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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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2
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Sabater-Arcis M, Moreno N, Sevilla T, Perez Alonso M, Bargiela A, Artero R. Msi2 enhances muscle dysfunction in a myotonic dystrophy type 1 mouse model. Biomed J 2023:100667. [PMID: 37797921 DOI: 10.1016/j.bj.2023.100667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 09/19/2023] [Accepted: 09/29/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND Myotonic dystrophy type 1 (DM1) is a rare neuromuscular disease caused by a CTG repeat expansion in the 3' untranslated region of the DM1 protein kinase gene. Characteristic degenerative muscle symptoms include myotonia, atrophy, and weakness. We previously proposed an Musashi homolog 2 (MSI2)>miR-7>autophagy axis whereby MSI2 overexpression repressed miR-7 biogenesis that subsequently de-repressed muscle catabolism through excessive autophagy. Because the DM1 HSALR mouse model expressing expanded CUG repeats shows weak muscle-wasting phenotypes, we hypothesized that MSI2 overexpression was sufficient to promote muscle dysfunction in vivo. METHODS By means of recombinant AAV murine MSI2 was overexpressed in neonates HSALR mice skeletal muscle to induce DM1-like phenotypes. RESULTS Sustained overexpression of the murine MSI2 protein in HSALR neonates induced autophagic flux and expression of critical autophagy proteins, increased central nuclei and reduced myofibers area, and weakened muscle strength. Importantly, these changes were independent of MBNL1, MBNL2, and Celf1 protein levels, which remained unchanged upon Msi2 overexpression. CONCLUSIONS Globally, molecular, histological, and functional data from these experiments in the HSALR mouse model confirms the pathological role of MSI2 expression levels as an atrophy-associated component that impacts the characteristic muscle dysfunction symptoms in DM1 patients.
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Affiliation(s)
- Maria Sabater-Arcis
- Human Translational Genomics Group, University Institute for Biotechnology and Biomedicine, Valencia, Spain; INCLIVA Biomedical Research Institute, Valencia, Spain.
| | - Nerea Moreno
- Human Translational Genomics Group, University Institute for Biotechnology and Biomedicine, Valencia, Spain; INCLIVA Biomedical Research Institute, Valencia, Spain.
| | - Teresa Sevilla
- Neuromuscular and Ataxias Research Group, Health Research Institute Hospital La Fe, Valencia, Spain; Centre for Biomedical Network Research on Rare Diseases, Valencia, Spain; Department of Medicine, University of Valencia, Valencia, Spain.
| | - Manuel Perez Alonso
- Human Translational Genomics Group, University Institute for Biotechnology and Biomedicine, Valencia, Spain; INCLIVA Biomedical Research Institute, Valencia, Spain.
| | - Ariadna Bargiela
- Neuromuscular and Ataxias Research Group, Health Research Institute Hospital La Fe, Valencia, Spain.
| | - Ruben Artero
- Human Translational Genomics Group, University Institute for Biotechnology and Biomedicine, Valencia, Spain; INCLIVA Biomedical Research Institute, Valencia, Spain.
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3
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Puri D, Sharma S, Samaddar S, Ravivarma S, Banerjee S, Ghosh-Roy A. Muscleblind-1 interacts with tubulin mRNAs to regulate the microtubule cytoskeleton in C. elegans mechanosensory neurons. PLoS Genet 2023; 19:e1010885. [PMID: 37603562 PMCID: PMC10470942 DOI: 10.1371/journal.pgen.1010885] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 08/31/2023] [Accepted: 07/26/2023] [Indexed: 08/23/2023] Open
Abstract
Regulation of the microtubule cytoskeleton is crucial for the development and maintenance of neuronal architecture, and recent studies have highlighted the significance of regulated RNA processing in the establishment and maintenance of neural circuits. In a genetic screen conducted using mechanosensory neurons of C. elegans, we identified a mutation in muscleblind-1/mbl-1 as a suppressor of loss of kinesin-13 family microtubule destabilizing factor klp-7. Muscleblind-1(MBL-1) is an RNA-binding protein that regulates the splicing, localization, and stability of RNA. Our findings demonstrate that mbl-1 is required cell-autonomously for axon growth and proper synapse positioning in the posterior lateral microtubule (PLM) neuron. Loss of mbl-1 leads to increased microtubule dynamics and mixed orientation of microtubules in the anterior neurite of PLM. These defects are also accompanied by abnormal axonal transport of the synaptic protein RAB-3 and reduction of gentle touch sensation in mbl-1 mutant. Our data also revealed that mbl-1 is genetically epistatic to mec-7 (β tubulin) and mec-12 (α tubulin) in regulating axon growth. Furthermore, mbl-1 is epistatic to sad-1, an ortholog of BRSK/Brain specific-serine/threonine kinase and a known regulator of synaptic machinery, for synapse formation at the correct location of the PLM neurite. Notably, the immunoprecipitation of MBL-1 resulted in the co-purification of mec-7, mec-12, and sad-1 mRNAs, suggesting a direct interaction between MBL-1 and these transcripts. Additionally, mbl-1 mutants exhibited reduced levels and stability of mec-7 and mec-12 transcripts. Our study establishes a previously unknown link between RNA-binding proteins and cytoskeletal machinery, highlighting their crucial roles in the development and maintenance of the nervous system.
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Affiliation(s)
- Dharmendra Puri
- National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Sunanda Sharma
- National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Sarbani Samaddar
- National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Sruthy Ravivarma
- National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Sourav Banerjee
- National Brain Research Centre, Manesar, Gurgaon, Haryana, India
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4
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Fralish Z, Lotz EM, Chavez T, Khodabukus A, Bursac N. Neuromuscular Development and Disease: Learning From in vitro and in vivo Models. Front Cell Dev Biol 2021; 9:764732. [PMID: 34778273 PMCID: PMC8579029 DOI: 10.3389/fcell.2021.764732] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/06/2021] [Indexed: 01/02/2023] Open
Abstract
The neuromuscular junction (NMJ) is a specialized cholinergic synaptic interface between a motor neuron and a skeletal muscle fiber that translates presynaptic electrical impulses into motor function. NMJ formation and maintenance require tightly regulated signaling and cellular communication among motor neurons, myogenic cells, and Schwann cells. Neuromuscular diseases (NMDs) can result in loss of NMJ function and motor input leading to paralysis or even death. Although small animal models have been instrumental in advancing our understanding of the NMJ structure and function, the complexities of studying this multi-tissue system in vivo and poor clinical outcomes of candidate therapies developed in small animal models has driven the need for in vitro models of functional human NMJ to complement animal studies. In this review, we discuss prevailing models of NMDs and highlight the current progress and ongoing challenges in developing human iPSC-derived (hiPSC) 3D cell culture models of functional NMJs. We first review in vivo development of motor neurons, skeletal muscle, Schwann cells, and the NMJ alongside current methods for directing the differentiation of relevant cell types from hiPSCs. We further compare the efficacy of modeling NMDs in animals and human cell culture systems in the context of five NMDs: amyotrophic lateral sclerosis, myasthenia gravis, Duchenne muscular dystrophy, myotonic dystrophy, and Pompe disease. Finally, we discuss further work necessary for hiPSC-derived NMJ models to function as effective personalized NMD platforms.
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Affiliation(s)
- Zachary Fralish
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, United States
| | - Ethan M Lotz
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, United States
| | - Taylor Chavez
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, United States
| | - Alastair Khodabukus
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, United States
| | - Nenad Bursac
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, United States
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5
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Matilainen O, Ribeiro ARS, Verbeeren J, Cetinbas M, Sood H, Sadreyev RI, Garcia SMDA. Loss of muscleblind splicing factor shortens Caenorhabditis elegans lifespan by reducing the activity of p38 MAPK/PMK-1 and transcription factors ATF-7 and Nrf/SKN-1. Genetics 2021; 219:6325509. [PMID: 34849877 PMCID: PMC8633093 DOI: 10.1093/genetics/iyab114] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/03/2021] [Indexed: 12/13/2022] Open
Abstract
Muscleblind-like splicing regulators (MBNLs) are RNA-binding factors that have an important role in developmental processes. Dysfunction of these factors is a key contributor of different neuromuscular degenerative disorders, including Myotonic Dystrophy type 1 (DM1). Since DM1 is a multisystemic disease characterized by symptoms resembling accelerated aging, we asked which cellular processes do MBNLs regulate that make them necessary for normal lifespan. By utilizing the model organism Caenorhabditis elegans, we found that loss of MBL-1 (the sole ortholog of mammalian MBNLs), which is known to be required for normal lifespan, shortens lifespan by decreasing the activity of p38 MAPK/PMK-1 as well as the function of transcription factors ATF-7 and SKN-1. Furthermore, we show that mitochondrial stress caused by the knockdown of mitochondrial electron transport chain components promotes the longevity of mbl-1 mutants in a partially PMK-1-dependent manner. Together, the data establish a mechanism of how DM1-associated loss of muscleblind affects lifespan. Furthermore, this study suggests that mitochondrial stress could alleviate symptoms caused by the dysfunction of muscleblind splicing factor, creating a potential approach to investigate for therapy.
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Affiliation(s)
- Olli Matilainen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790, Finland
| | - Ana R S Ribeiro
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790, Finland
| | - Jens Verbeeren
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790, Finland
| | - Murat Cetinbas
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Heini Sood
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790, Finland
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Susana M D A Garcia
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790, Finland
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6
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Tylock KM, Auerbach DS, Tang ZZ, Thornton CA, Dirksen RT. Biophysical mechanisms for QRS- and QTc-interval prolongation in mice with cardiac expression of expanded CUG-repeat RNA. J Gen Physiol 2021; 152:133632. [PMID: 31968060 PMCID: PMC7062505 DOI: 10.1085/jgp.201912450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/28/2019] [Accepted: 11/26/2019] [Indexed: 12/26/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1), the most common form of muscular dystrophy in adults, results from the expression of toxic gain-of-function transcripts containing expanded CUG-repeats. DM1 patients experience cardiac electrophysiological defects, including prolonged PR-, QRS-, and QT-intervals, that increase susceptibility to sudden cardiac death (SCD). However, the specific biophysical and molecular mechanisms that underlie the electrocardiograph (ECG) abnormalities and SCD in DM1 are unclear. Here, we addressed this issue using a novel transgenic mouse model that exhibits robust cardiac expression of expanded CUG-repeat RNA (LC15 mice). ECG measurements in conscious LC15 mice revealed significantly prolonged QRS- and corrected QT-intervals, but a normal PR-interval. Although spontaneous arrhythmias were not observed in conscious LC15 mice under nonchallenged conditions, acute administration of the sodium channel blocker flecainide prolonged the QRS-interval and unveiled an increased susceptibility to lethal ventricular arrhythmias. Current clamp measurements in ventricular myocytes from LC15 mice revealed significantly reduced action potential upstroke velocity at physiological pacing (9 Hz) and prolonged action potential duration at all stimulation rates (1–9 Hz). Voltage clamp experiments revealed significant rightward shifts in the voltage dependence of sodium channel activation and steady-state inactivation, as well as a marked reduction in outward potassium current density. Together, these findings indicate that expression of expanded CUG-repeat RNA in the murine heart results in reduced sodium and potassium channel activity that results in QRS- and QT-interval prolongation, respectively.
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Affiliation(s)
- Kevin M Tylock
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY
| | - David S Auerbach
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY.,Department of Pharmacology, Upstate Medical University, Syracuse, NY
| | - Zhen Zhi Tang
- Department of Neurology, University of Rochester Medical Center, Rochester, NY
| | - Charles A Thornton
- Department of Neurology, University of Rochester Medical Center, Rochester, NY
| | - Robert T Dirksen
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY
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7
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Fernández-Garibay X, Ortega MA, Cerro-Herreros E, Comelles J, Martínez E, Artero R, Fernández-Costa JM, Ramón-Azcón J. Bioengineered in vitro3D model of myotonic dystrophy type 1 human skeletal muscle. Biofabrication 2021; 13. [PMID: 33836519 DOI: 10.1088/1758-5090/abf6ae] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/09/2021] [Indexed: 02/06/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is the most common hereditary myopathy in the adult population. The disease is characterized by progressive skeletal muscle degeneration that produces severe disability. At present, there is still no effective treatment for DM1 patients, but the breakthroughs in understanding the molecular pathogenic mechanisms in DM1 have allowed the testing of new therapeutic strategies. Animal models andin vitrotwo-dimensional cell cultures have been essential for these advances. However, serious concerns exist regarding how faithfully these models reproduce the biological complexity of the disease. Biofabrication tools can be applied to engineer human three-dimensional (3D) culture systems that complement current preclinical research models. Here, we describe the development of the firstin vitro3D model of DM1 human skeletal muscle. Transdifferentiated myoblasts from patient-derived fibroblasts were encapsulated in micromolded gelatin methacryloyl-carboxymethyl cellulose methacrylate hydrogels through photomold patterning on functionalized glass coverslips. These hydrogels present a microstructured topography that promotes myoblasts alignment and differentiation resulting in highly aligned myotubes from both healthy and DM1 cells in a long-lasting cell culture. The DM1 3D microtissues recapitulate the molecular alterations detected in patient biopsies. Importantly, fusion index analyses demonstrate that 3D micropatterning significantly improved DM1 cell differentiation into multinucleated myotubes compared to standard cell cultures. Moreover, the characterization of the 3D cultures of DM1 myotubes detects phenotypes as the reduced thickness of myotubes that can be used for drug testing. Finally, we evaluated the therapeutic effect of antagomiR-23b administration on bioengineered DM1 skeletal muscle microtissues. AntagomiR-23b treatment rescues both molecular DM1 hallmarks and structural phenotype, restoring myotube diameter to healthy control sizes. Overall, these new microtissues represent an improvement over conventional cell culture models and can be used as biomimetic platforms to establish preclinical studies for myotonic dystrophy.
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Affiliation(s)
- Xiomara Fernández-Garibay
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri Reixac 10-12, E08028 Barcelona, Spain
| | - María A Ortega
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri Reixac 10-12, E08028 Barcelona, Spain
| | - Estefanía Cerro-Herreros
- University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Dr Moliner 50, E46100 Burjassot, Valencia, Spain.,Translational Genomics Group, Incliva Health Research Institute, Dr Moliner 50, E46100 Burjassot, Valencia, Spain.,Joint Unit Incliva- CIPF, Dr Moliner 50, E46100 Burjassot, Valencia, Spain
| | - Jordi Comelles
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri Reixac 10-12, E08028 Barcelona, Spain.,Department of Electronics and Biomedical Engineering, University of Barcelona (UB), c/Martí i Franquès 1-11, E08028 Barcelona, Spain
| | - Elena Martínez
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri Reixac 10-12, E08028 Barcelona, Spain.,Department of Electronics and Biomedical Engineering, University of Barcelona (UB), c/Martí i Franquès 1-11, E08028 Barcelona, Spain.,Centro de Investigación Biomédica en Red (CIBER), Av. Monforte de Lemos 3-5, Pabellón 11, Planta 0, E28029 Madrid, Spain
| | - Rubén Artero
- University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Dr Moliner 50, E46100 Burjassot, Valencia, Spain.,Translational Genomics Group, Incliva Health Research Institute, Dr Moliner 50, E46100 Burjassot, Valencia, Spain.,Joint Unit Incliva- CIPF, Dr Moliner 50, E46100 Burjassot, Valencia, Spain
| | - Juan M Fernández-Costa
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri Reixac 10-12, E08028 Barcelona, Spain
| | - Javier Ramón-Azcón
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri Reixac 10-12, E08028 Barcelona, Spain.,Institució Catalana de Reserca I Estudis Avançats (ICREA), Passeig de Lluís Companys, 23, E08010 Barcelona, Spain
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8
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Gan W, Chung-Davidson YW, Chen Z, Song S, Cui W, He W, Zhang Q, Li W, Li M, Ren J. Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish. Sci Rep 2021; 11:1815. [PMID: 33469041 PMCID: PMC7815744 DOI: 10.1038/s41598-020-80168-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023] Open
Abstract
Goldfish is an ornamental fish with diverse phenotypes. However, the limited genomic resources of goldfish hamper our understanding of the genetic basis for its phenotypic diversity. To provide enriched genomic resources and infer possible mechanisms underlying skin pigmentation, we performed a large-scale transcriptomic sequencing on 13 adult goldfish tissues, larvae at one- and three-days post hatch, and skin tissues with four different color pigmentation. A total of 25.52 Gb and 149.80 Gb clean data were obtained using the PacBio and Illumina platforms, respectively. Onto the goldfish reference genome, we mapped 137,674 non-redundant transcripts, of which 5.54% was known isoforms and 78.53% was novel isoforms of the reference genes, and the remaining 21,926 isoforms are novel isoforms of additional new genes. Both skin-specific and color-specific transcriptomic analyses showed that several significantly enriched genes were known to be involved in melanogenesis, tyrosine metabolism, PPAR signaling pathway, folate biosynthesis metabolism and so on. Thirteen differentially expressed genes across different color skins were associated with melanogenesis and pteridine synthesis including mitf, ednrb, mc1r, tyr, mlph and gch1, and xanthophore differentiation such as pax7, slc2a11 and slc2a15. These transcriptomic data revealed pathways involved in goldfish pigmentation and improved the gene annotation of the reference genome.
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Affiliation(s)
- Wu Gan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yu-Wen Chung-Davidson
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Zelin Chen
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Shiying Song
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Wenyao Cui
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Wei He
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Qinghua Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Mingyou Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China.
| | - Jianfeng Ren
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China.
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China.
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9
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An Overview of Alternative Splicing Defects Implicated in Myotonic Dystrophy Type I. Genes (Basel) 2020; 11:genes11091109. [PMID: 32971903 PMCID: PMC7564762 DOI: 10.3390/genes11091109] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 01/02/2023] Open
Abstract
Myotonic dystrophy type I (DM1) is the most common form of adult muscular dystrophy, caused by expansion of a CTG triplet repeat in the 3′ untranslated region (3′UTR) of the myotonic dystrophy protein kinase (DMPK) gene. The pathological CTG repeats result in protein trapping by expanded transcripts, a decreased DMPK translation and the disruption of the chromatin structure, affecting neighboring genes expression. The muscleblind-like (MBNL) and CUG-BP and ETR-3-like factors (CELF) are two families of tissue-specific regulators of developmentally programmed alternative splicing that act as antagonist regulators of several pre-mRNA targets, including troponin 2 (TNNT2), insulin receptor (INSR), chloride channel 1 (CLCN1) and MBNL2. Sequestration of MBNL proteins and up-regulation of CELF1 are key to DM1 pathology, inducing a spliceopathy that leads to a developmental remodelling of the transcriptome due to an adult-to-foetal splicing switch, which results in the loss of cell function and viability. Moreover, recent studies indicate that additional pathogenic mechanisms may also contribute to disease pathology, including a misregulation of cellular mRNA translation, localization and stability. This review focuses on the cause and effects of MBNL and CELF1 deregulation in DM1, describing the molecular mechanisms underlying alternative splicing misregulation for a deeper understanding of DM1 complexity. To contribute to this analysis, we have prepared a comprehensive list of transcript alterations involved in DM1 pathogenesis, as well as other deregulated mRNA processing pathways implications.
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10
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Voss DM, Sloan A, Spina R, Ames HM, Bar EE. The Alternative Splicing Factor, MBNL1, Inhibits Glioblastoma Tumor Initiation and Progression by Reducing Hypoxia-Induced Stemness. Cancer Res 2020; 80:4681-4692. [PMID: 32928918 DOI: 10.1158/0008-5472.can-20-1233] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/23/2020] [Accepted: 09/09/2020] [Indexed: 12/31/2022]
Abstract
Muscleblind-like proteins (MBNL) belong to a family of tissue-specific regulators of RNA metabolism that control premessenger RNA splicing. Inactivation of MBNL causes an adult-to-fetal alternative splicing transition, resulting in the development of myotonic dystrophy. We have previously shown that the aggressive brain cancer, glioblastoma (GBM), maintains stem-like features (glioma stem cell, GSC) through hypoxia-induced responses. Accordingly, we hypothesize here that hypoxia-induced responses in GBM might also include MBNL-based alternative splicing to promote tumor progression. When cultured in hypoxia condition, GSCs rapidly exported muscleblind-like-1 (MBNL1) out of the nucleus, resulting in significant inhibition of MBNL1 activity. Notably, hypoxia-regulated inhibition of MBNL1 also resulted in evidence of adult-to-fetal alternative splicing transitions. Forced expression of a constitutively active isoform of MBNL1 inhibited GSC self-renewal and tumor initiation in orthotopic transplantation models. Induced expression of MBNL1 in established orthotopic tumors dramatically inhibited tumor progression, resulting in significantly prolonged survival. This study reveals that MBNL1 plays an essential role in GBM stemness and tumor progression, where hypoxic responses within the tumor inhibit MBNL1 activity, promoting stem-like phenotypes and tumor growth. Reversing these effects on MBNL1 may therefore, yield potent tumor suppressor activities, uncovering new therapeutic opportunities to counter this disease. SIGNIFICANCE: This study describes an unexpected mechanism by which RNA-binding protein, MBNL1, activity is inhibited in hypoxia by a simple isoform switch to regulate glioma stem cell self-renewal, tumorigenicity, and progression.
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Affiliation(s)
- Dillon M Voss
- Department of Neurological Surgery, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Anthony Sloan
- Department of Neurological Surgery, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Raffaella Spina
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland.,Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, Maryland.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Heather M Ames
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Eli E Bar
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland. .,Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, Maryland.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
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11
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Chaudhuri A, Das S, Das B. Localization elements and zip codes in the intracellular transport and localization of messenger RNAs in Saccharomyces cerevisiae. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1591. [PMID: 32101377 DOI: 10.1002/wrna.1591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/13/2022]
Abstract
Intracellular trafficking and localization of mRNAs provide a mechanism of regulation of expression of genes with excellent spatial control. mRNA localization followed by localized translation appears to be a mechanism of targeted protein sorting to a specific cell-compartment, which is linked to the establishment of cell polarity, cell asymmetry, embryonic axis determination, and neuronal plasticity in metazoans. However, the complexity of the mechanism and the components of mRNA localization in higher organisms prompted the use of the unicellular organism Saccharomyces cerevisiae as a simplified model organism to study this vital process. Current knowledge indicates that a variety of mRNAs are asymmetrically and selectively localized to the tip of the bud of the daughter cells, to the vicinity of endoplasmic reticulum, mitochondria, and nucleus in this organism, which are connected to diverse cellular processes. Interestingly, specific cis-acting RNA localization elements (LEs) or RNA zip codes play a crucial role in the localization and trafficking of these localized mRNAs by providing critical binding sites for the specific RNA-binding proteins (RBPs). In this review, we present a comprehensive account of mRNA localization in S. cerevisiae, various types of localization elements influencing the mRNA localization, and the RBPs, which bind to these LEs to implement a number of vital physiological processes. Finally, we emphasize the significance of this process by highlighting their connection to several neuropathological disorders and cancers. This article is categorized under: RNA Export and Localization > RNA Localization.
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Affiliation(s)
- Anusha Chaudhuri
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Subhadeep Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
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12
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Huang K, Masuda A, Chen G, Bushra S, Kamon M, Araki T, Kinoshita M, Ohkawara B, Ito M, Ohno K. Inhibition of cyclooxygenase-1 by nonsteroidal anti-inflammatory drugs demethylates MeR2 enhancer and promotes Mbnl1 transcription in myogenic cells. Sci Rep 2020; 10:2558. [PMID: 32054946 PMCID: PMC7018979 DOI: 10.1038/s41598-020-59517-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
Muscleblind-like 1 (MBNL1) is a ubiquitously expressed RNA-binding protein, which is highly expressed in skeletal muscle. Abnormally expanded CUG-repeats in the DMPK gene cause myotonic dystrophy type 1 (DM1) by sequestration of MBNL1 to nuclear RNA foci and by upregulation of another RNA-binding protein, CUG-binding protein 1 (CUGBP1). We previously reported that a nonsteroidal anti-inflammatory drug (NSAID), phenylbutazone, upregulates MBNL1 expression in DM1 mouse model by demethylation of MeR2, an enhancer element in Mbnl1 intron 1. NSAIDs inhibit cyclooxygenase (COX), which is comprised of COX-1 and COX-2 isoforms. In this study, we screened 29 NSAIDs in C2C12 myoblasts, and found that 13 NSAIDs enhanced Mbnl1 expression, where COX-1-selective NSAIDs upregulated Mbnl1 more than COX-2-selective NSAIDs. Consistently, knockdown of COX-1, but not of COX-2, upregulated MBNL1 expression in C2C12 myoblasts and myotubes, as well as in myotubes differentiated from DM1 patient-derived induced pluripotent stem cells (iPSCs). Luciferase assay showed that COX-1-knockdown augmented the MeR2 enhancer activity. Furthermore, bisulfite sequencing analysis demonstrated that COX-1-knockdown suppressed methylation of MeR2. These results suggest that COX-1 inhibition upregulates Mbnl1 transcription through demethylation of the MeR2 enhancer. Taken together, our study provides new insights into the transcriptional regulation of Mbnl1 by the COX-1-mediated pathway.
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Affiliation(s)
- Kun Huang
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.
| | - Guiying Chen
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Samira Bushra
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Masayoshi Kamon
- Department of Peripheral Nervous System Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Toshiyuki Araki
- Department of Peripheral Nervous System Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | | | - Bisei Ohkawara
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Mikako Ito
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
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13
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In-silico prediction of role of chitosan, chondroitin sulphate and agar in process of wound healing towards scaffold development. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2020.100406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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14
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Shotwell CR, Cleary JD, Berglund JA. The potential of engineered eukaryotic RNA-binding proteins as molecular tools and therapeutics. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1573. [PMID: 31680457 DOI: 10.1002/wrna.1573] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/21/2019] [Accepted: 10/08/2019] [Indexed: 02/06/2023]
Abstract
Eukaroytic RNA-binding proteins (RBPs) recognize and process RNAs through recognition of their sequence motifs via RNA-binding domains (RBDs). RBPs usually consist of one or more RBDs and can include additional functional domains that modify or cleave RNA. Engineered RBPs have been used to answer basic biology questions, control gene expression, locate viral RNA in vivo, as well as many other tasks. Given the growing number of diseases associated with RNA and RBPs, engineered RBPs also have the potential to serve as therapeutics. This review provides an in depth description of recent advances in engineered RBPs and discusses opportunities and challenges in the field. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Methods > RNA Nanotechnology RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Carl R Shotwell
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida
| | - John D Cleary
- RNA Institute, University at Albany, Albany, New York
| | - J Andrew Berglund
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York
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15
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Hale MA, Richardson JI, Day RC, McConnell OL, Arboleda J, Wang ET, Berglund JA. An engineered RNA binding protein with improved splicing regulation. Nucleic Acids Res 2019; 46:3152-3168. [PMID: 29309648 PMCID: PMC5888374 DOI: 10.1093/nar/gkx1304] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 12/19/2017] [Indexed: 01/08/2023] Open
Abstract
The muscleblind-like (MBNL) family of proteins are key developmental regulators of alternative splicing. Sequestration of MBNL proteins by expanded CUG/CCUG repeat RNA transcripts is a major pathogenic mechanism in the neuromuscular disorder myotonic dystrophy (DM). MBNL1 contains four zinc finger (ZF) motifs that form two tandem RNA binding domains (ZF1-2 and ZF3-4) which each bind YGCY RNA motifs. In an effort to determine the differences in function between these domains, we designed and characterized synthetic MBNL proteins with duplicate ZF1-2 or ZF3-4 domains, referred to as MBNL-AA and MBNL-BB, respectively. Analysis of splicing regulation revealed that MBNL-AA had up to 5-fold increased splicing activity while MBNL-BB had 4-fold decreased activity compared to a MBNL protein with the canonical arrangement of zinc finger domains. RNA binding analysis revealed that the variations in splicing activity are due to differences in RNA binding specificities between the two ZF domains rather than binding affinity. Our findings indicate that ZF1-2 drives splicing regulation via recognition of YGCY RNA motifs while ZF3-4 acts as a general RNA binding domain. Our studies suggest that synthetic MBNL proteins with improved or altered splicing activity have the potential to be used as both tools for investigating splicing regulation and protein therapeutics for DM and other microsatellite diseases.
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Affiliation(s)
- Melissa A Hale
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.,Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA
| | - Jared I Richardson
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.,Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA
| | - Ryan C Day
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.,Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA
| | - Ona L McConnell
- Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA.,Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Juan Arboleda
- Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA.,Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Eric T Wang
- Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA.,Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - J Andrew Berglund
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.,Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA
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16
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Development of novel macrocyclic small molecules that target CTG trinucleotide repeats. Bioorg Med Chem 2019; 27:2978-2984. [PMID: 31113691 DOI: 10.1016/j.bmc.2019.05.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 05/07/2019] [Accepted: 05/13/2019] [Indexed: 11/23/2022]
Abstract
We describe the molecular design, synthesis, and investigation of a series of acridine-triaminotriazine macrocycles that selectively bind to CTG trinucleotide repeats in DNA with minimal nonspecific binding. The limited conformational flexibility enforces the stacking of the triaminotriazine and acridine units. Isothermal titration calorimetry studies and Job plot analyses revealed that the ligands bound to d(CTG) mismatched sites. The acridine and triaminotriazine units were shown to intramolecularly π-stack in aqueous solutions. Compared to a noncyclic analog, the macrocycles showed an almost 10-fold lower cytotoxicity in HeLa cells and up to 4-fold higher transcription inhibition of d(CTG·CAG)74.
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17
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Bovaird S, Patel D, Padilla JCA, Lécuyer E. Biological functions, regulatory mechanisms, and disease relevance of RNA localization pathways. FEBS Lett 2018; 592:2948-2972. [PMID: 30132838 DOI: 10.1002/1873-3468.13228] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/06/2018] [Accepted: 08/17/2018] [Indexed: 12/12/2022]
Abstract
The asymmetric subcellular distribution of RNA molecules from their sites of transcription to specific compartments of the cell is an important aspect of post-transcriptional gene regulation. This involves the interplay of intrinsic cis-regulatory elements within the RNA molecules with trans-acting RNA-binding proteins and associated factors. Together, these interactions dictate the intracellular localization route of RNAs, whose downstream impacts have wide-ranging implications in cellular physiology. In this review, we examine the mechanisms underlying RNA localization and discuss their biological significance. We also review the growing body of evidence pointing to aberrant RNA localization pathways in the development and progression of diseases.
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Affiliation(s)
- Samantha Bovaird
- Institut de recherches cliniques de Montréal (IRCM), QC, Canada.,Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Dhara Patel
- Institut de recherches cliniques de Montréal (IRCM), QC, Canada.,Molecular Biology Program, Faculty of Medicine, Université de Montréal, QC, Canada
| | - Juan-Carlos Alberto Padilla
- Institut de recherches cliniques de Montréal (IRCM), QC, Canada.,Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Eric Lécuyer
- Institut de recherches cliniques de Montréal (IRCM), QC, Canada.,Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada.,Molecular Biology Program, Faculty of Medicine, Université de Montréal, QC, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, QC, Canada
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18
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Matloka M, Klein AF, Rau F, Furling D. Cells of Matter- In Vitro Models for Myotonic Dystrophy. Front Neurol 2018; 9:361. [PMID: 29875732 PMCID: PMC5974047 DOI: 10.3389/fneur.2018.00361] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/03/2018] [Indexed: 12/17/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1 also known as Steinert disease) is a multisystemic disorder mainly characterized by myotonia, progressive muscle weakness and wasting, cognitive impairments, and cardiac defects. This autosomal dominant disease is caused by the expression of nuclear retained RNAs containing pathologic expanded CUG repeats that alter the function of RNA-binding proteins in a tissue-specific manner, leading ultimately to neuromuscular dysfunction and clinical symptoms. Although considerable knowledge has been gathered on myotonic dystrophy since its first description, the development of novel relevant disease models remains of high importance to investigate pathophysiologic mechanisms and to assess new therapeutic approaches. In addition to animal models, in vitro cell cultures provide a unique resource for both fundamental and translational research. This review discusses how cellular models broke ground to decipher molecular basis of DM1 and describes currently available cell models, ranging from exogenous expression of the CTG tracts to variable patients' derived cells.
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Affiliation(s)
| | | | | | - Denis Furling
- Sorbonne Université, INSERM, Association Institut de Myologie, Centre de Recherche en Myologie, Paris, France
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19
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Bhaumik P, Ghosh P, Biswas A, Ghosh S, Pal S, Sarkar B, Kumar Dey S. Rare Intronic Variations inTP73Gene Found in Patients with Alzheimer’sDisease. INT J HUM GENET 2018. [DOI: 10.1080/09723757.2017.1421438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Pranami Bhaumik
- Department of Biotechnology, School of Biotechnology and Biological Sciences, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly known as West Bengal University of Technology) BF – 142, Salt Lake City, Sector I. Kolkata 700 064, West Bengal, India
| | - Priyanka Ghosh
- Department of Biotechnology, School of Biotechnology and Biological Sciences, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly known as West Bengal University of Technology) BF – 142, Salt Lake City, Sector I. Kolkata 700 064, West Bengal, India
| | - Atanu Biswas
- Department of Neurology, Bangur Institute of Neurosciences, 52/1A, S.N. Pandit Street, Kolkata 700 025, West Bengal, India
| | - Sujay Ghosh
- Department of Zoology, University of Calcutta, (Ballygunge Science College Campus), 35 Ballygunge Circular Road., Kolkata 700 019, West Bengal, India
| | - Sandip Pal
- Department of Neurology, Burdwan Medical College, Burdwan 713 104, West Bengal, India
| | - Biswanath Sarkar
- DNA Laboratory, Anthropological Survey of India, 27 Jawaharlal Nehru Road Kolkata 700 016, West Bengal, India
| | - Subrata Kumar Dey
- Department of Biotechnology, School of Biotechnology and Biological Sciences, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly known as West Bengal University of Technology) BF – 142, Salt Lake City, Sector I. Kolkata 700 064, West Bengal, India
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20
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Konieczny P, Stepniak-Konieczna E, Taylor K, Sznajder LJ, Sobczak K. Autoregulation of MBNL1 function by exon 1 exclusion from MBNL1 transcript. Nucleic Acids Res 2017; 45:1760-1775. [PMID: 27903900 PMCID: PMC5389549 DOI: 10.1093/nar/gkw1158] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 11/07/2016] [Indexed: 01/14/2023] Open
Abstract
Muscleblind-like proteins (MBNLs) are regulators of RNA metabolism. During tissue differentiation the level of MBNLs increases, while their functional insufficiency plays a crucial role in myotonic dystrophy (DM). Deep sequencing of RNA molecules cross-linked to immunoprecipitated protein particles (CLIP-seq) revealed that MBNL1 binds to MBNL1 exon 1 (e1) encoding both the major part of 5΄UTR and an amino-terminal region of MBNL1 protein. We tested several hypotheses regarding the possible autoregulatory function of MBNL1 binding to its own transcript. Our data indicate that MBNLs induce skipping of e1 from precursor MBNL1 mRNA and that e1 exclusion may impact transcript association with polysomes and translation. Furthermore, e1-deficient protein isoform lacking the first two zinc fingers is highly unstable and its EGFP fusion protein has severely compromised splicing activity. We also show that MBNL1 can be transcribed from three different promoters and that the transcription initiation site determines the mode of e1 regulation. Taken together, we demonstrate that MBNL proteins control steady-state levels of MBNL1 through an interaction with e1 in its precursor mRNA. Insights from our study open a new avenue in therapies against DM based on manipulation of the transcription initiation site and e1 splicing of MBNL1 mRNA.
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Affiliation(s)
- Patryk Konieczny
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Ewa Stepniak-Konieczna
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Katarzyna Taylor
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Lukasz J Sznajder
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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21
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Zhang BW, Cai HF, Wei XF, Sun JJ, Lan XY, Lei CZ, Lin FP, Qi XL, Plath M, Chen H. miR-30-5p Regulates Muscle Differentiation and Alternative Splicing of Muscle-Related Genes by Targeting MBNL. Int J Mol Sci 2016; 17:ijms17020182. [PMID: 26840300 PMCID: PMC4783916 DOI: 10.3390/ijms17020182] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 12/26/2015] [Accepted: 01/22/2016] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs), a class of single stranded, small (~22 nucleotides), non-coding RNAs, play an important role in muscle development. We focused on the role of the miR-30-5p family during bovine muscle development from previous high-throughput sequencing results and analyzed their expression profiles. MHC and MyoG mRNAs expression as well as their proteins were suppressed in differentiated C2C12 cells, suggesting the importance of miR-30-5p in muscle development. MBNL, the candidate target of miR-30-5p, is an alternative splicing regulation factor. MBNL1 and MBNL3 have opposite effects on muscle differentiation. Our results confirmed that miR-30a-5p and miR-30e-5p repress the expression of MBNL1, MBNL2 and MBNL3, whereas miR-30b-5p inhibits MBNL1 and MBNL2 expression. This provides direct evidence that MBNL expression can be flexibly regulated by miR-30-5p. Previous studies showed that MBNL1 promotes exon inclusion of two muscle-related genes (Trim55 and INSR). Through RNA splicing studies, we found that miR-30-5p had an effect on their alternative splicing, which means miR-30-5p via MBNL1 could be integrated into muscle signaling pathways in which INSR or Trim55 are located. In conclusion, miR-30-5p could inhibit muscle cell differentiation and regulate the alternative splicing of Trim55 and INSR by targeting MBNL. These results promote the understanding of the function of miRNAs in muscle development.
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Affiliation(s)
- Bo-Wen Zhang
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Han-Fang Cai
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Xue-Feng Wei
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Jia-Jie Sun
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Xian-Yong Lan
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Chu-Zhao Lei
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Feng-Peng Lin
- Department of Animal Husbandry, Bureau of Biyang County of Henan province, Biyang 463700, Henan, China.
| | - Xing-Lei Qi
- Department of Animal Husbandry, Bureau of Biyang County of Henan province, Biyang 463700, Henan, China.
| | - Martin Plath
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Hong Chen
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
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22
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Zimmerman SC. A journey in bioinspired supramolecular chemistry: from molecular tweezers to small molecules that target myotonic dystrophy. Beilstein J Org Chem 2016; 12:125-38. [PMID: 26877815 PMCID: PMC4734311 DOI: 10.3762/bjoc.12.14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/06/2016] [Indexed: 12/02/2022] Open
Abstract
This review summarizes part of the author’s research in the area of supramolecular chemistry, beginning with his early life influences and early career efforts in molecular recognition, especially molecular tweezers. Although designed to complex DNA, these hosts proved more applicable to the field of host–guest chemistry. This early experience and interest in intercalation ultimately led to the current efforts to develop small molecule therapeutic agents for myotonic dystrophy using a rational design approach that heavily relies on principles of supramolecular chemistry. How this work was influenced by that of others in the field and the evolution of each area of research is highlighted with selected examples.
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Affiliation(s)
- Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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23
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Todorova T, Bock FJ, Chang P. PARP13 regulates cellular mRNA post-transcriptionally and functions as a pro-apoptotic factor by destabilizing TRAILR4 transcript. Nat Commun 2014; 5:5362. [PMID: 25382312 PMCID: PMC4228382 DOI: 10.1038/ncomms6362] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 09/23/2014] [Indexed: 12/27/2022] Open
Abstract
Poly(ADP-ribose) Polymerase-13 (PARP13/ZAP/ZC3HAV1) is an antiviral factor, active against specific RNA viruses such as MLV, SINV and HIV. During infection, PARP13 binds viral RNA via its four CCCH-type zinc finger domains and targets it for degradation by recruiting cellular mRNA decay factors such as the exosome complex and XRN1. Here we show that PARP13 binds to and regulates cellular mRNAs in the absence of viral infection. Knockdown of PARP13 results in the misregulation of hundreds of transcripts. Among the most upregulated transcripts is TRAILR4 that encodes a decoy receptor for TRAIL - a pro-apoptotic cytokine that is a promising target for the therapeutic inhibition of cancers. PARP13 destabilizes TRAILR4 mRNA posttranscriptionally in an exosome dependent manner by binding to a region in its 3’UTR. As a consequence, PARP13 represses TRAILR4 expression and increases cell sensitivity to TRAIL-mediated apoptosis, acting as a key regulator of the cellular response to TRAIL.
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Affiliation(s)
- Tanya Todorova
- 1] Department of Biology, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02139, USA [2] Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02139, USA
| | - Florian J Bock
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02139, USA
| | - Paul Chang
- 1] Department of Biology, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02139, USA [2] Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02139, USA
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24
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Konieczny P, Stepniak-Konieczna E, Sobczak K. MBNL proteins and their target RNAs, interaction and splicing regulation. Nucleic Acids Res 2014; 42:10873-87. [PMID: 25183524 PMCID: PMC4176163 DOI: 10.1093/nar/gku767] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Muscleblind-like (MBNL) proteins are key regulators of precursor and mature mRNA metabolism in mammals. Based on published and novel data, we explore models of tissue-specific MBNL interaction with RNA. We portray MBNL domains critical for RNA binding and splicing regulation, and the structure of MBNL's normal and pathogenic RNA targets, particularly in the context of myotonic dystrophy (DM), in which expanded CUG or CCUG repeat transcripts sequester several nuclear proteins including MBNLs. We also review the properties of MBNL/RNA complex, including recent data obtained from UV cross-linking and immunoprecipitation (CLIP-Seq), and discuss how this interaction shapes normal MBNL-dependent alternative splicing regulation. Finally, we review how this acquired knowledge about the pathogenic RNA structure and nature of MBNL sequestration can be translated into the design of therapeutic strategies against DM.
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Affiliation(s)
- Patryk Konieczny
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Ewa Stepniak-Konieczna
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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25
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Cheng AW, Shi J, Wong P, Luo KL, Trepman P, Wang ET, Choi H, Burge CB, Lodish HF. Muscleblind-like 1 (Mbnl1) regulates pre-mRNA alternative splicing during terminal erythropoiesis. Blood 2014; 124:598-610. [PMID: 24869935 PMCID: PMC4110662 DOI: 10.1182/blood-2013-12-542209] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 05/16/2014] [Indexed: 12/18/2022] Open
Abstract
The scope and roles of regulated isoform gene expression during erythroid terminal development are poorly understood. We identified hundreds of differentiation-associated isoform changes during terminal erythropoiesis. Sequences surrounding cassette exons of skipped exon events are enriched for motifs bound by the Muscleblind-like (MBNL) family of splicing factors. Knockdown of Mbnl1 in cultured murine fetal liver erythroid progenitors resulted in a strong block in erythroid differentiation and disrupted the developmentally regulated exon skipping of Ndel1 mRNA, which is bound by MBNL1 and critical for erythroid terminal proliferation. These findings reveal an unanticipated scope of the alternative splicing program and the importance of Mbnl1 during erythroid terminal differentiation.
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Affiliation(s)
- Albert W Cheng
- Whitehead Institute for Biomedical Research, Cambridge, MA; Computational and Systems Biology Program, and
| | - Jiahai Shi
- Whitehead Institute for Biomedical Research, Cambridge, MA
| | - Piu Wong
- Whitehead Institute for Biomedical Research, Cambridge, MA
| | - Katherine L Luo
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA; and
| | - Paula Trepman
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA; and
| | - Eric T Wang
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA; and Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA
| | - Heejo Choi
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA; and
| | - Christopher B Burge
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA; and
| | - Harvey F Lodish
- Whitehead Institute for Biomedical Research, Cambridge, MA; Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA; and
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26
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Wong CH, Nguyen L, Peh J, Luu LM, Sanchez J, Richardson SL, Tuccinardi T, Tsoi H, Chan WY, Chan HY, Baranger AM, Hergenrother PJ, Zimmerman SC. Targeting toxic RNAs that cause myotonic dystrophy type 1 (DM1) with a bisamidinium inhibitor. J Am Chem Soc 2014; 136:6355-61. [PMID: 24702247 PMCID: PMC4015652 DOI: 10.1021/ja5012146] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Indexed: 01/28/2023]
Abstract
A working hypothesis for the pathogenesis of myotonic dystrophy type 1 (DM1) involves the aberrant sequestration of an alternative splicing regulator, MBNL1, by expanded CUG repeats, r(CUG)(exp). It has been suggested that a reversal of the myotonia and potentially other symptoms of the DM1 disease can be achieved by inhibiting the toxic MBNL1-r(CUG)(exp) interaction. Using rational design, we discovered an RNA-groove binding inhibitor (ligand 3) that contains two triaminotriazine units connected by a bisamidinium linker. Ligand 3 binds r(CUG)12 with a low micromolar affinity (K(d) = 8 ± 2 μM) and disrupts the MBNL1-r(CUG)12 interaction in vitro (K(i) = 8 ± 2 μM). In addition, ligand 3 is cell and nucleus permeable, exhibits negligible toxicity to mammalian cells, dissolves MBNL1-r(CUG)(exp) ribonuclear foci, and restores misregulated splicing of IR and cTNT in a DM1 cell culture model. Importantly, suppression of r(CUG)(exp) RNA-induced toxicity in a DM1 Drosophila model was observed after treatment with ligand 3. These results suggest ligand 3 as a lead for the treatment of DM1.
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Affiliation(s)
- Chun-Ho Wong
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Lien Nguyen
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Jessie Peh
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Long M. Luu
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Jeannette
S. Sanchez
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Stacie L. Richardson
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | | | - Ho Tsoi
- Laboratory of Drosophila
Research and School of Life Sciences and School of Biomedical
Sciences, The Chinese University of Hong
Kong, Shatin, N.T., Hong Kong SAR, The People's Republic
of China
| | - Wood Yee Chan
- Laboratory of Drosophila
Research and School of Life Sciences and School of Biomedical
Sciences, The Chinese University of Hong
Kong, Shatin, N.T., Hong Kong SAR, The People's Republic
of China
| | - H. Y.
Edwin Chan
- Laboratory of Drosophila
Research and School of Life Sciences and School of Biomedical
Sciences, The Chinese University of Hong
Kong, Shatin, N.T., Hong Kong SAR, The People's Republic
of China
| | - Anne M. Baranger
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Paul J. Hergenrother
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Steven C. Zimmerman
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
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27
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Genome wide identification of aberrant alternative splicing events in myotonic dystrophy type 2. PLoS One 2014; 9:e93983. [PMID: 24722564 PMCID: PMC3983107 DOI: 10.1371/journal.pone.0093983] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 03/10/2014] [Indexed: 02/01/2023] Open
Abstract
Myotonic dystrophy type 2 (DM2) is a genetic, autosomal dominant disease due to expansion of tetraplet (CCTG) repetitions in the first intron of the ZNF9/CNBP gene. DM2 is a multisystemic disorder affecting the skeletal muscle, the heart, the eye and the endocrine system. According to the proposed pathological mechanism, the expanded tetraplets have an RNA toxic effect, disrupting the splicing of many mRNAs. Thus, the identification of aberrantly spliced transcripts is instrumental for our understanding of the molecular mechanisms underpinning the disease. The aim of this study was the identification of new aberrant alternative splicing events in DM2 patients. By genome wide analysis of 10 DM2 patients and 10 controls (CTR), we identified 273 alternative spliced exons in 218 genes. While many aberrant splicing events were already identified in the past, most were new. A subset of these events was validated by qPCR assays in 19 DM2 and 15 CTR subjects. To gain insight into the molecular pathways involving the identified aberrantly spliced genes, we performed a bioinformatics analysis with Ingenuity system. This analysis indicated a deregulation of development, cell survival, metabolism, calcium signaling and contractility. In conclusion, our genome wide analysis provided a database of aberrant splicing events in the skeletal muscle of DM2 patients. The affected genes are involved in numerous pathways and networks important for muscle physio-pathology, suggesting that the identified variants may contribute to DM2 pathogenesis.
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28
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Bargiela A, Llamusi B, Cerro-Herreros E, Artero R. Two enhancers control transcription of Drosophila muscleblind in the embryonic somatic musculature and in the central nervous system. PLoS One 2014; 9:e93125. [PMID: 24667536 PMCID: PMC3965525 DOI: 10.1371/journal.pone.0093125] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 03/01/2014] [Indexed: 12/19/2022] Open
Abstract
The phylogenetically conserved family of Muscleblind proteins are RNA-binding factors involved in a variety of gene expression processes including alternative splicing regulation, RNA stability and subcellular localization, and miRNA biogenesis, which typically contribute to cell-type specific differentiation. In humans, sequestration of Muscleblind-like proteins MBNL1 and MBNL2 has been implicated in degenerative disorders, particularly expansion diseases such as myotonic dystrophy type 1 and 2. Drosophila muscleblind was previously shown to be expressed in embryonic somatic and visceral muscle subtypes, and in the central nervous system, and to depend on Mef2 for transcriptional activation. Genomic approaches have pointed out candidate gene promoters and tissue-specific enhancers, but experimental confirmation of their regulatory roles was lacking. In our study, luciferase reporter assays in S2 cells confirmed that regions P1 (515 bp) and P2 (573 bp), involving the beginning of exon 1 and exon 2, respectively, were able to initiate RNA transcription. Similarly, transgenic Drosophila embryos carrying enhancer reporter constructs supported the existence of two regulatory regions which control embryonic expression of muscleblind in the central nerve cord (NE, neural enhancer; 830 bp) and somatic (skeletal) musculature (ME, muscle enhancer; 3.3 kb). Both NE and ME were able to boost expression from the Hsp70 heterologous promoter. In S2 cell assays most of the ME enhancer activation could be further narrowed down to a 1200 bp subregion (ME.3), which contains predicted binding sites for the Mef2 transcription factor. The present study constitutes the first characterization of muscleblind enhancers and will contribute to a deeper understanding of the transcriptional regulation of the gene.
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Affiliation(s)
- Ariadna Bargiela
- Translational Genomics Group, Department of Genetics, University of Valencia, Valencia, Spain
- INCLIVA Health Research Institute, Valencia, Spain
| | - Beatriz Llamusi
- Translational Genomics Group, Department of Genetics, University of Valencia, Valencia, Spain
- INCLIVA Health Research Institute, Valencia, Spain
| | - Estefanía Cerro-Herreros
- Translational Genomics Group, Department of Genetics, University of Valencia, Valencia, Spain
- INCLIVA Health Research Institute, Valencia, Spain
| | - Ruben Artero
- Translational Genomics Group, Department of Genetics, University of Valencia, Valencia, Spain
- INCLIVA Health Research Institute, Valencia, Spain
- * E-mail:
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29
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Spletter ML, Schnorrer F. Transcriptional regulation and alternative splicing cooperate in muscle fiber-type specification in flies and mammals. Exp Cell Res 2013; 321:90-8. [PMID: 24145055 PMCID: PMC4040393 DOI: 10.1016/j.yexcr.2013.10.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/06/2013] [Accepted: 10/09/2013] [Indexed: 11/21/2022]
Abstract
Muscles coordinate body movements throughout the animal kingdom. Each skeletal muscle is built of large, multi-nucleated cells, called myofibers, which are classified into several functionally distinct types. The typical fiber-type composition of each muscle arises during development, and in mammals is extensively adjusted in response to postnatal exercise. Understanding how functionally distinct muscle fiber-types arise is important for unraveling the molecular basis of diseases from cardiomyopathies to muscular dystrophies. In this review, we focus on recent advances in Drosophila and mammals in understanding how muscle fiber-type specification is controlled by the regulation of transcription and alternative splicing. We illustrate the cooperation of general myogenic transcription factors with muscle fiber-type specific transcriptional regulators as a basic principle for fiber-type specification, which is conserved from flies to mammals. We also examine how regulated alternative splicing of sarcomeric proteins in both flies and mammals can directly instruct the physiological and biophysical differences between fiber-types. Thus, research in Drosophila can provide important mechanistic insight into muscle fiber specification, which is relevant to homologous processes in mammals and to the pathology of muscle diseases.
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Affiliation(s)
- Maria L Spletter
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Frank Schnorrer
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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30
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Garcia-Alcover I, López Castel A, Perez-Alonso M, Artero R. In vivo strategies for drug discovery in myotonic dystrophy disorders. DRUG DISCOVERY TODAY. TECHNOLOGIES 2013; 10:e97-102. [PMID: 24050236 DOI: 10.1016/j.ddtec.2012.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Myotonic dystrophy (DM) is a complex neuromuscular genetic disease for which there is currently no valid therapy. The recent development of non-mammal animal models opened up the possibility of performing drug discovery in vivo, using as screening readout phenotypes with underlying molecular parallels to the disease. In this review we discuss the state of the art technologies already used in large scale drug screening and provide guidance for further development of novel technologies.
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31
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MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Nature 2013; 498:241-5. [PMID: 23739326 DOI: 10.1038/nature12270] [Citation(s) in RCA: 240] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 05/07/2013] [Indexed: 01/10/2023]
Abstract
Previous investigations of the core gene regulatory circuitry that controls the pluripotency of embryonic stem (ES) cells have largely focused on the roles of transcription, chromatin and non-coding RNA regulators. Alternative splicing represents a widely acting mode of gene regulation, yet its role in regulating ES-cell pluripotency and differentiation is poorly understood. Here we identify the muscleblind-like RNA binding proteins, MBNL1 and MBNL2, as conserved and direct negative regulators of a large program of cassette exon alternative splicing events that are differentially regulated between ES cells and other cell types. Knockdown of MBNL proteins in differentiated cells causes switching to an ES-cell-like alternative splicing pattern for approximately half of these events, whereas overexpression of MBNL proteins in ES cells promotes differentiated-cell-like alternative splicing patterns. Among the MBNL-regulated events is an ES-cell-specific alternative splicing switch in the forkhead family transcription factor FOXP1 that controls pluripotency. Consistent with a central and negative regulatory role for MBNL proteins in pluripotency, their knockdown significantly enhances the expression of key pluripotency genes and the formation of induced pluripotent stem cells during somatic cell reprogramming.
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32
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Malatesta M, Giagnacovo M, Costanzo M, Cisterna B, Cardani R, Meola G. Muscleblind-like1 undergoes ectopic relocation in the nuclei of skeletal muscles in myotonic dystrophy and sarcopenia. Eur J Histochem 2013; 57:e15. [PMID: 23807294 PMCID: PMC3794341 DOI: 10.4081/ejh.2013.e15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Revised: 02/13/2013] [Accepted: 02/14/2013] [Indexed: 01/24/2023] Open
Abstract
Muscleblind-like 1 (MBNL1) is an alternative splicing factor involved in postnatal development of skeletal muscles and heart in humans and mice, and its deregulation is known to be pivotal in the onset and development of myotonic dystrophy (DM). In fact, in DM patients this protein is ectopically sequestered into intranuclear foci, thus compromising the regulation of the alternative splicing of several genes. However, despite the numerous biochemical and molecular studies, scarce attention has been paid to the intranuclear location of MBNL1 outside the foci, although previous data demonstrated that in DM patients various splicing and cleavage factors undergo an abnormal intranuclear distribution suggestive of impaired RNA processing. Interestingly, these nuclear alterations strongly remind those observed in sarcopenia i.e., the loss of muscle mass and function which physiologically occurs during ageing. On this basis, in the present investigation the ultrastructural localization of MBNL1 was analyzed in the myonuclei of skeletal muscles from healthy and DM patients as well as from adult and old (sarcopenic) mice, in the attempt to elucidate possible changes in its distribution and amount. Our data demonstrate that in both dystrophic and sarcopenic muscles MBNL1 undergoes intranuclear relocation, accumulating in its usual functional sites but also ectopically moving to domains which are usually devoid of this protein in healthy adults. This accumulation/delocalization could contribute to hamper the functionality of the whole splicing machinery, leading to a lower nuclear metabolic activity and, consequently, to a less efficient protein synthesis. Moreover, the similar nuclear alterations found in DM and sarcopenia may account for the similar muscle tissue features (myofibre atrophy, fibre size variability and centrally located nuclei), and, in general, for the aging-reminiscent phenotype observed in DM patients.
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Affiliation(s)
- M Malatesta
- Dipartimento di Scienze Neurologiche, Neuropsicologiche, Morfologiche e Motorie, Sezione di Anatomia e Istologia, Università di Verona, 37134 Verona, Italy.
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33
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Fleming VA, Geng C, Ladd AN, Lou H. Alternative splicing of the neurofibromatosis type 1 pre-mRNA is regulated by the muscleblind-like proteins and the CUG-BP and ELAV-like factors. BMC Mol Biol 2012; 13:35. [PMID: 23227900 PMCID: PMC3558374 DOI: 10.1186/1471-2199-13-35] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/30/2012] [Indexed: 01/22/2023] Open
Abstract
Background Alternative splicing is often subjected to complex regulatory control that involves many protein factors and cis-acting RNA sequence elements. One major challenge is to identify all of the protein players and define how they control alternative expression of a particular exon in a combinatorial manner. The Muscleblind-like (MBNL) and CUG-BP and ELAV-Like family (CELF) proteins are splicing regulatory proteins, which function as antagonists in the regulation of several alternative exons. Currently only a limited number of common targets of MBNL and CELF are known that are antagonistically regulated by these two groups of proteins. Results Recently, we identified neurofibromatosis type 1 (NF1) exon 23a as a novel target of negative regulation by CELF proteins. Here we report that MBNL family members are positive regulators of this exon. Overexpression of MBNL proteins promote exon 23a inclusion in a low MBNL-expressing cell line, and simultaneous siRNA-mediated knockdown of MBNL1 and MBNL2 family members in a high MBNL-expressing cell line promotes exon 23a skipping. Importantly, these two groups of proteins antagonize each other in regulating inclusion of exon 23a. Furthermore, we analyzed the binding sites of these proteins in the intronic sequences upstream of exon 23a by UV cross-linking assays. We show that in vitro, in addition to the previously identified preferred binding sequence UGCUGU, the MBNL proteins need the neighboring sequences for optimal binding. Conclusion This study along with our previous work that demonstrated roles for Hu, CELF, and TIA-1 and TIAR proteins in the regulation of NF1 exon 23a establish that this exon is under tight, complex control.
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Affiliation(s)
- Victoria A Fleming
- Department of Genetics, Case Western Reserve University, Cleveland, OH, 44106, USA
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34
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Llamusi B, Bargiela A, Fernandez-Costa JM, Garcia-Lopez A, Klima R, Feiguin F, Artero R. Muscleblind, BSF and TBPH are mislocalized in the muscle sarcomere of a Drosophila myotonic dystrophy model. Dis Model Mech 2012; 6:184-96. [PMID: 23118342 PMCID: PMC3529350 DOI: 10.1242/dmm.009563] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a genetic disease caused by the pathological expansion of a CTG trinucleotide repeat in the 3′ UTR of the DMPK gene. In the DMPK transcripts, the CUG expansions sequester RNA-binding proteins into nuclear foci, including transcription factors and alternative splicing regulators such as MBNL1. MBNL1 sequestration has been associated with key features of DM1. However, the basis behind a number of molecular and histological alterations in DM1 remain unclear. To help identify new pathogenic components of the disease, we carried out a genetic screen using a Drosophila model of DM1 that expresses 480 interrupted CTG repeats, i(CTG)480, and a collection of 1215 transgenic RNA interference (RNAi) fly lines. Of the 34 modifiers identified, two RNA-binding proteins, TBPH (homolog of human TAR DNA-binding protein 43 or TDP-43) and BSF (Bicoid stability factor; homolog of human LRPPRC), were of particular interest. These factors modified i(CTG)480 phenotypes in the fly eye and wing, and TBPH silencing also suppressed CTG-induced defects in the flight muscles. In Drosophila flight muscle, TBPH, BSF and the fly ortholog of MBNL1, Muscleblind (Mbl), were detected in sarcomeric bands. Expression of i(CTG)480 resulted in changes in the sarcomeric patterns of these proteins, which could be restored by coexpression with human MBNL1. Epistasis studies showed that Mbl silencing was sufficient to induce a subcellular redistribution of TBPH and BSF proteins in the muscle, which mimicked the effect of i(CTG)480 expression. These results provide the first description of TBPH and BSF as targets of Mbl-mediated CTG toxicity, and they suggest an important role of these proteins in DM1 muscle pathology.
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Affiliation(s)
- Beatriz Llamusi
- Translational Genomics Group, Department of Genetics, University of Valencia, Doctor Moliner 50, 46100 Burjasot, Valencia, Spain
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35
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Udd B, Krahe R. The myotonic dystrophies: molecular, clinical, and therapeutic challenges. Lancet Neurol 2012; 11:891-905. [DOI: 10.1016/s1474-4422(12)70204-1] [Citation(s) in RCA: 335] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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36
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Combinatorial mutagenesis of MBNL1 zinc fingers elucidates distinct classes of regulatory events. Mol Cell Biol 2012; 32:4155-67. [PMID: 22890842 DOI: 10.1128/mcb.00274-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The RNA binding protein and alternative splicing factor Muscleblind-like 1 (MBNL1) has been a topic of intense study due to its role in myotonic dystrophy (DM) pathogenesis. MBNL1 contains four zinc finger (ZF) RNA binding domains arranged in two pairs. Through combinatorial mutagenesis of the ZF domains, we demonstrate that the pairs of ZFs have differential affinity for RNA and subsequently differential splicing activities. We evaluated splicing and binding activity for six MBNL1-mediated splicing events and found that the splicing activity profiles for the ZF mutants vary among transcripts. Clustering analysis of splicing profiles revealed that two distinct classes of MBNL1 pre-mRNA substrates exist. For some of the RNA transcripts tested, binding and splicing activity of the ZF mutants correlated. However, for some transcripts it appears that MBNL1 exerts robust splicing activity in the absence of RNA binding. We demonstrate that functionally distinct classes of MBNL1-mediated splicing events exist as defined by requirements for ZF-RNA interactions.
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37
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Drosophila muscleblind codes for proteins with one and two tandem zinc finger motifs. PLoS One 2012; 7:e34248. [PMID: 22479576 PMCID: PMC3315501 DOI: 10.1371/journal.pone.0034248] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 02/24/2012] [Indexed: 12/17/2022] Open
Abstract
Muscleblind-like proteins, Muscleblind (Mbl) in Drosophila and MBNL1-3 in vertebrates, are regulators of alternative splicing. Human MBNL1 is a key factor in the etiology of myotonic dystrophy (DM), a muscle wasting disease caused by the occurrence of toxic RNA molecules containing CUG/CCUG repeats. MBNL1 binds to these RNAs and is sequestered in nuclear foci preventing it from exerting its normal function, which ultimately leads to mis-spliced mRNAs, a major cause of the disease. Muscleblind-proteins bind to RNAs via N-terminal zinc fingers of the Cys(3)-His type. These zinc fingers are arranged in one (invertebrates) or two (vertebrates) tandem zinc finger (TZF) motifs with both fingers targeting GC steps in the RNA molecule. Here I show that mbl genes in Drosophila and in other insects also encode proteins with two TZF motifs, highly similar to vertebrate MBNL proteins. In Drosophila the different protein isoforms have overlapping but possibly divergent functions in vivo, evident by their unequal capacities to rescue the splicing defects observed in mbl mutant embryos. In addition, using whole transcriptome analysis, I identified several new splicing targets for Mbl in Drosophila embryos. Two of these novel targets, kkv (krotzkopf-verkehrt, coding for Chitin Synthase 1) and cora (coracle, coding for the Drosophila homolog of Protein 4.1), are not muscle-specific but expressed mainly in epidermal cells, indicating a function for mbl not only in muscles and the nervous system.
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