.4161/rna.25645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The SR family of proteins plays important regulatory roles in the control of alternative splicing in a wide range of organisms. These factors affect splicing through both positive and negative controls of splice site recognition by pre-spliceosomal factors. Recent studies indicate that the Drosophila SR factor Transformer 2 (Tra2) activates and represses splicing through distinct and separable effector regions of the protein. While the interactions of its Arg-Ser-rich activator region have been well studied, cofactors involved in splicing repression have yet to be found. Here we use a luciferase-based splicing reporter assay to screen for novel proteins necessary for Tra2-dependent repression of splicing. This approach identified Half pint, also known as Puf68, as a co-repressor required for Tra2-mediated autoregulation of the M1 intron. In vivo, Half pint is required for Tra2-dependent repression of M1 splicing but is not necessary for Tra2-dependent activation of doublesex splicing. Further experiments indicate that the effect of Hfp is sequence-specific and that it associates with these target transcripts in cells. Importantly, known M1 splicing regulatory elements are sufficient to sensitize a heterologous intron to Hfp regulation. Two alternative proteins deriving from Hfp transcripts, Hfp68, and Hfp58, were found to be expressed in vivo but differed dramatically in their effect on M1 splicing. Comparison of the cellular localization of these forms in S2 cells revealed that Hfp68 is predominantly localized to the nucleus while Hfp58 is distributed across both the nucleus and cytoplasm. This accords with their observed effects on splicing and suggests that differential compartmentalization may contribute to the specificity of these isoforms. Together, these studies reveal a function for Half pint in splicing repression and demonstrate it to be specifically required for Tra2-dependent intron inclusion.
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Affiliation(s)
- Shanzhi Wang
- Program in Genes and Development; The University of Texas Graduate School of Biomedical Sciences at Houston; Houston, TX USA; The University of Texas Graduate School of Biomedical Sciences at Houston; Houston, TX, USA; Department of Genetics; University of Texas M. D. Anderson Cancer Center; Houston, TX, USA
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20
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Guo R, Li Y, Ning J, Sun D, Lin L, Liu X. HnRNP A1/A2 and SF2/ASF regulate alternative splicing of interferon regulatory factor-3 and affect immunomodulatory functions in human non-small cell lung cancer cells. PLoS One 2013; 8:e62729. [PMID: 23658645 PMCID: PMC3639176 DOI: 10.1371/journal.pone.0062729] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 03/25/2013] [Indexed: 12/19/2022] Open
Abstract
Heterogeneous nuclear ribonucleoparticule A1/A2 (hnRNP A1/A2) and splicing factor 2/alternative splicing factor (SF2/ASF) are pivotal for precursor messenger RNA (pre-mRNA) splicing. Interferon regulatory factor-3 (IRF-3) plays critical roles in host defense against viral and microbial infection. Truncated IRF-3 proteins resulting from alternative splicing have been identified and characterized as functional antagonists to full-length IRF-3. In this study, we examined the molecular mechanism for splicing regulation of IRF-3 pre-mRNA and first reported the regulatory effect of hnRNP A1/A2 and SF2/ASF on IRF-3 splicing and activation. RNA interference-mediated depletion of hnRNP A1/A2 or SF2/ASF in human non-small cell lung cancer (NSCLC) cells increased exclusion of exons 2 and 3 of IRF-3 gene and reduced expression levels of IRF-3 protein and IRF-3 downstream effector molecules interferon-beta and CXCL10/IP-10. In addition, direct binding of hnRNP A1 and SF2/ASF to specific binding motifs in IRF-3 intron 1 was confirmed by RNA electrophoretic mobility shift assay. Subsequent minigene splicing assay showed that IRF-3 minigenes with mutated hnRNPA 1/A2 or SF2/ASF binding motifs increased exclusion of exons 2 and 3. Moreover, knockdown of hnRNP A1/A2 or SF2/ASF in NSCLC cells reinforced phytohemagglutinin-induced tumor necrosis factor-alpha release by peripheral blood mononuclear cells (PBMC) but suppressed that of interleukin-10 in NSCLC/PBMC co-cultures. Taken together, our results suggest that specific knockdown for hnRNP A1/A2 or SF2/ASF increase exclusion of exons 2 and 3 of IRF-3 pre-mRNA and influence immunomodulatory functions of human NSCLC cells.
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Affiliation(s)
- Rong Guo
- Department of Geriatrics, Peking University First Hospital, Beijing, China
| | - Yong Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Laboratory Animal, Peking University Cancer Hospital, Beijing Cancer Hospital, Beijing Institute for Cancer Research, Beijing, China
| | - Jinying Ning
- Department of Cell Biology, Crown Bioscience Incorporation (Beijing), Beijing, China
| | - Dan Sun
- Department of Geriatrics, Peking University First Hospital, Beijing, China
| | - Lianjun Lin
- Department of Geriatrics, Peking University First Hospital, Beijing, China
| | - Xinmin Liu
- Department of Geriatrics, Peking University First Hospital, Beijing, China
- * E-mail:
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21
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Pandit S, Zhou Y, Shiue L, Coutinho-Mansfield G, Li H, Qiu J, Huang J, Yeo GW, Ares M, Fu XD. Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing. Mol Cell 2013; 50:223-35. [PMID: 23562324 DOI: 10.1016/j.molcel.2013.03.001] [Citation(s) in RCA: 225] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 01/02/2013] [Accepted: 02/25/2013] [Indexed: 12/12/2022]
Abstract
SR proteins are well-characterized RNA binding proteins that promote exon inclusion by binding to exonic splicing enhancers (ESEs). However, it has been unclear whether regulatory rules deduced on model genes apply generally to activities of SR proteins in the cell. Here, we report global analyses of two prototypical SR proteins, SRSF1 (SF2/ASF) and SRSF2 (SC35), using splicing-sensitive arrays and CLIP-seq on mouse embryo fibroblasts (MEFs). Unexpectedly, we find that these SR proteins promote both inclusion and skipping of exons in vivo, but their binding patterns do not explain such opposite responses. Further analyses reveal that loss of one SR protein is accompanied by coordinated loss or compensatory gain in the interaction of other SR proteins at the affected exons. Therefore, specific effects on regulated splicing by one SR protein actually depend on a complex set of relationships with multiple other SR proteins in mammalian genomes.
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Affiliation(s)
- Shatakshi Pandit
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
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22
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Rimoldi V, Soldà G, Asselta R, Spena S, Stuani C, Buratti E, Duga S. Dual role of G-runs and hnRNP F in the regulation of a mutation-activated pseudoexon in the fibrinogen gamma-chain transcript. PLoS One 2013; 8:e59333. [PMID: 23533617 PMCID: PMC3606458 DOI: 10.1371/journal.pone.0059333] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 02/12/2013] [Indexed: 01/18/2023] Open
Abstract
Most pathological pseudoexon inclusion events originate from single activating mutations, suggesting that many intronic sequences are on the verge of becoming exons. However, the precise mechanisms controlling pseudoexon definition are still largely unexplored. Here, we investigated the cis-acting elements and trans-acting regulatory factors contributing to the regulation of a previously described fibrinogen gamma-chain (FGG) pseudoexon, which is activated by a deep-intronic mutation (IVS6-320A>T). This pseudoexon contains several G-run elements, which may be bound by heterogeneous nuclear ribonucleoproteins (hnRNPs) F and H. To explore the effect of these proteins on FGG pseudoexon inclusion, both silencing and overexpression experiments were performed in eukaryotic cells. While hnRNP H did not significantly affect pseudoexon splicing, hnRNP F promoted pseudoexon inclusion, indicating that these two proteins have only partially redundant functions. To verify the binding of hnRNP F and the possible involvement of other trans-acting splicing modulators, pulldown experiments were performed on the region of the pseudoexon characterized by both a G-run and enrichment for exonic splicing enhancers. This 25-bp-long region strongly binds hnRNP F/H and weakly interacts with Serine/Arginine-rich protein 40, which however was demonstrated to be dispensable for FGG pseudoexon inclusion in overexpression experiments. Deletion analysis, besides confirming the splicing-promoting role of the G-run within this 25-bp region, demonstrated that two additional hnRNP F binding sites might instead function as silencer elements. Taken together, our results indicate a major role of hnRNP F in regulating FGG pseudoexon inclusion, and strengthen the notion that G-runs may function either as splicing enhancers or silencers of the same exon.
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Affiliation(s)
- Valeria Rimoldi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Giulia Soldà
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Rosanna Asselta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Silvia Spena
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Stefano Duga
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
- * E-mail:
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23
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Becker K, Braune M, Benderska N, Buratti E, Baralle F, Villmann C, Stamm S, Eulenburg V, Becker CM. A retroelement modifies pre-mRNA splicing: the murine Glrb(spa) allele is a splicing signal polymorphism amplified by long interspersed nuclear element insertion. J Biol Chem 2012; 287:31185-94. [PMID: 22782896 DOI: 10.1074/jbc.m112.375691] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The glycine receptor-deficient mutant mouse spastic carries a full-length long interspersed nuclear element (LINE1) retrotransposon in intron 6 of the glycine receptor β subunit gene, Glrb(spa). The mutation arose in the C57BL/6J strain and is associated with skipping of exon 6 or a combination of the exons 5 and 6, thus resulting in a translational frameshift within the coding regions of the GlyR β subunit. The effect of the Glrb(spa) LINE1 insertion on pre-mRNA splicing was studied using a minigene approach. Sequence comparison as well as motif prediction and mutational analysis revealed that in addition to the LINE1 insertion the inactivation of an exonic splicing enhancer (ESE) within exon 6 is required for skipping of exon 6. Reconstitution of the ESE by substitution of a single residue was sufficient to prevent exon skipping. In addition to the ESE, two regions within the 5' and 3' UTR of the LINE1 were shown to be critical determinants for exon skipping, indicating that LINE1 acts as efficient modifier of subtle endogenous splicing phenotypes. Thus, the spastic allele of the murine glycine receptor β subunit gene is a two-hit mutation, where the hypomorphic alteration in an ESE is amplified by the insertion of a LINE1 element in the adjacent intron. Conversely, the LINE1 effect on splicing may be modulated by individual polymorphisms, depending on the insertional environment within the host genome.
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Affiliation(s)
- Kristina Becker
- Institut für Biochemie, Emil Fischer Zentrum, Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
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24
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Anderson ES, Lin CH, Xiao X, Stoilov P, Burge CB, Black DL. The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B. RNA (NEW YORK, N.Y.) 2012; 18:1041-9. [PMID: 22456266 PMCID: PMC3334691 DOI: 10.1261/rna.032912.112] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 02/24/2012] [Indexed: 05/24/2023]
Abstract
Modulation of alternative pre-mRNA splicing is a potential approach to therapeutic targeting for a variety of human diseases. We investigated the mechanism by which digitoxin, a member of the cardiotonic steroid class of drugs, regulates alternative splicing. Transcriptome-wide analysis identified a large set of alternative splicing events that change after digitoxin treatment. Within and adjacent to these regulated exons, we identified enrichment of potential binding sites for the splicing factors SRp20 (SRSF3/SFRS3) and Tra2-β (SFRS10/TRA2B). We further find that both of these proteins are depleted from cells by digitoxin treatment. Characterization of SRp20 and Tra2-β splicing targets revealed that many, but not all, digitoxin-induced splicing changes can be attributed to the depletion of one or both of these factors. Re-expression of SRp20 or Tra2-β after digitoxin treatment restores normal splicing of their targets, indicating that the digitoxin effect is directly due to these factors. These results demonstrate that cardiotonic steroids, long prescribed in the clinical treatment of heart failure, have broad effects on the cellular transcriptome through these and likely other RNA binding proteins. The approach described here can be used to identify targets of other potential therapeutics that act as alternative splicing modulators.
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Affiliation(s)
- Erik S. Anderson
- Molecular Biology Interdepartmental Graduate Program
- Medical Scientist Training Program
| | - Chia-Ho Lin
- Microbiology, Immunology and Molecular Genetics
- Howard Hughes Medical Institute
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology
- Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
| | - Peter Stoilov
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, USA
| | - Christopher B. Burge
- Department of Biology, Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
| | - Douglas L. Black
- Microbiology, Immunology and Molecular Genetics
- Howard Hughes Medical Institute
- Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
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25
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Regulation of alternative splicing within the supraspliceosome. J Struct Biol 2011; 177:152-9. [PMID: 22100336 DOI: 10.1016/j.jsb.2011.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 11/02/2011] [Accepted: 11/05/2011] [Indexed: 12/12/2022]
Abstract
Alternative splicing is a fundamental feature in regulating the eukaryotic transcriptome, as ~95% of multi-exon human Pol II transcripts are subject to this process. Regulated splicing operates through the combinatorial interplay of positive and negative regulatory signals present in the pre-mRNA, which are recognized by trans-acting factors. All these RNA and protein components are assembled in a gigantic, 21 MDa, ribonucleoprotein splicing machine - the supraspliceosome. Because most alternatively spliced mRNA isoforms vary between different cell and tissue types, the ability to perform alternative splicing is expected to be an integral part of the supraspliceosome, which constitutes the splicing machine in vivo. Here we show that both the constitutively and alternatively spliced mRNAs of the endogenous human pol II transcripts: hnRNP A/B, survival of motor neuron (SMN) and ADAR2 are predominantly found in supraspliceosomes. This finding is consistent with our observations that the splicing regulators hnRNP G as well as all phosphorylated SR proteins are predominantly associated with supraspliceosomes. We further show that changes in alternative splicing of hnRNP A/B, affected by up regulation of SRSF5 (SRp40) or by treatment with C6-ceramide, occur within supraspliceosomes. These observations support the proposed role of the supraspliceosome in splicing regulation and alternative splicing.
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26
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Ke S, Shang S, Kalachikov SM, Morozova I, Yu L, Russo JJ, Ju J, Chasin LA. Quantitative evaluation of all hexamers as exonic splicing elements. Genome Res 2011; 21:1360-74. [PMID: 21659425 DOI: 10.1101/gr.119628.110] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We describe a comprehensive quantitative measure of the splicing impact of a complete set of RNA 6-mer sequences by deep sequencing successfully spliced transcripts. All 4096 6-mers were substituted at five positions within two different internal exons in a 3-exon minigene, and millions of successfully spliced transcripts were sequenced after transfection of human cells. The results allowed the assignment of a relative splicing strength score to each mutant molecule. The effect of 6-mers on splicing often depended on their location; much of this context effect could be ascribed to the creation of different overlapping sequences at each site. Taking these overlaps into account, the splicing effect of each 6-mer could be quantified, and 6-mers could be designated as enhancers (ESEseqs) and silencers (ESSseqs), with an ESRseq score indicating their strength. Some 6-mers exhibited positional bias relative to the two splice sites. The distribution and conservation of these ESRseqs in and around human exons supported their classification. Predicted RNA secondary structure effects were also seen: Effective enhancers, silencers and 3' splice sites tend to be single stranded, and effective 5' splice sites tend to be double stranded. 6-mers that may form positive or negative synergy with another were also identified. Chromatin structure may also influence the splicing enhancement observed, as a good correspondence was found between splicing performance and the predicted nucleosome occupancy scores of 6-mers. This approach may prove of general use in defining nucleic acid regulatory motifs, substitute for functional SELEX in most cases, and provide insights about splicing mechanisms.
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Affiliation(s)
- Shengdong Ke
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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27
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Kralovicova J, Hwang G, Asplund AC, Churbanov A, Smith CIE, Vorechovsky I. Compensatory signals associated with the activation of human GC 5' splice sites. Nucleic Acids Res 2011; 39:7077-91. [PMID: 21609956 PMCID: PMC3167603 DOI: 10.1093/nar/gkr306] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
GC 5′ splice sites (5′ss) are present in ∼1% of human introns, but factors promoting their efficient selection are poorly understood. Here, we describe a case of X-linked agammaglobulinemia resulting from a GC 5′ss activated by a mutation in BTK intron 3. This GC 5′ss was intrinsically weak, yet it was selected in >90% primary transcripts in the presence of a strong and intact natural GT counterpart. We show that efficient selection of this GC 5′ss required a high density of GAA/CAA-containing splicing enhancers in the exonized segment and was promoted by SR proteins 9G8, Tra2β and SC35. The GC 5′ss was efficiently inhibited by splice-switching oligonucleotides targeting either the GC 5′ss itself or the enhancer. Comprehensive analysis of natural GC-AG introns and previously reported pathogenic GC 5′ss showed that their efficient activation was facilitated by higher densities of splicing enhancers and lower densities of silencers than their GT 5′ss equivalents. Removal of the GC-AG introns was promoted to a minor extent by the splice-site strength of adjacent exons and inhibited by flanking Alu repeats, with the first downstream Alus located on average at a longer distance from the GC 5′ss than other transposable elements. These results provide new insights into the splicing code that governs selection of noncanonical splice sites.
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Affiliation(s)
- Jana Kralovicova
- University of Southampton School of Medicine, Division of Human Genetics, Southampton SO16 6YD, UK
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28
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Ke S, Chasin LA. Context-dependent splicing regulation: exon definition, co-occurring motif pairs and tissue specificity. RNA Biol 2011; 8:384-8. [PMID: 21444999 DOI: 10.4161/rna.8.3.14458] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Splicing is a crucial process in gene expression in higher organisms because: 1) most vertebrate genes contain introns; and 2) alternative splicing is primarily responsible for increasing proteomic complexity and functional diversity. Intron definition, the coordination across an intron, is a mandatory step in the splicing process. However, exon definition, the coordination across an exon, is also thought to be required for the splicing of most vertebrate exons. Recent investigations of exon definition complexes provide insights into splicing dynamics. That splicing regulators act in a context-dependent mode is supported by a large collection of evidence. Splicing contexts generally can be classified as cis-element and trans-element contexts. A widespread cis-element context is defined by co-occurring motif pairs to which splicing regulatory factors bind to direct specific molecular interactions. Splicing regulation is also coordinated by trans-element contexts as exemplified by tissue specific splicing, where alternative exons can be coordinately regulated by a few splicing factors, the expression and/or activity of which are concertedly higher or lower in the corresponding tissues.
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Affiliation(s)
- Shengdong Ke
- Department of Biological Sciences, Columbia University, New York, NY, USA
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29
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Xiao X, Lee JH. Systems analysis of alternative splicing and its regulation. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 2:550-565. [PMID: 20836047 DOI: 10.1002/wsbm.84] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Alternative splicing (AS) has emerged as a key mechanism that accounts for gene expression diversity in metazoan organisms. Splicing is tightly regulated by a repertoire of RNA and protein factors and RNA sequence elements that function in a cooperative manner. Systems-level experimental and computational approaches have been instrumental in establishing comprehensive profiles of transcript variants generated by AS. In addition, systems biology approaches are starting to define how combinatorial splicing regulation shapes the complex splicing phenotypes observed in different tissue types and developmental stages and under different conditions. Here, we review recent progress in these areas.
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Affiliation(s)
- Xinshu Xiao
- Department of Physiological Science, University of California, Los Angeles, CA 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Jae-Hyung Lee
- Department of Physiological Science, University of California, Los Angeles, CA 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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30
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SR proteins induce alternative exon skipping through their activities on the flanking constitutive exons. Mol Cell Biol 2010; 31:793-802. [PMID: 21135118 DOI: 10.1128/mcb.01117-10] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SR proteins are well known to promote exon inclusion in regulated splicing through exonic splicing enhancers. SR proteins have also been reported to cause exon skipping, but little is known about the mechanism. We previously characterized SRSF1 (SF2/ASF)-dependent exon skipping of the CaMKIIδ gene during heart remodeling. By using mouse embryo fibroblasts derived from conditional SR protein knockout mice, we now show that SR protein-induced exon skipping depends on their prevalent actions on a flanking constitutive exon and requires collaboration of more than one SR protein. These findings, coupled with other established rules for SR proteins, provide a theoretical framework to understand the complex effect of SR protein-regulated splicing in mammalian cells. We further demonstrate that heart-specific CaMKIIδ splicing can be reconstituted in fibroblasts by downregulating SR proteins and upregulating a RBFOX protein and that SR protein overexpression impairs regulated CaMKIIδ splicing and neuronal differentiation in P19 cells, illustrating that SR protein-dependent exon skipping may constitute a key strategy for synergism with other splicing regulators in establishing tissue-specific alternative splicing critical for cell differentiation programs.
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31
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Costantino L, Claut L, Paracchini V, Coviello DA, Colombo C, Porcaro L, Capasso P, Zanardelli M, Pizzamiglio G, Degiorgio D, Seia M. A novel donor splice site characterized by CFTR mRNA analysis induces a new pseudo-exon in CF patients. J Cyst Fibros 2010; 9:411-8. [PMID: 20875776 DOI: 10.1016/j.jcf.2010.08.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 07/30/2010] [Accepted: 08/06/2010] [Indexed: 12/01/2022]
Abstract
BACKGROUND The CFTR gene is tightly regulated and differentially expressed in many mucosal epithelial cell types. There is evidence of an increasing number of genomic variations in the intronic regions influencing mRNA splicing, and also the level of normal CFTR transcript. METHODS In the present study, we investigate the molecular defect by RT-PCR analyzing the mRNA of 25 cystic fibrosis (CF) patients in whom only one or no CF allele had been identified after DNA analysis (of all the exons of the CFTR gene). RESULTS mRNA analysis led to the detection of a cryptic exon in two patients: the new exon is a 104 bp insertion between exons 10 and 11 and is caused by a new point mutation c.1584+18672 bp A>G (http://www.hgvs.org/mutnomen/) discovered in intron 10; moreover, they showed the absence of exon 9 skipping. CONCLUSIONS Our results confirm the utility of RNA analysis in discovering new mutations and in investigating their effect on normal splicing processes.
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Affiliation(s)
- Lucy Costantino
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda, 12, 20122 Milan, Italy
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32
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Shukla JN, Nagaraju J. Doublesex: a conserved downstream gene controlled by diverse upstream regulators. J Genet 2010; 89:341-56. [DOI: 10.1007/s12041-010-0046-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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33
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Dujardin G, Buratti E, Charlet-Berguerand N, Martins de Araujo M, Mbopda A, Le Jossic-Corcos C, Pagani F, Ferec C, Corcos L. CELF proteins regulate CFTR pre-mRNA splicing: essential role of the divergent domain of ETR-3. Nucleic Acids Res 2010; 38:7273-85. [PMID: 20631008 PMCID: PMC2978352 DOI: 10.1093/nar/gkq573] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Cystic fibrosis is a prominent genetic disease caused by mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Among the many disease-causing alterations are pre-mRNA splicing defects that can hamper mandatory exon inclusion. CFTR exon 9 splicing depends in part on a polymorphic UG(m)U(n) sequence at the end of intron 8, which can be bound by TDP-43, leading to partial exon 9 skipping. CELF proteins, like CUG-BP1 and ETR-3, can also bind UG repeats and regulate splicing. We show here that ETR-3, but not CUG-BP1, strongly stimulates exon 9 skipping, although both proteins bind efficiently to the same RNA motif as TDP-43 and with higher affinity. We further show that the skipping of this exon may be due to the functional antagonism between U2AF65 and ETR-3 binding onto the polymorphic U or UG stretch, respectively. Importantly, we demonstrate that the divergent domain of ETR-3 is critical for CFTR exon 9 skipping, as shown by deletion and domain-swapping experiments. We propose a model whereby several RNA-binding events account for the complex regulation of CFTR exon 9 inclusion, with strikingly distinct activities of ETR-3 and CUG-BP1, related to the structure of their divergent domain.
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Affiliation(s)
- Gwendal Dujardin
- Inserm U613-ECLA Team, Faculty of Medicine, 22 Avenue Camille Desmoulins, 29238 Brest Cedex 3, France
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34
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Dreumont N, Bourgeois CF, Lejeune F, Liu Y, Ehrmann IE, Elliott DJ, Stévenin J. Human RBMY regulates germline-specific splicing events by modulating the function of the serine/arginine-rich proteins 9G8 and Tra2-{beta}. J Cell Sci 2010; 123:40-50. [PMID: 20016065 DOI: 10.1242/jcs.055889] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
RBMY is a male germline RNA binding protein and potential alternative splicing regulator, but the lack of a convenient biological system has made its cellular functions elusive. We found that human RBMY fused to green fluorescent protein was strictly nuclear in transfected cells, but spatially enriched in areas around nuclear speckles with some components of the exon junction complex (EJC). Human RBMY (hRBMY) and the EJC components Magoh and Y14 also physically interacted but, unlike these two proteins, hRBMY protein did not shuttle to the cytoplasm. In addition, it relocalised into nucleolar caps after inhibition of RNA polymerase II transcription. Protein interactions were also detected between RBMY and splicing factors 9G8 and transformer-2 protein homolog beta (Tra2-beta), mediated by multiple regions of the RBMY protein that contain serine/arginine-rich dipeptides, but not by the single region lacking such dipeptides. These interactions modulated the splicing of several pre-mRNAs regulated by 9G8 and Tra2-beta. Importantly, ectopic expression of hRBMY stimulated the inclusion of a testis-enriched exon from the Acinus gene, whereas 9G8 and Tra2-beta repressed this exon. We propose that hRBMY associates with regions of the nucleus enriched in nascent RNA and participates in the regulation of specific splicing events in the germline by modulating the activity of constitutively expressed splicing factors.
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35
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Abstract
Alternative 5' splice site selection is one of the major pathways resulting in mRNA diversification. Regulation of this type of alternative splicing depends on the presence of regulatory elements that activate or repress the use of competing splice sites, usually leading to the preferential use of the proximal splice site. However, the mechanisms involved in proximal splice site selection and the thermodynamic advantage realized by proximal splice sites are not well understood. Here, we have carried out a systematic analysis of alternative 5' splice site usage using in vitro splicing assays. We show that observed rates of splicing correlate well with their U1 snRNA base pairing potential. Weak U1 snRNA interactions with the 5' splice site were significantly rescued by the proximity of the downstream exon, demonstrating that the intron definition mode of splice site recognition is highly efficient. In the context of competing splice sites, the proximity to the downstream 3' splice site was more influential in dictating splice site selection than the actual 5' splice site/U1 snRNA base pairing potential. Surprisingly, the kinetic analysis also demonstrated that an upstream competing 5' splice site enhances the rate of proximal splicing. These results reveal the discovery of a new splicing regulatory element, an upstream 5' splice site functioning as a splicing enhancer.
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36
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Rabin SJ, Kim JMH, Baughn M, Libby RT, Kim YJ, Fan Y, Libby RT, La Spada A, Stone B, Ravits J. Sporadic ALS has compartment-specific aberrant exon splicing and altered cell-matrix adhesion biology. Hum Mol Genet 2009; 19:313-28. [PMID: 19864493 PMCID: PMC2796893 DOI: 10.1093/hmg/ddp498] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive weakness from loss of motor neurons. The fundamental pathogenic mechanisms are unknown and recent evidence is implicating a significant role for abnormal exon splicing and RNA processing. Using new comprehensive genomic technologies, we studied exon splicing directly in 12 sporadic ALS and 10 control lumbar spinal cords acquired by a rapid autopsy system that processed nervous systems specifically for genomic studies. ALS patients had rostral onset and caudally advancing disease and abundant residual motor neurons in this region. We created two RNA pools, one from motor neurons collected by laser capture microdissection and one from the surrounding anterior horns. From each, we isolated RNA, amplified mRNA, profiled whole-genome exon splicing, and applied advanced bioinformatics. We employed rigorous quality control measures at all steps and validated findings by qPCR. In the motor neuron enriched mRNA pool, we found two distinct cohorts of mRNA signals, most of which were up-regulated: 148 differentially expressed genes (P ≤ 10−3) and 411 aberrantly spliced genes (P ≤ 10−5). The aberrantly spliced genes were highly enriched in cell adhesion (P ≤ 10−57), especially cell–matrix as opposed to cell–cell adhesion. Most of the enriching genes encode transmembrane or secreted as opposed to nuclear or cytoplasmic proteins. The differentially expressed genes were not biologically enriched. In the anterior horn enriched mRNA pool, we could not clearly identify mRNA signals or biological enrichment. These findings, perturbed and up-regulated cell–matrix adhesion, suggest possible mechanisms for the contiguously progressive nature of motor neuron degeneration. Data deposition: GeneChip raw data (CEL-files) have been deposited for public access in the Gene Expression Omnibus (GEO), www.ncbi.nlm.nih.gov/geo, accession number GSE18920.
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Affiliation(s)
- Stuart J Rabin
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
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37
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Du L, Gatti RA. Progress toward therapy with antisense-mediated splicing modulation. CURRENT OPINION IN MOLECULAR THERAPEUTICS 2009; 11:116-123. [PMID: 19330717 PMCID: PMC2753608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Antisense oligonucleotides (AO) or antisense RNA can complementarily bind to a target site in pre-mRNA and regulate gene splicing, either to restore gene function by reprogramming gene splicing or to inhibit gene expression by disrupting splicing. These two applications represent novel therapeutic strategies for several types of diseases such as genetic disorders, cancers and infectious diseases. In this review, the recent developments and applications of antisense-mediated splicing modulation in molecular therapy are discussed, with emphasis on advances in antisense-mediated splice targeting, applications in diseases and systematic delivery.
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Affiliation(s)
- Liutao Du
- Department of Pathology and Laboratory Medicine, The David Geffen School of Medicine at UCLA, 675 Charles Young Drive South, CA 90095-1732, USA.
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38
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Abstract
The SR protein family comprises a number of phylogenetically conserved and structurally related proteins with a characteristic domain rich in arginine and serine residues, known as the RS domain. They play significant roles in constitutive pre-mRNA splicing and are also important regulators of alternative splicing. In addition they participate in post-splicing activities, such as mRNA nuclear export, nonsense-mediated mRNA decay and mRNA translation. These wide-ranging roles of SR proteins highlight their importance as pivotal regulators of mRNA metabolism, and if these functions are disrupted, developmental defects or disease may result. Furthermore, animal models have shown a highly specific, non-redundant role for individual SR proteins in the regulation of developmental processes. Here, we will review the current literature to demonstrate how SR proteins are emerging as one of the master regulators of gene expression.
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39
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Solis AS, Peng R, Crawford JB, Phillips JA, Patton JG. Growth hormone deficiency and splicing fidelity: two serine/arginine-rich proteins, ASF/SF2 and SC35, act antagonistically. J Biol Chem 2008; 283:23619-26. [PMID: 18586677 DOI: 10.1074/jbc.m710175200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The majority of mutations that cause isolated growth hormone deficiency type II are the result of aberrant splicing of transcripts encoding human growth hormone. Such mutations increase skipping of exon 3 and encode a 17.5-kDa protein that acts as a dominant negative to block secretion of full-length protein produced from unaffected alleles. Previously, we identified a splicing regulatory element in exon 3 (exonic splicing enhancer 2 (ESE2)), but we had not determined the molecular mechanism by which this element prevents exon skipping. Here, we show that two members of the serine/arginine-rich (SR) protein superfamily (ASF/SF2 and SC35) act antagonistically to regulate exon 3 splicing. ASF/SF2 activates exon 3 inclusion, but SC35, acting through a region just downstream of ESE2, can block such activation. These findings explain the disease-causing mechanism of a patient mutation in ESE2 that creates a functional SC35-binding site that then acts synergistically with the downstream SC35 site to produce pathological levels of exon 3 skipping. Although the precedent for SR proteins acting as repressors is established, this is the first example of a patient mutation that creates a site through which an SR protein represses splicing.
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Affiliation(s)
- Amanda S Solis
- Department of Biological Sciences, Vanderbilt University, 2301 Vanderbilt Pl., Nashville, TN 37235, USA
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Wang Z, Burge CB. Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA (NEW YORK, N.Y.) 2008; 14:802-13. [PMID: 18369186 PMCID: PMC2327353 DOI: 10.1261/rna.876308] [Citation(s) in RCA: 697] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Alternative splicing of pre-mRNAs is a major contributor to both proteomic diversity and control of gene expression levels. Splicing is tightly regulated in different tissues and developmental stages, and its disruption can lead to a wide range of human diseases. An important long-term goal in the splicing field is to determine a set of rules or "code" for splicing that will enable prediction of the splicing pattern of any primary transcript from its sequence. Outside of the core splice site motifs, the bulk of the information required for splicing is thought to be contained in exonic and intronic cis-regulatory elements that function by recruitment of sequence-specific RNA-binding protein factors that either activate or repress the use of adjacent splice sites. Here, we summarize the current state of knowledge of splicing cis-regulatory elements and their context-dependent effects on splicing, emphasizing recent global/genome-wide studies and open questions.
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Affiliation(s)
- Zefeng Wang
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Gromak N, Talotti G, Proudfoot NJ, Pagani F. Modulating alternative splicing by cotranscriptional cleavage of nascent intronic RNA. RNA (NEW YORK, N.Y.) 2008; 14:359-366. [PMID: 18065715 PMCID: PMC2212250 DOI: 10.1261/rna.615508] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Accepted: 10/24/2007] [Indexed: 05/25/2023]
Abstract
Cotranscriptional cleavage mediated by a hammerhead ribozyme can affect alternative splicing if interposed between an exon and its intronic regulatory elements. This has been demonstrated using two different alternative splicing systems based on alpha-tropomyosin and fibronectin genes. We suggest that there is a requirement for intronic regulatory elements to be covalently attached to exons that are in turn tethered to the elongating polymerase. In the case of the alternatively spliced EDA exon of the fibronectin gene, we demonstrate that the newly identified intronic downstream regulatory element is associated with the splicing regulatory protein SRp20. Our results suggest that targeted hammerhead ribozyme cleavage within introns can be used as a tool to define splicing regulatory elements.
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Affiliation(s)
- Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
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