1
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Olthof AM, Schwoerer CF, Girardini KN, Weber AL, Doggett K, Mieruszynski S, Heath JK, Moore TE, Biran J, Kanadia RN. Taxonomy of introns and the evolution of minor introns. Nucleic Acids Res 2024:gkae550. [PMID: 38943346 DOI: 10.1093/nar/gkae550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 07/01/2024] Open
Abstract
Classification of introns, which is crucial to understanding their evolution and splicing, has historically been binary and has resulted in the naming of major and minor introns that are spliced by their namesake spliceosome. However, a broad range of intron consensus sequences exist, leading us to here reclassify introns as minor, minor-like, hybrid, major-like, major and non-canonical introns in 263 species across six eukaryotic supergroups. Through intron orthology analysis, we discovered that minor-like introns are a transitory node for intron conversion across evolution. Despite close resemblance of their consensus sequences to minor introns, these introns possess an AG dinucleotide at the -1 and -2 position of the 5' splice site, a salient feature of major introns. Through combined analysis of CoLa-seq, CLIP-seq for major and minor spliceosome components, and RNAseq from samples in which the minor spliceosome is inhibited we found that minor-like introns are also an intermediate class from a splicing mechanism perspective. Importantly, this analysis has provided insight into the sequence elements that have evolved to make minor-like introns amenable to recognition by both minor and major spliceosome components. We hope that this revised intron classification provides a new framework to study intron evolution and splicing.
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Affiliation(s)
- Anouk M Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
| | - Charles F Schwoerer
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
| | - Kaitlin N Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
| | - Audrey L Weber
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
| | - Karen Doggett
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Stephen Mieruszynski
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Joan K Heath
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Timothy E Moore
- Statistical Consulting Services, Center for Open Research Resources & Equipment, University of Connecticut, Storrs, CT, USA
| | - Jakob Biran
- Department of Poultry and Aquaculture, Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon, Israel
| | - Rahul N Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
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2
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Wuchty S, White AK, Olthof AM, Drake K, Hume AJ, Olejnik J, Aguiar-Pulido V, Mühlberger E, Kanadia RN. Minor intron-containing genes as an ancient backbone for viral infection? PNAS NEXUS 2024; 3:pgad479. [PMID: 38274120 PMCID: PMC10810330 DOI: 10.1093/pnasnexus/pgad479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024]
Abstract
Minor intron-containing genes (MIGs) account for <2% of all human protein-coding genes and are uniquely dependent on the minor spliceosome for proper excision. Despite their low numbers, we surprisingly found a significant enrichment of MIG-encoded proteins (MIG-Ps) in protein-protein interactomes and host factors of positive-sense RNA viruses, including SARS-CoV-1, SARS-CoV-2, MERS coronavirus, and Zika virus. Similarly, we observed a significant enrichment of MIG-Ps in the interactomes and sets of host factors of negative-sense RNA viruses such as Ebola virus, influenza A virus, and the retrovirus HIV-1. We also found an enrichment of MIG-Ps in double-stranded DNA viruses such as Epstein-Barr virus, human papillomavirus, and herpes simplex viruses. In general, MIG-Ps were highly connected and placed in central positions in a network of human-host protein interactions. Moreover, MIG-Ps that interact with viral proteins were enriched with essential genes. We also provide evidence that viral proteins interact with ancestral MIGs that date back to unicellular organisms and are mainly involved in basic cellular functions such as cell cycle, cell division, and signal transduction. Our results suggest that MIG-Ps form a stable, evolutionarily conserved backbone that viruses putatively tap to invade and propagate in human host cells.
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Affiliation(s)
- Stefan Wuchty
- Department of Computer Science, University of Miami, Coral Gables, FL 33146, USA
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
- Institute of Data Science and Computing, University of Miami, Coral Gables, FL 33146, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33134, USA
| | - Alisa K White
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Anouk M Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Kyle Drake
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Adam J Hume
- Department of Virology, Immunology and Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
- Center for Emerging Infectious Diseases Policy and Research, Boston University, Boston, MA 02118, USA
| | - Judith Olejnik
- Department of Virology, Immunology and Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | | | - Elke Mühlberger
- Department of Virology, Immunology and Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Rahul N Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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3
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Augspach A, Drake KD, Roma L, Qian E, Lee SR, Clarke D, Kumar S, Jaquet M, Gallon J, Bolis M, Triscott J, Galván JA, Chen Y, Thalmann GN, Kruithof-de Julio M, Theurillat JPP, Wuchty S, Gerstein M, Piscuoglio S, Kanadia RN, Rubin MA. Minor intron splicing is critical for survival of lethal prostate cancer. Mol Cell 2023; 83:1983-2002.e11. [PMID: 37295433 PMCID: PMC10637423 DOI: 10.1016/j.molcel.2023.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 03/29/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023]
Abstract
The evolutionarily conserved minor spliceosome (MiS) is required for protein expression of ∼714 minor intron-containing genes (MIGs) crucial for cell-cycle regulation, DNA repair, and MAP-kinase signaling. We explored the role of MIGs and MiS in cancer, taking prostate cancer (PCa) as an exemplar. Both androgen receptor signaling and elevated levels of U6atac, a MiS small nuclear RNA, regulate MiS activity, which is highest in advanced metastatic PCa. siU6atac-mediated MiS inhibition in PCa in vitro model systems resulted in aberrant minor intron splicing leading to cell-cycle G1 arrest. Small interfering RNA knocking down U6atac was ∼50% more efficient in lowering tumor burden in models of advanced therapy-resistant PCa compared with standard antiandrogen therapy. In lethal PCa, siU6atac disrupted the splicing of a crucial lineage dependency factor, the RE1-silencing factor (REST). Taken together, we have nominated MiS as a vulnerability for lethal PCa and potentially other cancers.
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Affiliation(s)
- Anke Augspach
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Kyle D Drake
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Luca Roma
- Institute of Pathology and Medical Genetics, University Hospital Basel, 4056 Basel, Switzerland
| | - Ellen Qian
- Department of Computer Science, Yale University, New Haven, CT 06520, USA; Yale College, New Haven, CT 06520, USA
| | - Se Ri Lee
- Department of Computer Science, Yale University, New Haven, CT 06520, USA; Yale College, New Haven, CT 06520, USA
| | - Declan Clarke
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Sushant Kumar
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Muriel Jaquet
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - John Gallon
- Institute of Pathology and Medical Genetics, University Hospital Basel, 4056 Basel, Switzerland
| | - Marco Bolis
- Institute of Oncology Research, 6500 Bellinzona, Switzerland; Computational Oncology Unit, Department of Oncology, Istituto di Ricerche Farmacologiche "Mario Negri" IRCCS, 20156 Milano, Italy
| | - Joanna Triscott
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - José A Galván
- Institute of Pathology, University of Bern, Bern 3008, Switzerland
| | - Yu Chen
- Human Oncology and Pathogenesis Program (HOPP), Memorial Sloan Kettering, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - George N Thalmann
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland; Department of Urology, Inselspital, Bern University Hospital, 3008 Bern, Switzerland
| | - Marianna Kruithof-de Julio
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland; Department of Urology, Inselspital, Bern University Hospital, 3008 Bern, Switzerland; Bern Center for Precision Medicine, University of Bern and Inselspital, 3008 Bern, Switzerland
| | - Jean-Philippe P Theurillat
- Institute of Oncology Research, 6500 Bellinzona, Switzerland; Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, Coral Gables, FL 33146, USA; Sylvester Comprehensive Cancer Center, University of Miami, Coral Gables, FL 33136, USA; Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Mark Gerstein
- Department of Computer Science, Yale University, New Haven, CT 06520, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Salvatore Piscuoglio
- Institute of Pathology and Medical Genetics, University Hospital Basel, 4056 Basel, Switzerland; Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Rahul N Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
| | - Mark A Rubin
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland; Bern Center for Precision Medicine, University of Bern and Inselspital, 3008 Bern, Switzerland.
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4
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Girardini KN, Olthof AM, Kanadia RN. Introns: the "dark matter" of the eukaryotic genome. Front Genet 2023; 14:1150212. [PMID: 37260773 PMCID: PMC10228655 DOI: 10.3389/fgene.2023.1150212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/28/2023] [Indexed: 06/02/2023] Open
Abstract
The emergence of introns was a significant evolutionary leap that is a major distinguishing feature between prokaryotic and eukaryotic genomes. While historically introns were regarded merely as the sequences that are removed to produce spliced transcripts encoding functional products, increasingly data suggests that introns play important roles in the regulation of gene expression. Here, we use an intron-centric lens to review the role of introns in eukaryotic gene expression. First, we focus on intron architecture and how it may influence mechanisms of splicing. Second, we focus on the implications of spliceosomal snRNAs and their variants on intron splicing. Finally, we discuss how the presence of introns and the need to splice them influences transcription regulation. Despite the abundance of introns in the eukaryotic genome and their emerging role regulating gene expression, a lot remains unexplored. Therefore, here we refer to introns as the "dark matter" of the eukaryotic genome and discuss some of the outstanding questions in the field.
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Affiliation(s)
- Kaitlin N. Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
| | - Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
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5
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Ding Z, Meng YR, Fan YJ, Xu YZ. Roles of minor spliceosome in intron recognition and the convergence with the better understood major spliceosome. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1761. [PMID: 36056453 DOI: 10.1002/wrna.1761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/06/2022] [Accepted: 08/06/2022] [Indexed: 01/31/2023]
Abstract
Catalyzed by spliceosomes in the nucleus, RNA splicing removes intronic sequences from precursor RNAs in eukaryotes to generate mature RNA, which also significantly increases proteome complexity and fine-tunes gene expression. Most metazoans have two coexisting spliceosomes; the major spliceosome, which removes >99.5% of introns, and the minor spliceosome, which removes far fewer introns (only 770 at present have been predicted in the human genome). Both spliceosomes are large and dynamic machineries, each consisting of five small nuclear RNAs (snRNAs) and more than 100 proteins. However, the dynamic assembly, catalysis, and protein composition of the minor spliceosome are still poorly understood. With different splicing signals, minor introns are rare and usually distributed alone and flanked by major introns in genes, raising questions of how they are recognized by the minor spliceosome and how their processing deals with the splicing of neighboring major introns. Due to large numbers of introns and close similarities between the two machinery, cooperative, and competitive recognition by the two spliceosomes has been investigated. Functionally, many minor-intron-containing genes are evolutionarily conserved and essential. Mutations in the minor spliceosome exhibit a variety of developmental defects in plants and animals and are linked to numerous human diseases. Here, we review recent progress in the understanding of minor splicing, compare currently known components of the two spliceosomes, survey minor introns in a wide range of organisms, discuss cooperation and competition of the two spliceosomes in splicing of minor-intron-containing genes, and contributions of minor splicing mutations in development and diseases. This article is categorized under: RNA Processing > Processing of Small RNAs RNA Processing > Splicing Mechanisms RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry.
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Affiliation(s)
- Zhan Ding
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan-Ran Meng
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China
| | - Yu-Jie Fan
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China
| | - Yong-Zhen Xu
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China
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6
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Iturrate A, Rivera-Barahona A, Flores CL, Otaify GA, Elhossini R, Perez-Sanz ML, Nevado J, Tenorio-Castano J, Triviño JC, Garcia-Gonzalo FR, Piceci-Sparascio F, De Luca A, Martínez L, Kalaycı T, Lapunzina P, Altunoglu U, Aglan M, Abdalla E, Ruiz-Perez VL. Mutations in SCNM1 cause orofaciodigital syndrome due to minor intron splicing defects affecting primary cilia. Am J Hum Genet 2022; 109:1828-1849. [PMID: 36084634 PMCID: PMC9606384 DOI: 10.1016/j.ajhg.2022.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 08/12/2022] [Indexed: 01/25/2023] Open
Abstract
Orofaciodigital syndrome (OFD) is a genetically heterogeneous ciliopathy characterized by anomalies of the oral cavity, face, and digits. We describe individuals with OFD from three unrelated families having bi-allelic loss-of-function variants in SCNM1 as the cause of their condition. SCNM1 encodes a protein recently shown to be a component of the human minor spliceosome. However, so far the effect of loss of SCNM1 function on human cells had not been assessed. Using a comparative transcriptome analysis between fibroblasts derived from an OFD-affected individual harboring SCNM1 mutations and control fibroblasts, we identified a set of genes with defective minor intron (U12) processing in the fibroblasts of the affected subject. These results were reproduced in SCNM1 knockout hTERT RPE-1 (RPE-1) cells engineered by CRISPR-Cas9-mediated editing and in SCNM1 siRNA-treated RPE-1 cultures. Notably, expression of TMEM107 and FAM92A encoding primary cilia and basal body proteins, respectively, and that of DERL2, ZC3H8, and C17orf75, were severely reduced in SCNM1-deficient cells. Primary fibroblasts containing SCNM1 mutations, as well as SCNM1 knockout and SCNM1 knockdown RPE-1 cells, were also found with abnormally elongated cilia. Conversely, cilia length and expression of SCNM1-regulated genes were restored in SCNM1-deficient fibroblasts following reintroduction of SCNM1 via retroviral delivery. Additionally, functional analysis in SCNM1-retrotransduced fibroblasts showed that SCNM1 is a positive mediator of Hedgehog (Hh) signaling. Our findings demonstrate that defective U12 intron splicing can lead to a typical ciliopathy such as OFD and reveal that primary cilia length and Hh signaling are regulated by the minor spliceosome through SCNM1 activity.
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Affiliation(s)
- Asier Iturrate
- Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28029 Madrid, Spain
| | - Ana Rivera-Barahona
- Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28029 Madrid, Spain,CIBER de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Carmen-Lisset Flores
- Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28029 Madrid, Spain
| | - Ghada A. Otaify
- Department of Clinical Genetics, Institute of Human Genetics and Genome Research, National Research Centre, Cairo, Egypt
| | - Rasha Elhossini
- Department of Clinical Genetics, Institute of Human Genetics and Genome Research, National Research Centre, Cairo, Egypt
| | - Marina L. Perez-Sanz
- Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28029 Madrid, Spain
| | - Julián Nevado
- CIBER de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain,Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IdiPAZ, ITHACA-ERN, 28046 Madrid, Spain
| | - Jair Tenorio-Castano
- CIBER de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain,Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IdiPAZ, ITHACA-ERN, 28046 Madrid, Spain
| | | | - Francesc R. Garcia-Gonzalo
- Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28029 Madrid, Spain,CIBER de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain,Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid, 28029 Madrid, Spain,Área de Cáncer y Genética Molecular Humana, Instituto de Investigaciones del Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Francesca Piceci-Sparascio
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy,Department of Experimental Medicine, “Sapienza” University of Rome, 00161 Rome, Italy
| | - Alessandro De Luca
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
| | - Leopoldo Martínez
- Departamento de Cirugía Pediátrica. Hospital Universitario La Paz-IdiPAZ, ITHACA-ERN, 28046 Madrid, Spain
| | - Tugba Kalaycı
- Medical Genetics Department, Istanbul Medical Faculty, Istanbul University, Istanbul 34093, Turkey
| | - Pablo Lapunzina
- CIBER de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain,Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IdiPAZ, ITHACA-ERN, 28046 Madrid, Spain
| | - Umut Altunoglu
- Medical Genetics Department, Koç University School of Medicine, Istanbul 34450, Turkey
| | - Mona Aglan
- Department of Clinical Genetics, Institute of Human Genetics and Genome Research, National Research Centre, Cairo, Egypt
| | - Ebtesam Abdalla
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt,Genetics Department, Armed Forces College of Medicine, Cairo, Egypt
| | - Victor L. Ruiz-Perez
- Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28029 Madrid, Spain,CIBER de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain,Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IdiPAZ, ITHACA-ERN, 28046 Madrid, Spain,Corresponding author
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7
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Weinstein R, Bishop K, Broadbridge E, Yu K, Carrington B, Elkahloun A, Zhen T, Pei W, Burgess SM, Liu P, Bresciani E, Sood R. Zrsr2 Is Essential for the Embryonic Development and Splicing of Minor Introns in RNA and Protein Processing Genes in Zebrafish. Int J Mol Sci 2022; 23:10668. [PMID: 36142581 PMCID: PMC9501576 DOI: 10.3390/ijms231810668] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022] Open
Abstract
ZRSR2 (zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2) is an essential splicing factor involved in 3' splice-site recognition as a component of both the major and minor spliceosomes that mediate the splicing of U2-type (major) and U12-type (minor) introns, respectively. Studies of ZRSR2-depleted cell lines and ZRSR2-mutated patient samples revealed its essential role in the U12-dependent minor spliceosome. However, the role of ZRSR2 during embryonic development is not clear, as its function is compensated for by Zrsr1 in mice. Here, we utilized the zebrafish model to investigate the role of zrsr2 during embryonic development. Using CRISPR/Cas9 technology, we generated a zrsr2-knockout zebrafish line, termed zrsr2hg129/hg129 (p.Trp167Argfs*9) and examined embryo development in the homozygous mutant embryos. zrsr2hg129/hg129 embryos displayed multiple developmental defects starting at 4 days post fertilization (dpf) and died after 8 dpf, suggesting that proper Zrsr2 function is required during embryonic development. The global transcriptome analysis of 3 dpf zrsr2hg129/hg129 embryos revealed that the loss of Zrsr2 results in the downregulation of essential metabolic pathways and the aberrant retention of minor introns in about one-third of all minor intron-containing genes in zebrafish. Overall, our study has demonstrated that the role of Zrsr2 as a component of the minor spliceosome is conserved and critical for proper embryonic development in zebrafish.
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Affiliation(s)
- Rachel Weinstein
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Bishop
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elizabeth Broadbridge
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kai Yu
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Blake Carrington
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abdel Elkahloun
- Microarray Core, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tao Zhen
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wuhong Pei
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shawn M. Burgess
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Liu
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erica Bresciani
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raman Sood
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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8
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Montañés-Agudo P, Casini S, Aufiero S, Ernault AC, van der Made I, Pinto YM, Remme CA, Creemers EE. Inhibition of minor intron splicing reduces Na+ and Ca2+ channel expression and function in cardiomyocytes. J Cell Sci 2021; 135:273616. [PMID: 34859816 PMCID: PMC8767276 DOI: 10.1242/jcs.259191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/26/2021] [Indexed: 12/04/2022] Open
Abstract
Eukaryotic genomes contain a tiny subset of ‘minor class’ introns with unique sequence elements that require their own splicing machinery. These minor introns are present in certain gene families with specific functions, such as voltage-gated Na+ and voltage-gated Ca2+ channels. Removal of minor introns by the minor spliceosome has been proposed as a post-transcriptional regulatory layer, which remains unexplored in the heart. Here, we investigate whether the minor spliceosome regulates electrophysiological properties of cardiomyocytes by knocking down the essential minor spliceosome small nuclear snRNA component U6atac in neonatal rat ventricular myocytes. Loss of U6atac led to robust minor intron retention within Scn5a and Cacna1c, resulting in reduced protein levels of Nav1.5 and Cav1.2 channels. Functional consequences were studied through patch-clamp analysis, and revealed reduced Na+ and L-type Ca2+ currents after loss of U6atac. In conclusion, minor intron splicing modulates voltage-dependent ion channel expression and function in cardiomyocytes. This may be of particular relevance in situations in which minor splicing activity changes, such as in genetic diseases affecting minor spliceosome components, or in acquired diseases in which minor spliceosome components are dysregulated, such as heart failure. Summary: Knockdown of minor spliceosome component U6atac in cardiomyocytes reveals that expression of the Na+ channel Scn5a and the L-type Ca2+ channel Cacna1c critically depend on minor intron splicing.
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Affiliation(s)
- Pablo Montañés-Agudo
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Simona Casini
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Simona Aufiero
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands.,Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Auriane C Ernault
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Ingeborg van der Made
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Yigal M Pinto
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Carol Ann Remme
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Esther E Creemers
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
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9
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White AK, Baumgartner M, Lee MF, Drake KD, Aquino GS, Kanadia RN. Trp53 ablation fails to prevent microcephaly in mouse pallium with impaired minor intron splicing. Development 2021; 148:272517. [PMID: 34557915 DOI: 10.1242/dev.199591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/17/2021] [Indexed: 12/21/2022]
Abstract
Minor spliceosome inhibition due to mutations in RNU4ATAC are linked to primary microcephaly. Ablation of Rnu11, which encodes a minor spliceosome snRNA, inhibits the minor spliceosome in the developing mouse pallium, causing microcephaly. There, cell cycle defects and p53-mediated apoptosis in response to DNA damage resulted in loss of radial glial cells (RGCs), underpinning microcephaly. Here, we ablated Trp53 to block cell death in Rnu11 cKO mice. We report that Trp53 ablation failed to prevent microcephaly in these double knockout (dKO) mice. We show that the transcriptome of the dKO pallium was more similar to the control compared with the Rnu11 cKO. We find aberrant minor intron splicing in minor intron-containing genes involved in cell cycle regulation, resulting in more severely impaired mitotic progression and cell cycle lengthening of RGCs in the dKO that was detected earlier than in the Rnu11 cKO. Furthermore, we discover a potential role of p53 in causing DNA damage in the developing pallium, as detection of γH2aX+ was delayed in the dKO. Thus, we postulate that microcephaly in minor spliceosome-related diseases is primarily caused by cell cycle defects.
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Affiliation(s)
- Alisa K White
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | | | - Madisen F Lee
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Kyle D Drake
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Gabriela S Aquino
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Rahul N Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA.,Institute of Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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10
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Barabino SML, Citterio E, Ronchi AE. Transcription Factors, R-Loops and Deubiquitinating Enzymes: Emerging Targets in Myelodysplastic Syndromes and Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13153753. [PMID: 34359655 PMCID: PMC8345071 DOI: 10.3390/cancers13153753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The advent of DNA massive sequencing technologies has allowed for the first time an extensive look into the heterogeneous spectrum of genes and mutations underpinning myelodysplastic syndromes (MDSs) and acute myeloid leukemia (AML). In this review, we wish to explore the most recent advances and the rationale for the potential therapeutic interest of three main actors in myelo-leukemic transformation: transcription factors that govern myeloid differentiation; RNA splicing factors, which ensure proper mRNA maturation and whose mutations increase R-loops formation; and deubiquitinating enzymes, which contribute to genome stability in hematopoietic stem cells (HSCs). Abstract Myeloid neoplasms encompass a very heterogeneous family of diseases characterized by the failure of the molecular mechanisms that ensure a balanced equilibrium between hematopoietic stem cells (HSCs) self-renewal and the proper production of differentiated cells. The origin of the driver mutations leading to preleukemia can be traced back to HSC/progenitor cells. Many properties typical to normal HSCs are exploited by leukemic stem cells (LSCs) to their advantage, leading to the emergence of a clonal population that can eventually progress to leukemia with variable latency and evolution. In fact, different subclones might in turn develop from the original malignant clone through accumulation of additional mutations, increasing their competitive fitness. This process ultimately leads to a complex cancer architecture where a mosaic of cellular clones—each carrying a unique set of mutations—coexists. The repertoire of genes whose mutations contribute to the progression toward leukemogenesis is broad. It encompasses genes involved in different cellular processes, including transcriptional regulation, epigenetics (DNA and histones modifications), DNA damage signaling and repair, chromosome segregation and replication (cohesin complex), RNA splicing, and signal transduction. Among these many players, transcription factors, RNA splicing proteins, and deubiquitinating enzymes are emerging as potential targets for therapeutic intervention.
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11
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Akinyi MV, Frilander MJ. At the Intersection of Major and Minor Spliceosomes: Crosstalk Mechanisms and Their Impact on Gene Expression. Front Genet 2021; 12:700744. [PMID: 34354740 PMCID: PMC8329584 DOI: 10.3389/fgene.2021.700744] [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: 04/26/2021] [Accepted: 06/28/2021] [Indexed: 11/17/2022] Open
Abstract
Many eukaryotic species contain two separate molecular machineries for removing non-coding intron sequences from pre-mRNA molecules. The majority of introns (more than 99.5% in humans) are recognized and excised by the major spliceosome, which utilizes relatively poorly conserved sequence elements at the 5′ and 3′ ends of the intron that are used for intron recognition and in subsequent catalysis. In contrast, the minor spliceosome targets a rare group of introns (approximately 0.5% in humans) with highly conserved sequences at the 5′ and 3′ ends of the intron. Minor introns coexist in the same genes with major introns and while the two intron types are spliced by separate spliceosomes, the two splicing machineries can interact with one another to shape mRNA processing events in genes containing minor introns. Here, we review known cooperative and competitive interactions between the two spliceosomes and discuss the mechanistic basis of the spliceosome crosstalk, its regulatory significance, and impact on spliceosome diseases.
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Affiliation(s)
- Maureen V Akinyi
- Institute of Biotechnology/Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Mikko J Frilander
- Institute of Biotechnology/Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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12
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Olthof AM, White AK, Mieruszynski S, Doggett K, Lee MF, Chakroun A, Abdel Aleem AK, Rousseau J, Magnani C, Roifman CM, Campeau PM, Heath JK, Kanadia RN. Disruption of exon-bridging interactions between the minor and major spliceosomes results in alternative splicing around minor introns. Nucleic Acids Res 2021; 49:3524-3545. [PMID: 33660780 PMCID: PMC8034651 DOI: 10.1093/nar/gkab118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 12/11/2022] Open
Abstract
Vertebrate genomes contain major (>99.5%) and minor (<0.5%) introns that are spliced by the major and minor spliceosomes, respectively. Major intron splicing follows the exon-definition model, whereby major spliceosome components first assemble across exons. However, since most genes with minor introns predominately consist of major introns, formation of exon-definition complexes in these genes would require interaction between the major and minor spliceosomes. Here, we report that minor spliceosome protein U11-59K binds to the major spliceosome U2AF complex, thereby supporting a model in which the minor spliceosome interacts with the major spliceosome across an exon to regulate the splicing of minor introns. Inhibition of minor spliceosome snRNAs and U11-59K disrupted exon-bridging interactions, leading to exon skipping by the major spliceosome. The resulting aberrant isoforms contained a premature stop codon, yet were not subjected to nonsense-mediated decay, but rather bound to polysomes. Importantly, we detected elevated levels of these alternatively spliced transcripts in individuals with minor spliceosome-related diseases such as Roifman syndrome, Lowry–Wood syndrome and early-onset cerebellar ataxia. In all, we report that the minor spliceosome informs splicing by the major spliceosome through exon-definition interactions and show that minor spliceosome inhibition results in aberrant alternative splicing in disease.
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Affiliation(s)
- Anouk M Olthof
- Physiology and Neurobiology Department, University of Connecticut, 75 N. Eagleville Road, Storrs, CT 06269, USA
| | - Alisa K White
- Physiology and Neurobiology Department, University of Connecticut, 75 N. Eagleville Road, Storrs, CT 06269, USA
| | - Stephen Mieruszynski
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Karen Doggett
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Madisen F Lee
- Physiology and Neurobiology Department, University of Connecticut, 75 N. Eagleville Road, Storrs, CT 06269, USA
| | | | | | - Justine Rousseau
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Cinzia Magnani
- Neonatology and Neonatal Intensive Care Unit, Maternal and Child Department, University of Parma, Parma, 43121, Italy
| | - Chaim M Roifman
- Division of Immunology and Allergy, Department of Pediatrics, The Hospital for Sick Children and the University of Toronto, Toronto, ON M5G 1X8, Canada.,The Canadian Centre for Primary Immunodeficiency and The Jeffrey Modell Research Laboratory for the Diagnosis of Primary Immunodeficiency, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Philippe M Campeau
- Department of Pediatrics, University of Montreal, Montreal, QC H4A 3J1, Canada
| | - Joan K Heath
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Rahul N Kanadia
- Physiology and Neurobiology Department, University of Connecticut, 75 N. Eagleville Road, Storrs, CT 06269, USA.,Institute for System Genomics, University of Connecticut, Storrs, CT 06269, USA
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13
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Drake KD, Lemoine C, Aquino GS, Vaeth AM, Kanadia RN. Loss of U11 small nuclear RNA in the developing mouse limb results in micromelia. Development 2020; 147:dev.190967. [PMID: 32665241 DOI: 10.1242/dev.190967] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/02/2020] [Indexed: 01/23/2023]
Abstract
Disruption of the minor spliceosome due to mutations in RNU4ATAC is linked to primordial dwarfism in microcephalic osteodysplastic primordial dwarfism type 1, Roifman syndrome, and Lowry-Wood syndrome. Similarly, primordial dwarfism in domesticated animals is linked to positive selection in minor spliceosome components. Despite being vital for limb development and size regulation, its role remains unexplored. Here, we disrupt minor spliceosome function in the developing mouse limb by ablating one of its essential components, U11 small nuclear RNA, which resulted in micromelia. Notably, earlier loss of U11 corresponded to increased severity. We find that limb size is reduced owing to elevated minor intron retention in minor intron-containing genes that regulate cell cycle. As a result, limb progenitor cells experience delayed prometaphase-to-metaphase transition and prolonged S-phase. Moreover, we observed death of rapidly dividing, distally located progenitors. Despite cell cycle defects and cell death, the spatial expression of key limb patterning genes was maintained. Overall, we show that the minor spliceosome is required for limb development via size control potentially shared in disease and domestication.
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Affiliation(s)
- Kyle D Drake
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Christopher Lemoine
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA.,Department of Surgery, School of Medicine, University of Connecticut, Farmington, CT 06030, USA
| | - Gabriela S Aquino
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Anna M Vaeth
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA.,Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rahul N Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA .,Institute for System Genomics, University of Connecticut, Storrs, CT 06269, USA
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