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Hwang H, Chen S, Ma M, Divyanshi, Fan HC, Borwick E, Böke E, Mei W, Yang J. Solubility phase transition of maternal RNAs during vertebrate oocyte-to-embryo transition. Dev Cell 2023; 58:2776-2788.e5. [PMID: 37922909 PMCID: PMC10841985 DOI: 10.1016/j.devcel.2023.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 07/01/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
The oocyte-to-embryo transition (OET) is regulated by maternal products stored in the oocyte cytoplasm, independent of transcription. How maternal products are precisely remodeled to dictate the OET remains largely unclear. In this work, we discover the dynamic solubility phase transition of maternal RNAs during Xenopus OET. We have identified 863 maternal transcripts that transition from a soluble state to a detergent-insoluble one after oocyte maturation. These RNAs are enriched in the animal hemisphere, and many of them encode key cell cycle regulators. In contrast, 165 transcripts, including nearly all Xenopus germline RNAs and some vegetally localized somatic RNAs, undergo an insoluble-to-soluble phase transition. This phenomenon is conserved in zebrafish. Our results demonstrate that the phase transition of germline RNAs influences their susceptibility to RNA degradation machinery and is mediated by the remodeling of germ plasm. This work thus identifies important remodeling mechanisms that act on RNAs to control vertebrate OET.
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Affiliation(s)
- Hyojeong Hwang
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, IL 61802, USA
| | - Sijie Chen
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, IL 61802, USA
| | - Meng Ma
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, IL 61802, USA
| | - Divyanshi
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Hao-Chun Fan
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, IL 61802, USA
| | - Elizabeth Borwick
- School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Elvan Böke
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Wenyan Mei
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, IL 61802, USA
| | - Jing Yang
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, IL 61802, USA
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, IL 61801, USA
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2
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Boccaccio GL, Thomas MG, García CC. Membraneless Organelles and Condensates Orchestrate Innate Immunity Against Viruses. J Mol Biol 2023; 435:167976. [PMID: 36702393 DOI: 10.1016/j.jmb.2023.167976] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023]
Abstract
The cellular defense against viruses involves the assembly of oligomers, granules and membraneless organelles (MLOs) that govern the activation of several arms of the innate immune response. Upon interaction with specific pathogen-derived ligands, a number of pattern recognition receptors (PRRs) undergo phase-separation thus triggering downstream signaling pathways. Among other relevant condensates, inflammasomes, apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC) specks, cyclic GMP-AMP synthase (cGAS) foci, protein kinase R (PKR) clusters, ribonuclease L-induced bodies (RLBs), stress granules (SGs), processing bodies (PBs) and promyelocytic leukemia protein nuclear bodies (PML NBs) play different roles in the immune response. In turn, viruses have evolved diverse strategies to evade the host defense. Viral DNA or RNA, as well as viral proteases or proteins carrying intrinsically disordered regions may interfere with condensate formation and function in multiple ways. In this review we discuss current and hypothetical mechanisms of viral escape that involve the disassembly, repurposing, or inactivation of membraneless condensates that govern innate immunity. We summarize emerging interconnections between these diverse condensates that ultimately determine the cellular outcome.
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Affiliation(s)
- Graciela Lidia Boccaccio
- Laboratorio de Biología Celular del ARN, Instituto Leloir (FIL) and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina; Departamento de Fisiología y Biología Molecular y Celular (FBMyC), Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - María Gabriela Thomas
- Laboratorio de Biología Celular del ARN, Instituto Leloir (FIL) and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina. https://www.twitter.com/_gabithomas
| | - Cybele Carina García
- Departamento de Química Biológica (QB), Facultad de Ciencias Exactas y Naturales (FCEN), and IQUIBICEN, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET) and Universidad de Buenos Aires, Buenos Aires, Argentina
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3
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Sato K, Sakai M, Ishii A, Maehata K, Takada Y, Yasuda K, Kotani T. Identification of embryonic RNA granules that act as sites of mRNA translation after changing their physical properties. iScience 2022; 25:104344. [PMID: 35620421 PMCID: PMC9127168 DOI: 10.1016/j.isci.2022.104344] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/16/2022] [Accepted: 04/27/2022] [Indexed: 11/08/2022] Open
Abstract
Fertilized eggs begin to translate mRNAs at appropriate times and placements to control development, but how the translation is regulated remains unclear. Here, we found that pou5f3 mRNA encoding a transcriptional factor essential for development formed granules in a dormant state in zebrafish oocytes. Although the number of pou5f3 granules remained constant, Pou5f3 protein accumulated after fertilization. Intriguingly, signals of newly synthesized peptides and a ribosomal protein became colocalized with pou5f3 granules after fertilization and, moreover, nascent Pou5f3 was shown to be synthesized in the granules. This functional change was accompanied by changes in the state and internal structure of granules. Dissolution of the granules reduced the rate of protein synthesis. Similarly, nanog and sox19b mRNAs in zebrafish and Pou5f1/Oct4 mRNA in mouse assembled into granules. Our results reveal that subcellular compartments, termed embryonic RNA granules, function as activation sites of translation after changing physical properties for directing vertebrate development.
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Affiliation(s)
- Keisuke Sato
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Moeko Sakai
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Anna Ishii
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kaori Maehata
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yuki Takada
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kyota Yasuda
- Department of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8526, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Hiroshima 739-8526, Japan
| | - Tomoya Kotani
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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4
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Fernández-Alvarez AJ, Thomas MG, Pascual ML, Habif M, Pimentel J, Corbat AA, Pessoa JP, La Spina PE, Boscaglia L, Plessis A, Carmo-Fonseca M, Grecco HE, Casado M, Boccaccio GL. Smaug1 membrane-less organelles respond to AMPK/mTOR and affect mitochondrial function‡. J Cell Sci 2021; 135:273619. [PMID: 34859817 DOI: 10.1242/jcs.253591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/15/2021] [Indexed: 11/20/2022] Open
Abstract
Smaug is a conserved translational regulator that binds numerous mRNAs, including nuclear transcripts that encode mitochondrial enzymes. Smaug orthologs form cytosolic membrane-less organelles (MLOs) in several organisms and cell types. We have performed single-molecule FISH assays that revealed that SDHB and UQCRC1 mRNAs associate with Smaug1 bodies in U2OS cells. Loss of function of Smaug1 and Smaug2 affected both mitochondrial respiration and morphology of the mitochondrial network. Phenotype rescue by Smaug1 transfection depends on the presence of its RNA binding domain. Moreover, we identified specific Smaug1 domains involved in MLO formation, and found that impaired Smaug1 MLO condensation correlates with mitochondrial defects. Mitochondrial Complex I inhibition by rotenone -but not strong mitochondrial uncoupling by CCCP- rapidly induced Smaug1 MLOs dissolution. Metformin and rapamycin elicited similar effects, which were blocked by pharmacological inhibition of AMPK. Finally, we found that Smaug1 MLO dissolution weakens the interaction with target mRNAs, thus enabling their release. We propose that mitochondrial respiration and the AMPK/mTOR balance controls the condensation and dissolution of Smaug1 MLOs, thus regulating nuclear mRNAs that encode key mitochondrial proteins.
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Affiliation(s)
- Ana J Fernández-Alvarez
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - María Gabriela Thomas
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Malena L Pascual
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Martín Habif
- Department of Physics, Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, and IFIBA, CONICET, C1428EHA Buenos Aires, Argentina
| | - Jerónimo Pimentel
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Agustín A Corbat
- Department of Physics, Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, and IFIBA, CONICET, C1428EHA Buenos Aires, Argentina
| | - João P Pessoa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Pablo E La Spina
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | | | - Anne Plessis
- Institut Jacques Monod, CNRS, UMR 7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Hernán E Grecco
- Department of Physics, Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, and IFIBA, CONICET, C1428EHA Buenos Aires, Argentina
| | - Marta Casado
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia 46010, Spain, and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid 28029, Spain
| | - Graciela L Boccaccio
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina.,Department of Molecular and Cellular Biology and Physiology (FBMyC), Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, C1428EHA Buenos Aires, Argentina
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5
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HuD regulates SOD1 expression during oxidative stress in differentiated neuroblastoma cells and sporadic ALS motor cortex. Neurobiol Dis 2020; 148:105211. [PMID: 33271327 DOI: 10.1016/j.nbd.2020.105211] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/09/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
The neuronal RNA-binding protein (RBP) HuD plays an important role in brain development, synaptic plasticity and neurodegenerative diseases such as Parkinson's (PD) and Alzheimer's (AD). Bioinformatics analysis of the human SOD1 mRNA 3' untranslated region (3'UTR) demonstrated the presence of HuD binding adenine-uridine (AU)-rich instability-conferring elements (AREs). Using differentiated SH-SY5Y cells along with brain tissues from sporadic amyotrophic lateral sclerosis (sALS) patients, we assessed HuD-dependent regulation of SOD1 mRNA. In vitro binding and mRNA decay assays demonstrate that HuD specifically binds to SOD1 ARE motifs promoting mRNA stabilization. In SH-SY5Y cells, overexpression of full-length HuD increased SOD1 mRNA and protein levels while a dominant negative form of the RBP downregulated its expression. HuD regulation of SOD1 mRNA was also found to be oxidative stress (OS)-dependent, as shown by the increased HuD binding and upregulation of this mRNA after H2O2 exposure. This treatment also induced a shift in alternative polyadenylation (APA) site usage in SOD1 3'UTR, increasing the levels of a long variant bearing HuD binding sites. The requirement of HuD for SOD1 upregulation during oxidative damage was validated using a specific siRNA that downregulated HuD protein levels to 36% and prevented upregulation of SOD1 and 91 additional genes. In the motor cortex from sALS patients, we found increases in SOD1 and HuD mRNAs and proteins, accompanied by greater HuD binding to this mRNA as confirmed by RNA-immunoprecipitation (RIP) assays. Altogether, our results suggest a role of HuD in the post-transcriptional regulation of SOD1 expression during ALS pathogenesis.
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6
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Choe HK, Cho J. Comprehensive Genome-Wide Approaches to Activity-Dependent Translational Control in Neurons. Int J Mol Sci 2020; 21:ijms21051592. [PMID: 32111062 PMCID: PMC7084349 DOI: 10.3390/ijms21051592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 02/06/2023] Open
Abstract
Activity-dependent regulation of gene expression is critical in experience-mediated changes in the brain. Although less appreciated than transcriptional control, translational control is a crucial regulatory step of activity-mediated gene expression in physiological and pathological conditions. In the first part of this review, we overview evidence demonstrating the importance of translational controls under the context of synaptic plasticity as well as learning and memory. Then, molecular mechanisms underlying the translational control, including post-translational modifications of translation factors, mTOR signaling pathway, and local translation, are explored. We also summarize how activity-dependent translational regulation is associated with neurodevelopmental and psychiatric disorders, such as autism spectrum disorder and depression. In the second part, we highlight how recent application of high-throughput sequencing techniques has added insight into genome-wide studies on translational regulation of neuronal genes. Sequencing-based strategies to identify molecular signatures of the active neuronal population responding to a specific stimulus are discussed. Overall, this review aims to highlight the implication of translational control for neuronal gene regulation and functions of the brain and to suggest prospects provided by the leading-edge techniques to study yet-unappreciated translational regulation in the nervous system.
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Affiliation(s)
- Han Kyoung Choe
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
- Correspondence: (H.K.C.); (J.C.)
| | - Jun Cho
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
- Correspondence: (H.K.C.); (J.C.)
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7
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Perez-Pepe M, Fernández-Alvarez AJ, Boccaccio GL. Life and Work of Stress Granules and Processing Bodies: New Insights into Their Formation and Function. Biochemistry 2018; 57:2488-2498. [PMID: 29595960 DOI: 10.1021/acs.biochem.8b00025] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The dynamic formation of stress granules (SGs), processing bodies (PBs), and related RNA organelles regulates diverse cellular processes, including the coordination of functionally connected messengers, the translational regulation at the synapse, and the control of viruses and retrotransposons. Recent studies have shown that pyruvate kinase and other enzymes localize in SGs and PBs, where they become protected from stress insults. These observations may have implications for enzyme regulation and metabolic control exerted by RNA-based organelles. The formation of these cellular bodies is governed by liquid-liquid phase separation (LLPS) processes, and it needs to be strictly controlled to prevent pathogenic aggregation. The intracellular concentration of key metabolites, such as ATP and sterol derivatives, may influence protein solubility, thus affecting the dynamics of liquid organelles. LLPS in vitro depends on the thermal diffusion of macromolecules, which is limited inside cells, where the condensation and dissolution of membrane-less organelles are helped by energy-driven processes. The active transport by the retrograde motor dynein helps SG assembly, whereas the anterograde motor kinesin mediates SG dissolution; a tug of war between these two molecular motors allows transient SG formation. There is evidence that the efficiency of dynein-mediated transport increases with the number of motor molecules associated with the cargo. The dynein-dependent transport may be influenced by cargo size as larger cargos can load a larger number of motors. We propose a model based on this emergent property of dynein motors, which would be collectively stronger during SG condensation and weaker during SG breakdown, thus allowing kinesin-mediated dispersion.
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Affiliation(s)
- Marcelo Perez-Pepe
- Instituto Leloir and Instituto de Investigaciones Bioquı́micas de Buenos Aires (IIBBA)-CONICET , Buenos Aires , Argentina
| | - Ana J Fernández-Alvarez
- Instituto Leloir and Instituto de Investigaciones Bioquı́micas de Buenos Aires (IIBBA)-CONICET , Buenos Aires , Argentina
| | - Graciela L Boccaccio
- Instituto Leloir and Instituto de Investigaciones Bioquı́micas de Buenos Aires (IIBBA)-CONICET , Buenos Aires , Argentina
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8
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Scarpin MR, Sigaut L, Temprana SG, Boccaccio GL, Pietrasanta LI, Muschietti JP. Two Arabidopsis late pollen transcripts are detected in cytoplasmic granules. PLANT DIRECT 2017; 1:e00012. [PMID: 31245661 PMCID: PMC6508577 DOI: 10.1002/pld3.12] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/11/2017] [Accepted: 08/24/2017] [Indexed: 05/19/2023]
Abstract
Many of mRNAs synthesized during pollen development are translated after germination, and we hypothesize that they are stored in cytoplasmic granules. We analyzed the cellular localization of the SKS14 and AT59 Arabidopsis mRNAs, which are orthologues of the tobacco NTP303 and tomato LAT59 pollen mRNAs, respectively, by artificially labeling the transcripts with a MS2-GFP chimera. A MATLAB-automated image analysis helped to identify the presence of cytoplasmic SKS14 and AT59 mRNA granules in mature pollen grains. These mRNA granules partially colocalized with VCS and DCP1, two processing body (PB) proteins. Finally, we found a temporal correlation between SKS14 protein accumulation and the disappearance of SKS14 mRNA granules during pollen germination. These results contribute to unveil a mechanism for translational regulation in Arabidopsis thaliana pollen.
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Affiliation(s)
- María R. Scarpin
- Instituto de Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres” (INGEBI‐CONICET)Buenos AiresArgentina
| | - Lorena Sigaut
- Instituto de Física de Buenos Aires (IFIBA‐CONICET)Departamento de FísicaFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresCiudad UniversitariaBuenos AiresArgentina
| | - Silvio G. Temprana
- Fundación Instituto LeloirIIBBA‐CONICETFacultad de Ciencias Exactas y NaturalesDepartamento de Fisiología y Biología Molecular y CelularUniversidad de Buenos AiresCiudad UniversitariaBuenos AiresArgentina
| | - Graciela L. Boccaccio
- Fundación Instituto LeloirIIBBA‐CONICETFacultad de Ciencias Exactas y NaturalesDepartamento de Fisiología y Biología Molecular y CelularUniversidad de Buenos AiresCiudad UniversitariaBuenos AiresArgentina
| | - Lía I. Pietrasanta
- Instituto de Física de Buenos Aires (IFIBA‐CONICET)Departamento de FísicaFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresCiudad UniversitariaBuenos AiresArgentina
- Centro de Microscopías AvanzadasFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresCiudad UniversitariaBuenos AiresArgentina
| | - Jorge P. Muschietti
- Instituto de Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres” (INGEBI‐CONICET)Buenos AiresArgentina
- Departamento de Biodiversidad y Biología ExperimentalFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresCiudad UniversitariaBuenos AiresArgentina
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9
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Roesler R. Molecular mechanisms controlling protein synthesis in memory reconsolidation. Neurobiol Learn Mem 2017; 142:30-40. [DOI: 10.1016/j.nlm.2017.04.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 10/19/2022]
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10
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Wang JKT, Langfelder P, Horvath S, Palazzolo MJ. Exosomes and Homeostatic Synaptic Plasticity Are Linked to Each other and to Huntington's, Parkinson's, and Other Neurodegenerative Diseases by Database-Enabled Analyses of Comprehensively Curated Datasets. Front Neurosci 2017; 11:149. [PMID: 28611571 PMCID: PMC5374209 DOI: 10.3389/fnins.2017.00149] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/09/2017] [Indexed: 12/15/2022] Open
Abstract
Huntington's disease (HD) is a progressive and autosomal dominant neurodegeneration caused by CAG expansion in the huntingtin gene (HTT), but the pathophysiological mechanism of mutant HTT (mHTT) remains unclear. To study HD using systems biological methodologies on all published data, we undertook the first comprehensive curation of two key PubMed HD datasets: perturbation genes that impact mHTT-driven endpoints and therefore are putatively linked causally to pathogenic mechanisms, and the protein interactome of HTT that reflects its biology. We perused PubMed articles containing co-citation of gene IDs and MeSH terms of interest to generate mechanistic gene sets for iterative enrichment analyses and rank ordering. The HD Perturbation database of 1,218 genes highly overlaps the HTT Interactome of 1,619 genes, suggesting links between normal HTT biology and mHTT pathology. These two HD datasets are enriched for protein networks of key genes underlying two mechanisms not previously implicated in HD nor in each other: exosome synaptic functions and homeostatic synaptic plasticity. Moreover, proteins, possibly including HTT, and miRNA detected in exosomes from a wide variety of sources also highly overlap the HD datasets, suggesting both mechanistic and biomarker links. Finally, the HTT Interactome highly intersects protein networks of pathogenic genes underlying Parkinson's, Alzheimer's and eight non-HD polyglutamine diseases, ALS, and spinal muscular atrophy. These protein networks in turn highly overlap the exosome and homeostatic synaptic plasticity gene sets. Thus, we hypothesize that HTT and other neurodegeneration pathogenic genes form a large interlocking protein network involved in exosome and homeostatic synaptic functions, particularly where the two mechanisms intersect. Mutant pathogenic proteins cause dysfunctions at distinct points in this network, each altering the two mechanisms in specific fashion that contributes to distinct disease pathologies, depending on the gene mutation and the cellular and biological context. This protein network is rich with drug targets, and exosomes may provide disease biomarkers, thus enabling drug discovery. All the curated datasets are made available for other investigators. Elucidating the roles of pathogenic neurodegeneration genes in exosome and homeostatic synaptic functions may provide a unifying framework for the age-dependent, progressive and tissue selective nature of multiple neurodegenerative diseases.
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Affiliation(s)
| | - Peter Langfelder
- Department of Human Genetics, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA, USA
| | - Michael J Palazzolo
- Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of CaliforniaLos Angeles, CA, USA
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11
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Faus-Garriga J, Novoa I, Ozaita A. mTOR signaling in proteostasis and its relevance to autism spectrum disorders. AIMS BIOPHYSICS 2017. [DOI: 10.3934/biophy.2017.1.63] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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12
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Bryant CD, Yazdani N. RNA-binding proteins, neural development and the addictions. GENES BRAIN AND BEHAVIOR 2016; 15:169-86. [PMID: 26643147 DOI: 10.1111/gbb.12273] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/30/2015] [Accepted: 11/09/2015] [Indexed: 12/25/2022]
Abstract
Transcriptional and post-transcriptional regulation of gene expression defines the neurobiological mechanisms that bridge genetic and environmental risk factors with neurobehavioral dysfunction underlying the addictions. More than 1000 genes in the eukaryotic genome code for multifunctional RNA-binding proteins (RBPs) that can regulate all levels of RNA biogenesis. More than 50% of these RBPs are expressed in the brain where they regulate alternative splicing, transport, localization, stability and translation of RNAs during development and adulthood. Dysfunction of RBPs can exert global effects on their targetomes that underlie neurodegenerative disorders such as Alzheimer's and Parkinson's diseases as well as neurodevelopmental disorders, including autism and schizophrenia. Here, we consider the evidence that RBPs influence key molecular targets, neurodevelopment, synaptic plasticity and neurobehavioral dysfunction underlying the addictions. Increasingly well-powered genome-wide association studies in humans and mammalian model organisms combined with ever more precise transcriptomic and proteomic approaches will continue to uncover novel and possibly selective roles for RBPs in the addictions. Key challenges include identifying the biological functions of the dynamic RBP targetomes from specific cell types throughout subcellular space (e.g. the nuclear spliceome vs. the synaptic translatome) and time and manipulating RBP programs through post-transcriptional modifications to prevent or reverse aberrant neurodevelopment and plasticity underlying the addictions.
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Affiliation(s)
- C D Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - N Yazdani
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
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13
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De Conti L, Baralle M, Buratti E. Neurodegeneration and RNA-binding proteins. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27659427 DOI: 10.1002/wrna.1394] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/06/2016] [Accepted: 08/18/2016] [Indexed: 12/12/2022]
Abstract
In the eukaryotic nucleus, RNA-binding proteins (RBPs) play a very important role in the life cycle of both coding and noncoding RNAs. As soon as they are transcribed, in fact, all RNA molecules within a cell are bound by distinct sets of RBPs that have the task of regulating its correct processing, transport, stability, and function/translation up to its final degradation. These tasks are particularly important in cells that have a complex RNA metabolism, such as neurons. Not surprisingly, therefore, recent findings have shown that the misregulation of genes involved in RNA metabolism or the autophagy/proteasome pathway plays an important role in the onset and progression of several neurodegenerative diseases. In this article, we aim to review the recent advances that link neurodegenerative processes and RBP proteins. WIREs RNA 2017, 8:e1394. doi: 10.1002/wrna.1394 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Laura De Conti
- Biotechnology Development Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Marco Baralle
- Biotechnology Development Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Emanuele Buratti
- Molecular Pathology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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14
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Misra M, Edmund H, Ennis D, Schlueter MA, Marot JE, Tambasco J, Barlow I, Sigurbjornsdottir S, Mathew R, Vallés AM, Wojciech W, Roth S, Davis I, Leptin M, Gavis ER. A Genome-Wide Screen for Dendritically Localized RNAs Identifies Genes Required for Dendrite Morphogenesis. G3 (BETHESDA, MD.) 2016; 6:2397-405. [PMID: 27260999 PMCID: PMC4978894 DOI: 10.1534/g3.116.030353] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 05/27/2016] [Indexed: 12/15/2022]
Abstract
Localizing messenger RNAs at specific subcellular sites is a conserved mechanism for targeting the synthesis of cytoplasmic proteins to distinct subcellular domains, thereby generating the asymmetric protein distributions necessary for cellular and developmental polarity. However, the full range of transcripts that are asymmetrically distributed in specialized cell types, and the significance of their localization, especially in the nervous system, are not known. We used the EP-MS2 method, which combines EP transposon insertion with the MS2/MCP in vivo fluorescent labeling system, to screen for novel localized transcripts in polarized cells, focusing on the highly branched Drosophila class IV dendritic arborization neurons. Of a total of 541 lines screened, we identified 55 EP-MS2 insertions producing transcripts that were enriched in neuronal processes, particularly in dendrites. The 47 genes identified by these insertions encode molecularly diverse proteins, and are enriched for genes that function in neuronal development and physiology. RNAi-mediated knockdown confirmed roles for many of the candidate genes in dendrite morphogenesis. We propose that the transport of mRNAs encoded by these genes into the dendrites allows their expression to be regulated on a local scale during the dynamic developmental processes of dendrite outgrowth, branching, and/or remodeling.
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Affiliation(s)
- Mala Misra
- Department of Molecular Biology, Princeton University, NJ 08544
| | - Hendia Edmund
- Department of Molecular Biology, Princeton University, NJ 08544
| | - Darragh Ennis
- Department of Biochemistry, The University of Oxford, OX1 3QU, United Kingdom
| | | | - Jessica E Marot
- Department of Molecular Biology, Princeton University, NJ 08544
| | - Janet Tambasco
- Department of Molecular Biology, Princeton University, NJ 08544
| | - Ida Barlow
- Department of Molecular Biology, Princeton University, NJ 08544
| | | | - Renjith Mathew
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Ana Maria Vallés
- Department of Biochemistry, The University of Oxford, OX1 3QU, United Kingdom
| | - Waldemar Wojciech
- Biocenter, Institute of Developmental Biology, University of Cologne, 50674 Cologne, Germany
| | - Siegfried Roth
- Biocenter, Institute of Developmental Biology, University of Cologne, 50674 Cologne, Germany
| | - Ilan Davis
- Department of Biochemistry, The University of Oxford, OX1 3QU, United Kingdom
| | - Maria Leptin
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany Institute of Genetics, University of Cologne, 50674 Germany
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15
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Bowden HA, Dormann D. Altered mRNP granule dynamics in FTLD pathogenesis. J Neurochem 2016; 138 Suppl 1:112-33. [PMID: 26938019 DOI: 10.1111/jnc.13601] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 12/13/2022]
Abstract
In neurons, RNA-binding proteins (RBPs) play a key role in post-transcriptional gene regulation, for example alternative splicing, mRNA localization in neurites and local translation upon synaptic stimulation. There is increasing evidence that defective or mislocalized RBPs - and consequently altered mRNA processing - lead to neuronal dysfunction and cause neurodegeneration, including frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Cytosolic RBP aggregates containing TAR DNA-binding protein of 43 kDa (TDP-43) or fused in sarcoma (FUS) are a common hallmark of both disorders. There is mounting evidence that translationally silent mRNP granules, such as stress granules or transport granules, play an important role in the formation of these RBP aggregates. These granules are thought to be 'catalytic convertors' of RBP aggregation by providing a high local concentration of RBPs. As recently shown in vitro, RBPs that contain a so-called low-complexity domain start to 'solidify' and eventually aggregate at high protein concentrations. The same may happen in mRNP granules in vivo, leading to 'solidified' granules that lose their dynamic properties and ability to fulfill their physiological functions. This may result in a disturbed stress response, altered mRNA transport and local translation, and formation of pathological TDP-43 or FUS aggregates, all of which may contribute to neuronal dysfunction and neurodegeneration. Here, we discuss the general functional properties of these mRNP granules, how their dynamics may be disrupted in frontotemporal lobar degeneration/amyotrophic lateral sclerosis, for example by loss or gain of function of TDP-43 and FUS, and how this may contribute to the development of RBP aggregates and neurotoxicity. In this review, we discuss how dynamic mRNP granules, such as stress granules or neuronal transport granules, may be converted into pathological aggregates containing misfolded RNA-binding proteins (RBPs), such as TDP-43 and FUS. Abnormal interactions between low-complexity domains in RBPs may cause dynamic mRNP granules to solidify and become dysfunctional. This may result in a disturbed stress response, altered mRNA transport and local translation, as well as RBP aggregation, all of which may contribute to neuronal dysfunction and neurodegeneration.
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Affiliation(s)
- Hilary A Bowden
- Graduate School of Systemic Neurosciences (GSN), Planegg-Martinsried, Germany
| | - Dorothee Dormann
- BioMedical Center (BMC), Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany.,Graduate School of Systemic Neurosciences (GSN), Planegg-Martinsried, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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16
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Raab-Graham KF, Workman ER, Namjoshi S, Niere F. Pushing the threshold: How NMDAR antagonists induce homeostasis through protein synthesis to remedy depression. Brain Res 2016; 1647:94-104. [PMID: 27125595 DOI: 10.1016/j.brainres.2016.04.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 04/04/2016] [Accepted: 04/07/2016] [Indexed: 12/17/2022]
Abstract
Healthy neurons have an optimal operating range, coded globally by the frequency of action potentials or locally by calcium. The maintenance of this range is governed by homeostatic plasticity. Here, we discuss how new approaches to treat depression alter synaptic activity. These approaches induce the neuron to recruit homeostatic mechanisms to relieve depression. Homeostasis generally implies that the direction of activity necessary to restore the neuron's critical operating range is opposite in direction to its current activity pattern. Unconventional antidepressant therapies-deep brain stimulation and NMDAR antagonists-alter the neuron's "depressed" state by pushing the neuron's current activity in the same direction but to the extreme edge. These therapies rally the intrinsic drive of neurons in the opposite direction, thereby allowing the cell to return to baseline activity, form new synapses, and restore proper communication. In this review, we discuss seminal studies on protein synthesis dependent homeostatic plasticity and their contribution to our understanding of molecular mechanisms underlying the effectiveness of NMDAR antagonists as rapid antidepressants. Rapid antidepressant efficacy is likely to require a cascade of mRNA translational regulation. Emerging evidence suggests that changes in synaptic strength or intrinsic excitability converge on the same protein synthesis pathways, relieving depressive symptoms. Thus, we address the question: Are there multiple homeostatic mechanisms that induce the neuron and neuronal circuits to self-correct to regulate mood in vivo? Targeting alternative ways to induce homeostatic protein synthesis may provide, faster, safer, and longer lasting antidepressants. This article is part of a Special Issue entitled SI:RNA Metabolism in Disease.
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Affiliation(s)
- Kimberly F Raab-Graham
- Center for Learning and Memory, Department of Neuroscience, Institute of Neuroscience, University of Texas at Austin, Austin, TX 78712, United States; Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX 78712, United States; Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States.
| | - Emily R Workman
- Center for Learning and Memory, Department of Neuroscience, Institute of Neuroscience, University of Texas at Austin, Austin, TX 78712, United States; Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX 78712, United States
| | - Sanjeev Namjoshi
- Center for Learning and Memory, Department of Neuroscience, Institute of Neuroscience, University of Texas at Austin, Austin, TX 78712, United States; Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States
| | - Farr Niere
- Center for Learning and Memory, Department of Neuroscience, Institute of Neuroscience, University of Texas at Austin, Austin, TX 78712, United States; Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX 78712, United States
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17
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Herms J, Dorostkar MM. Dendritic Spine Pathology in Neurodegenerative Diseases. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2016; 11:221-50. [PMID: 26907528 DOI: 10.1146/annurev-pathol-012615-044216] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Substantial progress has been made toward understanding the neuropathology, genetic origins, and epidemiology of neurodegenerative diseases, including Alzheimer's disease; tauopathies, such as frontotemporal dementia; α-synucleinopathies, such as Parkinson's disease or dementia with Lewy bodies; Huntington's disease; and amyotrophic lateral sclerosis with dementia, as well as prion diseases. Recent evidence has implicated dendritic spine dysfunction as an important substrate of the pathogenesis of dementia in these disorders. Dendritic spines are specialized structures, extending from the neuronal processes, on which excitatory synaptic contacts are formed, and the loss of dendritic spines correlates with the loss of synaptic function. We review the literature that has implicated direct or indirect structural alterations at dendritic spines in the pathogenesis of major neurodegenerative diseases, focusing on those that lead to dementias such as Alzheimer's, Parkinson's, and Huntington's diseases, as well as frontotemporal dementia and prion diseases. We stress the importance of in vivo studies in animal models.
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Affiliation(s)
- Jochen Herms
- Center for Neuropathology and Prion Research, Ludwig Maximilian University, 81377 Munich, Germany; .,Munich Cluster for Systems Neurology, Ludwig Maximilian University, 81377 Munich, Germany.,German Center for Neurodegenerative Diseases, 81377 Munich, Germany
| | - Mario M Dorostkar
- Center for Neuropathology and Prion Research, Ludwig Maximilian University, 81377 Munich, Germany;
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18
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Thomas MG, Boccaccio GL. Novel mRNA-silencing bodies at the synapse: A never-ending story. Commun Integr Biol 2016; 9:e1139251. [PMID: 27195060 PMCID: PMC4857779 DOI: 10.1080/19420889.2016.1139251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/02/2016] [Accepted: 01/04/2016] [Indexed: 01/08/2023] Open
Abstract
Several cellular responses depend on translational regulation and in most cases, this involves the formation of cytoplasmic granules that contain repressed mRNAs. In neurons, numerous mRNAs travel along dendrites to be locally regulated upon synapse activity and we have recently shown that the exoribonuclease XRN1 forms dynamic aggregates at the post synapse that respond to specific stimuli.1 These foci were termed SX-bodies and are distinct from stress granules (SGs), processing bodies (PBs) and other RNA granules previously described. Together with Smaug1-foci and FMRP-granules, the SX-bodies contribute to dynamically shape the transcriptome available for translation at the post-synapse.
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Affiliation(s)
- María Gabriela Thomas
- Fundación Instituto Leloir, Buenos Aires, Argentina; Instituto de Investigaciones Bioquímicas Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
| | - Graciela Lidia Boccaccio
- Fundación Instituto Leloir, Buenos Aires, Argentina; Instituto de Investigaciones Bioquímicas Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina; Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Buenos Aires, Argentina
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19
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Abstract
We report a novel spherical nucleic acid (SNA) gold nanoparticle conjugate, termed the Sticky-flare, which enables facile quantification of RNA expression in live cells and spatiotemporal analysis of RNA transport and localization. The Sticky-flare is capable of entering live cells without the need for transfection agents and recognizing target RNA transcripts in a sequence-specific manner. On recognition, the Sticky-flare transfers a fluorophore-conjugated reporter to the transcript, resulting in a turning on of fluorescence in a quantifiable manner and the fluorescent labeling of targeted transcripts. The latter allows the RNA to be tracked via fluorescence microscopy as it is transported throughout the cell. We use this novel nanoconjugate to analyze the expression level and spatial distribution of β-actin mRNA in HeLa cells and to observe the real-time transport of β-actin mRNA in mouse embryonic fibroblasts. Furthermore, we investigate the application of Sticky-flares for tracking transcripts that undergo more extensive compartmentalization by fluorophore-labeling U1 small nuclear RNA and observing its distribution in the nucleus of live cells.
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20
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Callaerts-Vegh Z, Ahmed T, Vermaercke B, Marynen P, Balschun D, Froyen G, D'Hooge R. Nxf7 deficiency impairs social exploration and spatio-cognitive abilities as well as hippocampal synaptic plasticity in mice. Front Behav Neurosci 2015. [PMID: 26217206 PMCID: PMC4498129 DOI: 10.3389/fnbeh.2015.00179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nuclear RNA export factors (NXF) are conserved in all metazoans and are deemed essential for shuttling RNA across the nuclear envelope and other post-transcriptional processes (such as mRNA metabolism, storage and stability). Disruption of human NXF5 has been implicated in intellectual and psychosocial disabilities. In the present report, we use recently described Nxf7 knockout (KO) mice as an experimental model to analyze in detail the behavioral consequences of clinical NXF5 deficiency. We examined male Nxf7 KO mice using an extended cognitive and behavioral test battery, and recorded extracellular field potentials in the hippocampal CA1 region. We observed various cognitive and behavioral changes including alterations in social exploration, impaired spatial learning and spatio-cognitive abilities. We also defined a new experimental paradigm to discriminate search strategies in Morris water maze and showed significant differences between Nxf7 KO and control animals. Furthermore, while we observed no difference in a nose poke suppression in an conditioned emotional response (CER) protocol, Nxf7 KO mice were impaired in discriminating between differentially reinforced cues in an auditory fear conditioning protocol. This distinct neurocognitive phenotype was accompanied by impaired hippocampal Long-term potentiation (LTP), while long-term depression (LTD) was not affected by Nxf7 deficiency. Our data demonstrate that disruption of murine Nxf7 leads to behavioral phenotypes that may relate to the intellectual and social deficits in patients with NXF5 deficiency.
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Affiliation(s)
| | - Tariq Ahmed
- Laboratory of Biological Psychology, University of Leuven, KU Leuven Leuven, Belgium
| | - Ben Vermaercke
- Laboratory of Biological Psychology, University of Leuven, KU Leuven Leuven, Belgium
| | - Peter Marynen
- Human Genome Laboratory, University of Leuven and VIB Center for the Biology of Disease Leuven, Belgium
| | - Detlef Balschun
- Laboratory of Biological Psychology, University of Leuven, KU Leuven Leuven, Belgium
| | - Guy Froyen
- Human Genome Laboratory, University of Leuven and VIB Center for the Biology of Disease Leuven, Belgium
| | - Rudi D'Hooge
- Laboratory of Biological Psychology, University of Leuven, KU Leuven Leuven, Belgium
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Dorostkar MM, Zou C, Blazquez-Llorca L, Herms J. Analyzing dendritic spine pathology in Alzheimer's disease: problems and opportunities. Acta Neuropathol 2015; 130:1-19. [PMID: 26063233 PMCID: PMC4469300 DOI: 10.1007/s00401-015-1449-5] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 06/02/2015] [Accepted: 06/02/2015] [Indexed: 12/22/2022]
Abstract
Synaptic failure is an immediate cause of cognitive decline and memory dysfunction in Alzheimer’s disease. Dendritic spines are specialized structures on neuronal processes, on which excitatory synaptic contacts take place and the loss of dendritic spines directly correlates with the loss of synaptic function. Dendritic spines are readily accessible for both in vitro and in vivo experiments and have, therefore, been studied in great detail in Alzheimer’s disease mouse models. To date, a large number of different mechanisms have been proposed to cause dendritic spine dysfunction and loss in Alzheimer’s disease. For instance, amyloid beta fibrils, diffusible oligomers or the intracellular accumulation of amyloid beta have been found to alter the function and structure of dendritic spines by distinct mechanisms. Furthermore, tau hyperphosphorylation and microglia activation, which are thought to be consequences of amyloidosis in Alzheimer’s disease, may also contribute to spine loss. Lastly, genetic and therapeutic interventions employed to model the disease and elucidate its pathogenetic mechanisms in experimental animals may cause alterations of dendritic spines on their own. However, to date none of these mechanisms have been translated into successful therapeutic approaches for the human disease. Here, we critically review the most intensely studied mechanisms of spine loss in Alzheimer’s disease as well as the possible pitfalls inherent in the animal models of such a complex neurodegenerative disorder.
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Affiliation(s)
- Mario M. Dorostkar
- />Ludwig-Maximilians University Munich, Center for Neuropathology and Prion Research, Feodor-Lynen-Str. 23, 81377 Munich, Germany
| | - Chengyu Zou
- />Ludwig-Maximilians University Munich, Center for Neuropathology and Prion Research, Feodor-Lynen-Str. 23, 81377 Munich, Germany
- />Graduate School of Systemic Neuroscience, Ludwig-Maximilians-University Munich, Munich, Germany
- />German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen-Str. 23, 81377 Munich, Germany
| | - Lidia Blazquez-Llorca
- />Ludwig-Maximilians University Munich, Center for Neuropathology and Prion Research, Feodor-Lynen-Str. 23, 81377 Munich, Germany
- />German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen-Str. 23, 81377 Munich, Germany
| | - Jochen Herms
- />German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen-Str. 23, 81377 Munich, Germany
- />Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
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22
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Novel Mechanisms of Spinal Cord Plasticity in a Mouse Model of Motoneuron Disease. BIOMED RESEARCH INTERNATIONAL 2015; 2015:654637. [PMID: 26064939 PMCID: PMC4433663 DOI: 10.1155/2015/654637] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/16/2014] [Indexed: 12/15/2022]
Abstract
A hopeful spinal cord repairing strategy involves the activation of neural precursor cells. Unfortunately, their ability to generate neurons after injury appears limited. Another process promoting functional recovery is synaptic plasticity. We have previously studied some mechanisms of spinal plasticity involving BDNF, Shh, Notch-1, Numb, and Noggin, by using a mouse model of motoneuron depletion induced by cholera toxin-B saporin. TDP-43 is a nuclear RNA/DNA binding protein involved in amyotrophic lateral sclerosis. Interestingly, TDP-43 could be localized at the synapse and affect synaptic strength. Here, we would like to deepen the investigation of this model of spinal plasticity. After lesion, we observed a glial reaction and an activity-dependent modification of Shh, Noggin, and Numb proteins. By using multivariate regression models, we found that Shh and Noggin could affect motor performance and that these proteins could be associated with both TDP-43 and Numb. Our data suggest that TDP-43 is likely an important regulator of synaptic plasticity, probably in collaboration with other proteins involved in both neurogenesis and synaptic plasticity. Moreover, given the rapidly increasing knowledge about spinal cord plasticity, we believe that further efforts to achieve spinal cord repair by stimulating the intrinsic potential of spinal cord will produce interesting results.
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23
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Pimentel J, Boccaccio GL. Translation and silencing in RNA granules: a tale of sand grains. Front Mol Neurosci 2014; 7:68. [PMID: 25100944 PMCID: PMC4107967 DOI: 10.3389/fnmol.2014.00068] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/05/2014] [Indexed: 01/19/2023] Open
Abstract
The transcriptome at the synapse consists of thousands of messengers encoding several cellular functions, including a significant number of receptors and ion channels and associated proteins. The concerted translational regulation of all these molecules contributes to the dynamic control of synaptic strength. Cumulative evidence supports that dendritic RNA granules and mRNA-silencing foci play an important role in translational regulation. Several relevant RBPs – FMRP; FUS/TLS; TDP-43; Staufen; Smaug; Pumilio; CPEB; HuD; ZBP1; and DDX6 among others – form granules that contain dormant mRNAs repressed by multiple pathways. Recent reports indicate that dendritic granules may contain stalled polysomes, and furthermore, active translation may occur in association with RNA granules. Here, we discuss the molecules and pathways involved in this continuum of RNA granules that contain masked mRNAs, mRNAs trapped in inactive polysomes or mRNAs engaged in translation.
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Affiliation(s)
| | - Graciela L Boccaccio
- Instituto Leloir Buenos Aires, Argentina ; Instituto de Investigaciones Bioquímicas Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas Buenos Aires, Argentina ; Facultad de Ciencias Exactas y Naturales, University of Buenos Aires Buenos Aires, Argentina
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