1
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Wright CJ, Smith CWJ, Jiggins CD. Alternative splicing as a source of phenotypic diversity. Nat Rev Genet 2022; 23:697-710. [PMID: 35821097 DOI: 10.1038/s41576-022-00514-4] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2022] [Indexed: 12/27/2022]
Abstract
A major goal of evolutionary genetics is to understand the genetic processes that give rise to phenotypic diversity in multicellular organisms. Alternative splicing generates multiple transcripts from a single gene, enriching the diversity of proteins and phenotypic traits. It is well established that alternative splicing contributes to key innovations over long evolutionary timescales, such as brain development in bilaterians. However, recent developments in long-read sequencing and the generation of high-quality genome assemblies for diverse organisms has facilitated comparisons of splicing profiles between closely related species, providing insights into how alternative splicing evolves over shorter timescales. Although most splicing variants are probably non-functional, alternative splicing is nonetheless emerging as a dynamic, evolutionarily labile process that can facilitate adaptation and contribute to species divergence.
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Affiliation(s)
- Charlotte J Wright
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK. .,Department of Zoology, University of Cambridge, Cambridge, UK.
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK.
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2
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Qu A, Bai Y, Zhang X, Zeng J, Pu F, Wu L, Xu P, Zhou T. Tissue-Specific Analysis of Alternative Splicing Events and Differential Isoform Expression in Large Yellow Croaker (Larimichthys crocea) After Cryptocaryon irritans Infection. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:640-654. [PMID: 35624193 DOI: 10.1007/s10126-022-10133-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
The large yellow croaker (Larimichthys crocea) is one of the most important mariculture fish in China. Recently, cryptocaryonosis caused by Cryptocryon irritans infection has brought huge economic losses and threatens the healthy and sustainable development of the L. crocea industry. However, the molecular mechanism and regulation process for L. crocea resistance to C. irritans infection has not been fully researched. Alternative splicing (AS) is an important post-transcriptional regulatory mechanism that allows cells to produce transcriptional and proteomic diversity. The results of AS are tissue dependent, and the expression of tissue-specific transcription subtype genes is determined by AS and transcriptional regulation. However, studies on the tissue specificity of AS events in L. crocea following infection with C. irritans have not been performed. In this study, the L. crocea were artificially infected with C. irritans; their skin and gill were collected at 0 h, 24 h, 48 h, 72 h, and 96 h post infection. After sequencing and differential expression analysis, a set of 452, 692, 934, 711, 534, and 297 differential alternative splicing (DAS) events were identified in 0 h, 12 h, 24 h, 48 h, 72 h, and 96 h post infection respectively. Furthermore, 4160 differentially expressed isoforms (DEIs) and 4209 DEI genes were identified from all time point groups. GO enrichment and pathway analysis indicated that many genes of DAS and DEIs were rich in immune-related GO terms and KEGG pathways, such as the Toll and Imd signaling pathway, NOD-like receptor signaling pathway, TNF signaling pathway, and TNF signaling pathway. Among hub DEI genes, alternative splicing-related genes (cwc25, prpf8, and sf3a3), skin function-related gene (fa2h), and oxygen deprivation-related gene (hyo1) were found in DEI genes. This study provided insight into the temporal change of DAS and DEIs between skin and gill of L. crocea against C. irritans infection and revealed that these differences might play immune-related roles in the infection process.
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Affiliation(s)
- Ang Qu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Yulin Bai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Xinyi Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Junjia Zeng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Fei Pu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Linni Wu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Peng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Tao Zhou
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
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3
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Lostal W, Roudaut C, Faivre M, Charton K, Suel L, Bourg N, Best H, Smith JE, Gohlke J, Corre G, Li X, Elbeck Z, Knöll R, Deschamps JY, Granzier H, Richard I. Titin splicing regulates cardiotoxicity associated with calpain 3 gene therapy for limb-girdle muscular dystrophy type 2A. Sci Transl Med 2020; 11:11/520/eaat6072. [PMID: 31776291 DOI: 10.1126/scitranslmed.aat6072] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 10/31/2019] [Indexed: 01/31/2023]
Abstract
Limb-girdle muscular dystrophy type 2A (LGMD2A or LGMDR1) is a neuromuscular disorder caused by mutations in the calpain 3 gene (CAPN3). Previous experiments using adeno-associated viral (AAV) vector-mediated calpain 3 gene transfer in mice indicated cardiac toxicity associated with the ectopic expression of the calpain 3 transgene. Here, we performed a preliminary dose study in a severe double-knockout mouse model deficient in calpain 3 and dysferlin. We evaluated safety and biodistribution of AAV9-desmin-hCAPN3 vector administration to nonhuman primates (NHPs) with a dose of 3 × 1013 viral genomes/kg. Vector administration did not lead to observable adverse effects or to detectable toxicity in NHP. Of note, the transgene expression did not produce any abnormal changes in cardiac morphology or function of injected animals while reaching therapeutic expression in skeletal muscle. Additional investigation on the underlying causes of cardiac toxicity observed after gene transfer in mice and the role of titin in this phenomenon suggest species-specific titin splicing. Mice have a reduced capacity for buffering calpain 3 activity compared to NHPs and humans. Our studies highlight a complex interplay between calpain 3 and titin binding sites and demonstrate an effective and safe profile for systemic calpain 3 vector delivery in NHP, providing critical support for the clinical potential of calpain 3 gene therapy in humans.
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Affiliation(s)
- William Lostal
- Généthon INSERM, U951, INTEGRARE Research Unit, Evry F-91002, France
| | - Carinne Roudaut
- Généthon INSERM, U951, INTEGRARE Research Unit, Evry F-91002, France
| | - Marine Faivre
- Généthon INSERM, U951, INTEGRARE Research Unit, Evry F-91002, France
| | - Karine Charton
- Généthon INSERM, U951, INTEGRARE Research Unit, Evry F-91002, France
| | - Laurence Suel
- Généthon INSERM, U951, INTEGRARE Research Unit, Evry F-91002, France
| | - Nathalie Bourg
- Généthon INSERM, U951, INTEGRARE Research Unit, Evry F-91002, France
| | - Heather Best
- Généthon INSERM, U951, INTEGRARE Research Unit, Evry F-91002, France
| | | | | | - Guillaume Corre
- Généthon INSERM, U951, INTEGRARE Research Unit, Evry F-91002, France
| | - Xidan Li
- Department of Medicine, Karolinska Institute, Stockholm SE-171 77, Sweden
| | - Zaher Elbeck
- Department of Medicine, Karolinska Institute, Stockholm SE-171 77, Sweden
| | - Ralph Knöll
- Department of Medicine, Karolinska Institute, Stockholm SE-171 77, Sweden.,AstraZeneca, R&D, Innovative Medicines & Early Development, Cardiovascular, Renal and Metabolic Diseases (CVRM), Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Jack-Yves Deschamps
- Emergency and Critical Care Unit, ONIRIS, School of Veterinary Medicine, La Chantrerie, 44307 Nantes Cedex 03, France
| | | | - Isabelle Richard
- Généthon INSERM, U951, INTEGRARE Research Unit, Evry F-91002, France.
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4
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Imkeller K, Ambrosi G, Boutros M, Huber W. gscreend: modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection. Genome Biol 2020; 21:53. [PMID: 32122365 PMCID: PMC7052974 DOI: 10.1186/s13059-020-1939-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 01/19/2020] [Indexed: 02/06/2023] Open
Abstract
Pooled CRISPR screens are a powerful tool to probe genotype-phenotype relationships at genome-wide scale. However, criteria for optimal design are missing, and it remains unclear how experimental parameters affect results. Here, we report that random decreases in gRNA abundance are more likely than increases due to bottle-neck effects during the cell proliferation phase. Failure to consider this asymmetry leads to loss of detection power. We provide a new statistical test that addresses this problem and improves hit detection at reduced experiment size. The method is implemented in the R package gscreend, which is available at http://bioconductor.org/packages/gscreend.
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Affiliation(s)
- Katharina Imkeller
- German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Giulia Ambrosi
- German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
| | - Michael Boutros
- German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory, Heidelberg, Germany
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5
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Rbfox-Splicing Factors Maintain Skeletal Muscle Mass by Regulating Calpain3 and Proteostasis. Cell Rep 2019; 24:197-208. [PMID: 29972780 DOI: 10.1016/j.celrep.2018.06.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/27/2017] [Accepted: 06/01/2018] [Indexed: 01/01/2023] Open
Abstract
Maintenance of skeletal muscle mass requires a dynamic balance between protein synthesis and tightly controlled protein degradation by the calpain, autophagy-lysosome, and ubiquitin-proteasome systems (proteostasis). Several sensing and gene-regulatory mechanisms act together to maintain this balance in response to changing conditions. Here, we show that deletion of the highly conserved Rbfox1 and Rbfox2 alternative splicing regulators in adult mouse skeletal muscle causes rapid, severe loss of muscle mass. Rbfox deletion did not cause a reduction in global protein synthesis, but it led to altered splicing of hundreds of gene transcripts, including capn3, which produced an active form of calpain3 protease. Rbfox knockout also led to a reduction in autophagy flux, likely producing a compensatory increase in general protein degradation by the proteasome. Our results indicate that the Rbfox-splicing factors are essential for the maintenance of skeletal muscle mass and proteostasis.
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6
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Kellermayer D, Smith JE, Granzier H. Titin mutations and muscle disease. Pflugers Arch 2019; 471:673-682. [PMID: 30919088 DOI: 10.1007/s00424-019-02272-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/11/2019] [Indexed: 12/12/2022]
Abstract
The introduction of next-generation sequencing technology has revealed that mutations in the gene that encodes titin (TTN) are linked to multiple skeletal and cardiac myopathies. The most prominent of these myopathies is dilated cardiomyopathy (DCM). Over 60 genes are linked to the etiology of DCM, but by far, the leading cause of DCM is mutations in TTN with truncating variants in TTN (TTNtvs) associated with familial DCM in ∼ 20% of the cases. Titin is a large (3-4 MDa) and abundant protein that forms the third myofilament type of striated muscle where it spans half the sarcomere, from the Z-disk to the M-line. The underlying mechanisms by which titin mutations induce disease are poorly understood and targeted therapies are not available. Here, we review what is known about TTN mutations in muscle disease, with a major focus on DCM. We highlight that exon skipping might provide a possible therapeutic avenue to address diseases that arise from TTNtvs.
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Affiliation(s)
- Dalma Kellermayer
- Department of Cellular and Molecular Medicine, University of Arizona, MRB 325. 1656 E Mabel Street, Tucson, AZ, 85724-5217, USA.,Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ, 85721, USA
| | - John E Smith
- Department of Cellular and Molecular Medicine, University of Arizona, MRB 325. 1656 E Mabel Street, Tucson, AZ, 85724-5217, USA.,Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ, 85721, USA
| | - Henk Granzier
- Department of Cellular and Molecular Medicine, University of Arizona, MRB 325. 1656 E Mabel Street, Tucson, AZ, 85724-5217, USA. .,Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ, 85721, USA.
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7
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Cheong TC, Blasco RB, Chiarle R. The CRISPR/Cas9 System as a Tool to Engineer Chromosomal Translocation In Vivo. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:39-48. [PMID: 29956290 DOI: 10.1007/978-981-13-0593-1_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The CRISPR/Cas9 system has emerged as a powerful tool to edit the genome. Among many applications, the system generates the exciting possibility of engineering small and large portions of chromosomes to induce a variety of structural alterations such as deletions, inversions, insertions and inter-chromosomal translocations. Furthermore, the availability of viral vectors that express Cas9 has been critical to deliver the CRISPR/Cas9 system directly in vivo to induce chromosomal rearrangements. This review provides an overview of the state-of-the-art CRISPR/Cas9 technology to model a variety of rearrangements in vivo in animal models.
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Affiliation(s)
- Taek-Chin Cheong
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Rafael B Blasco
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA.
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8
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Savarese M, Jonson PH, Huovinen S, Paulin L, Auvinen P, Udd B, Hackman P. The complexity of titin splicing pattern in human adult skeletal muscles. Skelet Muscle 2018; 8:11. [PMID: 29598826 PMCID: PMC5874998 DOI: 10.1186/s13395-018-0156-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/05/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Mutations in the titin gene (TTN) cause a large spectrum of diseases affecting skeletal and/or cardiac muscle. TTN includes 363 coding exons, a repeated region with a high degree of complexity, isoform-specific elements, and metatranscript-only exons thought to be expressed only during fetal development. Although three main classes of isoforms have been described so far, alternative splicing events (ASEs) in different tissues or in different developmental and physiological states have been reported. METHODS To achieve a comprehensive view of titin ASEs in adult human skeletal muscles, we performed a RNA-Sequencing experiment on 42 human biopsies collected from 12 anatomically different skeletal muscles of 11 individuals without any skeletal-muscle disorders. RESULTS We confirmed that the skeletal muscle N2A isoforms are highly prevalent, but we found an elevated number of alternative splicing events, some at a very high level. These include previously unknown exon skipping events and alternative 5' and 3' splice sites. Our data suggests the partial inclusion in the TTN transcript of some metatranscript-only exons and the partial exclusion of canonical N2A exons. CONCLUSIONS This study provides an extensive picture of the complex TTN splicing pattern in human adult skeletal muscle, which is crucial for a proper clinical interpretation of TTN variants.
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Affiliation(s)
- Marco Savarese
- Folkhälsan Research Center, University of Helsinki, Helsinki, Finland. .,Folkhälsan Institute of Genetics, Department of Medical Genetics, University of Helsinki, Biomedicum, Haartmaninkatu 8, Pb 63, 00014, Helsinki, Finland.
| | - Per Harald Jonson
- Folkhälsan Research Center, University of Helsinki, Helsinki, Finland
| | - Sanna Huovinen
- Department of Pathology, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Bjarne Udd
- Folkhälsan Research Center, University of Helsinki, Helsinki, Finland.,Department of Pathology, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland.,Vaasa Central Hospital, Vaasa, Finland
| | - Peter Hackman
- Folkhälsan Research Center, University of Helsinki, Helsinki, Finland
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9
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Abstract
The past several years have seen an explosion in development of applications for the CRISPR-Cas9 system, from efficient genome editing, to high-throughput screening, to recruitment of a range of DNA and chromatin-modifying enzymes. While homology-directed repair (HDR) coupled with Cas9 nuclease cleavage has been used with great success to repair and re-write genomes, recently developed base-editing systems present a useful orthogonal strategy to engineer nucleotide substitutions. Base editing relies on recruitment of cytidine deaminases to introduce changes (rather than double-stranded breaks and donor templates) and offers potential improvements in efficiency while limiting damage and simplifying the delivery of editing machinery. At the same time, these systems enable novel mutagenesis strategies to introduce sequence diversity for engineering and discovery. Here, we review the different base-editing platforms, including their deaminase recruitment strategies and editing outcomes, and compare them to other CRISPR genome-editing technologies. Additionally, we discuss how these systems have been applied in therapeutic, engineering, and research settings. Lastly, we explore future directions of this emerging technology.
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10
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Hess GT, Tycko J, Yao D, Bassik MC. Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes. Mol Cell 2017; 68:26-43. [PMID: 28985508 PMCID: PMC5997582 DOI: 10.1016/j.molcel.2017.09.029] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 12/26/2022]
Abstract
The past several years have seen an explosion in development of applications for the CRISPR-Cas9 system, from efficient genome editing, to high-throughput screening, to recruitment of a range of DNA and chromatin-modifying enzymes. While homology-directed repair (HDR) coupled with Cas9 nuclease cleavage has been used with great success to repair and re-write genomes, recently developed base-editing systems present a useful orthogonal strategy to engineer nucleotide substitutions. Base editing relies on recruitment of cytidine deaminases to introduce changes (rather than double-stranded breaks and donor templates) and offers potential improvements in efficiency while limiting damage and simplifying the delivery of editing machinery. At the same time, these systems enable novel mutagenesis strategies to introduce sequence diversity for engineering and discovery. Here, we review the different base-editing platforms, including their deaminase recruitment strategies and editing outcomes, and compare them to other CRISPR genome-editing technologies. Additionally, we discuss how these systems have been applied in therapeutic, engineering, and research settings. Lastly, we explore future directions of this emerging technology.
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Affiliation(s)
- Gaelen T Hess
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - Josh Tycko
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - David Yao
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - Michael C Bassik
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA.
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11
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Brinegar AE, Xia Z, Loehr JA, Li W, Rodney GG, Cooper TA. Extensive alternative splicing transitions during postnatal skeletal muscle development are required for calcium handling functions. eLife 2017; 6:27192. [PMID: 28826478 PMCID: PMC5577920 DOI: 10.7554/elife.27192] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/04/2017] [Indexed: 01/08/2023] Open
Abstract
Postnatal development of skeletal muscle is a highly dynamic period of tissue remodeling. Here, we used RNA-seq to identify transcriptome changes from late embryonic to adult mouse muscle and demonstrate that alternative splicing developmental transitions impact muscle physiology. The first 2 weeks after birth are particularly dynamic for differential gene expression and alternative splicing transitions, and calcium-handling functions are significantly enriched among genes that undergo alternative splicing. We focused on the postnatal splicing transitions of the three calcineurin A genes, calcium-dependent phosphatases that regulate multiple aspects of muscle biology. Redirected splicing of calcineurin A to the fetal isoforms in adult muscle and in differentiated C2C12 slows the timing of muscle relaxation, promotes nuclear localization of calcineurin target Nfatc3, and/or affects expression of Nfatc transcription targets. The results demonstrate a previously unknown specificity of calcineurin isoforms as well as the broader impact of alternative splicing during muscle postnatal development.
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Affiliation(s)
- Amy E Brinegar
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, United States.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, United States
| | - Zheng Xia
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, United States.,Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, United States
| | - James Anthony Loehr
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, United States
| | - Wei Li
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, United States.,Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, United States
| | - George Gerald Rodney
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, United States
| | - Thomas A Cooper
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, United States.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, United States.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, United States
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12
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Lalonde S, Stone OA, Lessard S, Lavertu A, Desjardins J, Beaudoin M, Rivas M, Stainier DYR, Lettre G. Frameshift indels introduced by genome editing can lead to in-frame exon skipping. PLoS One 2017; 12:e0178700. [PMID: 28570605 PMCID: PMC5453576 DOI: 10.1371/journal.pone.0178700] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 05/17/2017] [Indexed: 12/31/2022] Open
Abstract
The introduction of frameshift indels by genome editing has emerged as a powerful technique to study the functions of uncharacterized genes in cell lines and model organisms. Such mutations should lead to mRNA degradation owing to nonsense-mediated mRNA decay or the production of severely truncated proteins. Here, we show that frameshift indels engineered by genome editing can also lead to skipping of “multiple of three nucleotides” exons. Such splicing events result in in-frame mRNA that may encode fully or partially functional proteins. We also characterize a segregating nonsense variant (rs2273865) located in a “multiple of three nucleotides” exon of LGALS8 that increases exon skipping in human erythroblast samples. Our results highlight the potentially frequent contribution of exonic splicing regulatory elements and are important for the interpretation of negative results in genome editing experiments. Moreover, they may contribute to a better annotation of loss-of-function mutations in the human genome.
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Affiliation(s)
| | - Oliver A. Stone
- Department of Biochemistry & Biophysics, UCSF, San Francisco, California, United States of America
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Samuel Lessard
- Montreal Heart Institute, Montreal, Quebec, Canada
- Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Adam Lavertu
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
| | | | | | - Manuel Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
| | - Didier Y. R. Stainier
- Department of Biochemistry & Biophysics, UCSF, San Francisco, California, United States of America
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Guillaume Lettre
- Montreal Heart Institute, Montreal, Quebec, Canada
- Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
- * E-mail:
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13
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Alternative splicing as a regulator of development and tissue identity. Nat Rev Mol Cell Biol 2017; 18:437-451. [PMID: 28488700 DOI: 10.1038/nrm.2017.27] [Citation(s) in RCA: 750] [Impact Index Per Article: 107.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Alternative splicing of eukaryotic transcripts is a mechanism that enables cells to generate vast protein diversity from a limited number of genes. The mechanisms and outcomes of alternative splicing of individual transcripts are relatively well understood, and recent efforts have been directed towards studying splicing networks. It has become apparent that coordinated splicing networks regulate tissue and organ development, and that alternative splicing has important physiological functions in different developmental processes in humans.
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14
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Hackman P, Udd B, Bönnemann CG, Ferreiro A. 219th ENMC International Workshop Titinopathies International database of titin mutations and phenotypes, Heemskerk, The Netherlands, 29 April-1 May 2016. Neuromuscul Disord 2017; 27:396-407. [PMID: 28214268 DOI: 10.1016/j.nmd.2017.01.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/12/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Peter Hackman
- Folkhälsan Institute of Genetics, University of Helsinki, Finland.
| | - Bjarne Udd
- Neuromuscular Research Center, Tampere University, Finland
| | | | - Ana Ferreiro
- Unité de Biologie Fonctionnelle et Adaptative, Université Paris Diderot/CNRS, France; Reference Center for Neuromuscular Disorders, Pitié-Salpêtrière Hospital, AP-HP, France
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