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D'Andrea L, Audano M, Pedretti S, Pelucchi S, Stringhi R, Imperato G, De Cesare G, Cambria C, Laporte MH, Zamboni N, Antonucci F, Di Luca M, Mitro N, Marcello E. Glucose-derived glutamate drives neuronal terminal differentiation in vitro. EMBO Rep 2024; 25:991-1021. [PMID: 38243137 PMCID: PMC10933318 DOI: 10.1038/s44319-023-00048-8] [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: 07/13/2023] [Revised: 12/01/2023] [Accepted: 12/19/2023] [Indexed: 01/21/2024] Open
Abstract
Neuronal maturation is the phase during which neurons acquire their final characteristics in terms of morphology, electrical activity, and metabolism. However, little is known about the metabolic pathways governing neuronal maturation. Here, we investigate the contribution of the main metabolic pathways, namely glucose, glutamine, and fatty acid oxidation, during the maturation of primary rat hippocampal neurons. Blunting glucose oxidation through the genetic and chemical inhibition of the mitochondrial pyruvate transporter reveals that this protein is critical for the production of glutamate, which is required for neuronal arborization, proper dendritic elongation, and spine formation. Glutamate supplementation in the early phase of differentiation restores morphological defects and synaptic function in mitochondrial pyruvate transporter-inhibited cells. Furthermore, the selective activation of metabotropic glutamate receptors restores the impairment of neuronal differentiation due to the reduced generation of glucose-derived glutamate and rescues synaptic local translation. Fatty acid oxidation does not impact neuronal maturation. Whereas glutamine metabolism is important for mitochondria, it is not for endogenous glutamate production. Our results provide insights into the role of glucose-derived glutamate as a key player in neuronal terminal differentiation.
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Affiliation(s)
- Laura D'Andrea
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti", Via Giuseppe Balzaretti 9, 20133, Milan, Italy
| | - Matteo Audano
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti", Via Giuseppe Balzaretti 9, 20133, Milan, Italy
| | - Silvia Pedretti
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti", Via Giuseppe Balzaretti 9, 20133, Milan, Italy
| | - Silvia Pelucchi
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti", Via Giuseppe Balzaretti 9, 20133, Milan, Italy
| | - Ramona Stringhi
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti", Via Giuseppe Balzaretti 9, 20133, Milan, Italy
| | - Gabriele Imperato
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti", Via Giuseppe Balzaretti 9, 20133, Milan, Italy
| | - Giulia De Cesare
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti", Via Giuseppe Balzaretti 9, 20133, Milan, Italy
| | - Clara Cambria
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), Via F.lli Cervi 93, Segrate, 20054 Milan and via Vanvitelli 32, Milan, Italy
| | - Marine H Laporte
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Flavia Antonucci
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), Via F.lli Cervi 93, Segrate, 20054 Milan and via Vanvitelli 32, Milan, Italy
- Institute of Neuroscience, IN-CNR, Milan, Italy
| | - Monica Di Luca
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti", Via Giuseppe Balzaretti 9, 20133, Milan, Italy
| | - Nico Mitro
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti", Via Giuseppe Balzaretti 9, 20133, Milan, Italy.
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.
| | - Elena Marcello
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti", Via Giuseppe Balzaretti 9, 20133, Milan, Italy.
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2
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Pechmann S. Single-cell expression predicts neuron-specific protein homeostasis networks. Open Biol 2024; 14:230386. [PMID: 38262604 PMCID: PMC10805596 DOI: 10.1098/rsob.230386] [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: 04/22/2023] [Accepted: 11/17/2023] [Indexed: 01/25/2024] Open
Abstract
The protein homeostasis network keeps proteins in their correct shapes and avoids unwanted aggregation. In turn, the accumulation of aberrantly misfolded proteins has been directly associated with the onset of ageing-associated neurodegenerative diseases such as Alzheimer's and Parkinson's. However, a detailed and rational understanding of how protein homeostasis is achieved in health, and how it can be targeted for therapeutic intervention in diseases remains missing. Here, large-scale single-cell expression data from the Allen Brain Map are analysed to investigate the transcription regulation of the core protein homeostasis network across the human brain. Remarkably, distinct expression profiles suggest specialized protein homeostasis networks with systematic adaptations in excitatory neurons, inhibitory neurons and non-neuronal cells. Moreover, several chaperones and Ubiquitin ligases are found transcriptionally coregulated with genes important for synapse formation and maintenance, thus linking protein homeostasis to the regulation of neuronal function. Finally, evolutionary analyses highlight the conservation of an elevated interaction density in the chaperone network, suggesting that one of the most exciting aspects of chaperone action may yet be discovered in their collective action at the systems level. More generally, our work highlights the power of computational analyses for breaking down complexity and gaining complementary insights into fundamental biological problems.
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3
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Ravichandran K, Khargonkar T, Samaddar S, Banerjee S. CRISPR Based Programmable RNA Editing in Primary Hippocampal Neurons. Curr Protoc 2023; 3:e886. [PMID: 37755318 DOI: 10.1002/cpz1.886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Investigating the RNA regulation landscape primarily relies on understanding how RNA-protein interactions are governed in various cell types, including neurons. Analysis of RNA-protein interactions in physiological environments warrants the development of new tools that rely on RNA manipulation. Recently, a CRISPR-based RNA-editing tool (dCas13b-ADAR2DD ) was developed to mitigate disease-associated point mutations in cell lines. Here, we explored the targeted sequence editing potential of the tool (dCas13b-ADAR2DD system) by adapting it to manipulate RNA function to visualize RNA editing in primary hippocampal neurons. This two-component system includes a programmable guide RNA (gRNA) complementary to the target RNA and a catalytically dead version of the Cas13b enzyme fused to ADAR. The RNA editing protocol outlined in this article relies on gRNA-dependent targeting of the dCas13b-ADAR fusion protein to the mutant form of the Dendra2 transcript. Dendra2 is not required for intrinsic cellular functioning. It was ectopically expressed for fluorescent detection as a proof-of-principle demonstration of targeted RNA editing. We first abrogated the fluorescence of Dendra2 by introducing a nonsense mutation that precludes the formation of the functional protein. To visualize the efficacy of the RNA editing in neurons, we used the dCas13b-ADAR2DD system to edit specific nucleotides within the Dendra2 mRNA to restore the amino acid codes critical for Dendra2 fluorescence. This method lays the foundation for future studies on the dynamics of activity-induced RNA-protein interactions in neurons and can be extended to manipulate the endogenous RNome in diverse neuronal subtypes. Furthermore, this methodology will enable investigators to visualize the spatial and temporal resolution of RNA-protein interactions without altering the genomes via conventional methods. © 2023 Wiley Periodicals LLC. Support Protocol: Preparation of mouse primary hippocampal culture Basic Protocol: Targeted editing of RNA.
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4
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Harbin NH, Lustberg DJ, Hurst C, Pare J, Crotty KM, Waters AL, Yeligar SM, Smith Y, Seyfried NT, Weinshenker D, Hepler JR. RGS14 limits seizure-induced mitochondrial oxidative stress and pathology in hippocampus. Neurobiol Dis 2023; 181:106128. [PMID: 37075948 PMCID: PMC10259180 DOI: 10.1016/j.nbd.2023.106128] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/02/2023] [Accepted: 04/14/2023] [Indexed: 04/21/2023] Open
Abstract
RGS14 is a complex multifunctional scaffolding protein that is highly enriched within pyramidal cells (PCs) of hippocampal area CA2. In these neurons, RGS14 suppresses glutamate-induced calcium influx and related G protein and ERK signaling in dendritic spines to restrain postsynaptic signaling and plasticity. Previous findings show that, unlike PCs of hippocampal areas CA1 and CA3, CA2 PCs are resistant to a number of neurological insults, including degeneration caused by temporal lobe epilepsy (TLE). While RGS14 is protective against peripheral injury, similar roles for RGS14 during pathological injury in hippocampus remain unexplored. Recent studies showed that area CA2 modulates hippocampal excitability, generates epileptiform activity and promotes hippocampal pathology in animal models and patients with TLE. Because RGS14 suppresses CA2 excitability and signaling, we hypothesized that RGS14 would moderate seizure behavior and early hippocampal pathology following seizure activity, possibly affording protection to CA2 PCs. Using kainic acid (KA) to induce status epilepticus (KA-SE) in mice, we show that the loss of RGS14 (RGS14 KO) accelerated onset of limbic motor seizures and mortality compared to wild type (WT) mice, and that KA-SE upregulated RGS14 protein expression in CA2 and CA1 PCs of WT. Our proteomics data show that the loss of RGS14 impacted the expression of a number of proteins at baseline and after KA-SE, many of which associated unexpectedly with mitochondrial function and oxidative stress. RGS14 was shown to localize to the mitochondria in CA2 PCs of mice and reduce mitochondrial respiration in vitro. As a readout of oxidative stress, we found that RGS14 KO dramatically increased 3- nitrotyrosine levels in CA2 PCs, which was greatly exacerbated following KA-SE and correlated with a lack of superoxide dismutase 2 (SOD2) induction. Assessing for hallmarks of seizure pathology in RGS14 KO, we unexpectedly found no differences in neuronal injury in CA2 PCs. However, we observed a striking and surprising lack of microgliosis in CA1 and CA2 of RGS14 KO compared to WT. Together, our data demonstrate a newly appreciated role for RGS14 in limiting intense seizure activity and pathology in hippocampus. Our findings are consistent with a model where RGS14 limits seizure onset and mortality and, after seizure, is upregulated to support mitochondrial function, prevent oxidative stress in CA2 PCs, and promote microglial activation in hippocampus.
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Affiliation(s)
- N H Harbin
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Rd, 5001 Rollins Research Ctr, Atlanta, GA 30322, United States.
| | - D J Lustberg
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, GA 30322, United States
| | - C Hurst
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Rd, 4001 Rollins Research Center, Atlanta, GA 30322, United States.
| | - J Pare
- Emory National Primate Research Center, Emory University, 954, Gatewood Rd NE, Atlanta, GA 30329, United States.
| | - K M Crotty
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, 1364 Clifton Road NE, Suite H-153, Atlanta, GA 30322, United States; Atlanta Veterans Affairs Health Care System, 1670 Clairmont Road, Decatur, GA 30033, United States.
| | - A L Waters
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Rd, 5001 Rollins Research Ctr, Atlanta, GA 30322, United States.
| | - S M Yeligar
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, 1364 Clifton Road NE, Suite H-153, Atlanta, GA 30322, United States; Atlanta Veterans Affairs Health Care System, 1670 Clairmont Road, Decatur, GA 30033, United States.
| | - Y Smith
- Emory National Primate Research Center, Emory University, 954, Gatewood Rd NE, Atlanta, GA 30329, United States; Department of Neurology, Emory University School of Medicine, 12 Executive Park Dr NE, Atlanta, GA, 30322, United States.
| | - N T Seyfried
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Rd, 4001 Rollins Research Center, Atlanta, GA 30322, United States.
| | - D Weinshenker
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, GA 30322, United States.
| | - J R Hepler
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 1510 Clifton Rd, 5001 Rollins Research Ctr, Atlanta, GA 30322, United States.
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5
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Harbin NH, Lustberg DJ, Hurst C, Pare JF, Crotty KM, Waters AL, Yeligar SM, Smith Y, Seyfried NT, Weinshenker D, Hepler JR. RGS14 is neuroprotective against seizure-induced mitochondrial oxidative stress and pathology in hippocampus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526349. [PMID: 36778349 PMCID: PMC9915580 DOI: 10.1101/2023.02.01.526349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RGS14 is a complex multifunctional scaffolding protein that is highly enriched within pyramidal cells (PCs) of hippocampal area CA2. There, RGS14 suppresses glutamate-induced calcium influx and related G protein and ERK signaling in dendritic spines to restrain postsynaptic signaling and plasticity. Previous findings show that, unlike PCs of hippocampal areas CA1 and CA3, CA2 PCs are resistant to a number of neurological insults, including degeneration caused by temporal lobe epilepsy (TLE). While RGS14 is protective against peripheral injury, similar roles for RGS14 during pathological injury in hippocampus remain unexplored. Recent studies show that area CA2 modulates hippocampal excitability, generates epileptiform activity and promotes hippocampal pathology in animal models and patients with TLE. Because RGS14 suppresses CA2 excitability and signaling, we hypothesized that RGS14 would moderate seizure behavior and early hippocampal pathology following seizure activity. Using kainic acid (KA) to induce status epilepticus (KA-SE) in mice, we show loss of RGS14 (RGS14 KO) accelerated onset of limbic motor seizures and mortality compared to wild type (WT) mice, and that KA-SE upregulated RGS14 protein expression in CA2 and CA1 PCs of WT. Utilizing proteomics, we saw loss of RGS14 impacted the expression of a number of proteins at baseline and after KA-SE, many of which associated unexpectedly with mitochondrial function and oxidative stress. RGS14 was shown to localize to the mitochondria in CA2 PCs of mice and reduce mitochondrial respiration in vitro . As a readout of oxidative stress, we found RGS14 KO dramatically increased 3-nitrotyrosine levels in CA2 PCs, which was greatly exacerbated following KA-SE and correlated with a lack of superoxide dismutase 2 (SOD2) induction. Assessing for hallmarks of seizure pathology in RGS14 KO, we observed worse neuronal injury in area CA3 (but none in CA2 or CA1), and a lack of microgliosis in CA1 and CA2 compared to WT. Together, our data demonstrates a newly appreciated neuroprotective role for RGS14 against intense seizure activity in hippocampus. Our findings are consistent with a model where, after seizure, RGS14 is upregulated to support mitochondrial function and prevent oxidative stress in CA2 PCs, limit seizure onset and hippocampal neuronal injury, and promote microglial activation in hippocampus.
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6
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Christensen JR, Reck-Peterson SL. Hitchhiking Across Kingdoms: Cotransport of Cargos in Fungal, Animal, and Plant Cells. Annu Rev Cell Dev Biol 2022; 38:155-178. [PMID: 35905769 PMCID: PMC10967659 DOI: 10.1146/annurev-cellbio-120420-104341] [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] [Indexed: 11/09/2022]
Abstract
Eukaryotic cells across the tree of life organize their subcellular components via intracellular transport mechanisms. In canonical transport, myosin, kinesin, and dynein motor proteins interact with cargos via adaptor proteins and move along filamentous actin or microtubule tracks. In contrast to this canonical mode, hitchhiking is a newly discovered mode of intracellular transport in which a cargo attaches itself to an already-motile cargo rather than directly associating with a motor protein itself. Many cargos including messenger RNAs, protein complexes, and organelles hitchhike on membrane-bound cargos. Hitchhiking-like behaviors have been shown to impact cellular processes including local protein translation, long-distance signaling, and organelle network reorganization. Here, we review instances of cargo hitchhiking in fungal, animal, and plant cells and discuss the potential cellular and evolutionary importance of hitchhiking in these different contexts.
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Affiliation(s)
- Jenna R Christensen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA; ,
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA; ,
- Department of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, La Jolla, California, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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Genes Responsible for H2S Production and Metabolism Are Involved in Learning and Memory in Drosophila melanogaster. Biomolecules 2022; 12:biom12060751. [PMID: 35740876 PMCID: PMC9221306 DOI: 10.3390/biom12060751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 12/13/2022] Open
Abstract
The gasotransmitter hydrogen sulfide (H2S) produced by the transsulfuration pathway (TSP) is an important biological mediator, involved in many physiological and pathological processes in multiple higher organisms, including humans. Cystathionine-β-synthase (CBS) and cystathionine-γ-lyase (CSE) enzymes play a central role in H2S production and metabolism. Here, we investigated the role of H2S in learning and memory processes by exploring several Drosophila melanogaster strains with single and double deletions of CBS and CSE developed by the CRISPR/Cas9 technique. We monitored the learning and memory parameters of these strains using the mating rejection courtship paradigm and demonstrated that the deletion of the CBS gene, which is expressed predominantly in the central nervous system, and double deletions completely block short- and long-term memory formation in fruit flies. On the other hand, the flies with CSE deletion preserve short- and long-term memory but fail to exhibit long-term memory retention. Transcriptome profiling of the heads of the males from the strains with deletions in Gene Ontology terms revealed a strong down-regulation of many genes involved in learning and memory, reproductive behavior, cognition, and the oxidation–reduction process in all strains with CBS deletion, indicating an important role of the hydrogen sulfide production in these vital processes.
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8
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RGS14 Regulation of Post-Synaptic Signaling and Spine Plasticity in Brain. Int J Mol Sci 2021; 22:ijms22136823. [PMID: 34201943 PMCID: PMC8268017 DOI: 10.3390/ijms22136823] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/12/2021] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
The regulator of G-protein signaling 14 (RGS14) is a multifunctional signaling protein that regulates post synaptic plasticity in neurons. RGS14 is expressed in the brain regions essential for learning, memory, emotion, and stimulus-induced behaviors, including the basal ganglia, limbic system, and cortex. Behaviorally, RGS14 regulates spatial and object memory, female-specific responses to cued fear conditioning, and environmental- and psychostimulant-induced locomotion. At the cellular level, RGS14 acts as a scaffolding protein that integrates G protein, Ras/ERK, and calcium/calmodulin signaling pathways essential for spine plasticity and cell signaling, allowing RGS14 to naturally suppress long-term potentiation (LTP) and structural plasticity in hippocampal area CA2 pyramidal cells. Recent proteomics findings indicate that RGS14 also engages the actomyosin system in the brain, perhaps to impact spine morphogenesis. Of note, RGS14 is also a nucleocytoplasmic shuttling protein, where its role in the nucleus remains uncertain. Balanced nuclear import/export and dendritic spine localization are likely essential for RGS14 neuronal functions as a regulator of synaptic plasticity. Supporting this idea, human genetic variants disrupting RGS14 localization also disrupt RGS14’s effects on plasticity. This review will focus on the known and unexplored roles of RGS14 in cell signaling, physiology, disease and behavior.
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Bridges MC, Daulagala AC, Kourtidis A. LNCcation: lncRNA localization and function. J Cell Biol 2021; 220:e202009045. [PMID: 33464299 PMCID: PMC7816648 DOI: 10.1083/jcb.202009045] [Citation(s) in RCA: 658] [Impact Index Per Article: 219.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/20/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022] Open
Abstract
Subcellular localization of RNAs has gained attention in recent years as a prevalent phenomenon that influences numerous cellular processes. This is also evident for the large and relatively novel class of long noncoding RNAs (lncRNAs). Because lncRNAs are defined as RNA transcripts >200 nucleotides that do not encode protein, they are themselves the functional units, making their subcellular localization critical to their function. The discovery of tens of thousands of lncRNAs and the cumulative evidence involving them in almost every cellular activity render assessment of their subcellular localization essential to fully understanding their biology. In this review, we summarize current knowledge of lncRNA subcellular localization, factors controlling their localization, emerging themes, including the role of lncRNA isoforms and the involvement of lncRNAs in phase separation bodies, and the implications of lncRNA localization on their function and on cellular behavior. We also discuss gaps in the current knowledge as well as opportunities that these provide for novel avenues of investigation.
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Affiliation(s)
| | | | - Antonis Kourtidis
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC
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10
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Mossanen-Parsi A, Parisi D, Browne-Marke N, Bharudin I, Connell SR, Mayans O, Fucini P, Morozov IY, Caddick MX. Histone mRNA is subject to 3' uridylation and re-adenylation in Aspergillus nidulans. Mol Microbiol 2020; 115:238-254. [PMID: 33047379 DOI: 10.1111/mmi.14613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 11/29/2022]
Abstract
The role of post-transcriptional RNA modification is of growing interest. One example is the addition of non-templated uridine residues to the 3' end of transcripts. In mammalian systems, uridylation is integral to cell cycle control of histone mRNA levels. This regulatory mechanism is dependent on the nonsense-mediated decay (NMD) component, Upf1, which promotes histone mRNA uridylation and degradation in response to the arrest of DNA synthesis. We have identified a similar system in Aspergillus nidulans, where Upf1 is required for the regulation of histone mRNA levels. However, other NMD components are also implicated, distinguishing it from the mammalian system. As in human cells, 3' uridylation of histone mRNA is induced upon replication arrest. Disruption of this 3' tagging has a significant but limited effect on histone transcript regulation, consistent with multiple mechanisms acting to regulate mRNA levels. Interestingly, 3' end degraded transcripts are also subject to re-adenylation. Both mRNA pyrimidine tagging and re-adenylation are dependent on the same terminal-nucleotidyltransferases, CutA, and CutB, and we show this is consistent with the in vitro activities of both enzymes. Based on these data we argue that mRNA 3' tagging has diverse and distinct roles associated with transcript degradation, functionality and regulation.
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Affiliation(s)
- Amir Mossanen-Parsi
- Institute of Systems, Molecular and Integrative Biology, The University of Liverpool, Liverpool, UK
| | - Daniele Parisi
- Institute of Systems, Molecular and Integrative Biology, The University of Liverpool, Liverpool, UK.,Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | | | - Izwan Bharudin
- Institute of Systems, Molecular and Integrative Biology, The University of Liverpool, Liverpool, UK
| | - Sean R Connell
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Olga Mayans
- Institute of Systems, Molecular and Integrative Biology, The University of Liverpool, Liverpool, UK
| | - Paola Fucini
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Igor Y Morozov
- Institute of Systems, Molecular and Integrative Biology, The University of Liverpool, Liverpool, UK.,Centre for Sport, Exercise and Life Sciences, Coventry University, Coventry, UK
| | - Mark X Caddick
- Institute of Systems, Molecular and Integrative Biology, The University of Liverpool, Liverpool, UK
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11
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Park AJ, Shetty MS, Baraban JM, Abel T. Selective role of the translin/trax RNase complex in hippocampal synaptic plasticity. Mol Brain 2020; 13:145. [PMID: 33172471 PMCID: PMC7653721 DOI: 10.1186/s13041-020-00691-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 10/30/2020] [Indexed: 01/09/2023] Open
Abstract
Activity-dependent local protein synthesis is critical for synapse-specific, persistent plasticity. Abnormalities in local protein synthesis have been implicated in psychiatric disorders. We have recently identified the translin/trax microRNA-degrading enzyme as a novel mediator of protein synthesis at activated synapses. Additionally, translin knockout (KO) mice, which lack translin/trax, exhibit some of the behavioral abnormalities found in a mouse model of fragile X syndrome (fragile X mental retardation protein-FMRP-KO mice). Therefore, identifying signaling pathways interacting with translin/trax to support persistent synaptic plasticity is a translationally relevant goal. Here, as a first step to achieve this goal, we have assessed the requirement of translin/trax for multiple hippocampal synaptic plasticity paradigms that rely on distinct molecular mechanisms. We found that mice lacking translin/trax exhibited selective impairment in a form of persistent hippocampal plasticity, which requires postsynaptic protein kinase A (PKA) activity. In contrast, enduring forms of plasticity that are dependent on presynaptic PKA were unaffected. Furthermore, these mice did not display exaggerated metabotropic glutamate receptor-mediated long-term synaptic depression (mGluR-LTD), a hallmark of the FMRP KO mice. On the contrary, translin KO mice exhibited deficits in N-methyl-d-aspartate receptor (NMDAR) dependent LTD, a phenotype not observed in the FMRP knockouts. Taken together, these findings demonstrate that translin/trax mediates long-term synaptic plasticity that is dependent on postsynaptic PKA signaling and suggest that translin/trax and FMRP play distinct roles in hippocampal synaptic plasticity.
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Affiliation(s)
- Alan Jung Park
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA. .,Gogos Lab, Mortimer B. Zuckerman Mind Brain Behavior Institute, Jerome L. Greene Science Center, Columbia University, L5-053, 3227 Broadway, New York, NY, 10027, USA.
| | - Mahesh Shivarama Shetty
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 2-471 Bowen Science Building, 51 Newton Road, Iowa City, IA, 52242, USA.,Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 2312 Pappajohn Biomedical Discovery Building, 169 Newton Road, Iowa City, 52242, IA, USA
| | - Jay M Baraban
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ted Abel
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 2-471 Bowen Science Building, 51 Newton Road, Iowa City, IA, 52242, USA. .,Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 2312 Pappajohn Biomedical Discovery Building, 169 Newton Road, Iowa City, 52242, IA, USA.
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12
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Gobbo F, Cattaneo A. Neuronal Activity at Synapse Resolution: Reporters and Effectors for Synaptic Neuroscience. Front Mol Neurosci 2020; 13:572312. [PMID: 33192296 PMCID: PMC7609880 DOI: 10.3389/fnmol.2020.572312] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/31/2020] [Indexed: 12/15/2022] Open
Abstract
The development of methods for the activity-dependent tagging of neurons enabled a new way to tackle the problem of engram identification at the cellular level, giving rise to groundbreaking findings in the field of memory studies. However, the resolution of activity-dependent tagging remains limited to the whole-cell level. Notably, events taking place at the synapse level play a critical role in the establishment of new memories, and strong experimental evidence shows that learning and synaptic plasticity are tightly linked. Here, we provide a comprehensive review of the currently available techniques that enable to identify and track the neuronal activity with synaptic spatial resolution. We also present recent technologies that allow to selectively interfere with specific subsets of synapses. Lastly, we discuss how these technologies can be applied to the study of learning and memory.
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Affiliation(s)
- Francesco Gobbo
- Bio@SNS Laboratory of Biology, Scuola Normale Superiore, Pisa, Italy
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Antonino Cattaneo
- Bio@SNS Laboratory of Biology, Scuola Normale Superiore, Pisa, Italy
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13
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Polinski JM, Kron N, Smith DR, Bodnar AG. Unique age-related transcriptional signature in the nervous system of the long-lived red sea urchin Mesocentrotus franciscanus. Sci Rep 2020; 10:9182. [PMID: 32514014 PMCID: PMC7280269 DOI: 10.1038/s41598-020-66052-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/12/2020] [Indexed: 11/23/2022] Open
Abstract
The red sea urchin, Mesocentrotus franciscanus, is one the earth’s longest-lived animals, reported to live more than 100 years with indeterminate growth, life-long reproduction and no increase in mortality rate with age. To gain insight into mechanisms associated with longevity and negligible senescence, age-related transcriptional profiles were examined in tissues of the red sea urchin. Genome-wide transcriptional profiling using RNA-Seq revealed few age-related changes in gene expression in muscle and esophagus tissue. In contrast, radial nerve showed an unexpected level of complexity with the expression of 3,370 genes significantly altered more than two-fold with age, including genes involved in nerve function, signaling, metabolism, transcriptional regulation and chromatin modification. There was an age-related upregulation in expression of genes involved in synaptogenesis, axonogenesis and neuroprotection suggesting preservation of neuronal processes with age. There was also an upregulation in expression of positive regulators and key components of the AMPK pathway, autophagy, proteasome function, and the unfolded protein response. This unique age-related gene expression profile in the red sea urchin nervous system may play a role in mitigating the detrimental effects of aging in this long-lived animal.
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Affiliation(s)
- Jennifer M Polinski
- Gloucester Marine Genomics Institute, 417 Main Street, Gloucester, MA, 01930, USA
| | - Nicholas Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, United States
| | - Douglas R Smith
- Gloucester Marine Genomics Institute, 417 Main Street, Gloucester, MA, 01930, USA
| | - Andrea G Bodnar
- Gloucester Marine Genomics Institute, 417 Main Street, Gloucester, MA, 01930, USA.
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14
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Canclini L, Cal K, Bardier C, Ruiz P, Mercer JA, Calliari A. Calcium triggers the dissociation of myosin-Va from ribosomes in ribonucleoprotein complexes. FEBS Lett 2020; 594:2311-2321. [PMID: 32412091 DOI: 10.1002/1873-3468.13813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 11/08/2022]
Abstract
The sorting of RNAs to specific regions of the cell for local translation represents an important mechanism directing protein distribution and cell compartmentalization. While significant progress has been made in understanding the mechanisms underlying the transport and localization of mRNAs, the mechanisms governing ribosome mobilization are less well understood. Ribosomes present in the cytoplasm of multiple cell types can form ribonucleoprotein complexes that also contain myosin-Va (Myo5a), a processive, actin-dependent molecular motor. Here, we report that Myo5a can be disassociated from ribosomes when ribonucleoprotein complexes are exposed to calcium, both in vitro and in vivo. We suggest that Myo5a may act as a molecular switch able to anchor or release ribosomes from the actin cytoskeleton in response to intracellular signaling.
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Affiliation(s)
- Lucía Canclini
- Department of Genetics, Instituto de Investigaciones Biológicas 'Clemente Estable' (MEC), Montevideo, Uruguay
| | - Karina Cal
- Department of Biosciences, Facultad de Veterinaria, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Camila Bardier
- Department of Genetics, Instituto de Investigaciones Biológicas 'Clemente Estable' (MEC), Montevideo, Uruguay
| | - Paul Ruiz
- Department of Biosciences, Facultad de Veterinaria, Universidad de la República (UdelaR), Montevideo, Uruguay
| | | | - Aldo Calliari
- Department of Biosciences, Facultad de Veterinaria, Universidad de la República (UdelaR), Montevideo, Uruguay
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15
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Carter SD, Hampton CM, Langlois R, Melero R, Farino ZJ, Calderon MJ, Li W, Wallace CT, Tran NH, Grassucci RA, Siegmund SE, Pemberton J, Morgenstern TJ, Eisenman L, Aguilar JI, Greenberg NL, Levy ES, Yi E, Mitchell WG, Rice WJ, Wigge C, Pilli J, George EW, Aslanoglou D, Courel M, Freyberg RJ, Javitch JA, Wills ZP, Area-Gomez E, Shiva S, Bartolini F, Volchuk A, Murray SA, Aridor M, Fish KN, Walter P, Balla T, Fass D, Wolf SG, Watkins SC, Carazo JM, Jensen GJ, Frank J, Freyberg Z. Ribosome-associated vesicles: A dynamic subcompartment of the endoplasmic reticulum in secretory cells. SCIENCE ADVANCES 2020; 6:eaay9572. [PMID: 32270040 PMCID: PMC7112762 DOI: 10.1126/sciadv.aay9572] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/13/2020] [Indexed: 05/21/2023]
Abstract
The endoplasmic reticulum (ER) is a highly dynamic network of membranes. Here, we combine live-cell microscopy with in situ cryo-electron tomography to directly visualize ER dynamics in several secretory cell types including pancreatic β-cells and neurons under near-native conditions. Using these imaging approaches, we identify a novel, mobile form of ER, ribosome-associated vesicles (RAVs), found primarily in the cell periphery, which is conserved across different cell types and species. We show that RAVs exist as distinct, highly dynamic structures separate from the intact ER reticular architecture that interact with mitochondria via direct intermembrane contacts. These findings describe a new ER subcompartment within cells.
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Affiliation(s)
- Stephen D. Carter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Cheri M. Hampton
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Robert Langlois
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Roberto Melero
- Biocomputing Unit, Centro Nacional de Biotecnología–CSIC, Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Zachary J. Farino
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Michael J. Calderon
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Wen Li
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Callen T. Wallace
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ngoc Han Tran
- HHMI, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robert A. Grassucci
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Stephanie E. Siegmund
- Department of Cellular, Molecular and Biophysical Studies, Columbia University Medical Center, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY 10032, USA
| | - Joshua Pemberton
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Travis J. Morgenstern
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Leanna Eisenman
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jenny I. Aguilar
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Nili L. Greenberg
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Elana S. Levy
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Edward Yi
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - William G. Mitchell
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | | | | | - Jyotsna Pilli
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Emily W. George
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Despoina Aslanoglou
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Maïté Courel
- CNRS-UMR7622, Institut de Biologie Paris-Seine, Université Pierre & Marie Curie, 75252 Paris, France
| | - Robin J. Freyberg
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jonathan A. Javitch
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Zachary P. Wills
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Estela Area-Gomez
- Department of Neurology, Columbia University, New York, NY 10032, USA
| | - Sruti Shiva
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Francesca Bartolini
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Allen Volchuk
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sandra A. Murray
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Meir Aridor
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Kenneth N. Fish
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Peter Walter
- HHMI, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sharon G. Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Simon C. Watkins
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - José María Carazo
- Biocomputing Unit, Centro Nacional de Biotecnología–CSIC, Darwin 3, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Grant J. Jensen
- HHMI, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Zachary Freyberg
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
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16
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Roy R, Shiina N, Wang DO. More dynamic, more quantitative, unexpectedly intricate: Advanced understanding on synaptic RNA localization in learning and memory. Neurobiol Learn Mem 2019; 168:107149. [PMID: 31881355 DOI: 10.1016/j.nlm.2019.107149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/25/2019] [Accepted: 12/23/2019] [Indexed: 01/13/2023]
Abstract
Synaptic signaling exhibits great diversity, complexity, and plasticity which necessitates maintenance and rapid modification of a local proteome. One solution neurons actively exploit to meet such demands is the strategic deposition of mRNAs encoding proteins for both basal and experience-driven activities into ribonucleoprotein complexes at the synapse. Transcripts localized in this manner can be rapidly accessed for translation in response to a diverse range of stimuli in a temporal- and spatially-restricted manner. Here we review recent findings on localized RNAs and RNA binding proteins in the context of learning and memory, as revealed by cutting-edge in-vitro and in-vivo technologies capable of yielding quantitative and dynamic information. The new technologies include proteomic and transcriptomic analyses, high-resolution multiplexed RNA imaging, single-molecule RNA tracking in living neurons, animal models and human neuron cell models. Among many recent advances in the field, RNA chemical modification has emerged as one of the new regulatory layers of gene expression at synapse that is complex and yet largely unexplored. These exciting new discoveries have enhanced our understanding of the modulation mechanisms of synaptic gene expression and their roles in cognition.
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Affiliation(s)
- Rohini Roy
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Nobuyuki Shiina
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Japan; Department of Basic Biology, SOKENDAI, Okazaki, Japan; Exploratory Research Center on Life and Living Systems, Okazaki, Japan.
| | - Dan Ohtan Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Liaoning, China; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; The Keihanshin Consortium for Fostering the Next Generation of Global Leaders in Research (K-CONNEX), Kyoto University, Kyoto, Japan.
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17
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Dubes S, Favereaux A, Thoumine O, Letellier M. miRNA-Dependent Control of Homeostatic Plasticity in Neurons. Front Cell Neurosci 2019; 13:536. [PMID: 31866828 PMCID: PMC6906196 DOI: 10.3389/fncel.2019.00536] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/19/2019] [Indexed: 11/13/2022] Open
Abstract
Homeostatic plasticity is a form of plasticity in which neurons compensate for changes in neuronal activity through the control of key physiological parameters such as the number and the strength of their synaptic inputs and intrinsic excitability. Recent studies revealed that miRNAs, which are small non-coding RNAs repressing mRNA translation, participate in this process by controlling the translation of multiple effectors such as glutamate transporters, receptors, signaling molecules and voltage-gated ion channels. In this review, we present and discuss the role of miRNAs in both cell-wide and compartmentalized forms of homeostatic plasticity as well as their implication in pathological processes associated with homeostatic failure.
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Affiliation(s)
- Sandra Dubes
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux, France
- CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux, France
| | - Alexandre Favereaux
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux, France
- CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux, France
| | - Olivier Thoumine
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux, France
- CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux, France
| | - Mathieu Letellier
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux, France
- CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux, France
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18
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Bauer KE, Segura I, Gaspar I, Scheuss V, Illig C, Ammer G, Hutten S, Basyuk E, Fernández-Moya SM, Ehses J, Bertrand E, Kiebler MA. Live cell imaging reveals 3'-UTR dependent mRNA sorting to synapses. Nat Commun 2019; 10:3178. [PMID: 31320644 PMCID: PMC6639396 DOI: 10.1038/s41467-019-11123-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 06/25/2019] [Indexed: 12/20/2022] Open
Abstract
mRNA transport restricts translation to specific subcellular locations, which is the basis for many cellular functions. However, the precise process of mRNA sorting to synapses in neurons remains elusive. Here we use Rgs4 mRNA to investigate 3′-UTR-dependent transport by MS2 live-cell imaging. The majority of observed RNA granules display 3′-UTR independent bidirectional transport in dendrites. Importantly, the Rgs4 3′-UTR causes an anterograde transport bias, which requires the Staufen2 protein. Moreover, the 3′-UTR mediates dynamic, sustained mRNA recruitment to synapses. Visualization at high temporal resolution enables us to show mRNA patrolling dendrites, allowing transient interaction with multiple synapses, in agreement with the sushi-belt model. Modulation of neuronal activity by either chemical silencing or local glutamate uncaging regulates both the 3′-UTR-dependent transport bias and synaptic recruitment. This dynamic and reversible mRNA recruitment to active synapses would allow translation and synaptic remodeling in a spatially and temporally adaptive manner. Asymmetric subcellular mRNA distribution is important for local translation of neuronal mRNAs. Here the authors employed MS2 live-cell imaging and showed that the reporter mRNA containing the 3’ UTR of Rgs4 shows an anterograde transport bias, dependent on neuronal activity and the protein Staufen2, and mediates sustained mRNA recruitment to synapses.
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Affiliation(s)
- Karl E Bauer
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Inmaculada Segura
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Imre Gaspar
- EMBL, Meyerhofstraße 1, 69117, Heidelberg, Germany.,Institute of Molecular Biotechnology, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Volker Scheuss
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Christin Illig
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Georg Ammer
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany.,MPI of Neurobiology, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Saskia Hutten
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Eugénia Basyuk
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France.,Institut de Génétique Humaine de Montpellier, CNRS UMR9002, Université de Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France
| | - Sandra M Fernández-Moya
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Janina Ehses
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France
| | - Michael A Kiebler
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany.
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19
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Ravindran S, Nalavadi VC, Muddashetty RS. BDNF Induced Translation of Limk1 in Developing Neurons Regulates Dendrite Growth by Fine-Tuning Cofilin1 Activity. Front Mol Neurosci 2019; 12:64. [PMID: 30949027 PMCID: PMC6436473 DOI: 10.3389/fnmol.2019.00064] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 02/26/2019] [Indexed: 11/13/2022] Open
Abstract
Dendritic growth and branching are highly regulated processes and are essential for establishing proper neuronal connectivity. There is a critical phase of early dendrite development when these are heavily regulated by external cues such as trophic factors. Brain-derived neurotrophic factor (BDNF) is a major trophic factor known to enhance dendrite growth in cortical neurons, but the molecular underpinnings of this response are not completely understood. We have identified that BDNF induced translational regulation is an important mechanism governing dendrite development in cultured rat cortical neurons. We show that BDNF treatment for 1 h in young neurons leads to translational up-regulation of an important actin regulatory protein LIM domain kinase 1 (Limk1), increasing its level locally in the dendrites. Limk1 is a member of serine/threonine (Ser/Thr) family kinases downstream of the Rho-GTPase pathway. BDNF induced increase in Limk1 levels leads to increased phosphorylation of its target protein cofilin1. We observed that these changes are maintained for long durations of up to 48 h and are mediating increase in number of primary dendrites and total dendrite length. Thus, we show that BDNF induced protein synthesis leads to fine-tuning of the actin cytoskeletal reassembly and thereby mediate dendrite development.
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Affiliation(s)
- Sreenath Ravindran
- Center for Brain Development and Repair (CBDR), Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Vijayalaxmi C Nalavadi
- Center for Brain Development and Repair (CBDR), Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, India
| | - Ravi S Muddashetty
- Center for Brain Development and Repair (CBDR), Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, India
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20
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Cenik ES, Meng X, Tang NH, Hall RN, Arribere JA, Cenik C, Jin Y, Fire A. Maternal Ribosomes Are Sufficient for Tissue Diversification during Embryonic Development in C. elegans. Dev Cell 2019; 48:811-826.e6. [PMID: 30799226 DOI: 10.1016/j.devcel.2019.01.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 11/06/2018] [Accepted: 01/21/2019] [Indexed: 12/20/2022]
Abstract
Caenorhabditis elegans provides an amenable system to explore whether newly composed ribosomes are required to progress through development. Despite the complex pattern of tissues that are formed during embryonic development, we found that null homozygotes lacking any of the five different ribosomal proteins (RPs) can produce fully functional first-stage larvae, with similar developmental competence seen upon complete deletion of the multi-copy ribosomal RNA locus. These animals, relying on maternal but not zygotic contribution of ribosomal components, are capable of completing embryogenesis. In the absence of new ribosomal components, the resulting animals are arrested before progression from the first larval stage and fail in two assays for postembryonic plasticity of neuronal structure. Mosaic analyses of larvae that are a mixture of ribosome-competent and non-competent cells suggest a global regulatory mechanism in which ribosomal insufficiency in a subset of cells triggers organism-wide growth arrest.
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Affiliation(s)
- Elif Sarinay Cenik
- Department of Pathology, Stanford University Medical School, Stanford, CA, USA; Department of Molecular Biosciences, University of Texas Austin, Austin, TX, USA
| | - Xuefeng Meng
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Ngang Heok Tang
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, San Diego, CA, USA
| | | | - Joshua A Arribere
- Department of MCD Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas Austin, Austin, TX, USA
| | - Yishi Jin
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Andrew Fire
- Department of Pathology, Stanford University Medical School, Stanford, CA, USA.
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21
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Patel AA, Ganepola GA, Rutledge JR, Chang DH. The Potential Role of Dysregulated miRNAs in Alzheimer’s Disease Pathogenesis and Progression. J Alzheimers Dis 2019; 67:1123-1145. [DOI: 10.3233/jad-181078] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ankur A. Patel
- Department of Research, Center for Cancer Research and Genomic Medicine, The Valley Hospital, Paramus, NJ, USA
| | - Ganepola A.P. Ganepola
- Department of Research, Center for Cancer Research and Genomic Medicine, The Valley Hospital, Paramus, NJ, USA
| | - John R. Rutledge
- Department of Oncology Special Program, The Daniel and Gloria Blumenthal Cancer Center, The Valley Hospital, Paramus, NJ, USA
| | - David H. Chang
- Department of Research, Center for Cancer Research and Genomic Medicine, The Valley Hospital, Paramus, NJ, USA
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22
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Langille JJ, Brown RE. The Synaptic Theory of Memory: A Historical Survey and Reconciliation of Recent Opposition. Front Syst Neurosci 2018; 12:52. [PMID: 30416432 PMCID: PMC6212519 DOI: 10.3389/fnsys.2018.00052] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/28/2018] [Indexed: 01/12/2023] Open
Abstract
Trettenbrein (2016) has argued that the concept of the synapse as the locus of memory is outdated and has made six critiques of this concept. In this article, we examine these six critiques and suggest that the current theories of the neurobiology of memory and the empirical data indicate that synaptic activation is the first step in a chain of cellular and biochemical events that lead to memories formed in cell assemblies and neural networks that rely on synaptic modification for their formation. These neural networks and their modified synaptic connections can account for the cognitive basis of learning and memory and for memory deterioration in neurological disorders. We first discuss Hebb's (1949) theory that synaptic change and the formation of cell assemblies and phase sequences can link neurophysiology to cognitive processes. We then examine each of Trettenbrein's (2016) critiques of the synaptic theory in light of Hebb's theories and recent empirical data. We examine the biochemical basis of memory formation and the necessity of synaptic modification to form the neural networks underlying learning and memory. We then examine the use of Hebb's theories of synaptic change and cell assemblies for integrating neurophysiological and cognitive conceptions of learning and memory. We conclude with an examination of the applications of the Hebb synapse and cell assembly theories to the study of the neuroscience of learning and memory, the development of computational models of memory and the construction of "intelligent" robots. We conclude that the synaptic theory of memory has not met its demise, but is essential to our understanding of the neural basis of memory, which has two components: synaptic plasticity and intrinsic plasticity.
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Affiliation(s)
| | - Richard E. Brown
- Department of Psychology and Neuroscience, Dalhousie University, Halifax, NS, Canada
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23
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Nakahata Y, Yasuda R. Plasticity of Spine Structure: Local Signaling, Translation and Cytoskeletal Reorganization. Front Synaptic Neurosci 2018; 10:29. [PMID: 30210329 PMCID: PMC6123351 DOI: 10.3389/fnsyn.2018.00029] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/07/2018] [Indexed: 12/31/2022] Open
Abstract
Dendritic spines are small protrusive structures on dendritic surfaces, and function as postsynaptic compartments for excitatory synapses. Plasticity of spine structure is associated with many forms of long-term neuronal plasticity, learning and memory. Inside these small dendritic compartments, biochemical states and protein-protein interactions are dynamically modulated by synaptic activity, leading to the regulation of protein synthesis and reorganization of cytoskeletal architecture. This in turn causes plasticity of structure and function of the spine. Technical advances in monitoring molecular behaviors in single dendritic spines have revealed that each signaling pathway is differently regulated across multiple spatiotemporal domains. The spatial pattern of signaling activity expands from a single spine to the nearby dendritic area, dendritic branch and the nucleus, regulating different cellular events at each spatial scale. Temporally, biochemical events are typically triggered by short Ca2+ pulses (~10–100 ms). However, these signals can then trigger activation of downstream protein cascades that can last from milliseconds to hours. Recent imaging studies provide many insights into the biochemical processes governing signaling events of molecular assemblies at different spatial localizations. Here, we highlight recent findings of signaling dynamics during synaptic plasticity and discuss their roles in long-term structural plasticity of dendritic spines.
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Affiliation(s)
- Yoshihisa Nakahata
- Neuronal Signal Transduction, Max Planck Florida Institute for Neuroscience (MPFI), Jupiter, FL, United States
| | - Ryohei Yasuda
- Neuronal Signal Transduction, Max Planck Florida Institute for Neuroscience (MPFI), Jupiter, FL, United States
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Merkurjev D, Hong WT, Iida K, Oomoto I, Goldie BJ, Yamaguti H, Ohara T, Kawaguchi SY, Hirano T, Martin KC, Pellegrini M, Wang DO. Synaptic N6-methyladenosine (m6A) epitranscriptome reveals functional partitioning of localized transcripts. Nat Neurosci 2018; 21:1004-1014. [DOI: 10.1038/s41593-018-0173-6] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 05/14/2018] [Indexed: 01/21/2023]
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25
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Neuronal RNP granules: from physiological to pathological assemblies. Biol Chem 2018; 399:623-635. [DOI: 10.1515/hsz-2018-0141] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/30/2018] [Indexed: 12/11/2022]
Abstract
Abstract
Neuronal cells rely on macro- and micro-cellular compartmentalization to rapidly process information, and respond locally to external stimuli. Such a cellular organization is achieved via the assembly of neuronal ribonucleoprotein (RNP) granules, dynamic membrane-less organelles enriched in RNAs and associated regulatory proteins. In this review, we discuss how these high-order structures transport mRNAs to dendrites and axons, and how they contribute to the spatio-temporal regulation of localized mRNA translation. We also highlight how recent biophysical studies have shed light on the mechanisms underlying neuronal RNP granule dynamic assembly, remodeling and maturation, in both physiological and pathological contexts.
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Wanke KA, Devanna P, Vernes SC. Understanding Neurodevelopmental Disorders: The Promise of Regulatory Variation in the 3'UTRome. Biol Psychiatry 2018; 83:548-557. [PMID: 29289333 DOI: 10.1016/j.biopsych.2017.11.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 11/02/2017] [Accepted: 11/02/2017] [Indexed: 01/28/2023]
Abstract
Neurodevelopmental disorders have a strong genetic component, but despite widespread efforts, the specific genetic factors underlying these disorders remain undefined for a large proportion of affected individuals. Given the accessibility of exome sequencing, this problem has thus far been addressed from a protein-centric standpoint; however, protein-coding regions only make up ∼1% to 2% of the human genome. With the advent of whole genome sequencing we are in the midst of a paradigm shift as it is now possible to interrogate the entire sequence of the human genome (coding and noncoding) to fill in the missing heritability of complex disorders. These new technologies bring new challenges, as the number of noncoding variants identified per individual can be overwhelming, making it prudent to focus on noncoding regions of known function, for which the effects of variation can be predicted and directly tested to assess pathogenicity. The 3'UTRome is a region of the noncoding genome that perfectly fulfills these criteria and is of high interest when searching for pathogenic variation related to complex neurodevelopmental disorders. Herein, we review the regulatory roles of the 3'UTRome as binding sites for microRNAs or RNA binding proteins, or during alternative polyadenylation. We detail existing evidence that these regions contribute to neurodevelopmental disorders and outline strategies for identification and validation of novel putatively pathogenic variation in these regions. This evidence suggests that studying the 3'UTRome will lead to the identification of new risk factors, new candidate disease genes, and a better understanding of the molecular mechanisms contributing to neurodevelopmental disorders.
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Affiliation(s)
- Kai A Wanke
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Paolo Devanna
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands.
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Kourtidis A, Anastasiadis PZ. Close encounters of the RNAi kind: the silencing life of the adherens junctions. Curr Opin Cell Biol 2018; 54:30-36. [PMID: 29587176 DOI: 10.1016/j.ceb.2018.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/01/2018] [Accepted: 03/06/2018] [Indexed: 11/19/2022]
Abstract
The adherens junction has been historically considered an essential structural component of epithelial tissues. Although primarily discussed as targets of signaling pathways responsible for cell fate and tissue remodeling, they have also emerged as critical signaling regulators in developmental processes or in disease progression. The recent discovery of a functional localized RNA interference (RNAi) machinery at epithelial adherens junctions revealed a new layer of signaling regulation that is directly associated with the structure itself. This and other findings also indicate that our view of the subcellular localization of RNAi requires revisiting. A number of questions emerge regarding the physiological role and the modes of regulation of the junctional RNAi machinery, pointing towards new directions of investigation.
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Affiliation(s)
- Antonis Kourtidis
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA.
| | - Panos Z Anastasiadis
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA.
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28
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Cho C, Michailidis V, Martin LJ. Revealing brain mechanisms of mTOR-mediated translational regulation: Implications for chronic pain. NEUROBIOLOGY OF PAIN 2018; 4:27-34. [PMID: 31194026 PMCID: PMC6550104 DOI: 10.1016/j.ynpai.2018.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 12/27/2022]
Abstract
mTOR is a major regulator of protein translation. mTOR serves an important role in neural plasticity. mTOR signalling in the brain as a pathology for neurological disorder is known. mTOR signalling in the brain as a chronic pain mechanism is understudied.
In the spinal cord, altered protein transcription and translation have received a lot of recent attention for their role in neural plasticity, a major mechanism leading to the development of chronic pain. However, changes in brain plasticity are also associated with the maintenance of pain symptoms, but these cellular mechanisms remain less clear. The mechanistic/mammalian target of rapamycin (mTOR) is a master regulator of protein synthesis, and controls several neuronal functions, including neural plasticity. While aberrant changes in mTOR signaling are associated with sensitization of the pain pathway (sensory neurons and spinal cord), there are various nervous system diseases that have pain as a comorbidity and altered mTOR activity in the brain. Here, we provide a brief review of mTOR changes in the brain that are associated with some neurological disorders and focus on how these changes may be relevant to the pain of the underlying condition and chronic pain itself.
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Affiliation(s)
- Chulmin Cho
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Vassilia Michailidis
- Deptartment of Cell and Systems Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Loren J. Martin
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Deptartment of Cell and Systems Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Corresponding author at: Department of Psychology, University of Toronto Mississauga, 3359 Mississauga Rd., Mississauga, ON L5L 1C6, Canada.
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Leighton LJ, Ke K, Zajaczkowski EL, Edmunds J, Spitale RC, Bredy TW. Experience-dependent neural plasticity, learning, and memory in the era of epitranscriptomics. GENES, BRAIN, AND BEHAVIOR 2018; 17:e12426. [PMID: 28926184 PMCID: PMC5858957 DOI: 10.1111/gbb.12426] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 12/23/2022]
Abstract
In this short review, we highlight recent findings in the emerging field of epitranscriptomic mechanisms and discuss their potential role in neural plasticity, learning and memory. These include the influence of RNA modifications on activity-induced RNA structure states, RNA editing and RNA localization, and how qualitative state changes in RNA increase the functional diversity and information-carrying capacity of RNA molecules. We predict that RNA modifications may be just as important for synaptic plasticity and memory as quantitative changes in transcript and protein abundance, but with the added advantage of not being required to signal back to the nucleus, and therefore better suited to be coordinated with the temporal dynamics of learning.
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Affiliation(s)
- Laura J. Leighton
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia 4072
| | - Ke Ke
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA 92697
| | - Esmi L. Zajaczkowski
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia 4072
| | - Jordan Edmunds
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia 4072
| | - Robert C. Spitale
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA 92697
| | - Timothy W. Bredy
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia 4072
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30
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Kourtidis A, Necela B, Lin WH, Lu R, Feathers RW, Asmann YW, Thompson EA, Anastasiadis PZ. Cadherin complexes recruit mRNAs and RISC to regulate epithelial cell signaling. J Cell Biol 2017; 216:3073-3085. [PMID: 28877994 PMCID: PMC5626537 DOI: 10.1083/jcb.201612125] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 06/15/2017] [Accepted: 07/27/2017] [Indexed: 02/07/2023] Open
Abstract
Cumulative evidence demonstrates that most RNAs exhibit specific subcellular distribution. However, the mechanisms regulating this phenomenon and its functional consequences are still under investigation. Here, we reveal that cadherin complexes at the apical zonula adherens (ZA) of epithelial adherens junctions recruit the core components of the RNA-induced silencing complex (RISC) Ago2, GW182, and PABPC1, as well as a set of 522 messenger RNAs (mRNAs) and 28 mature microRNAs (miRNAs or miRs), via PLEKHA7. Top canonical pathways represented by these mRNAs include Wnt/β-catenin, TGF-β, and stem cell signaling. We specifically demonstrate the presence and silencing of MYC, JUN, and SOX2 mRNAs by miR-24 and miR-200c at the ZA. PLEKHA7 knockdown dissociates RISC from the ZA, decreases loading of the ZA-associated mRNAs and miRNAs to Ago2, and results in a corresponding increase of MYC, JUN, and SOX2 protein expression. The present work reveals a mechanism that directly links junction integrity to the silencing of a set of mRNAs that critically affect epithelial homeostasis.
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Affiliation(s)
- Antonis Kourtidis
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL .,Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC
| | - Brian Necela
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL
| | - Wan-Hsin Lin
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL
| | - Ruifeng Lu
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL
| | | | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL
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Namjoshi SV, Raab-Graham KF. Screening the Molecular Framework Underlying Local Dendritic mRNA Translation. Front Mol Neurosci 2017; 10:45. [PMID: 28286470 PMCID: PMC5323403 DOI: 10.3389/fnmol.2017.00045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/10/2017] [Indexed: 12/13/2022] Open
Abstract
In the last decade, bioinformatic analyses of high-throughput proteomics and transcriptomics data have enabled researchers to gain insight into the molecular networks that may underlie lasting changes in synaptic efficacy. Development and utilization of these techniques have advanced the field of learning and memory significantly. It is now possible to move from the study of activity-dependent changes of a single protein to modeling entire network changes that require local protein synthesis. This data revolution has necessitated the development of alternative computational and statistical techniques to analyze and understand the patterns contained within. Thus, the focus of this review is to provide a synopsis of the journey and evolution toward big data techniques to address still unanswered questions regarding how synapses are modified to strengthen neuronal circuits. We first review the seminal studies that demonstrated the pivotal role played by local mRNA translation as the mechanism underlying the enhancement of enduring synaptic activity. In the interest of those who are new to the field, we provide a brief overview of molecular biology and biochemical techniques utilized for sample preparation to identify locally translated proteins using RNA sequencing and proteomics, as well as the computational approaches used to analyze these data. While many mRNAs have been identified, few have been shown to be locally synthesized. To this end, we review techniques currently being utilized to visualize new protein synthesis, a task that has proven to be the most difficult aspect of the field. Finally, we provide examples of future applications to test the physiological relevance of locally synthesized proteins identified by big data approaches.
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Affiliation(s)
- Sanjeev V Namjoshi
- Center for Learning and Memory, The University of Texas at Austin, AustinTX, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, AustinTX, USA
| | - Kimberly F Raab-Graham
- Center for Learning and Memory, The University of Texas at Austin, AustinTX, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, AustinTX, USA; Department of Physiology and Pharmacology, Wake Forest Health Sciences, Medical Center Boulevard, Winston-SalemNC, USA
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32
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Kejiou NS, Palazzo AF. mRNA localization as a rheostat to regulate subcellular gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [DOI: 10.1002/wrna.1416] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Nevraj S. Kejiou
- Department of Biochemistry; University of Toronto; Toronto Canada
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In vivocharacterization of the aspartyl-tRNA synthetase DARS: Homing in on the leukodystrophy HBSL. Neurobiol Dis 2016; 97:24-35. [PMID: 27816769 DOI: 10.1016/j.nbd.2016.10.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/12/2016] [Accepted: 10/30/2016] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The recently diagnosed leukodystrophy Hypomyelination with Brain stem and Spinal cord involvement and Leg spasticity (HBSL) is caused by mutations of the cytoplasmic aspartyl-tRNA synthetase geneDARS. The physiological role of DARS in translation is to accurately pair aspartate with its cognate tRNA. Clinically, HBSL subjects show a distinct pattern of hypomyelination and develop progressive leg spasticity, variable cognitive impairment and epilepsy. To elucidate the underlying pathomechanism, we comprehensively assessed endogenous DARS expression in mice. Additionally, aiming at creating the first mammalian HBSL model, we genetically engineered and phenotyped mutant mice with a targetedDarslocus. RESULTS DARS, although expressed in all organs, shows a distinct expression pattern in the adult brain with little immunoreactivity in macroglia but enrichment in neuronal subpopulations of the hippocampus, cerebellum, and cortex. Within neurons, DARS is mainly located in the cell soma where it co-localizes with other components of the translation machinery. Intriguingly, DARS is also present along neurites and at synapses, where it potentially contributes to local protein synthesis.Dars-null mice are not viable and die before embryonic day 11. Heterozygous mice with only one functionalDarsallele display substantially reduced DARS levels in the brain; yet these mutants show no gross abnormalities, including unchanged motor performance. However, we detected reduced pre-pulse inhibition of the acoustic startle response indicating dysfunction of attentional processing inDars+/-mice. CONCLUSIONS Our results, for the first time, show an in-depth characterization of the DARS tissue distribution in mice, revealing surprisingly little uniformity across brain regions or between the major neural cell types. The complete loss of DARS function is not tolerated in mice suggesting that the identified HBSL mutations in humans retain some residual enzyme activity. The mild phenotype of heterozygousDars-null carriers indicates that even partial restoration of DARS levels would be therapeutically relevant. Despite the fact that they do not resemble the full spectrum of clinical symptoms, the robust pre-pulse inhibition phenotype ofDars+/-mice will be instrumental for future preclinical therapeutic efficacy studies. In summary, our data is an important contribution to a better understanding of DARS function and HBSL pathology.
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34
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Majumder P, Chu JF, Chatterjee B, Swamy KBS, Shen CKJ. Co-regulation of mRNA translation by TDP-43 and Fragile X Syndrome protein FMRP. Acta Neuropathol 2016; 132:721-738. [PMID: 27518042 PMCID: PMC5073124 DOI: 10.1007/s00401-016-1603-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 07/28/2016] [Accepted: 07/28/2016] [Indexed: 01/15/2023]
Abstract
For proper mammalian brain development and functioning, the translation of many neuronal mRNAs needs to be repressed without neuronal activity stimulations. We have discovered that the expression of a subclass of neuronal proteins essential for neurodevelopment and neuron plasticity is co-regulated at the translational level by TDP-43 and the Fragile X Syndrome protein FMRP. Using molecular, cellular and imaging approaches, we show that these two RNA-binding proteins (RBP) co-repress the translation initiation of Rac1, Map1b and GluR1 mRNAs, and consequently the hippocampal spinogenesis. The co-repression occurs through binding of TDP-43 to mRNA(s) at specific UG/GU sequences and recruitment of the inhibitory CYFIP1-FMRP complex by its glycine-rich domain. This novel regulatory scenario could be utilized to silence a significant portion of around 160 common target mRNAs of the two RBPs. The study establishes a functional/physical partnership between FMRP and TDP-43 that mechanistically links several neurodevelopmental disorders and neurodegenerative diseases.
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Schmidt BZ, Lehmann M, Gutbier S, Nembo E, Noel S, Smirnova L, Forsby A, Hescheler J, Avci HX, Hartung T, Leist M, Kobolák J, Dinnyés A. In vitro acute and developmental neurotoxicity screening: an overview of cellular platforms and high-throughput technical possibilities. Arch Toxicol 2016; 91:1-33. [PMID: 27492622 DOI: 10.1007/s00204-016-1805-9] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 07/07/2016] [Indexed: 01/03/2023]
Abstract
Neurotoxicity and developmental neurotoxicity are important issues of chemical hazard assessment. Since the interpretation of animal data and their extrapolation to man is challenging, and the amount of substances with information gaps exceeds present animal testing capacities, there is a big demand for in vitro tests to provide initial information and to prioritize for further evaluation. During the last decade, many in vitro tests emerged. These are based on animal cells, human tumour cell lines, primary cells, immortalized cell lines, embryonic stem cells, or induced pluripotent stem cells. They differ in their read-outs and range from simple viability assays to complex functional endpoints such as neural crest cell migration. Monitoring of toxicological effects on differentiation often requires multiomics approaches, while the acute disturbance of neuronal functions may be analysed by assessing electrophysiological features. Extrapolation from in vitro data to humans requires a deep understanding of the test system biology, of the endpoints used, and of the applicability domains of the tests. Moreover, it is important that these be combined in the right way to assess toxicity. Therefore, knowledge on the advantages and disadvantages of all cellular platforms, endpoints, and analytical methods is essential when establishing in vitro test systems for different aspects of neurotoxicity. The elements of a test, and their evaluation, are discussed here in the context of comprehensive prediction of potential hazardous effects of a compound. We summarize the main cellular characteristics underlying neurotoxicity, present an overview of cellular platforms and read-out combinations assessing distinct parts of acute and developmental neurotoxicology, and highlight especially the use of stem cell-based test systems to close gaps in the available battery of tests.
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Affiliation(s)
- Béla Z Schmidt
- BioTalentum Ltd., Gödöllő, Hungary.,Stem Cell Biology and Embryology Unit, Department of Development and Regeneration, Stem Cell Institute Leuven, KU Leuven, Leuven, Belgium
| | - Martin Lehmann
- BioTalentum Ltd., Gödöllő, Hungary.,Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Simon Gutbier
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Constance, Germany
| | - Erastus Nembo
- BioTalentum Ltd., Gödöllő, Hungary.,Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Sabrina Noel
- Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain, Brussels, Belgium
| | - Lena Smirnova
- Center for Alternatives to Animal Testing, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Anna Forsby
- Swedish Toxicology Research Center (Swetox), Södertälje, Sweden.,Department of Neurochemistry, Stockholm University, Stockholm, Sweden
| | - Jürgen Hescheler
- Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Hasan X Avci
- BioTalentum Ltd., Gödöllő, Hungary.,Department of Medical Chemistry, University of Szeged, Szeged, Hungary
| | - Thomas Hartung
- Center for Alternatives to Animal Testing, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Marcel Leist
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Constance, Germany
| | | | - András Dinnyés
- BioTalentum Ltd., Gödöllő, Hungary. .,Molecular Animal Biotechnology Laboratory, Szent István University, Gödöllő, 2100, Hungary.
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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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37
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Richter JD, Bassell GJ, Klann E. Dysregulation and restoration of translational homeostasis in fragile X syndrome. Nat Rev Neurosci 2015; 16:595-605. [PMID: 26350240 DOI: 10.1038/nrn4001] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fragile X syndrome (FXS), the most-frequently inherited form of intellectual disability and the most-prevalent single-gene cause of autism, results from a lack of fragile X mental retardation protein (FMRP), an RNA-binding protein that acts, in most cases, to repress translation. Multiple pharmacological and genetic manipulations that target receptors, scaffolding proteins, kinases and translational control proteins can rescue neuronal morphology, synaptic function and behavioural phenotypes in FXS model mice, presumably by reducing excessive neuronal translation to normal levels. Such rescue strategies might also be explored in the future to identify the mRNAs that are critical for FXS pathophysiology.
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Affiliation(s)
- Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01545, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Eric Klann
- Center for Neural Science, New York University, New York City, New York 10003, USA
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