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Sibarov DA, Tsytsarev V, Volnova A, Vaganova AN, Alves J, Rojas L, Sanabria P, Ignashchenkova A, Savage ED, Inyushin M. Arc protein, a remnant of ancient retrovirus, forms virus-like particles, which are abundantly generated by neurons during epileptic seizures, and affects epileptic susceptibility in rodent models. Front Neurol 2023; 14:1201104. [PMID: 37483450 PMCID: PMC10361770 DOI: 10.3389/fneur.2023.1201104] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/02/2023] [Indexed: 07/25/2023] Open
Abstract
A product of the immediate early gene Arc (Activity-regulated cytoskeleton-associated protein or Arc protein) of retroviral ancestry resides in the genome of all tetrapods for millions of years and is expressed endogenously in neurons. It is a well-known protein, very important for synaptic plasticity and memory consolidation. Activity-dependent Arc expression concentrated in glutamatergic synapses affects the long-time synaptic strength of those excitatory synapses. Because it modulates excitatory-inhibitory balance in a neuronal network, the Arc gene itself was found to be related to the pathogenesis of epilepsy. General Arc knockout rodent models develop a susceptibility to epileptic seizures. Because of activity dependence, synaptic Arc protein synthesis also is affected by seizures. Interestingly, it was found that Arc protein in synapses of active neurons self-assemble in capsids of retrovirus-like particles, which can transfer genetic information between neurons, at least across neuronal synaptic boutons. Released Arc particles can be accumulated in astrocytes after seizures. It is still not known how capsid assembling and transmission timescale is affected by seizures. This scientific field is relatively novel and is experiencing swift transformation as it grapples with difficult concepts in light of evolving experimental findings. We summarize the emergent literature on the subject and also discuss the specific rodent models for studying Arc effects in epilepsy. We summarized both to clarify the possible role of Arc-related pseudo-viral particles in epileptic disorders, which may be helpful to researchers interested in this growing area of investigation.
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Affiliation(s)
- Dmitry A. Sibarov
- Sechenov Institute of Evolutionary Physiology and Biochemistry of the Russian Academy of Sciences, Saint Petersburg, Russia
| | - Vassiliy Tsytsarev
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Anna Volnova
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Anastasia N. Vaganova
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Janaina Alves
- School of Medicine, Universidad Central del Caribe, Bayamón, PR, United States
| | - Legier Rojas
- School of Medicine, Universidad Central del Caribe, Bayamón, PR, United States
| | - Priscila Sanabria
- School of Medicine, Universidad Central del Caribe, Bayamón, PR, United States
| | | | | | - Mikhail Inyushin
- School of Medicine, Universidad Central del Caribe, Bayamón, PR, United States
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2
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Zeitz C, Roger JE, Audo I, Michiels C, Sánchez-Farías N, Varin J, Frederiksen H, Wilmet B, Callebert J, Gimenez ML, Bouzidi N, Blond F, Guilllonneau X, Fouquet S, Léveillard T, Smirnov V, Vincent A, Héon E, Sahel JA, Kloeckener-Gruissem B, Sennlaub F, Morgans CW, Duvoisin RM, Tkatchenko AV, Picaud S. Shedding light on myopia by studying complete congenital stationary night blindness. Prog Retin Eye Res 2023; 93:101155. [PMID: 36669906 DOI: 10.1016/j.preteyeres.2022.101155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 01/20/2023]
Abstract
Myopia is the most common eye disorder, caused by heterogeneous genetic and environmental factors. Rare progressive and stationary inherited retinal disorders are often associated with high myopia. Genes implicated in myopia encode proteins involved in a variety of biological processes including eye morphogenesis, extracellular matrix organization, visual perception, circadian rhythms, and retinal signaling. Differentially expressed genes (DEGs) identified in animal models mimicking myopia are helpful in suggesting candidate genes implicated in human myopia. Complete congenital stationary night blindness (cCSNB) in humans and animal models represents an ON-bipolar cell signal transmission defect and is also associated with high myopia. Thus, it represents also an interesting model to identify myopia-related genes, as well as disease mechanisms. While the origin of night blindness is molecularly well established, further research is needed to elucidate the mechanisms of myopia development in subjects with cCSNB. Using whole transcriptome analysis on three different mouse models of cCSNB (in Gpr179-/-, Lrit3-/- and Grm6-/-), we identified novel actors of the retinal signaling cascade, which are also novel candidate genes for myopia. Meta-analysis of our transcriptomic data with published transcriptomic databases and genome-wide association studies from myopia cases led us to propose new biological/cellular processes/mechanisms potentially at the origin of myopia in cCSNB subjects. The results provide a foundation to guide the development of pharmacological myopia therapies.
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Affiliation(s)
- Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.
| | - Jérome E Roger
- Paris-Saclay Institute of Neuroscience, CERTO-Retina France, CNRS, Université Paris-Saclay, Saclay, France
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; CHNO des Quinze-Vingts, INSERM-DGOS CIC 1423, Paris, France
| | | | | | - Juliette Varin
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Helen Frederiksen
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Baptiste Wilmet
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Jacques Callebert
- Service of Biochemistry and Molecular Biology, INSERM U942, Hospital Lariboisière, APHP, Paris, France
| | | | - Nassima Bouzidi
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Frederic Blond
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Stéphane Fouquet
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Vasily Smirnov
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Ajoy Vincent
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada; Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Elise Héon
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada; Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; CHNO des Quinze-Vingts, INSERM-DGOS CIC 1423, Paris, France; Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Florian Sennlaub
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Catherine W Morgans
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Robert M Duvoisin
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Andrei V Tkatchenko
- Oujiang Laboratory, Zhejiang Laboratory for Regenerative Medicine, Vision and Brain Health, Wenzhou, China; Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University, New York, NY, USA
| | - Serge Picaud
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
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3
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Calis D, Hess M, Marchetta P, Singer W, Modro J, Nelissen E, Prickaerts J, Sandner P, Lukowski R, Ruth P, Knipper M, Rüttiger L. Acute deletion of the central MR/GR steroid receptor correlates with changes in LTP, auditory neural gain, and GC-A cGMP signaling. Front Mol Neurosci 2023; 16:1017761. [PMID: 36873102 PMCID: PMC9983609 DOI: 10.3389/fnmol.2023.1017761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/18/2023] [Indexed: 02/19/2023] Open
Abstract
The complex mechanism by which stress can affect sensory processes such as hearing is still poorly understood. In a previous study, the mineralocorticoid (MR) and/or glucocorticoid receptor (GR) were deleted in frontal brain regions but not cochlear regions using a CaMKIIα-based tamoxifen-inducible Cre ERT2/loxP approach. These mice exhibit either a diminished (MRTMXcKO) or disinhibited (GRTMXcKO) auditory nerve activity. In the present study, we observed that mice differentially were (MRTMXcKO) or were not (GRTMXcKO) able to compensate for altered auditory nerve activity in the central auditory pathway. As previous findings demonstrated a link between central auditory compensation and memory-dependent adaptation processes, we analyzed hippocampal paired-pulse facilitation (PPF) and long-term potentiation (LTP). To determine which molecular mechanisms may impact differences in synaptic plasticity, we analyzed Arc/Arg3.1, known to control AMPA receptor trafficking, as well as regulators of tissue perfusion and energy consumption (NO-GC and GC-A). We observed that the changes in PPF of MRTMXcKOs mirrored the changes in their auditory nerve activity, whereas changes in the LTP of MRTMXcKOs and GRTMXcKOs mirrored instead the changes in their central compensation capacity. Enhanced GR expression levels in MRTMXcKOs suggest that MRs typically suppress GR expression. We observed that hippocampal LTP, GC-A mRNA expression levels, and ABR wave IV/I ratio were all enhanced in animals with elevated GR (MRTMXcKOs) but were all lower or not mobilized in animals with impaired GR expression levels (GRTMXcKOs and MRGRTMXcKOs). This suggests that GC-A may link LTP and auditory neural gain through GR-dependent processes. In addition, enhanced NO-GC expression levels in MR, GR, and MRGRTMXcKOs suggest that both receptors suppress NO-GC; on the other hand, elevated Arc/Arg3.1 levels in MRTMXcKOs and MRGRTMXcKOs but not GRTMXcKOs suggest that MR suppresses Arc/Arg3.1 expression levels. Conclusively, MR through GR inhibition may define the threshold for hemodynamic responses for LTP and auditory neural gain associated with GC-A.
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Affiliation(s)
- Dila Calis
- Department of Otolaryngology, Head and Neck Surgery, Tübingen Hearing Research Centre, Molecular Physiology of Hearing, University of Tübingen, Tübingen, Germany
| | - Morgan Hess
- Department of Otolaryngology, Head and Neck Surgery, Tübingen Hearing Research Centre, Molecular Physiology of Hearing, University of Tübingen, Tübingen, Germany
| | - Philine Marchetta
- Department of Otolaryngology, Head and Neck Surgery, Tübingen Hearing Research Centre, Molecular Physiology of Hearing, University of Tübingen, Tübingen, Germany
| | - Wibke Singer
- Department of Otolaryngology, Head and Neck Surgery, Tübingen Hearing Research Centre, Molecular Physiology of Hearing, University of Tübingen, Tübingen, Germany
| | - Julian Modro
- Department of Otolaryngology, Head and Neck Surgery, Tübingen Hearing Research Centre, Molecular Physiology of Hearing, University of Tübingen, Tübingen, Germany
| | - Ellis Nelissen
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, Netherlands
| | - Jos Prickaerts
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, Netherlands
| | - Peter Sandner
- Bayer Health Care Pharmaceuticals, Global Drug Discovery Pharma Research Centre Wuppertal, Wuppertal, Germany
| | - Robert Lukowski
- Institute of Pharmacy, Pharmacology, Toxicology and Clinical Pharmacy, University of Tübingen, Tübingen, Germany
| | - Peter Ruth
- Institute of Pharmacy, Pharmacology, Toxicology and Clinical Pharmacy, University of Tübingen, Tübingen, Germany
| | - Marlies Knipper
- Department of Otolaryngology, Head and Neck Surgery, Tübingen Hearing Research Centre, Molecular Physiology of Hearing, University of Tübingen, Tübingen, Germany
| | - Lukas Rüttiger
- Department of Otolaryngology, Head and Neck Surgery, Tübingen Hearing Research Centre, Molecular Physiology of Hearing, University of Tübingen, Tübingen, Germany
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Le P, Ahmed N, Yeo GW. Illuminating RNA biology through imaging. Nat Cell Biol 2022; 24:815-824. [PMID: 35697782 PMCID: PMC11132331 DOI: 10.1038/s41556-022-00933-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 05/06/2022] [Indexed: 12/14/2022]
Abstract
RNA processing plays a central role in accurately transmitting genetic information into functional RNA and protein regulators. To fully appreciate the RNA life-cycle, tools to observe RNA with high spatial and temporal resolution are critical. Here we review recent advances in RNA imaging and highlight how they will propel the field of RNA biology. We discuss current trends in RNA imaging and their potential to elucidate unanswered questions in RNA biology.
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Affiliation(s)
- Phuong Le
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Noorsher Ahmed
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA.
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5
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mRNA Trafficking in the Nervous System: A Key Mechanism of the Involvement of Activity-Regulated Cytoskeleton-Associated Protein (Arc) in Synaptic Plasticity. Neural Plast 2021; 2021:3468795. [PMID: 34603440 PMCID: PMC8486535 DOI: 10.1155/2021/3468795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/15/2021] [Accepted: 09/07/2021] [Indexed: 12/18/2022] Open
Abstract
Synaptic activity mediates information storage and memory consolidation in the brain and requires a fast de novo synthesis of mRNAs in the nucleus and proteins in synapses. Intracellular localization of a protein can be achieved by mRNA trafficking and localized translation. Activity-regulated cytoskeleton-associated protein (Arc) is a master regulator of synaptic plasticity and plays an important role in controlling large signaling networks implicated in learning, memory consolidation, and behavior. Transcription of the Arc gene may be induced by a short behavioral event, resulting in synaptic activation. Arc mRNA is exported into the cytoplasm and can be trafficked into the dendrite of an activated synapse where it is docked and translated. The structure of Arc is similar to the viral GAG (group-specific antigen) protein, and phylogenic analysis suggests that Arc may originate from the family of Ty3/Gypsy retrotransposons. Therefore, Arc might evolve through “domestication” of retroviruses. Arc can form a capsid-like structure that encapsulates a retrovirus-like sentence in the 3′-UTR (untranslated region) of Arc mRNA. Such complex can be loaded into extracellular vesicles and transported to other neurons or muscle cells carrying not only genetic information but also regulatory signals within neuronal networks. Therefore, Arc mRNA inter- and intramolecular trafficking is essential for the modulation of synaptic activity required for memory consolidation and cognitive functions. Recent studies with single-molecule imaging in live neurons confirmed and extended the role of Arc mRNA trafficking in synaptic plasticity.
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6
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Das S, Vera M, Gandin V, Singer RH, Tutucci E. Intracellular mRNA transport and localized translation. Nat Rev Mol Cell Biol 2021; 22:483-504. [PMID: 33837370 PMCID: PMC9346928 DOI: 10.1038/s41580-021-00356-8] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2021] [Indexed: 02/08/2023]
Abstract
Fine-tuning cellular physiology in response to intracellular and environmental cues requires precise temporal and spatial control of gene expression. High-resolution imaging technologies to detect mRNAs and their translation state have revealed that all living organisms localize mRNAs in subcellular compartments and create translation hotspots, enabling cells to tune gene expression locally. Therefore, mRNA localization is a conserved and integral part of gene expression regulation from prokaryotic to eukaryotic cells. In this Review, we discuss the mechanisms of mRNA transport and local mRNA translation across the kingdoms of life and at organellar, subcellular and multicellular resolution. We also discuss the properties of messenger ribonucleoprotein and higher order RNA granules and how they may influence mRNA transport and local protein synthesis. Finally, we summarize the technological developments that allow us to study mRNA localization and local translation through the simultaneous detection of mRNAs and proteins in single cells, mRNA and nascent protein single-molecule imaging, and bulk RNA and protein detection methods.
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Affiliation(s)
- Sulagna Das
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY, USA
| | - Maria Vera
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | | | - Robert H. Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY, USA.,Janelia Research Campus of the HHMI, Ashburn, VA, USA.,;
| | - Evelina Tutucci
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,;
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7
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Hedde PN, Malacrida L, Barylko B, Binns DD, Albanesi JP, Jameson DM. Membrane Remodeling by Arc/Arg3.1. Front Mol Biosci 2021; 8:630625. [PMID: 33763452 PMCID: PMC7982473 DOI: 10.3389/fmolb.2021.630625] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/11/2021] [Indexed: 11/13/2022] Open
Abstract
The activity-regulated cytoskeletal-associated protein (Arc, also known as Arg3.1) is an immediate early gene product induced by activity/experience and required for multiple modes of synaptic plasticity. Both long-term potentiation (LTP) and long-term depression (LTD) are impaired upon Arc deletion, as well as the ability to form long-term spatial, taste and fear memories. The best-characterized cellular function of Arc is enhancement of the endocytic internalization of AMPA receptors (AMPARs) in dendritic spines. Solution of the crystal structure of a C-terminal segment of Arc revealed a striking similarity to the capsid domain of HIV Gag. It was subsequently shown that Arc assembles into viral capsid-like structures that enclose Arc mRNA, are released into the extracellular space, and are internalized by neighboring cells. Thus, Arc is unique in participating in plasma membrane budding both into and out of the cell. In this report we study the interaction of Arc with membranes using giant unilamellar vesicles (GUVs). Using the fluorescent lipid probe LAURDAN, we find that Arc promotes the formation of smaller vesicles that penetrate into the GUV interior. Our results suggest that Arc induces negative membrane curvature and may therefore facilitate the formation of mRNA-containing extracellular vesicles from the plasma membrane.
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Affiliation(s)
- Per Niklas Hedde
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, HI, United States.,Laboratory for Fluorescence Dynamics, University of California, Irvine , CA, United States
| | - Leonel Malacrida
- Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo , Uruguay.,Advanced Bioimaging Unit, Institute Pasteur of Montevideo-Universidad de la República, Montevideo, Uruguay
| | - Barbara Barylko
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Derk D Binns
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Joseph P Albanesi
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - David M Jameson
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, HI, United States
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8
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Hedde PN, Malacrida L, Barylko B, Binns DD, Albanesi JP, Jameson DM. Membrane Remodeling by Arc/Arg3.1. Front Mol Biosci 2021; 8:630625. [PMID: 33763452 DOI: 10.3389/fmolb.2021.630625/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/11/2021] [Indexed: 05/23/2023] Open
Abstract
The activity-regulated cytoskeletal-associated protein (Arc, also known as Arg3.1) is an immediate early gene product induced by activity/experience and required for multiple modes of synaptic plasticity. Both long-term potentiation (LTP) and long-term depression (LTD) are impaired upon Arc deletion, as well as the ability to form long-term spatial, taste and fear memories. The best-characterized cellular function of Arc is enhancement of the endocytic internalization of AMPA receptors (AMPARs) in dendritic spines. Solution of the crystal structure of a C-terminal segment of Arc revealed a striking similarity to the capsid domain of HIV Gag. It was subsequently shown that Arc assembles into viral capsid-like structures that enclose Arc mRNA, are released into the extracellular space, and are internalized by neighboring cells. Thus, Arc is unique in participating in plasma membrane budding both into and out of the cell. In this report we study the interaction of Arc with membranes using giant unilamellar vesicles (GUVs). Using the fluorescent lipid probe LAURDAN, we find that Arc promotes the formation of smaller vesicles that penetrate into the GUV interior. Our results suggest that Arc induces negative membrane curvature and may therefore facilitate the formation of mRNA-containing extracellular vesicles from the plasma membrane.
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Affiliation(s)
- Per Niklas Hedde
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, HI, United States
- Laboratory for Fluorescence Dynamics, University of California, Irvine , CA, United States
| | - Leonel Malacrida
- Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo , Uruguay
- Advanced Bioimaging Unit, Institute Pasteur of Montevideo-Universidad de la República, Montevideo, Uruguay
| | - Barbara Barylko
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Derk D Binns
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Joseph P Albanesi
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - David M Jameson
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, HI, United States
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10
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Yakout DW, Shree N, Mabb AM. Effect of pharmacological manipulations on Arc function. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2020; 2:100013. [PMID: 34909648 PMCID: PMC8663979 DOI: 10.1016/j.crphar.2020.100013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/11/2020] [Accepted: 12/17/2020] [Indexed: 12/20/2022] Open
Abstract
Activity-regulated cytoskeleton-associated protein (Arc) is a brain-enriched immediate early gene that regulates important mechanisms implicated in learning and memory. Arc levels are controlled through a balance of induction and degradation in an activity-dependent manner. Arc further undergoes multiple post-translational modifications that regulate its stability, localization and function. Recent studies demonstrate that these features of Arc can be pharmacologically manipulated. In this review, we discuss some of these compounds, with an emphasis on drugs of abuse and psychotropic drugs. We also discuss inflammatory states that regulate Arc.
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Affiliation(s)
- Dina W. Yakout
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
| | - Nitheyaa Shree
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
| | - Angela M. Mabb
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
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11
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Bressloff PC. Target competition for resources under multiple search-and-capture events with stochastic resetting. Proc Math Phys Eng Sci 2020; 476:20200475. [PMID: 33223946 PMCID: PMC7655747 DOI: 10.1098/rspa.2020.0475] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/15/2020] [Indexed: 12/19/2022] Open
Abstract
We develop a general framework for analysing the distribution of resources in a population of targets under multiple independent search-and-capture events. Each event involves a single particle executing a stochastic search that resets to a fixed location x r at a random sequence of times. Whenever the particle is captured by a target, it delivers a packet of resources and then returns to x r , where it is reloaded with cargo and a new round of search and capture begins. Using renewal theory, we determine the mean number of resources in each target as a function of the splitting probabilities and unconditional mean first passage times of the corresponding search process without resetting. We then use asymptotic PDE methods to determine the effects of resetting on the distribution of resources generated by diffusive search in a bounded two-dimensional domain with N small interior targets. We show that slow resetting increases the total number of resources M tot across all targets provided that ∑ j = 1 N G ( x r , x j ) < 0 , where G is the Neumann Green's function and x j is the location of the j-th target. This implies that M tot can be optimized by varying r. We also show that the k-th target has a competitive advantage if ∑ j = 1 N G ( x r , x j ) > N G ( x r , x k ) .
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Affiliation(s)
- P. C. Bressloff
- Department of Mathematics, University of Utah, 155 South 1400 East, Salt Lake City, UT 84112, USA
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12
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Bressloff PC. Queueing theory of search processes with stochastic resetting. Phys Rev E 2020; 102:032109. [PMID: 33075909 DOI: 10.1103/physreve.102.032109] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 08/21/2020] [Indexed: 06/11/2023]
Abstract
We use queueing theory to develop a general framework for analyzing search processes with stochastic resetting, under the additional assumption that following absorption by a target, the particle (searcher) delivers a packet of resources to the target and the search process restarts at the reset point x_{r}. This leads to a sequence of search-and-capture events, whereby resources accumulate in the target under the combined effects of resource supply and degradation. Combining the theory of G/M/∞ queues with a renewal method for analyzing resetting processes, we derive general expressions for the mean and variance of the number of resource packets within the target at steady state. These expressions apply to both exponential and nonexponential resetting protocols and take into account delays arising from various factors such as finite return times, refractory periods, and delays due to the loading or unloading of resources. In the case of exponential resetting, we show how the resource statistics can be expressed in terms of the MFPTs T_{r}(x_{r}) and T_{r+γ}(x_{r}), where r is the resetting rate and γ is the degradation rate. This allows us to derive various general results concerning the dependence of the mean and variance on the parameters r,γ. Our results are illustrated using several specific examples. Finally, we show how fluctuations can be reduced either by allowing the delivery of multiple packets that degrade independently or by having multiple independent searchers.
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Affiliation(s)
- Paul C Bressloff
- Department of Mathematics, University of Utah, Salt Lake City, Utah 84112, USA
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13
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Braselmann E, Rathbun C, Richards EM, Palmer AE. Illuminating RNA Biology: Tools for Imaging RNA in Live Mammalian Cells. Cell Chem Biol 2020; 27:891-903. [PMID: 32640188 PMCID: PMC7595133 DOI: 10.1016/j.chembiol.2020.06.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/30/2020] [Accepted: 06/15/2020] [Indexed: 01/06/2023]
Abstract
The central dogma teaches us that DNA makes RNA, which in turn makes proteins, the main building blocks of the cell. But this over simplified linear transmission of information overlooks the vast majority of the genome produces RNAs that do not encode proteins and the myriad ways that RNA regulates cellular functions. Historically, one of the challenges in illuminating RNA biology has been the lack of tools for visualizing RNA in live cells. But clever approaches for exploiting RNA binding proteins, in vitro RNA evolution, and chemical biology have resulted in significant advances in RNA visualization tools in recent years. This review provides an overview of current tools for tagging RNA with fluorescent probes and tracking their dynamics, localization andfunction in live mammalian cells.
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Affiliation(s)
- Esther Braselmann
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Colin Rathbun
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Erin M Richards
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Amy E Palmer
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA.
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14
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Mofatteh M. mRNA localization and local translation in neurons. AIMS Neurosci 2020; 7:299-310. [PMID: 32995487 PMCID: PMC7519968 DOI: 10.3934/neuroscience.2020016] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/05/2020] [Indexed: 12/15/2022] Open
Abstract
The spatial and temporal regulation of gene expression in neurons is an important step in creating functional and structural neuronal networks. The complexity of neurons require differential expression of various proteins in different compartments. Highly polarised cells, such as neurons, respond rapidly to different external stimuli by changing their local protein abundance and composition. Neurons can have extensions up to a meter away from their cell body in humans, so it is easy to envisage why they need to manage the synthesis of new proteins locally and on-demand. Recent research has demonstrated that neurons can control the expression of different proteins by localising translationally silent mRNAs, followed by subsequent translation. Neurons use mRNA localization and local translation to achieve different purposes during their life cycle. While developing neurons rely on mRNA localization for axon guidance and synaptogenesis, mature neurons can use mRNA localization for maintenance of essential physiological processes. mRNA localization also plays a role in response to neuron injury to regenerate and restore neuronal connections. Recent microscopic imaging techniques such as live imaging of fluorescently tagged molecules combined with genetic and biochemical studies in neurons have illustrated evolutionarily conserved mechanisms for targeting mRNAs into their correct compartments. This review provides an overview of mRNA localization and local translation in vertebrate and invertebrate neurons and discusses the mechanism by which mRNAs are trafficked into axons. Furthermore, the role of mRNA localization in synaptic activation, as well as axonal injury is explored.
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Affiliation(s)
- Mohammad Mofatteh
- Lincoln College, University of Oxford, Turl Street, Oxford, OX1 3DR, United Kingdom.,Merton College, University of Oxford, Merton Street, Oxford, OX1 4DJ, United Kingdom.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, United Kingdom
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15
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Fujita H, Oikawa R, Hayakawa M, Tomoike F, Kimura Y, Okuno H, Hatashita Y, Fiallos Oliveros C, Bito H, Ohshima T, Tsuneda S, Abe H, Inoue T. Quantification of native mRNA dynamics in living neurons using fluorescence correlation spectroscopy and reduction-triggered fluorescent probes. J Biol Chem 2020; 295:7923-7940. [PMID: 32341124 PMCID: PMC7278347 DOI: 10.1074/jbc.ra119.010921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 04/22/2020] [Indexed: 11/06/2022] Open
Abstract
RNA localization in subcellular compartments is essential for spatial and temporal regulation of protein expression in neurons. Several techniques have been developed to visualize mRNAs inside cells, but the study of the behavior of endogenous and nonengineered mRNAs in living neurons has just started. In this study, we combined reduction-triggered fluorescent (RETF) probes and fluorescence correlation spectroscopy (FCS) to investigate the diffusion properties of activity-regulated cytoskeleton-associated protein (Arc) and inositol 1,4,5-trisphosphate receptor type 1 (Ip3r1) mRNAs. This approach enabled us to discriminate between RNA-bound and unbound fluorescent probes and to quantify mRNA diffusion parameters and concentrations in living rat primary hippocampal neurons. Specifically, we detected the induction of Arc mRNA production after neuronal activation in real time. Results from computer simulations with mRNA diffusion coefficients obtained in these analyses supported the idea that free diffusion is incapable of transporting mRNA of sizes close to those of Arc or Ip3r1 to distal dendrites. In conclusion, the combined RETF-FCS approach reported here enables analyses of the dynamics of endogenous, unmodified mRNAs in living neurons, affording a glimpse into the intracellular dynamics of RNA in live cells.
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Affiliation(s)
- Hirotaka Fujita
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Ryota Oikawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Aichi, Japan
| | - Mayu Hayakawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Aichi, Japan
| | - Fumiaki Tomoike
- Department of Chemistry, Graduate School of Science, Nagoya University, Aichi, Japan
| | - Yasuaki Kimura
- Department of Chemistry, Graduate School of Science, Nagoya University, Aichi, Japan
| | - Hiroyuki Okuno
- Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Yoshiki Hatashita
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Carolina Fiallos Oliveros
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Haruhiko Bito
- Department of Neurochemistry, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Toshio Ohshima
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Aichi, Japan
| | - Takafumi Inoue
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
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16
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Engel KL, Arora A, Goering R, Lo HYG, Taliaferro JM. Mechanisms and consequences of subcellular RNA localization across diverse cell types. Traffic 2020; 21:404-418. [PMID: 32291836 PMCID: PMC7304542 DOI: 10.1111/tra.12730] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 02/07/2023]
Abstract
Essentially all cells contain a variety of spatially restricted regions that are important for carrying out specialized functions. Often, these regions contain specialized transcriptomes that facilitate these functions by providing transcripts for localized translation. These transcripts play a functional role in maintaining cell physiology by enabling a quick response to changes in the cellular environment. Here, we review how RNA molecules are trafficked within cells, with a focus on the subcellular locations to which they are trafficked, mechanisms that regulate their transport and clinical disorders associated with misregulation of the process.
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Affiliation(s)
- Krysta L Engel
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ankita Arora
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Raeann Goering
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Hei-Yong G Lo
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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17
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Wu H, Zhou J, Zhu T, Cohen I, Dictenberg J. A kinesin adapter directly mediates dendritic mRNA localization during neural development in mice. J Biol Chem 2020; 295:6605-6628. [PMID: 32111743 DOI: 10.1074/jbc.ra118.005616] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 08/19/2019] [Indexed: 11/06/2022] Open
Abstract
Motor protein-based active transport is essential for mRNA localization and local translation in animal cells, yet how mRNA granules interact with motor proteins remains poorly understood. Using an unbiased yeast two-hybrid screen for interactions between murine RNA-binding proteins (RBPs) and motor proteins, here we identified protein interaction with APP tail-1 (PAT1) as a potential direct adapter between zipcode-binding protein 1 (ZBP1, a β-actin RBP) and the kinesin-I motor complex. The amino acid sequence of mouse PAT1 is similar to that of the kinesin light chain (KLC), and we found that PAT1 binds to KLC directly. Studying PAT1 in mouse primary hippocampal neuronal cultures from both sexes and using structured illumination microscopic imaging of these neurons, we observed that brain-derived neurotrophic factor (BDNF) enhances co-localization of dendritic ZBP1 and PAT1 within granules that also contain kinesin-I. PAT1 is essential for BDNF-stimulated neuronal growth cone development and dendritic protrusion formation, and we noted that ZBP1 and PAT1 co-locate along with β-actin mRNA in actively transported granules in living neurons. Acute disruption of the PAT1-ZBP1 interaction in neurons with PAT1 siRNA or a dominant-negative ZBP1 construct diminished localization of β-actin mRNA but not of Ca2+/calmodulin-dependent protein kinase IIα (CaMKIIα) mRNA in dendrites. The aberrant β-actin mRNA localization resulted in abnormal dendritic protrusions and growth cone dynamics. These results suggest a critical role for PAT1 in BDNF-induced β-actin mRNA transport during postnatal development and reveal a new molecular mechanism for mRNA localization in vertebrates.
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Affiliation(s)
- Hao Wu
- Department of Biological Sciences, Hunter College, City University of New York, New York, New York 10065 .,Biology Program, Graduate School and University Center, City University of New York, New York, New York 10016
| | - Jing Zhou
- Biology Program, Graduate School and University Center, City University of New York, New York, New York 10016.,Biology Department, Lehman College, City University of New York, Bronx, New York 10468
| | - Tianhui Zhu
- Department of Biological Sciences, Hunter College, City University of New York, New York, New York 10065.,Biology Program, Graduate School and University Center, City University of New York, New York, New York 10016
| | - Ivan Cohen
- Department of Biological Sciences, Hunter College, City University of New York, New York, New York 10065
| | - Jason Dictenberg
- Cell Biology, State University of New York Downstate, Brooklyn, New York 11226 .,Biotechnology Incubator, AccelBio, Brooklyn, New York 11226
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18
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Cottee MA, Letham SC, Young GR, Stoye JP, Taylor IA. Structure of Drosophila melanogaster ARC1 reveals a repurposed molecule with characteristics of retroviral Gag. SCIENCE ADVANCES 2020; 6:eaay6354. [PMID: 31911950 PMCID: PMC6938703 DOI: 10.1126/sciadv.aay6354] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/06/2019] [Indexed: 06/10/2023]
Abstract
The tetrapod neuronal protein ARC and its Drosophila melanogaster homolog, dARC1, have important but differing roles in neuronal development. Both are thought to originate through exaptation of ancient Ty3/Gypsy retrotransposon Gag, with their novel function relying on an original capacity for self-assembly and encapsidation of nucleic acids. Here, we present the crystal structure of dARC1 CA and examine the relationship between dARC1, mammalian ARC, and the CA protein of circulating retroviruses. We show that while the overall architecture is highly related to that of orthoretroviral and spumaretroviral CA, there are substantial deviations in both amino- and carboxyl-terminal domains, potentially affecting recruitment of partner proteins and particle assembly. The degree of sequence and structural divergence suggests that Ty3/Gypsy Gag has been exapted on two separate occasions and that, although mammalian ARC and dARC1 share functional similarity, the structures have undergone different adaptations after appropriation into the tetrapod and insect genomes.
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Affiliation(s)
- Matthew A. Cottee
- Macromolecular Structure Laboratory, The Francis Crick Institute, Midland Road, London NW1 1AT, UK
| | - Suzanne C. Letham
- Macromolecular Structure Laboratory, The Francis Crick Institute, Midland Road, London NW1 1AT, UK
| | - George R. Young
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Midland Road, London NW1 1AT, UK
| | - Jonathan P. Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Midland Road, London NW1 1AT, UK
- Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, Midland Road, London NW1 1AT, UK
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19
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Noya SB, Colameo D, Brüning F, Spinnler A, Mircsof D, Opitz L, Mann M, Tyagarajan SK, Robles MS, Brown SA. The forebrain synaptic transcriptome is organized by clocks but its proteome is driven by sleep. Science 2019; 366:366/6462/eaav2642. [DOI: 10.1126/science.aav2642] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 09/03/2019] [Indexed: 12/13/2022]
Abstract
Neurons have adapted mechanisms to traffic RNA and protein into distant dendritic and axonal arbors. Taking a biochemical approach, we reveal that forebrain synaptic transcript accumulation shows overwhelmingly daily rhythms, with two-thirds of synaptic transcripts showing time-of-day–dependent abundance independent of oscillations in the soma. These transcripts formed two sharp temporal and functional clusters, with transcripts preceding dawn related to metabolism and translation and those anticipating dusk related to synaptic transmission. Characterization of the synaptic proteome around the clock demonstrates the functional relevance of temporal gating for synaptic processes and energy homeostasis. Unexpectedly, sleep deprivation completely abolished proteome but not transcript oscillations. Altogether, the emerging picture is one of a circadian anticipation of messenger RNA needs in the synapse followed by translation as demanded by sleep-wake cycles.
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Affiliation(s)
- Sara B. Noya
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - David Colameo
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Franziska Brüning
- Institute of Medical Psychology, Medical Faculty, LMU Munich, Germany
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andrea Spinnler
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Dennis Mircsof
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Lennart Opitz
- Functional Genomics Center Zurich, University of Zurich–Eidgenosissche Technische Hochschule, Zurich, Switzerland
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Shiva K. Tyagarajan
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Maria S. Robles
- Institute of Medical Psychology, Medical Faculty, LMU Munich, Germany
| | - Steven A. Brown
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
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20
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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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21
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Moissoglu K, Yasuda K, Wang T, Chrisafis G, Mili S. Translational regulation of protrusion-localized RNAs involves silencing and clustering after transport. eLife 2019; 8:44752. [PMID: 31290739 PMCID: PMC6639073 DOI: 10.7554/elife.44752] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 07/08/2019] [Indexed: 02/06/2023] Open
Abstract
Localization of RNAs to various subcellular destinations is a widely used mechanism that regulates a large proportion of transcripts in polarized cells. In many cases, such localized transcripts mediate spatial control of gene expression by being translationally silent while in transit and locally activated at their destination. Here, we investigate the translation of RNAs localized at dynamic cellular protrusions of human and mouse, migrating, mesenchymal cells. In contrast to the model described above, we find that protrusion-localized RNAs are not locally activated solely at protrusions, but can be translated with similar efficiency in both internal and peripheral locations. Interestingly, protrusion-localized RNAs are translated at extending protrusions, they become translationally silenced in retracting protrusions and this silencing is accompanied by coalescence of single RNAs into larger heterogeneous RNA clusters. This work describes a distinct mode of translational regulation of localized RNAs, which we propose is used to regulate protein activities during dynamic cellular responses.
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Affiliation(s)
- Konstadinos Moissoglu
- Laboratory of Cellular and Molecular Biology,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Kyota Yasuda
- Laboratory of Cellular and Molecular Biology,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.,Program of Mathematical and Life Sciences, Graduate School of Integrated Science for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research, Suita, Japan
| | - Tianhong Wang
- Laboratory of Cellular and Molecular Biology,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - George Chrisafis
- Laboratory of Cellular and Molecular Biology,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Stavroula Mili
- Laboratory of Cellular and Molecular Biology,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
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22
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Bioinformatics Approaches to Gain Insights into cis-Regulatory Motifs Involved in mRNA Localization. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:165-194. [PMID: 31811635 DOI: 10.1007/978-3-030-31434-7_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Messenger RNA (mRNA) is a fundamental intermediate in the expression of proteins. As an integral part of this important process, protein production can be localized by the targeting of mRNA to a specific subcellular compartment. The subcellular destination of mRNA is suggested to be governed by a region of its primary sequence or secondary structure, which consequently dictates the recruitment of trans-acting factors, such as RNA-binding proteins or regulatory RNAs, to form a messenger ribonucleoprotein particle. This molecular ensemble is requisite for precise and spatiotemporal control of gene expression. In the context of RNA localization, the description of the binding preferences of an RNA-binding protein defines a motif, and one, or more, instance of a given motif is defined as a localization element (zip code). In this chapter, we first discuss the cis-regulatory motifs previously identified as mRNA localization elements. We then describe motif representation in terms of entropy and information content and offer an overview of motif databases and search algorithms. Finally, we provide an outline of the motif topology of asymmetrically localized mRNA molecules.
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23
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Single-molecule analysis of endogenous β-actin mRNA trafficking reveals a mechanism for compartmentalized mRNA localization in axons. Proc Natl Acad Sci U S A 2018; 115:E9697-E9706. [PMID: 30254174 PMCID: PMC6187124 DOI: 10.1073/pnas.1806189115] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
De novo protein synthesis in neuronal axons plays important roles in neural circuit formation, maintenance, and disease. Key to the selectivity of axonal protein synthesis is whether an mRNA is present at the right place to be translated, but the mechanisms behind axonal mRNA localization remain poorly understood. In this work, we quantitatively analyze the link between axonal β-actin mRNA trafficking and its localization patterns. By developing a single-molecule approach to live-image β-actin mRNAs in axons, we explore the biophysical drivers behind β-actin mRNA motion and uncover a mechanism for generating increased density at the axon tip by differences in motor protein-driven transport speeds. These results provide mechanistic insight into the control of local translation through mRNA trafficking. During embryonic nervous system assembly, mRNA localization is precisely regulated in growing axons, affording subcellular autonomy by allowing controlled protein expression in space and time. Different sets of mRNAs exhibit different localization patterns across the axon. However, little is known about how mRNAs move in axons or how these patterns are generated. Here, we couple molecular beacon technology with highly inclined and laminated optical sheet microscopy to image single molecules of identified endogenous mRNA in growing axons. By combining quantitative single-molecule imaging with biophysical motion models, we show that β-actin mRNA travels mainly as single copies and exhibits different motion-type frequencies in different axonal subcompartments. We find that β-actin mRNA density is fourfold enriched in the growth cone central domain compared with the axon shaft and that a modicum of directed transport is vital for delivery of mRNA to the axon tip. Through mathematical modeling we further demonstrate that directional differences in motor-driven mRNA transport speeds are sufficient to generate β-actin mRNA enrichment at the growth cone. Our results provide insight into how mRNAs are trafficked in axons and a mechanism for generating different mRNA densities across axonal subcompartments.
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24
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Bressloff PC, Maclaurin JN. Stochastic Hybrid Systems in Cellular Neuroscience. JOURNAL OF MATHEMATICAL NEUROSCIENCE 2018; 8:12. [PMID: 30136005 PMCID: PMC6104574 DOI: 10.1186/s13408-018-0067-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/05/2018] [Indexed: 06/08/2023]
Abstract
We review recent work on the theory and applications of stochastic hybrid systems in cellular neuroscience. A stochastic hybrid system or piecewise deterministic Markov process involves the coupling between a piecewise deterministic differential equation and a time-homogeneous Markov chain on some discrete space. The latter typically represents some random switching process. We begin by summarizing the basic theory of stochastic hybrid systems, including various approximation schemes in the fast switching (weak noise) limit. In subsequent sections, we consider various applications of stochastic hybrid systems, including stochastic ion channels and membrane voltage fluctuations, stochastic gap junctions and diffusion in randomly switching environments, and intracellular transport in axons and dendrites. Finally, we describe recent work on phase reduction methods for stochastic hybrid limit cycle oscillators.
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25
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Janz P, Hauser P, Heining K, Nestel S, Kirsch M, Egert U, Haas CA. Position- and Time-Dependent Arc Expression Links Neuronal Activity to Synaptic Plasticity During Epileptogenesis. Front Cell Neurosci 2018; 12:244. [PMID: 30154698 PMCID: PMC6102356 DOI: 10.3389/fncel.2018.00244] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/18/2018] [Indexed: 12/14/2022] Open
Abstract
In mesial temporal lobe epilepsy (mTLE) an initial precipitating injury can trigger aberrant wiring of neuronal circuits causing seizure activity. While circuit reorganization is known to be largely activity-dependent, the interactions between neuronal activity and synaptic plasticity during the development of mTLE remain poorly understood. Therefore, the present study aimed at delineating the spatiotemporal relationship between epileptic activity, activity-dependent gene expression and synaptic plasticity during kainic acid-induced epileptogenesis in mice. We show that during epileptogenesis the sclerotic hippocampus differed from non-sclerotic regions by displaying a consistently lower power of paroxysmal discharges. However, the power of these discharges steadily increased during epileptogenesis. This increase was paralleled by the upregulation of the activity-related cytoskeleton protein (Arc) gene expression in dentate granule cells (DGCs) of the sclerotic hippocampus. Importantly, we found that Arc mRNA-upregulating DGCs exhibited increased spine densities and spine sizes, but at the same time decreased AMPA-type glutamate receptor (AMPAR) densities. Finally, we show that in vivo optogenetic stimulation of DGC synapses evoked robust seizure activity in epileptic mice, but failed to induce dendritic translocation of Arc mRNA as under healthy conditions, supporting the theory of a breakdown of the dentate gate in mTLE. We conclude that during epileptogenesis epileptic activity emerges early and persists in the whole hippocampus, however, only the sclerotic part shows modulation of discharge amplitudes accompanied by plasticity of DGCs. In this context, we identified Arc as a putative mediator between seizure activity and synaptic plasticity.
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Affiliation(s)
- Philipp Janz
- Experimental Epilepsy Research, Department of Neurosurgery, University Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Pascal Hauser
- Experimental Epilepsy Research, Department of Neurosurgery, University Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Katharina Heining
- Faculty of Biology, University of Freiburg, Freiburg, Germany.,Laboratory for Biomicrotechnology, Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany.,Bernstein Center Freiburg, University of Freiburg, Freiburg, Germany
| | - Sigrun Nestel
- Institute for Anatomy and Cell Biology, Department of Neuroanatomy, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias Kirsch
- Institute for Anatomy and Cell Biology, Department of Neuroanatomy, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,BrainLinks-BrainTools Cluster of Excellence, University of Freiburg, Freiburg, Germany
| | - Ulrich Egert
- Laboratory for Biomicrotechnology, Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany.,Bernstein Center Freiburg, University of Freiburg, Freiburg, Germany.,BrainLinks-BrainTools Cluster of Excellence, University of Freiburg, Freiburg, Germany
| | - Carola A Haas
- Experimental Epilepsy Research, Department of Neurosurgery, University Medical Center, University of Freiburg, Freiburg, Germany.,Bernstein Center Freiburg, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,BrainLinks-BrainTools Cluster of Excellence, University of Freiburg, Freiburg, Germany
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26
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Das S, Moon HC, Singer RH, Park HY. A transgenic mouse for imaging activity-dependent dynamics of endogenous Arc mRNA in live neurons. SCIENCE ADVANCES 2018; 4:eaar3448. [PMID: 29938222 PMCID: PMC6010337 DOI: 10.1126/sciadv.aar3448] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 05/10/2018] [Indexed: 05/05/2023]
Abstract
Localized translation plays a crucial role in synaptic plasticity and memory consolidation. However, it has not been possible to follow the dynamics of memory-associated mRNAs in living neurons in response to neuronal activity in real time. We have generated a novel mouse model where the endogenous Arc/Arg3.1 gene is tagged in its 3' untranslated region with stem-loops that bind a bacteriophage PP7 coat protein (PCP), allowing visualization of individual mRNAs in real time. The physiological response of the tagged gene to neuronal activity is identical to endogenous Arc and reports the true dynamics of Arc mRNA from transcription to degradation. The transcription dynamics of Arc in cultured hippocampal neurons revealed two novel results: (i) A robust transcriptional burst with prolonged ON state occurs after stimulation, and (ii) transcription cycles continue even after initial stimulation is removed. The correlation of stimulation with Arc transcription and mRNA transport in individual neurons revealed that stimulus-induced Ca2+ activity was necessary but not sufficient for triggering Arc transcription and that blocking neuronal activity did not affect the dendritic transport of newly synthesized Arc mRNAs. This mouse will provide an important reagent to investigate how individual neurons transduce activity into spatiotemporal regulation of gene expression at the synapse.
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Affiliation(s)
- Sulagna Das
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hyungseok C. Moon
- Department of Physics and Astronomy, Seoul National University, Seoul 08826, Korea
| | - Robert H. Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
- Corresponding author. (H.Y.P.); (R.H.S.)
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul 08826, Korea
- The Institute of Applied Physics, Seoul National University, Seoul 08826, Korea
- Corresponding author. (H.Y.P.); (R.H.S.)
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27
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Ashley J, Cordy B, Lucia D, Fradkin LG, Budnik V, Thomson T. Retrovirus-like Gag Protein Arc1 Binds RNA and Traffics across Synaptic Boutons. Cell 2018; 172:262-274.e11. [PMID: 29328915 PMCID: PMC5793882 DOI: 10.1016/j.cell.2017.12.022] [Citation(s) in RCA: 272] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 08/15/2017] [Accepted: 12/18/2017] [Indexed: 12/31/2022]
Abstract
Arc/Arg3.1 is required for synaptic plasticity and cognition, and mutations in this gene are linked to autism and schizophrenia. Arc bears a domain resembling retroviral/retrotransposon Gag-like proteins, which multimerize into a capsid that packages viral RNA. The significance of such a domain in a plasticity molecule is uncertain. Here, we report that the Drosophila Arc1 protein forms capsid-like structures that bind darc1 mRNA in neurons and is loaded into extracellular vesicles that are transferred from motorneurons to muscles. This loading and transfer depends on the darc1-mRNA 3' untranslated region, which contains retrotransposon-like sequences. Disrupting transfer blocks synaptic plasticity, suggesting that transfer of dArc1 complexed with its mRNA is required for this function. Notably, cultured cells also release extracellular vesicles containing the Gag region of the Copia retrotransposon complexed with its own mRNA. Taken together, our results point to a trans-synaptic mRNA transport mechanism involving retrovirus-like capsids and extracellular vesicles.
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Affiliation(s)
- James Ashley
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Benjamin Cordy
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Diandra Lucia
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lee G Fradkin
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Vivian Budnik
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Travis Thomson
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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28
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Wilkerson JR, Albanesi JP, Huber KM. Roles for Arc in metabotropic glutamate receptor-dependent LTD and synapse elimination: Implications in health and disease. Semin Cell Dev Biol 2017; 77:51-62. [PMID: 28969983 DOI: 10.1016/j.semcdb.2017.09.035] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/21/2017] [Accepted: 09/26/2017] [Indexed: 10/18/2022]
Abstract
The Arc gene is robustly transcribed in specific neural ensembles in response to experience-driven activity. Upon induction, Arc mRNA is transported to dendrites, where it can be rapidly and locally translated by activation of metabotropic glutamate receptors (mGluR1/5). mGluR-induced dendritic synthesis of Arc is implicated in weakening or elimination of excitatory synapses by triggering endocytosis of postsynaptic AMPARs in both hippocampal CA1 and cerebellar Purkinje neurons. Importantly, CA1 neurons with experience-induced Arc mRNA are susceptible, or primed for mGluR-induced long-term synaptic depression (mGluR-LTD). Here we review mechanisms and function of Arc in mGluR-LTD and synapse elimination and propose roles for these forms of plasticity in Arc-dependent formation of sparse neural representations of learned experience. We also discuss accumulating evidence linking dysregulation of Arc and mGluR-LTD in human cognitive disorders such as intellectual disability, autism and Alzheimer's disease.
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Affiliation(s)
- Julia R Wilkerson
- Departments of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States
| | - Joseph P Albanesi
- Departments of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States
| | - Kimberly M Huber
- Departments of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States.
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29
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Urbanek MO, Michalak M, Krzyzosiak WJ. 2D and 3D FISH of expanded repeat RNAs in human lymphoblasts. Methods 2017; 120:49-57. [PMID: 28404480 DOI: 10.1016/j.ymeth.2017.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/09/2017] [Accepted: 04/05/2017] [Indexed: 12/18/2022] Open
Abstract
The first methods for visualizing RNAs within cells were designed for simple imaging of specific transcripts in cells or tissues and since then significant technical advances have been made in this field. Today, high-resolution images can be obtained, enabling visualization of single transcript molecules, quantitative analyses of images, and precise localization of RNAs within cells as well as co-localization of transcripts with specific proteins or other molecules. In addition, tracking of RNA dynamics within single cell has become possible. RNA imaging techniques have been utilized for investigating the role of mutant RNAs in a number of human disorders caused by simple microsatellite expansions. These diseases include myotonic dystrophy type 1 and 2, amyotrophic lateral sclerosis/frontotemporal dementia, fragile X-associated tremor/ataxia syndrome, and Huntington's disease. Mutant RNAs with expanded repeats tend to aggregate predominantly within cell nuclei, forming structures called RNA foci. In this study, we demonstrate methods for fluorescent visualization of RNAs in both fixed and living cells using the example of RNAs containing various expanded repeat tracts (CUG, CCUG, GGGGCC, CGG, and CAG) from experiment design to image analysis. We describe in detail 2D and 3D fluorescence in situ hybridization (FISH) protocols for imaging expanded repeats RNAs, and we review briefly live imaging techniques used to characterize RNA foci formed by mutant RNAs. These methods could be used to image the entire cellular pathway of RNAs, from transcription to degradation.
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Affiliation(s)
- Martyna O Urbanek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland
| | - Michal Michalak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland.
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30
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Lee BH, Bae SW, Shim JJ, Park SY, Park HY. Imaging Single-mRNA Localization and Translation in Live Neurons. Mol Cells 2016; 39:841-846. [PMID: 28030897 PMCID: PMC5223100 DOI: 10.14348/molcells.2016.0277] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 01/18/2023] Open
Abstract
Local protein synthesis mediates precise spatio-temporal regulation of gene expression for neuronal functions such as long-term plasticity, axon guidance and regeneration. To reveal the underlying mechanisms of local translation, it is crucial to understand mRNA transport, localization and translation in live neurons. Among various techniques for mRNA analysis, fluorescence microscopy has been widely used as the most direct method to study localization of mRNA. Live-cell imaging of single RNA molecules is particularly advantageous to dissect the highly heterogeneous and dynamic nature of messenger ribonucleoprotein (mRNP) complexes in neurons. Here, we review recent advances in the study of mRNA localization and translation in live neurons using novel techniques for single-RNA imaging.
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Affiliation(s)
- Byung Hun Lee
- Department of Physics and Astronomy, Seoul National University, Seoul 08826,
Korea
| | - Seong-Woo Bae
- Department of Physics and Astronomy, Seoul National University, Seoul 08826,
Korea
| | - Jaeyoun Jay Shim
- Department of Physics and Astronomy, Seoul National University, Seoul 08826,
Korea
| | - Sung Young Park
- Center for RNA Research, Institute for Basic Science, Seoul 08826,
Korea
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul 08826,
Korea
- The Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826,
Korea
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31
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Lampasona AA, Czaplinski K. RNA voyeurism: A coming of age story. Methods 2016; 98:10-17. [DOI: 10.1016/j.ymeth.2015.11.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 10/22/2022] Open
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32
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Williams AH, O'Donnell C, Sejnowski TJ, O'Leary T. Dendritic trafficking faces physiologically critical speed-precision tradeoffs. eLife 2016; 5:e20556. [PMID: 28034367 PMCID: PMC5201421 DOI: 10.7554/elife.20556] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/29/2016] [Indexed: 01/27/2023] Open
Abstract
Nervous system function requires intracellular transport of channels, receptors, mRNAs, and other cargo throughout complex neuronal morphologies. Local signals such as synaptic input can regulate cargo trafficking, motivating the leading conceptual model of neuron-wide transport, sometimes called the 'sushi-belt model' (Doyle and Kiebler, 2011). Current theories and experiments are based on this model, yet its predictions are not rigorously understood. We formalized the sushi belt model mathematically, and show that it can achieve arbitrarily complex spatial distributions of cargo in reconstructed morphologies. However, the model also predicts an unavoidable, morphology dependent tradeoff between speed, precision and metabolic efficiency of cargo transport. With experimental estimates of trafficking kinetics, the model predicts delays of many hours or days for modestly accurate and efficient cargo delivery throughout a dendritic tree. These findings challenge current understanding of the efficacy of nucleus-to-synapse trafficking and may explain the prevalence of local biosynthesis in neurons.
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Affiliation(s)
- Alex H Williams
- Department of Neurosciences, University of California, San Diego, La Jolla, United States,Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States,Department of Neurobiology, Stanford University, Stanford, United States, (AHW)
| | - Cian O'Donnell
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States,Department of Computer Science, University of Bristol, Bristol, United Kingdom
| | - Terrence J Sejnowski
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States,Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Timothy O'Leary
- Volen Center and Biology Department, Brandeis University, Waltham, United States,Department of Engineering, University of Cambridge, Cambridge, United Kingdom, (TO)
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33
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New Insights on Retrieval-Induced and Ongoing Memory Consolidation: Lessons from Arc. Neural Plast 2015; 2015:184083. [PMID: 26380114 PMCID: PMC4561316 DOI: 10.1155/2015/184083] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/26/2015] [Accepted: 03/03/2015] [Indexed: 01/08/2023] Open
Abstract
The mainstream view on the neurobiological mechanisms underlying memory formation states that memory traces reside on the network of cells activated during initial acquisition that becomes active again upon retrieval (reactivation). These activation and reactivation processes have been called "conjunctive trace." This process implies that singular molecular events must occur during acquisition, strengthening the connection between the implicated cells whose synchronous activity must underlie subsequent reactivations. The strongest experimental support for the conjunctive trace model comes from the study of immediate early genes such as c-fos, zif268, and activity-regulated cytoskeletal-associated protein. The expressions of these genes are reliably induced by behaviorally relevant neuronal activity and their products often play a central role in long-term memory formation. In this review, we propose that the peculiar characteristics of Arc protein, such as its optimal expression after ongoing experience or familiar behavior, together with its versatile and central functions in synaptic plasticity could explain how familiarization and recognition memories are stored and preserved in the mammalian brain.
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34
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Urbanek MO, Galka-Marciniak P, Olejniczak M, Krzyzosiak WJ. RNA imaging in living cells - methods and applications. RNA Biol 2015; 11:1083-95. [PMID: 25483044 PMCID: PMC4615301 DOI: 10.4161/rna.35506] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Numerous types of transcripts perform multiple functions in cells, and these functions are mainly facilitated by the interactions of the RNA with various proteins and other RNAs. Insight into the dynamics of RNA biosynthesis, processing and cellular activities is highly desirable because this knowledge will deepen our understanding of cell physiology and help explain the mechanisms of RNA-mediated pathologies. In this review, we discuss the live RNA imaging systems that have been developed to date. We highlight information on the design of these systems, briefly discuss their advantages and limitations and provide examples of their numerous applications in various organisms and cell types. We present a detailed examination of one application of RNA imaging systems: this application aims to explain the role of mutant transcripts in human disease pathogenesis caused by triplet repeat expansions. Thus, this review introduces live RNA imaging systems and provides a glimpse into their various applications.
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Affiliation(s)
- Martyna O Urbanek
- a Department of Molecular Biomedicine; Institute of Bioorganic Chemistry; Polish Academy of Sciences ; Poznan , Poland
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35
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Abstract
The dentate gyrus (DG) plays a critical role in memory formation and maintenance. Fitting this specialized role, the DG has many unique characteristics. In addition to being one of the few places in which new neurons are continually added in adulthood, the region also shows a unique long-term sustained transcriptional response of the immediate-early gene Arc to sensory input. Although we know that adult-generated granule cells are reliably recruited into behaviorally-driven neuronal network, it remains unknown whether they display robust late-phase sustained transcription in response to activity like their developmentally-generated counterparts. Since this late-phase of transcription is required for enduring plasticity, knowing if sustained transcription appears as soon as these cells are incorporated provides information on their potential for plasticity. To address this question, adult F344 rats were injected with BrdU (50mg/kg/day for 5 days) and 4 weeks later explored a novel environment. Arc expression in both BrdU- and BrdU+ neurons was determined 0.5h, 1h, 2h, 6h, 8h, 12h, or 24h following this behavior. Recently-generated granule cells showed a robust sustained Arc expression following a discrete behavioral experience. These data provide information on a potential mechanism to sculpt the representations of events occurring within hours of each other to create uncorrelated representations of episodes despite a highly excitable population of neurons.
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Affiliation(s)
- Alicia Meconi
- Department of Psychology, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada
| | - Erika Lui
- Department of Psychology, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada
| | - Diano F Marrone
- Department of Psychology, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada; McKnight Brain Institute, University of Arizona, Tucson, AZ 85724, USA.
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36
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Buxbaum AR, Yoon YJ, Singer RH, Park HY. Single-molecule insights into mRNA dynamics in neurons. Trends Cell Biol 2015; 25:468-75. [PMID: 26052005 DOI: 10.1016/j.tcb.2015.05.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 05/07/2015] [Accepted: 05/08/2015] [Indexed: 10/23/2022]
Abstract
Targeting of mRNAs to neuronal dendrites and axons plays an integral role in intracellular signaling, development, and synaptic plasticity. Single-molecule imaging of mRNAs in neurons and brain tissue has led to enhanced understanding of mRNA dynamics. Here we discuss aspects of mRNA regulation as revealed by single-molecule detection, which has led to quantitative analyses of mRNA diversity, localization, transport, and translation. These exciting new discoveries propel our understanding of the life of an mRNA in a neuron and how its activity is regulated at the single-molecule level.
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Affiliation(s)
- Adina R Buxbaum
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Young J Yoon
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Hye Yoon Park
- Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA; Department of Physics and Astronomy, Seoul National University, Seoul 151-747, Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul 151-742, Korea.
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37
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Sosanya NM, Cacheaux LP, Workman ER, Niere F, Perrone-Bizzozero NI, Raab-Graham KF. Mammalian Target of Rapamycin (mTOR) Tagging Promotes Dendritic Branch Variability through the Capture of Ca2+/Calmodulin-dependent Protein Kinase II α (CaMKIIα) mRNAs by the RNA-binding Protein HuD. J Biol Chem 2015; 290:16357-71. [PMID: 25944900 DOI: 10.1074/jbc.m114.599399] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Indexed: 02/05/2023] Open
Abstract
The fate of a memory, whether stored or forgotten, is determined by the ability of an active or tagged synapse to undergo changes in synaptic efficacy requiring protein synthesis of plasticity-related proteins. A synapse can be tagged, but without the "capture" of plasticity-related proteins, it will not undergo long lasting forms of plasticity (synaptic tagging and capture hypothesis). What the "tag" is and how plasticity-related proteins are captured at tagged synapses are unknown. Ca(2+)/calmodulin-dependent protein kinase II α (CaMKIIα) is critical in learning and memory and is synthesized locally in neuronal dendrites. The mechanistic (mammalian) target of rapamycin (mTOR) is a protein kinase that increases CaMKIIα protein expression; however, the mechanism and site of dendritic expression are unknown. Herein, we show that mTOR activity mediates the branch-specific expression of CaMKIIα, favoring one secondary, daughter branch over the other in a single neuron. mTOR inhibition decreased the dendritic levels of CaMKIIα protein and mRNA by shortening its poly(A) tail. Overexpression of the RNA-stabilizing protein HuD increased CaMKIIα protein levels and preserved its selective expression in one daughter branch over the other when mTOR was inhibited. Unexpectedly, deleting the third RNA recognition motif of HuD, the domain that binds the poly(A) tail, eliminated the branch-specific expression of CaMKIIα when mTOR was active. These results provide a model for one molecular mechanism that may underlie the synaptic tagging and capture hypothesis where mTOR is the tag, preventing deadenylation of CaMKIIα mRNA, whereas HuD captures and promotes its expression in a branch-specific manner.
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Affiliation(s)
- Natasha M Sosanya
- From the Center for Learning and Memory, Department of Neuroscience, Institute for Cell Biology, and United States Army Institute of Surgical Research, Joint Base San Antonio-Fort Sam, Houston, Texas 78234, and
| | - Luisa P Cacheaux
- From the Center for Learning and Memory, Department of Neuroscience
| | - Emily R Workman
- From the Center for Learning and Memory, Department of Neuroscience, Institute for Neuroscience, University of Texas, Austin, Texas 78712
| | - Farr Niere
- From the Center for Learning and Memory, Department of Neuroscience
| | - Nora I Perrone-Bizzozero
- Department of Neurosciences, Psychiatry and Behavioral Sciences, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131
| | - Kimberly F Raab-Graham
- From the Center for Learning and Memory, Department of Neuroscience, Institute for Cell Biology, and Institute for Neuroscience, University of Texas, Austin, Texas 78712,
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38
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Steward O, Farris S, Pirbhoy PS, Darnell J, Driesche SJV. Localization and local translation of Arc/Arg3.1 mRNA at synapses: some observations and paradoxes. Front Mol Neurosci 2015; 7:101. [PMID: 25628532 PMCID: PMC4290588 DOI: 10.3389/fnmol.2014.00101] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 12/11/2014] [Indexed: 11/13/2022] Open
Abstract
Arc is a unique immediate early gene whose expression is induced as synapses are being modified during learning. The uniqueness comes from the fact that newly synthesized Arc mRNA is rapidly transported throughout dendrites where it localizes near synapses that were recently activated. Here, we summarize aspects of Arc mRNA translation in dendrites in vivo, focusing especially on features of its expression that are paradoxical or that donot fit in with current models of how Arc protein operates. Findings from in vivo studies that donot quite fit include: (1) Following induction of LTP in vivo, Arc mRNA and protein localize near active synapses, but are also distributed throughout dendrites. In contrast, Arc mRNA localizes selectively near active synapses when stimulation is continued as Arc mRNA is transported into dendrites; (2) Strong induction of Arc expression as a result of a seizure does not lead to a rundown of synaptic efficacy in vivo as would be predicted by the hypothesis that high levels of Arc cause glutamate receptor endocytosis and LTD. (3) Arc protein is synthesized in the perinuclear cytoplasm rapidly after transcriptional activation, indicating that at least a pool of Arc mRNA is not translationally repressed to allow for dendritic delivery; (4) Increases in Arc mRNA in dendrites are not paralleled by increases in levels of exon junction complex (EJC) proteins. These results of studies of mRNA trafficking in neurons in vivo provide a new perspective on the possible roles of Arc in activity-dependent synaptic modifications.
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Affiliation(s)
- Oswald Steward
- Reeve-Irvine Research Center, University of California Irvine Irvine, CA, USA ; Department of Anatomy and Neurobiology, University of California Irvine Irvine, CA, USA ; Department of Neurobiology and Behavior, University of California Irvine Irvine, CA, USA ; Center for the Neurobiology of Learning and Memory, University of California Irvine Irvine, CA, USA
| | - Shannon Farris
- Reeve-Irvine Research Center, University of California Irvine Irvine, CA, USA ; Department of Anatomy and Neurobiology, University of California Irvine Irvine, CA, USA
| | - Patricia S Pirbhoy
- Reeve-Irvine Research Center, University of California Irvine Irvine, CA, USA ; Department of Neurobiology and Behavior, University of California Irvine Irvine, CA, USA
| | - Jennifer Darnell
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University New York, NY, USA
| | - Sarah J Van Driesche
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University New York, NY, USA
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In the right place at the right time: visualizing and understanding mRNA localization. Nat Rev Mol Cell Biol 2014; 16:95-109. [PMID: 25549890 DOI: 10.1038/nrm3918] [Citation(s) in RCA: 379] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The spatial regulation of protein translation is an efficient way to create functional and structural asymmetries in cells. Recent research has furthered our understanding of how individual cells spatially organize protein synthesis, by applying innovative technology to characterize the relationship between mRNAs and their regulatory proteins, single-mRNA trafficking dynamics, physiological effects of abrogating mRNA localization in vivo and for endogenous mRNA labelling. The implementation of new imaging technologies has yielded valuable information on mRNA localization, for example, by observing single molecules in tissues. The emerging movements and localization patterns of mRNAs in morphologically distinct unicellular organisms and in neurons have illuminated shared and specialized mechanisms of mRNA localization, and this information is complemented by transgenic and biochemical techniques that reveal the biological consequences of mRNA mislocalization.
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Abstract
Synaptic plasticity, learning, and memory require high temporal and spatial control of gene expression. These processes are thought to rely mainly on asymmetric mRNA transport to synapses. Already in the early days of studying mRNA transport, Wilhelm and Vale proposed a multi-step process in 1993. Since then, we have gained important novel insights into how these individual steps are controlled by research performed in various cell types and organisms. Here, we present the latest view on how dendritic mRNA localization is achieved and how local translation at the synapse is regulated. In particular, we propose that the recently observed heterogeneity of RNA-protein particle assembly in neurons might be the key for how precise gene expression in the brain is achieved. In addition, we focus on latest data dealing with translational activation of translationally repressed mRNPs at a synapse that experiences learning-induced changes in its morphology and function. Together, these new findings shed new light on how precise regulatory mechanisms can lead to synaptic plasticity and memory formation.
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Affiliation(s)
- Saskia Hutten
- a Department of Anatomy and Cell Biology ; Ludwig-Maximilians-University ; Munich , Germany
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Gardiol A, St Johnston D. Staufen targets coracle mRNA to Drosophila neuromuscular junctions and regulates GluRIIA synaptic accumulation and bouton number. Dev Biol 2014; 392:153-67. [PMID: 24951879 PMCID: PMC4111903 DOI: 10.1016/j.ydbio.2014.06.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/08/2014] [Accepted: 06/09/2014] [Indexed: 11/28/2022]
Abstract
The post-synaptic translation of localised mRNAs has been postulated to underlie several forms of plasticity at vertebrate synapses, but the mechanisms that target mRNAs to these postsynaptic sites are not well understood. Here we show that the evolutionary conserved dsRNA binding protein, Staufen, localises to the postsynaptic side of the Drosophila neuromuscular junction (NMJ), where it is required for the localisation of coracle mRNA and protein. Staufen plays a well-characterised role in the localisation of oskar mRNA to the oocyte posterior, where Staufen dsRNA-binding domain 5 is specifically required for its translation. Removal of Staufen dsRNA-binding domain 5, disrupts the postsynaptic accumulation of Coracle protein without affecting the localisation of cora mRNA, suggesting that Staufen similarly regulates Coracle translation. Tropomyosin II, which functions with Staufen in oskar mRNA localisation, is also required for coracle mRNA localisation, suggesting that similar mechanisms target mRNAs to the NMJ and the oocyte posterior. Coracle, the orthologue of vertebrate band 4.1, functions in the anchoring of the glutamate receptor IIA subunit (GluRIIA) at the synapse. Consistent with this, staufen mutant larvae show reduced accumulation of GluRIIA at synapses. The NMJs of staufen mutant larvae have also a reduced number of synaptic boutons. Altogether, this suggests that this novel Staufen-dependent mRNA localisation and local translation pathway may play a role in the developmentally regulated growth of the NMJ.
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Affiliation(s)
- Alejandra Gardiol
- The WellcomeCRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, United Kingdom
| | - Daniel St Johnston
- The WellcomeCRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, United Kingdom.
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Czaplinski K. Understanding mRNA trafficking: Are we there yet? Semin Cell Dev Biol 2014; 32:63-70. [DOI: 10.1016/j.semcdb.2014.04.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 04/17/2014] [Indexed: 10/25/2022]
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Caffino L, Giannotti G, Malpighi C, Racagni G, Filip M, Fumagalli F. Long-Term Abstinence from Developmental Cocaine Exposure Alters Arc/Arg3.1 Modulation in the Rat Medial Prefrontal Cortex. Neurotox Res 2014; 26:299-306. [DOI: 10.1007/s12640-014-9472-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/20/2014] [Accepted: 04/21/2014] [Indexed: 01/22/2023]
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Zhang X, Zajac AL, Huang L, Behlke MA, Tsourkas A. Imaging the directed transport of single engineered RNA transcripts in real-time using ratiometric bimolecular beacons. PLoS One 2014; 9:e85813. [PMID: 24454933 PMCID: PMC3893274 DOI: 10.1371/journal.pone.0085813] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 12/02/2013] [Indexed: 11/26/2022] Open
Abstract
The relationship between RNA expression and cell function can often be difficult to decipher due to the presence of both temporal and sub-cellular processing of RNA. These intricacies of RNA regulation can often be overlooked when only acquiring global measurements of RNA expression. This has led to development of several tools that allow for the real-time imaging of individual engineered RNA transcripts in living cells. Here, we describe a new technique that utilizes an oligonucleotide-based probe, ratiometric bimolecular beacon (RBMB), to image RNA transcripts that were engineered to contain 96-tandem repeats of the RBMB target sequence in the 3′-untranslated region. Binding of RBMBs to the target RNA resulted in discrete bright fluorescent spots, representing individual transcripts, that could be imaged in real-time. Since RBMBs are a synthetic probe, the use of photostable, bright, and red-shifted fluorophores led to a high signal-to-background. RNA motion was readily characterized by both mean squared displacement and moment scaling spectrum analyses. These analyses revealed clear examples of directed, Brownian, and subdiffusive movements.
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Affiliation(s)
- Xuemei Zhang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Allison L. Zajac
- Cell Biology and Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lingyan Huang
- Integrated DNA Technologies, Inc., Coralville, Iowa, United States of America
| | - Mark A. Behlke
- Integrated DNA Technologies, Inc., Coralville, Iowa, United States of America
| | - Andrew Tsourkas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Kim TK, Sul JY, Helmfors H, Langel U, Kim J, Eberwine J. Dendritic glutamate receptor mRNAs show contingent local hotspot-dependent translational dynamics. Cell Rep 2013; 5:114-25. [PMID: 24075992 DOI: 10.1016/j.celrep.2013.08.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 07/24/2013] [Accepted: 08/14/2013] [Indexed: 11/16/2022] Open
Abstract
Protein synthesis in neuronal dendrites underlies long-term memory formation in the brain. Local translation of reporter mRNAs has demonstrated translation in dendrites at focal points called translational hotspots. Various reports have shown that hundreds to thousands of mRNAs are localized to dendrites, yet the dynamics of translation of multiple dendritic mRNAs has remained elusive. Here, we show that the protein translational activities of two dendritically localized mRNAs are spatiotemporally complex but constrained by the translational hotspots in which they are colocalized. Cotransfection of glutamate receptor 2 (GluR2) and GluR4 mRNAs (engineered to encode different fluorescent proteins) into rat hippocampal neurons demonstrates a heterogeneous distribution of translational hotspots for the two mRNAs along dendrites. Stimulation with s-3,5-dihydroxy-phenylglycine modifies the translational dynamics of both of these RNAs in a complex saturable manner. These results suggest that the translational hotspot is a primary structural regulator of the simultaneous yet differential translation of multiple mRNAs in the neuronal dendrite.
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Affiliation(s)
- Tae Kyung Kim
- Department of Pharmacology, Perelman School of Medicine, Philadelphia, PA 19104-6084, USA
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Li M, Liu WJ, Lu B, Wang YH, Liu JG. Differential expression of Arc in the mesocorticolimbic system is involved in drug and natural rewarding behavior in rats. Acta Pharmacol Sin 2013; 34:1013-24. [PMID: 23708554 DOI: 10.1038/aps.2013.28] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 03/06/2013] [Indexed: 12/25/2022] Open
Abstract
AIM To investigate the different effects of heroin and milk in activating the corticostriatal system that plays a critical role in reward reinforcement learning. METHODS Male SD rats were trained daily for 15 d to self-administer heroin or milk tablets in a classic runway drug self-administration model. Immunohistochemical assay was used to quantify Arc protein expression in the medial prefrontal cortex (mPFC), the nucleus accumbens (NAc), the dorsomedial striatum (DMS) and the ventrolateral striatum (VLS) in response to chronic self-administration of heroin or milk tablets. NMDA receptor antagonist MK801 (0.1 mg/kg) or dopamine D1 receptor antagonist SCH23390 (0.03 mg/kg) were intravenously injected at the same time as heroin was infused intravenously. RESULTS Runway training with heroin resulted in robust enhancement of Arc expression in the mPFC, the NAc and the DMS on d 1, 7, and 15, and in the VLS on d 1 and d 7. However, runway training with milk led to increased Arc expression in the mPFC, the NAc and the DMS only on d 7 and/or d 15 but not on d 1. Moreover, runway training with milk failed to induce increased Arc protein in the VLS. Both heroin-seeking behavior and Arc protein expression were blocked by MK801 or SCH23390 administration. CONCLUSION The VLS is likely to be critically involved in drug-seeking behavior. The NMDA- and D1 receptor-dependent Arc expression is important in drug-seeking behavior.
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Pathak GK, Love JM, Chetta J, Shah SB. A comparative quantitative assessment of axonal and dendritic mRNA transport in maturing hippocampal neurons. PLoS One 2013; 8:e65917. [PMID: 23894274 PMCID: PMC3718819 DOI: 10.1371/journal.pone.0065917] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/30/2013] [Indexed: 12/16/2022] Open
Abstract
Translation of mRNA in axons and dendrites enables a rapid supply of proteins to specific sites of localization within the neuron. Distinct mRNA-containing cargoes, including granules and mitochondrial mRNA, are transported within neuronal projections. The distributions of these cargoes appear to change during neuronal development, but details on the dynamics of mRNA transport during these transitions remain to be elucidated. For this study, we have developed imaging and image processing methods to quantify several transport parameters that can define the dynamics of RNA transport and localization. Using these methods, we characterized the transport of mitochondrial and non-mitochondrial mRNA in differentiated axons and dendrites of cultured hippocampal neurons varying in developmental maturity. Our results suggest differences in the transport profiles of mitochondrial and non-mitochondrial mRNA, and differences in transport parameters at different time points, and between axons and dendrites. Furthermore, within the non-mitochondrial mRNA pool, we observed two distinct populations that differed in their fluorescence intensity and velocity. The net axonal velocity of the brighter pool was highest at day 7 (0.002±0.001 µm/s, mean ± SEM), raising the possibility of a presynaptic requirement for mRNA during early stages of synapse formation. In contrast, the net dendritic velocity of the brighter pool increased steadily as neurons matured, with a significant difference between day 12 (0.0013±0.0006 µm/s ) and day 4 (−0.003±0.001 µm/s) suggesting a postsynaptic role for mRNAs in more mature neurons. The dim population showed similar trends, though velocities were two orders of magnitude higher than of the bright particles. This study provides a baseline for further studies on mRNA transport, and has important implications for the regulation of neuronal plasticity during neuronal development and in response to neuronal injury.
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Affiliation(s)
- Gunja K. Pathak
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - James M. Love
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Joshua Chetta
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Sameer B. Shah
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
- Departments of Orthopaedic Surgery and Bioengineering, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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Eliscovich C, Buxbaum AR, Katz ZB, Singer RH. mRNA on the move: the road to its biological destiny. J Biol Chem 2013; 288:20361-8. [PMID: 23720759 DOI: 10.1074/jbc.r113.452094] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cells have evolved to regulate the asymmetric distribution of specific mRNA targets to institute spatial and temporal control over gene expression. Over the last few decades, evidence has mounted as to the importance of localization elements in the mRNA sequence and their respective RNA-binding proteins. Live imaging methodologies have shown mechanistic details of this phenomenon. In this minireview, we focus on the advanced biochemical and cell imaging techniques used to tweeze out the finer aspects of mechanisms of mRNA movement.
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Affiliation(s)
- Carolina Eliscovich
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA
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Hayashi G, Okamoto A. Probe design for the effective fluorescence imaging of intracellular RNA. CHEM REC 2013; 13:209-17. [PMID: 23495145 DOI: 10.1002/tcr.201200026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Indexed: 01/18/2023]
Abstract
Over the past two decades, the spatiotemporal analysis of fluorescently labeled single RNA species has provided a broad insight into the synthesis, localization, degradation, and transport of RNA. To elucidate the dynamic behavior of functional RNAs in living cells, researchers throughout the world have proposed numerous fluorometric strategies for intracellular RNA imaging. Because, like most other biological molecules, RNA is intrinsically nonfluorescent, the development of methods for the labeling of RNAs of interest with fluorescent molecules is essential. Several artificial tag sequences have been attached onto the 3' end of target RNAs and used as scaffolds for interacting with their fluorescent counterparts. In this Personal Account, we focus on the methods that have been developed to show how RNAs expressed in cells can be labeled and visualized by fluorescent proteins, small molecules, or nucleic acids. Each of these methods is designed to increase the sensitivity and specificity for imaging or to decrease the background fluorescence.
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Affiliation(s)
- Gosuke Hayashi
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Tokyo 153-8904, Japan
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Dynes JL, Steward O. Arc mRNA docks precisely at the base of individual dendritic spines indicating the existence of a specialized microdomain for synapse-specific mRNA translation. J Comp Neurol 2013; 520:3105-19. [PMID: 22350812 DOI: 10.1002/cne.23073] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Arc (aka Arg 3.1) is induced by neural activity and learning experience. Arc mRNA is rapidly exported into dendrites where it localizes near activated synapses. By imaging green fluorescent protein (GFP)-tagged mRNA in living neurons in culture, we show that fusion transcripts containing the Arc 30'UTR (untranslated region) localize with remarkable precision in a microdomain at the base of dendritic spines. Transcripts with the Arc 30'UTR that encode a reporter protein rather than Arc show precise localization. Localization persists in the presence of translation inhibitors, indicating that localization does not require ongoing translation. Similarly, polyribosome complexes remained stably positioned at spine bases in brain tissue treated with the translation inhibitor (puromycin) that releases ribosomes from mRNA. Single particle tracking revealed that Arc mRNA particles positioned at spine bases exhibited highly constrained submicron movements. These observations imply the existence of a microdomain at the spine base where Arc mRNA docks in association with a previously unknown mRNA-binding structural element.
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Affiliation(s)
- Joseph L Dynes
- Reeve-Irvine Research Center, University of California at Irvine, Irvine, California 92697, USA
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