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Kikuchi M, Viet J, Nagata K, Sato M, David G, Audic Y, Silverman MA, Yamamoto M, Akatsu H, Hashizume Y, Takeda S, Akamine S, Miyamoto T, Uozumi R, Gotoh S, Mori K, Ikeda M, Paillard L, Morihara T. Gene-gene functional relationships in Alzheimer's disease: CELF1 regulates KLC1 alternative splicing. Biochem Biophys Res Commun 2024; 721:150025. [PMID: 38768546 DOI: 10.1016/j.bbrc.2024.150025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/16/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024]
Abstract
The causes of Alzheimer's disease (AD) are poorly understood, although many genes are known to be involved in this pathology. To gain insights into the underlying molecular mechanisms, it is essential to identify the relationships between individual AD genes. Previous work has shown that the splice variant E of KLC1 (KLC1_vE) promotes AD, and that the CELF1 gene, which encodes an RNA-binding protein involved in splicing regulation, is at a risk locus for AD. Here, we identified a functional link between CELF1 and KLC1 in AD pathogenesis. Transcriptomic data from human samples from different ethnic groups revealed that CELF1 mRNA levels are low in AD brains, and the splicing pattern of KLC1 is strongly correlated with CELF1 expression levels. Specifically, KLC1_vE is negatively correlated with CELF1. Depletion and overexpression experiments in cultured cells demonstrated that the CELF1 protein down-regulates KLC1_vE. In a cross-linking and immunoprecipitation sequencing (CLIP-seq) database, CELF1 directly binds to KLC1 RNA, following which it likely modulates terminal exon usage, hence KLC1_vE formation. These findings reveal a new pathogenic pathway where a risk allele of CELF1 is associated with reduced CELF1 expression, which up-regulates KLC1_vE to promote AD.
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Affiliation(s)
- Masataka Kikuchi
- Department of Genome Informatics, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Justine Viet
- Université de Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes), UMR 6290, F-35000, Rennes, France
| | - Kenichi Nagata
- Department of Functional Anatomy and Neuroscience, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Masahiro Sato
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Geraldine David
- Université de Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes), UMR 6290, F-35000, Rennes, France
| | - Yann Audic
- Université de Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes), UMR 6290, F-35000, Rennes, France
| | - Michael A Silverman
- Department of Biological Sciences, Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, Canada
| | - Mitsuko Yamamoto
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hiroyasu Akatsu
- Department of Community-based Medical Education, Graduate School of Medicine, Nagoya City University, Nagoya, Japan; Choju Medical/Neuropathological Institute, Fukushimura Hospital, Toyohashi, Japan
| | | | - Shuko Takeda
- Department of Clinical Gene Therapy, Graduate School of Medicine, Osaka University, Suita, Japan; Osaka Psychiatric Medical Center, Osaka Psychiatric Research Center, Hirakata, Japan
| | - Shoshin Akamine
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Tesshin Miyamoto
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Ryota Uozumi
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Shiho Gotoh
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Kohji Mori
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Manabu Ikeda
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Luc Paillard
- Université de Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes), UMR 6290, F-35000, Rennes, France.
| | - Takashi Morihara
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan; Toyonaka Municipal Hospital, Toyonaka, Japan.
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David G, Reboutier D, Deschamps S, Méreau A, Taylor W, Padilla-Parra S, Tramier M, Audic Y, Paillard L. The RNA-binding proteins CELF1 and ELAVL1 cooperatively control the alternative splicing of CD44. Biochem Biophys Res Commun 2022; 626:79-84. [DOI: 10.1016/j.bbrc.2022.07.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/29/2022]
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Picchio L, Legagneux V, Deschamps S, Renaud Y, Chauveau S, Paillard L, Jagla K. Bruno-3 regulates sarcomere component expression and contributes to muscle phenotypes of myotonic dystrophy type 1. Dis Model Mech 2018; 11:dmm.031849. [PMID: 29716962 PMCID: PMC5992612 DOI: 10.1242/dmm.031849] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 04/18/2018] [Indexed: 01/22/2023] Open
Abstract
Steinert disease, or myotonic dystrophy type 1 (DM1), is a multisystemic disorder caused by toxic noncoding CUG repeat transcripts, leading to altered levels of two RNA binding factors, MBNL1 and CELF1. The contribution of CELF1 to DM1 phenotypes is controversial. Here, we show that the Drosophila CELF1 family member, Bru-3, contributes to pathogenic muscle defects observed in a Drosophila model of DM1. Bru-3 displays predominantly cytoplasmic expression in muscles and its muscle-specific overexpression causes a range of phenotypes also observed in the fly DM1 model, including affected motility, fiber splitting, reduced myofiber length and altered myoblast fusion. Interestingly, comparative genome-wide transcriptomic analyses revealed that Bru-3 negatively regulates levels of mRNAs encoding a set of sarcomere components, including Actn transcripts. Conversely, it acts as a positive regulator of Actn translation. As CELF1 displays predominantly cytoplasmic expression in differentiating C2C12 myotubes and binds to Actn mRNA, we hypothesize that it might exert analogous functions in vertebrate muscles. Altogether, we propose that cytoplasmic Bru-3 contributes to DM1 pathogenesis in a Drosophila model by regulating sarcomeric transcripts and protein levels.
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Affiliation(s)
- Lucie Picchio
- GReD (Genetics, Reproduction and Development Laboratory), INSERM 1103, CNRS 6293, University of Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
| | - Vincent Legagneux
- IGDR (Institut de Génétique et Développement de Rennes), UMR 6290 CNRS, Université de Rennes, 2 Avenue Léon Bernard, 35000 Rennes, France.,Inserm UMR1085 IRSET, Université de Rennes 1, 35000 Rennes, France.,CNRS-Université de Rennes1-INRIA, UMR6074 IRISA, 35000 Rennes, France
| | - Stephane Deschamps
- IGDR (Institut de Génétique et Développement de Rennes), UMR 6290 CNRS, Université de Rennes, 2 Avenue Léon Bernard, 35000 Rennes, France
| | - Yoan Renaud
- GReD (Genetics, Reproduction and Development Laboratory), INSERM 1103, CNRS 6293, University of Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
| | - Sabine Chauveau
- GReD (Genetics, Reproduction and Development Laboratory), INSERM 1103, CNRS 6293, University of Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
| | - Luc Paillard
- IGDR (Institut de Génétique et Développement de Rennes), UMR 6290 CNRS, Université de Rennes, 2 Avenue Léon Bernard, 35000 Rennes, France
| | - Krzysztof Jagla
- GReD (Genetics, Reproduction and Development Laboratory), INSERM 1103, CNRS 6293, University of Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France
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Siddam AD, Gautier-Courteille C, Perez-Campos L, Anand D, Kakrana A, Dang CA, Legagneux V, Méreau A, Viet J, Gross JM, Paillard L, Lachke SA. The RNA-binding protein Celf1 post-transcriptionally regulates p27Kip1 and Dnase2b to control fiber cell nuclear degradation in lens development. PLoS Genet 2018; 14:e1007278. [PMID: 29565969 PMCID: PMC5889275 DOI: 10.1371/journal.pgen.1007278] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 04/06/2018] [Accepted: 02/26/2018] [Indexed: 11/18/2022] Open
Abstract
Opacification of the ocular lens, termed cataract, is a common cause of blindness. To become transparent, lens fiber cells undergo degradation of their organelles, including their nuclei, presenting a fundamental question: does signaling/transcription sufficiently explain differentiation of cells progressing toward compromised transcriptional potential? We report that a conserved RNA-binding protein Celf1 post-transcriptionally controls key genes to regulate lens fiber cell differentiation. Celf1-targeted knockout mice and celf1-knockdown zebrafish and Xenopus morphants have severe eye defects/cataract. Celf1 spatiotemporally down-regulates the cyclin-dependent kinase (Cdk) inhibitor p27Kip1 by interacting with its 5' UTR and mediating translation inhibition. Celf1 deficiency causes ectopic up-regulation of p21Cip1. Further, Celf1 directly binds to the mRNA of the nuclease Dnase2b to maintain its high levels. Together these events are necessary for Cdk1-mediated lamin A/C phosphorylation to initiate nuclear envelope breakdown and DNA degradation in fiber cells. Moreover, Celf1 controls alternative splicing of the membrane-organization factor beta-spectrin and regulates F-actin-crosslinking factor Actn2 mRNA levels, thereby controlling fiber cell morphology. Thus, we illustrate new Celf1-regulated molecular mechanisms in lens development, suggesting that post-transcriptional regulatory RNA-binding proteins have evolved conserved functions to control vertebrate oculogenesis.
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Affiliation(s)
- Archana D. Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE, United States of America
| | - Carole Gautier-Courteille
- Institut de Génétique et Développement de Rennes, Université de Rennes 1, CNRS UMR6290, Rennes, France
| | - Linette Perez-Campos
- Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
- Department of Molecular Biosciences, University of Texas, Austin, TX, United States of America
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, United States of America
| | - Atul Kakrana
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
| | - Christine A. Dang
- Department of Biological Sciences, University of Delaware, Newark, DE, United States of America
| | - Vincent Legagneux
- Institut de Génétique et Développement de Rennes, Université de Rennes 1, CNRS UMR6290, Rennes, France
| | - Agnès Méreau
- Institut de Génétique et Développement de Rennes, Université de Rennes 1, CNRS UMR6290, Rennes, France
| | - Justine Viet
- Institut de Génétique et Développement de Rennes, Université de Rennes 1, CNRS UMR6290, Rennes, France
| | - Jeffrey M. Gross
- Department of Molecular Biosciences, University of Texas, Austin, TX, United States of America
- Department of Ophthalmology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Luc Paillard
- Institut de Génétique et Développement de Rennes, Université de Rennes 1, CNRS UMR6290, Rennes, France
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, United States of America
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
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Le Tonquèze O, Gschloessl B, Legagneux V, Paillard L, Audic Y. Identification of CELF1 RNA targets by CLIP-seq in human HeLa cells. GENOMICS DATA 2016; 8:97-103. [PMID: 27222809 PMCID: PMC4872370 DOI: 10.1016/j.gdata.2016.04.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/15/2016] [Accepted: 04/16/2016] [Indexed: 02/06/2023]
Abstract
The specific interactions between RNA-binding proteins and their target RNAs are an essential level to control gene expression. By combining ultra-violet cross-linking and immunoprecipitation (CLIP) and massive SoliD sequencing we identified the RNAs bound by the RNA-binding protein CELF1, in human HeLa cells. The CELF1 binding sites deduced from the sequence data allow characterizing specific features of CELF1-RNA association. We present therefore the first map of CELF1 binding sites in human cells.
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Affiliation(s)
| | | | | | | | - Yann Audic
- Corresponding author at: Centre National de la Recherche Scientifique (CNRS), Institut de Génétique et Développement, UMR6290, Rennes, France.Centre National de la Recherche Scientifique (CNRS)Institut de Génétique et DéveloppementUMR6290France
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Hypogonadism Associated with Cyp19a1 (Aromatase) Posttranscriptional Upregulation in Celf1 Knockout Mice. Mol Cell Biol 2015; 35:3244-53. [PMID: 26169831 DOI: 10.1128/mcb.00074-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 07/06/2015] [Indexed: 12/19/2022] Open
Abstract
CELF1 is a multifunctional RNA-binding protein that controls several aspects of RNA fate. The targeted disruption of the Celf1 gene in mice causes male infertility due to impaired spermiogenesis, the postmeiotic differentiation of male gametes. Here, we investigated the molecular reasons that underlie this testicular phenotype. By measuring sex hormone levels, we detected low concentrations of testosterone in Celf1-null mice. We investigated the effect of Celf1 disruption on the expression levels of steroidogenic enzyme genes, and we observed that Cyp19a1 was upregulated. Cyp19a1 encodes aromatase, which transforms testosterone into estradiol. Administration of testosterone or the aromatase inhibitor letrozole partly rescued the spermiogenesis defects, indicating that a lack of testosterone associated with excessive aromatase contributes to the testicular phenotype. In vivo and in vitro interaction assays demonstrated that CELF1 binds to Cyp19a1 mRNA, and reporter assays supported the conclusion that CELF1 directly represses Cyp19a1 translation. We conclude that CELF1 downregulates Cyp19a1 (Aromatase) posttranscriptionally to achieve high concentrations of testosterone compatible with spermiogenesis completion. We discuss the implications of these findings with respect to reproductive defects in men, including patients suffering from isolated hypogonadotropic hypogonadism and myotonic dystrophy type I.
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CUGBP1 promotes cell proliferation and suppresses apoptosis via down-regulating C/EBPα in human non-small cell lung cancers. Med Oncol 2015; 32:82. [DOI: 10.1007/s12032-015-0544-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 02/13/2015] [Indexed: 12/13/2022]
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Lentivirus-mediated knockdown of CUGBP1 suppresses gastric cancer cell proliferation in vitro. Appl Biochem Biotechnol 2014; 173:1529-36. [PMID: 24818870 DOI: 10.1007/s12010-014-0937-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 04/21/2014] [Indexed: 10/25/2022]
Abstract
Gastric cancer is the second most common cause of cancer-related death worldwide. This study was designed to examine the role of CUGBP1 in cell growth via an RNA interference (RNAi) lentivirus system in gastric cancer cells in vitro. The expression of CUGBP1 was much stronger in gastric cancer tissues than that in adjacent normal tissues. The lentivirus-mediated knockdown of CUGBP1 resulted in a significant reduction of CUGBP1 expression in MGC-803 gastric cancer cells. The cell viability was remarkably decreased by 50 % after 5 days of infection, as determined by MTT assay. Moreover, the size and the number of colonies formed in MGC-803 cells were markedly reduced in the absence of CUGBP1. Furthermore, the silencing of CUGBP1 downregulated the expression levels of cyclin B1 and cyclin D1, which are involved in cell cycle control. These results clearly indicated that CUGBP1 is essential for the growth of gastric cancer cells. Therefore, silencing of CUGBP1 by RNAi could be developed as a promising therapeutic approach for gastric cancer.
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Vlasova-St Louis I, Bohjanen PR. Coordinate regulation of mRNA decay networks by GU-rich elements and CELF1. Curr Opin Genet Dev 2011; 21:444-51. [PMID: 21497082 DOI: 10.1016/j.gde.2011.03.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 03/21/2011] [Indexed: 01/03/2023]
Abstract
The GU-rich element (GRE) was identified as a conserved sequence enriched in the 3' UTR of human transcripts that exhibited rapid mRNA turnover. In mammalian cells, binding to GREs by the protein CELF1 coordinates mRNA decay of networks of transcripts involved in cell growth, migration, and apoptosis. Depending on the context, GREs and CELF1 also regulate pre-mRNA splicing and translation. GREs are highly conserved throughout evolution and play important roles in the development of organisms ranging from worms to man. In humans, abnormal GRE-mediated regulation contributes to disease states and cancer. Thus, GREs and CELF proteins serve critical functions in gene expression regulation and define an important evolutionarily conserved posttranscriptional regulatory network.
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Affiliation(s)
- Irina Vlasova-St Louis
- Department of Microbiology, Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, MN, USA
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