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Chekulaeva M. Mechanistic insights into the basis of widespread RNA localization. Nat Cell Biol 2024; 26:1037-1046. [PMID: 38956277 DOI: 10.1038/s41556-024-01444-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/20/2024] [Indexed: 07/04/2024]
Abstract
The importance of subcellular mRNA localization is well established, but the underlying mechanisms mostly remain an enigma. Early studies suggested that specific mRNA sequences recruit RNA-binding proteins (RBPs) to regulate mRNA localization. However, despite the observation of thousands of localized mRNAs, only a handful of these sequences and RBPs have been identified. This suggests the existence of alternative, and possibly predominant, mechanisms for mRNA localization. Here I re-examine currently described mRNA localization mechanisms and explore alternative models that could account for its widespread occurrence.
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Affiliation(s)
- Marina Chekulaeva
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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2
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Crawford RA, Eastham M, Pool MR, Ashe MP. Orchestrated centers for the production of proteins or "translation factories". WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1867. [PMID: 39048533 DOI: 10.1002/wrna.1867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/20/2024] [Accepted: 06/07/2024] [Indexed: 07/27/2024]
Abstract
The mechanics of how proteins are generated from mRNA is increasingly well understood. However, much less is known about how protein production is coordinated and orchestrated within the crowded intracellular environment, especially in eukaryotic cells. Recent studies suggest that localized sites exist for the coordinated production of specific proteins. These sites have been termed "translation factories" and roles in protein complex formation, protein localization, inheritance, and translation regulation have been postulated. In this article, we review the evidence supporting the translation of mRNA at these sites, the details of their mechanism of formation, and their likely functional significance. Finally, we consider the key uncertainties regarding these elusive structures in cells. This article is categorized under: Translation Translation > Mechanisms RNA Export and Localization > RNA Localization Translation > Regulation.
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Affiliation(s)
- Robert A Crawford
- Division of Molecular and Cellular Function, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Matthew Eastham
- Division of Molecular and Cellular Function, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Martin R Pool
- Division of Molecular and Cellular Function, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Mark P Ashe
- Division of Molecular and Cellular Function, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
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3
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De Pace R, Ghosh S, Ryan VH, Sohn M, Jarnik M, Rezvan Sangsari P, Morgan NY, Dale RK, Ward ME, Bonifacino JS. Messenger RNA transport on lysosomal vesicles maintains axonal mitochondrial homeostasis and prevents axonal degeneration. Nat Neurosci 2024; 27:1087-1102. [PMID: 38600167 PMCID: PMC11156585 DOI: 10.1038/s41593-024-01619-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
In neurons, RNA granules are transported along the axon for local translation away from the soma. Recent studies indicate that some of this transport involves hitchhiking of RNA granules on lysosome-related vesicles. In the present study, we leveraged the ability to prevent transport of these vesicles into the axon by knockout of the lysosome-kinesin adaptor BLOC-one-related complex (BORC) to identify a subset of axonal mRNAs that depend on lysosome-related vesicles for transport. We found that BORC knockout causes depletion of a large group of axonal mRNAs mainly encoding ribosomal and mitochondrial/oxidative phosphorylation proteins. This depletion results in mitochondrial defects and eventually leads to axonal degeneration in human induced pluripotent stem cell (iPSC)-derived and mouse neurons. Pathway analyses of the depleted mRNAs revealed a mechanistic connection of BORC deficiency with common neurodegenerative disorders. These results demonstrate that mRNA transport on lysosome-related vesicles is critical for the maintenance of axonal homeostasis and that its failure causes axonal degeneration.
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Affiliation(s)
- Raffaella De Pace
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Saikat Ghosh
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Veronica H Ryan
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Mira Sohn
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Michal Jarnik
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Paniz Rezvan Sangsari
- Biomedical Engineering and Physical Science Shared Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Nicole Y Morgan
- Biomedical Engineering and Physical Science Shared Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Michael E Ward
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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Hacisuleyman E, Hale CR, Noble N, Luo JD, Fak JJ, Saito M, Chen J, Weissman JS, Darnell RB. Neuronal activity rapidly reprograms dendritic translation via eIF4G2:uORF binding. Nat Neurosci 2024; 27:822-835. [PMID: 38589584 PMCID: PMC11088998 DOI: 10.1038/s41593-024-01615-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 03/05/2024] [Indexed: 04/10/2024]
Abstract
Learning and memory require activity-induced changes in dendritic translation, but which mRNAs are involved and how they are regulated are unclear. In this study, to monitor how depolarization impacts local dendritic biology, we employed a dendritically targeted proximity labeling approach followed by crosslinking immunoprecipitation, ribosome profiling and mass spectrometry. Depolarization of primary cortical neurons with KCl or the glutamate agonist DHPG caused rapid reprogramming of dendritic protein expression, where changes in dendritic mRNAs and proteins are weakly correlated. For a subset of pre-localized messages, depolarization increased the translation of upstream open reading frames (uORFs) and their downstream coding sequences, enabling localized production of proteins involved in long-term potentiation, cell signaling and energy metabolism. This activity-dependent translation was accompanied by the phosphorylation and recruitment of the non-canonical translation initiation factor eIF4G2, and the translated uORFs were sufficient to confer depolarization-induced, eIF4G2-dependent translational control. These studies uncovered an unanticipated mechanism by which activity-dependent uORF translational control by eIF4G2 couples activity to local dendritic remodeling.
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Affiliation(s)
- Ezgi Hacisuleyman
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA.
| | - Caryn R Hale
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Natalie Noble
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - John J Fak
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA
| | - Misa Saito
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA
| | - Jin Chen
- Department of Pharmacology and Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Altos Labs, Bay Area Institute of Science, Redwood City, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Robert B Darnell
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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Xu J, Hörner M, Nagel M, Korneck M, Noß M, Hauser S, Schöls L, Admard J, Casadei N, Schüle R. Unraveling Axonal Transcriptional Landscapes: Insights from iPSC-Derived Cortical Neurons and Implications for Motor Neuron Degeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586780. [PMID: 38585749 PMCID: PMC10996649 DOI: 10.1101/2024.03.26.586780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Neuronal function and pathology are deeply influenced by the distinct molecular profiles of the axon and soma. Traditional studies have often overlooked these differences due to the technical challenges of compartment specific analysis. In this study, we employ a robust RNA-sequencing (RNA-seq) approach, using microfluidic devices, to generate high-quality axonal transcriptomes from iPSC-derived cortical neurons (CNs). We achieve high specificity of axonal fractions, ensuring sample purity without contamination. Comparative analysis revealed a unique and specific transcriptional landscape in axonal compartments, characterized by diverse transcript types, including protein-coding mRNAs, ribosomal proteins (RPs), mitochondrial-encoded RNAs, and long non-coding RNAs (lncRNAs). Previous works have reported the existence of transcription factors (TFs) in the axon. Here, we detect a subset of previously unreported TFs specific to the axon and indicative of their active participation in transcriptional regulation. To investigate transcripts and pathways essential for central motor neuron (MN) degeneration and maintenance we analyzed KIF1C-knockout (KO) CNs, modeling hereditary spastic paraplegia (HSP), a disorder associated with prominent length-dependent degeneration of central MN axons. We found that several key factors crucial for survival and health were absent in KIF1C-KO axons, highlighting a possible role of these also in other neurodegenerative diseases. Taken together, this study underscores the utility of microfluidic devices in studying compartment-specific transcriptomics in human neuronal models and reveals complex molecular dynamics of axonal biology. The impact of KIF1C on the axonal transcriptome not only deepens our understanding of MN diseases but also presents a promising avenue for exploration of compartment specific disease mechanisms.
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Shoshkes-Carmel M. Telocytes in the Luminal GI Tract. Cell Mol Gastroenterol Hepatol 2024; 17:697-701. [PMID: 38342300 PMCID: PMC10958115 DOI: 10.1016/j.jcmgh.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/13/2024]
Abstract
Telocytes are unique mesenchymal cells characterized by multiple remarkably long cytoplasmic extensions that extend hundreds of micron away from the cell body. Through these extensions, telocytes establish a 3-dimensional network by connecting with other telocytes and various cell types within the tissue. In the intestine, telocytes have emerged as an essential component of the stem cell niche, providing Wnt proteins that are critical for the proliferation of stem and progenitor cells. However, the analysis of single-cell RNA sequencing has revealed other stromal populations and mechanisms for niche organization, raising questions about the role of telocytes as a component of the stem cell niche. This review explores the current state-of-the-art, existing controversies, and potential future directions related to telocytes in the luminal gastrointestinal tract.
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Affiliation(s)
- Michal Shoshkes-Carmel
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel.
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Veeraraghavan P, Engmann AK, Hatch JJ, Itoh Y, Nguyen D, Addison T, Macklis JD. Dynamic subtype- and context-specific subcellular RNA regulation in growth cones of developing neurons of the cerebral cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.24.559186. [PMID: 38328182 PMCID: PMC10849483 DOI: 10.1101/2023.09.24.559186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Molecular mechanisms that cells employ to compartmentalize function via localization of function-specific RNA and translation are only partially elucidated. We investigate long-range projection neurons of the cerebral cortex as highly polarized exemplars to elucidate dynamic regulation of RNA localization, stability, and translation within growth cones (GCs), leading tips of growing axons. Comparison of GC-localized transcriptomes between two distinct subtypes of projection neurons- interhemispheric-callosal and corticothalamic- across developmental stages identifies both distinct and shared subcellular machinery, and intriguingly highlights enrichment of genes associated with neurodevelopmental and neuropsychiatric disorders. Developmental context-specific components of GC-localized transcriptomes identify known and novel potential regulators of distinct phases of circuit formation: long-distance growth, target area innervation, and synapse formation. Further, we investigate mechanisms by which transcripts are enriched and dynamically regulated in GCs, and identify GC-enriched motifs in 3' untranslated regions. As one example, we identify cytoplasmic adenylation element binding protein 4 (CPEB4), an RNA binding protein regulating localization and translation of mRNAs encoding molecular machinery important for axonal branching and complexity. We also identify RNA binding motif single stranded interacting protein 1 (RBMS1) as a dynamically expressed regulator of RNA stabilization that enables successful callosal circuit formation. Subtly aberrant associative and integrative cortical circuitry can profoundly affect cortical function, often causing neurodevelopmental and neuropsychiatric disorders. Elucidation of context-specific subcellular RNA regulation for GC- and soma-localized molecular controls over precise circuit development, maintenance, and function offers generalizable insights for other polarized cells, and might contribute substantially to understanding neurodevelopmental and behavioral-cognitive disorders and toward targeted therapeutics.
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Affiliation(s)
- Priya Veeraraghavan
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Anne K. Engmann
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - John J. Hatch
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Yasuhiro Itoh
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Duane Nguyen
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Thomas Addison
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Jeffrey D. Macklis
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
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Thompson AC, Aizenman CD. Characterization of Na + currents regulating intrinsic excitability of optic tectal neurons. Life Sci Alliance 2024; 7:e202302232. [PMID: 37918964 PMCID: PMC10622587 DOI: 10.26508/lsa.202302232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023] Open
Abstract
Developing neurons adapt their intrinsic excitability to maintain stable output despite changing synaptic input. The mechanisms behind this process remain unclear. In this study, we examined Xenopus optic tectal neurons and found that the expressions of Nav1.1 and Nav1.6 voltage-gated Na+ channels are regulated during changes in intrinsic excitability, both during development and becsuse of changes in visual experience. Using whole-cell electrophysiology, we demonstrate the existence of distinct, fast, persistent, and resurgent Na+ currents in the tectum, and show that these Na+ currents are co-regulated with changes in Nav channel expression. Using antisense RNA to suppress the expression of specific Nav subunits, we found that up-regulation of Nav1.6 expression, but not Nav1.1, was necessary for experience-dependent increases in Na+ currents and intrinsic excitability. Furthermore, this regulation was also necessary for normal development of sensory guided behaviors. These data suggest that the regulation of Na+ currents through the modulation of Nav1.6 expression, and to a lesser extent Nav1.1, plays a crucial role in controlling the intrinsic excitability of tectal neurons and guiding normal development of the tectal circuitry.
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Affiliation(s)
- Adrian C Thompson
- https://ror.org/05gq02987 Department of Neuroscience, Brown University, Providence, RI, USA
| | - Carlos D Aizenman
- https://ror.org/05gq02987 Department of Neuroscience, Brown University, Providence, RI, USA
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9
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Pade LR, Stepler KE, Portero EP, DeLaney K, Nemes P. Biological mass spectrometry enables spatiotemporal 'omics: From tissues to cells to organelles. MASS SPECTROMETRY REVIEWS 2024; 43:106-138. [PMID: 36647247 PMCID: PMC10668589 DOI: 10.1002/mas.21824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 06/17/2023]
Abstract
Biological processes unfold across broad spatial and temporal dimensions, and measurement of the underlying molecular world is essential to their understanding. Interdisciplinary efforts advanced mass spectrometry (MS) into a tour de force for assessing virtually all levels of the molecular architecture, some in exquisite detection sensitivity and scalability in space-time. In this review, we offer vignettes of milestones in technology innovations that ushered sample collection and processing, chemical separation, ionization, and 'omics analyses to progressively finer resolutions in the realms of tissue biopsies and limited cell populations, single cells, and subcellular organelles. Also highlighted are methodologies that empowered the acquisition and analysis of multidimensional MS data sets to reveal proteomes, peptidomes, and metabolomes in ever-deepening coverage in these limited and dynamic specimens. In pursuit of richer knowledge of biological processes, we discuss efforts pioneering the integration of orthogonal approaches from molecular and functional studies, both within and beyond MS. With established and emerging community-wide efforts ensuring scientific rigor and reproducibility, spatiotemporal MS emerged as an exciting and powerful resource to study biological systems in space-time.
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Affiliation(s)
- Leena R. Pade
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kaitlyn E. Stepler
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Erika P. Portero
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kellen DeLaney
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
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Cagnetta R, Flanagan JG, Sonenberg N. Control of Selective mRNA Translation in Neuronal Subcellular Compartments in Health and Disease. J Neurosci 2023; 43:7247-7263. [PMID: 37914402 PMCID: PMC10621772 DOI: 10.1523/jneurosci.2240-22.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 11/03/2023] Open
Abstract
In multiple cell types, mRNAs are transported to subcellular compartments, where local translation enables rapid, spatially localized, and specific responses to external stimuli. Mounting evidence has uncovered important roles played by local translation in vivo in axon survival, axon regeneration, and neural wiring, as well as strong links between dysregulation of local translation and neurologic disorders. Omic studies have revealed that >1000 mRNAs are present and can be selectively locally translated in the presynaptic and postsynaptic compartments from development to adulthood in vivo A large proportion of the locally translated mRNAs is specifically upregulated or downregulated in response to distinct extracellular signals. Given that the local translatome is large, selectively translated, and cue-specifically remodeled, a fundamental question concerns how selective translation is achieved locally. Here, we review the emerging regulatory mechanisms of local selective translation in neuronal subcellular compartments, their mRNA targets, and their orchestration. We discuss mechanisms of local selective translation that remain unexplored. Finally, we describe clinical implications and potential therapeutic strategies in light of the latest advances in gene therapy.
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Affiliation(s)
- Roberta Cagnetta
- Department of Biochemistry and Goodman Cancer Institute, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - John G Flanagan
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, Massachusetts 02115
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Institute, McGill University, Montreal, Quebec H3A 1A3, Canada
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McKenna ED, Sarbanes SL, Cummings SW, Roll-Mecak A. The Tubulin Code, from Molecules to Health and Disease. Annu Rev Cell Dev Biol 2023; 39:331-361. [PMID: 37843925 DOI: 10.1146/annurev-cellbio-030123-032748] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Microtubules are essential dynamic polymers composed of α/β-tubulin heterodimers. They support intracellular trafficking, cell division, cellular motility, and other essential cellular processes. In many species, both α-tubulin and β-tubulin are encoded by multiple genes with distinct expression profiles and functionality. Microtubules are further diversified through abundant posttranslational modifications, which are added and removed by a suite of enzymes to form complex, stereotyped cellular arrays. The genetic and chemical diversity of tubulin constitute a tubulin code that regulates intrinsic microtubule properties and is read by cellular effectors, such as molecular motors and microtubule-associated proteins, to provide spatial and temporal specificity to microtubules in cells. In this review, we synthesize the rapidly expanding tubulin code literature and highlight limitations and opportunities for the field. As complex microtubule arrays underlie essential physiological processes, a better understanding of how cells employ the tubulin code has important implications for human disease ranging from cancer to neurological disorders.
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Affiliation(s)
- Elizabeth D McKenna
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA;
| | - Stephanie L Sarbanes
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA;
| | - Steven W Cummings
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA;
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA;
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland, USA
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徐 晨, 王 寅, 魏 东, 李 文, 钱 晔, 潘 新, 雷 大. [Advances of spatial omics in the individualized diagnosis and treatment of head and neck cancer]. LIN CHUANG ER BI YAN HOU TOU JING WAI KE ZA ZHI = JOURNAL OF CLINICAL OTORHINOLARYNGOLOGY, HEAD, AND NECK SURGERY 2023; 37:729-733;739. [PMID: 37830120 PMCID: PMC10722126 DOI: 10.13201/j.issn.2096-7993.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Indexed: 10/14/2023]
Abstract
Spatialomics is another research hotspot of biotechnology after single-cell sequencing technology, which can make up for the defect that single-cell sequencing technology can not obtain cell spatial distribution information. Spatialomics mainly studies the relative position of cells in tissue samples to reveal the effect of cell spatial distribution on diseases. In recent years, spatialomics has made new progress in the pathogenesis, target exploration, drug development and many other aspects of head and neck tumors. This paper summarizes the latest progress of spatialomics in the diagnosis and treatment of head and neck cancer.
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Affiliation(s)
- 晨阳 徐
- 山东大学齐鲁医院耳鼻咽喉科,国家卫生健康委员会耳鼻喉科学重点实验室(山东大学)(济南,250012)Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission Key Laboratory of Otorhinolaryngology[Shandong University], Jinan, 250012, China
| | - 寅 王
- 山东大学齐鲁医院耳鼻咽喉科,国家卫生健康委员会耳鼻喉科学重点实验室(山东大学)(济南,250012)Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission Key Laboratory of Otorhinolaryngology[Shandong University], Jinan, 250012, China
| | - 东敏 魏
- 山东大学齐鲁医院耳鼻咽喉科,国家卫生健康委员会耳鼻喉科学重点实验室(山东大学)(济南,250012)Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission Key Laboratory of Otorhinolaryngology[Shandong University], Jinan, 250012, China
| | - 文明 李
- 山东大学齐鲁医院耳鼻咽喉科,国家卫生健康委员会耳鼻喉科学重点实验室(山东大学)(济南,250012)Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission Key Laboratory of Otorhinolaryngology[Shandong University], Jinan, 250012, China
| | - 晔 钱
- 山东大学齐鲁医院耳鼻咽喉科,国家卫生健康委员会耳鼻喉科学重点实验室(山东大学)(济南,250012)Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission Key Laboratory of Otorhinolaryngology[Shandong University], Jinan, 250012, China
| | - 新良 潘
- 山东大学齐鲁医院耳鼻咽喉科,国家卫生健康委员会耳鼻喉科学重点实验室(山东大学)(济南,250012)Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission Key Laboratory of Otorhinolaryngology[Shandong University], Jinan, 250012, China
| | - 大鹏 雷
- 山东大学齐鲁医院耳鼻咽喉科,国家卫生健康委员会耳鼻喉科学重点实验室(山东大学)(济南,250012)Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission Key Laboratory of Otorhinolaryngology[Shandong University], Jinan, 250012, China
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13
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Loedige I, Baranovskii A, Mendonsa S, Dantsuji S, Popitsch N, Breimann L, Zerna N, Cherepanov V, Milek M, Ameres S, Chekulaeva M. mRNA stability and m 6A are major determinants of subcellular mRNA localization in neurons. Mol Cell 2023; 83:2709-2725.e10. [PMID: 37451262 PMCID: PMC10529935 DOI: 10.1016/j.molcel.2023.06.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/04/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
For cells to perform their biological functions, they need to adopt specific shapes and form functionally distinct subcellular compartments. This is achieved in part via an asymmetric distribution of mRNAs within cells. Currently, the main model of mRNA localization involves specific sequences called "zipcodes" that direct mRNAs to their proper locations. However, while thousands of mRNAs localize within cells, only a few zipcodes have been identified, suggesting that additional mechanisms contribute to localization. Here, we assess the role of mRNA stability in localization by combining the isolation of the soma and neurites of mouse primary cortical and mESC-derived neurons, SLAM-seq, m6A-RIP-seq, the perturbation of mRNA destabilization mechanisms, and the analysis of multiple mRNA localization datasets. We show that depletion of mRNA destabilization elements, such as m6A, AU-rich elements, and suboptimal codons, functions as a mechanism that mediates the localization of mRNAs associated with housekeeping functions to neurites in several types of neurons.
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Affiliation(s)
- Inga Loedige
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Artem Baranovskii
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Samantha Mendonsa
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Sayaka Dantsuji
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Niko Popitsch
- Max Perutz Labs, University of Vienna, Vienna BioCenter, 1030 Vienna, Austria
| | - Laura Breimann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nadja Zerna
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Vsevolod Cherepanov
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Miha Milek
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Stefan Ameres
- Max Perutz Labs, University of Vienna, Vienna BioCenter, 1030 Vienna, Austria
| | - Marina Chekulaeva
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany.
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14
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Paşcalău R, Badea TC. Signaling - transcription interactions in mouse retinal ganglion cells early axon pathfinding -a literature review. FRONTIERS IN OPHTHALMOLOGY 2023; 3:1180142. [PMID: 38983012 PMCID: PMC11182120 DOI: 10.3389/fopht.2023.1180142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 04/21/2023] [Indexed: 07/11/2024]
Abstract
Sending an axon out of the eye and into the target brain nuclei is the defining feature of retinal ganglion cells (RGCs). The literature on RGC axon pathfinding is vast, but it focuses mostly on decision making events such as midline crossing at the optic chiasm or retinotopic mapping at the target nuclei. In comparison, the exit of RGC axons out of the eye is much less explored. The first checkpoint on the RGC axons' path is the optic cup - optic stalk junction (OC-OS). OC-OS development and the exit of the RGC pioneer axons out of the eye are coordinated spatially and temporally. By the time the optic nerve head domain is specified, the optic fissure margins are in contact and the fusion process is ongoing, the first RGCs are born in its proximity and send pioneer axons in the optic stalk. RGC differentiation continues in centrifugal waves. Later born RGC axons fasciculate with the more mature axons. Growth cones at the end of the axons respond to guidance cues to adopt a centripetal direction, maintain nerve fiber layer restriction and to leave the optic cup. Although there is extensive information on OC-OS development, we still have important unanswered questions regarding its contribution to the exit of the RGC axons out of the eye. We are still to distinguish the morphogens of the OC-OS from the axon guidance molecules which are expressed in the same place at the same time. The early RGC transcription programs responsible for axon emergence and pathfinding are also unknown. This review summarizes the molecular mechanisms for early RGC axon guidance by contextualizing mouse knock-out studies on OC-OS development with the recent transcriptomic studies on developing RGCs in an attempt to contribute to the understanding of human optic nerve developmental anomalies. The published data summarized here suggests that the developing optic nerve head provides a physical channel (the closing optic fissure) as well as molecular guidance cues for the pioneer RGC axons to exit the eye.
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Affiliation(s)
- Raluca Paşcalău
- Research and Development Institute, Transilvania University of Braşov, Braşov, Romania
- Ophthalmology Clinic, Cluj County Emergency Hospital, Cluj-Napoca, Romania
| | - Tudor Constantin Badea
- Research and Development Institute, Transilvania University of Braşov, Braşov, Romania
- National Center for Brain Research, Institutul de Cercetări pentru Inteligență Artificială, Romanian Academy, Bucharest, Romania
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15
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Yang Z, Yu J, Zhang J, Song H, Ye H, Liu J, Wang N, Che P, Long G, Wang Y, Park J, Ji SJ. Facilitation of axonal transcriptome analysis with quantitative microfluidic devices. LAB ON A CHIP 2023; 23:2217-2227. [PMID: 37067243 DOI: 10.1039/d2lc01183b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Microfluidic chambers are powerful tools for studying axonal mRNA localization and translation in neurons. In addition to specific manipulation and measurements of axons, microfluidic chambers are used for collecting axonal materials to perform axonal transcriptome analysis. However, traditional bipartite and tripartite chambers have limitations either in purity or quantity of collected axons. Here, we improved the design of traditional chambers. Moreover, we developed two new quantitative chambers, multi-compartmental quantitative bipartite chamber (MQBC) and long quantitative tripartite chamber (LQTC). Compared with the traditional chambers, MQBC and LQTC could dramatically increase the efficiency in collecting axonal RNA. Finally, we applied these chambers to do comparative axon transcriptome analysis of different types of neurons. Thus, our newly designed quantitative chambers significantly improve axon collection efficiency and facilitate axonal transcriptome analysis.
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Affiliation(s)
- Zhuoxuan Yang
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Jun Yu
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Jian Zhang
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Huixue Song
- School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Haixia Ye
- School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Jianhui Liu
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Nijia Wang
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Pengfei Che
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Gaoxin Long
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Yunxuan Wang
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Jaewon Park
- School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
- OJeong Resilience Institute (OJERI), Korea University, Seoul, 02841, Korea.
| | - Sheng-Jian Ji
- School of Life Sciences, Department of Neuroscience, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
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16
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Sun C, Schuman E. A multi-omics view of neuronal subcellular protein synthesis. Curr Opin Neurobiol 2023; 80:102705. [PMID: 36913750 DOI: 10.1016/j.conb.2023.102705] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 03/13/2023]
Abstract
While it has long been known that protein synthesis is necessary for long-term memory in the brain, the logistics of neuronal protein synthesis is complicated by the extensive subcellular compartmentalization of the neuron. Local protein synthesis solves many of the logistic problems posed by the extreme complexity of dendritic and axonal arbors and the huge number of synapses. Here we review recent multi-omic and quantitative studies that elaborate a systems view of decentralized neuronal protein synthesis. We highlight recent insights from the transcriptomic, translatomic, and proteomic levels, discuss the nuanced logic of local protein synthesis for different protein features, and list the missing information needed to build a comprehensive logistic model for neuronal protein supply.
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Affiliation(s)
- Chao Sun
- Max Planck Institute for Brain Research, Frankfurt, Germany; Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Denmark; Aarhus University, Department of Molecular Biology and Genetics, Universitetsbyen 81, 8000 Aarhus C, Denmark. https://twitter.com/LukeChaoSun
| | - Erin Schuman
- Max Planck Institute for Brain Research, Frankfurt, Germany.
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17
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Goering R, Arora A, Pockalny MC, Taliaferro JM. RNA localization mechanisms transcend cell morphology. eLife 2023; 12:e80040. [PMID: 36867563 PMCID: PMC9984196 DOI: 10.7554/elife.80040] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 01/24/2023] [Indexed: 03/04/2023] Open
Abstract
RNA molecules are localized to specific subcellular regions through interactions between RNA regulatory elements and RNA binding proteins (RBPs). Generally, our knowledge of the mechanistic details behind the localization of a given RNA is restricted to a particular cell type. Here, we show that RNA/RBP interactions that regulate RNA localization in one cell type predictably regulate localization in other cell types with vastly different morphologies. To determine transcriptome-wide RNA spatial distributions across the apicobasal axis of human intestinal epithelial cells, we used our recently developed RNA proximity labeling technique, Halo-seq. We found that mRNAs encoding ribosomal proteins (RP mRNAs) were strongly localized to the basal pole of these cells. Using reporter transcripts and single-molecule RNA FISH, we found that pyrimidine-rich motifs in the 5' UTRs of RP mRNAs were sufficient to drive basal RNA localization. Interestingly, the same motifs were also sufficient to drive RNA localization to the neurites of mouse neuronal cells. In both cell types, the regulatory activity of this motif was dependent on it being in the 5' UTR of the transcript, was abolished upon perturbation of the RNA-binding protein LARP1, and was reduced upon inhibition of kinesin-1. To extend these findings, we compared subcellular RNAseq data from neuronal and epithelial cells. We found that the basal compartment of epithelial cells and the projections of neuronal cells were enriched for highly similar sets of RNAs, indicating that broadly similar mechanisms may be transporting RNAs to these morphologically distinct locations. These findings identify the first RNA element known to regulate RNA localization across the apicobasal axis of epithelial cells, establish LARP1 as an RNA localization regulator, and demonstrate that RNA localization mechanisms cut across cell morphologies.
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Affiliation(s)
- Raeann Goering
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
- RNA Bioscience Initiative, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Ankita Arora
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Megan C Pockalny
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
- RNA Bioscience Initiative, University of Colorado Anschutz Medical CampusAuroraUnited States
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18
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Massively parallel identification of mRNA localization elements in primary cortical neurons. Nat Neurosci 2023; 26:394-405. [PMID: 36646877 PMCID: PMC9991926 DOI: 10.1038/s41593-022-01243-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/01/2022] [Indexed: 01/18/2023]
Abstract
Cells adopt highly polarized shapes and form distinct subcellular compartments in many cases due to the localization of many mRNAs to specific areas, where they are translated into proteins with local functions. This mRNA localization is mediated by specific cis-regulatory elements in mRNAs, commonly called 'zipcodes'. Although there are hundreds of localized mRNAs, only a few zipcodes have been characterized. Here we describe a novel neuronal zipcode identification protocol (N-zip) that can identify zipcodes across hundreds of 3' untranslated regions. This approach combines a method of separating the principal subcellular compartments of neurons-cell bodies and neurites-with a massively parallel reporter assay. N-zip identifies the let-7 binding site and (AU)n motif as de novo zipcodes in mouse primary cortical neurons. Our analysis also provides, to our knowledge, the first demonstration of an miRNA affecting mRNA localization and suggests a strategy for detecting many more zipcodes.
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19
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Jung J, Ohk J, Kim H, Holt CE, Park HJ, Jung H. mRNA transport, translation, and decay in adult mammalian central nervous system axons. Neuron 2023; 111:650-668.e4. [PMID: 36584679 DOI: 10.1016/j.neuron.2022.12.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/31/2022] [Accepted: 12/08/2022] [Indexed: 12/30/2022]
Abstract
Localized mRNA translation regulates synapse function and axon maintenance, but how compartment-specific mRNA repertoires are regulated is largely unknown. We developed an axonal transcriptome capture method that allows deep sequencing of metabolically labeled mRNAs from retinal ganglion cell axon terminals in mouse. Comparing axonal-to-somal transcriptomes and axonal translatome-to-transcriptome enables genome-wide visualization of mRNA transport and translation and unveils potential regulators tuned to each process. FMRP and TDP-43 stand out as key regulators of transport, and experiments in Fmr1 knockout mice validate FMRP's role in the axonal transportation of synapse-related mRNAs. Pulse-and-chase experiments enable genome-wide assessment of mRNA stability in axons and reveal a strong coupling between mRNA translation and decay. Measuring the absolute mRNA abundance per axon terminal shows that the adult axonal transcriptome is stably maintained by persistent transport. Our datasets provide a rich resource for unique insights into RNA-based mechanisms in maintaining presynaptic structure and function in vivo.
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Affiliation(s)
- Jane Jung
- Department of Anatomy, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jiyeon Ohk
- Department of Anatomy, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyeyoung Kim
- Department of Anatomy, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Christine E Holt
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Hyun Jung Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.
| | - Hosung Jung
- Department of Anatomy, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.
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20
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Bourke AM, Schwarz A, Schuman EM. De-centralizing the Central Dogma: mRNA translation in space and time. Mol Cell 2023; 83:452-468. [PMID: 36669490 DOI: 10.1016/j.molcel.2022.12.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/16/2022] [Accepted: 12/28/2022] [Indexed: 01/20/2023]
Abstract
As our understanding of the cell interior has grown, we have come to appreciate that most cellular operations are localized, that is, they occur at discrete and identifiable locations or domains. These cellular domains contain enzymes, machines, and other components necessary to carry out and regulate these localized operations. Here, we review these features of one such operation: the localization and translation of mRNAs within subcellular compartments observed across cell types and organisms. We describe the conceptual advantages and the "ingredients" and mechanisms of local translation. We focus on the nature and features of localized mRNAs, how they travel and get localized, and how this process is regulated. We also evaluate our current understanding of protein synthesis machines (ribosomes) and their cadre of regulatory elements, that is, the translation factors.
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Affiliation(s)
- Ashley M Bourke
- Max Planck Institute for Brain Research, Max von Laue Strasse 4, 60438 Frankfurt, Germany
| | - Andre Schwarz
- Max Planck Institute for Brain Research, Max von Laue Strasse 4, 60438 Frankfurt, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Max von Laue Strasse 4, 60438 Frankfurt, Germany.
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21
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Pinho-Correia LM, Prokop A. Maintaining essential microtubule bundles in meter-long axons: a role for local tubulin biogenesis? Brain Res Bull 2023; 193:131-145. [PMID: 36535305 DOI: 10.1016/j.brainresbull.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Axons are the narrow, up-to-meter long cellular processes of neurons that form the biological cables wiring our nervous system. Most axons must survive for an organism's lifetime, i.e. up to a century in humans. Axonal maintenance depends on loose bundles of microtubules that run without interruption all along axons. The continued turn-over and the extension of microtubule bundles during developmental, regenerative or plastic growth requires the availability of α/β-tubulin heterodimers up to a meter away from the cell body. The underlying regulation in axons is poorly understood and hardly features in past and contemporary research. Here we discuss potential mechanisms, particularly focussing on the possibility of local tubulin biogenesis in axons. Current knowledge might suggest that local translation of tubulin takes place in axons, but far less is known about the post-translational machinery of tubulin biogenesis involving three chaperone complexes: prefoldin, CCT and TBC. We discuss functional understanding of these chaperones from a range of model organisms including yeast, plants, flies and mice, and explain what is known from human diseases. Microtubules across species depend on these chaperones, and they are clearly required in the nervous system. However, most chaperones display a high degree of functional pleiotropy, partly through independent functions of individual subunits outside their complexes, thus posing a challenge to experimental studies. Notably, we found hardly any studies that investigate their presence and function particularly in axons, thus highlighting an important gap in our understanding of axon biology and pathology.
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Affiliation(s)
- Liliana Maria Pinho-Correia
- The University of Manchester, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biology, Manchester, UK
| | - Andreas Prokop
- The University of Manchester, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biology, Manchester, UK.
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22
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Gale JR, Gedeon JY, Donnelly CJ, Gold MS. Local translation in primary afferents and its contribution to pain. Pain 2022; 163:2302-2314. [PMID: 35438669 PMCID: PMC9579217 DOI: 10.1097/j.pain.0000000000002658] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 04/08/2022] [Indexed: 02/06/2023]
Abstract
ABSTRACT Chronic pain remains a significant problem due to its prevalence, impact, and limited therapeutic options. Progress in addressing chronic pain is dependent on a better understanding of underlying mechanisms. Although the available evidence suggests that changes within the central nervous system contribute to the initiation and maintenance of chronic pain, it also suggests that the primary afferent plays a critical role in all phases of the manifestation of chronic pain in most of those who suffer. Most notable among the changes in primary afferents is an increase in excitability or sensitization. A number of mechanisms have been identified that contribute to primary afferent sensitization with evidence for both increases in pronociceptive signaling molecules, such as voltage-gated sodium channels, and decreases in antinociceptive signaling molecules, such as voltage-dependent or calcium-dependent potassium channels. Furthermore, these changes in signaling molecules seem to reflect changes in gene expression as well as posttranslational processing. A mechanism of sensitization that has received far less attention, however, is the local or axonal translation of these signaling molecules. A growing body of evidence indicates that this process not only is dynamically regulated but also contributes to the initiation and maintenance of chronic pain. Here, we review the biology of local translation in primary afferents and its relevance to pain pathobiology.
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Affiliation(s)
- Jenna R Gale
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Jeremy Y Gedeon
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | | | - Michael S Gold
- Corresponding author: Michael S Gold, PhD, Department of Neurobiology, University of Pittsburgh School of Medicine, 200 Lothrop Street, Pittsburgh, PA 15213, P: 412-383-5367,
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23
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Hees JT, Harbauer AB. Metabolic Regulation of Mitochondrial Protein Biogenesis from a Neuronal Perspective. Biomolecules 2022; 12:1595. [PMID: 36358945 PMCID: PMC9687362 DOI: 10.3390/biom12111595] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 09/29/2023] Open
Abstract
Neurons critically depend on mitochondria for ATP production and Ca2+ buffering. They are highly compartmentalized cells and therefore a finely tuned mitochondrial network constantly adapting to the local requirements is necessary. For neuronal maintenance, old or damaged mitochondria need to be degraded, while the functional mitochondrial pool needs to be replenished with freshly synthesized components. Mitochondrial biogenesis is known to be primarily regulated via the PGC-1α-NRF1/2-TFAM pathway at the transcriptional level. However, while transcriptional regulation of mitochondrial genes can change the global mitochondrial content in neurons, it does not explain how a morphologically complex cell such as a neuron adapts to local differences in mitochondrial demand. In this review, we discuss regulatory mechanisms controlling mitochondrial biogenesis thereby making a case for differential regulation at the transcriptional and translational level. In neurons, additional regulation can occur due to the axonal localization of mRNAs encoding mitochondrial proteins. Hitchhiking of mRNAs on organelles including mitochondria as well as contact site formation between mitochondria and endolysosomes are required for local mitochondrial biogenesis in axons linking defects in any of these organelles to the mitochondrial dysfunction seen in various neurological disorders.
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Affiliation(s)
- Jara Tabitha Hees
- TUM Medical Graduate Center, Technical University of Munich, 81675 Munich, Germany
- Max Planck Institute for Biological Intelligence, in Foundation, 82152 Planegg-Martinsried, Germany
| | - Angelika Bettina Harbauer
- Max Planck Institute for Biological Intelligence, in Foundation, 82152 Planegg-Martinsried, Germany
- Institute of Neuronal Cell Biology, Technical University of Munich, 80802 Munich, Germany
- Munich Cluster for Systems Neurology, 81377 Munich, Germany
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24
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Dumrongprechachan V, Salisbury RB, Butler L, MacDonald ML, Kozorovitskiy Y. Dynamic proteomic and phosphoproteomic atlas of corticostriatal axons in neurodevelopment. eLife 2022; 11:e78847. [PMID: 36239373 PMCID: PMC9629834 DOI: 10.7554/elife.78847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022] Open
Abstract
Mammalian axonal development begins in embryonic stages and continues postnatally. After birth, axonal proteomic landscape changes rapidly, coordinated by transcription, protein turnover, and post-translational modifications. Comprehensive profiling of axonal proteomes across neurodevelopment is limited, with most studies lacking cell-type and neural circuit specificity, resulting in substantial information loss. We create a Cre-dependent APEX2 reporter mouse line and map cell-type-specific proteome of corticostriatal projections across postnatal development. We synthesize analysis frameworks to define temporal patterns of axonal proteome and phosphoproteome, identifying co-regulated proteins and phosphorylations associated with genetic risk for human brain disorders. We discover proline-directed kinases as major developmental regulators. APEX2 transgenic reporter proximity labeling offers flexible strategies for subcellular proteomics with cell type specificity in early neurodevelopment, a critical period for neuropsychiatric disease.
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Affiliation(s)
- Vasin Dumrongprechachan
- Department of Neurobiology, Northwestern UniversityEvanstonUnited States
- The Chemistry of Life Processes Institute, Northwestern UniversityEvanstonUnited States
| | - Ryan B Salisbury
- Department of Psychiatry, University of PittsburghPittsburghUnited States
| | - Lindsey Butler
- Department of Neurobiology, Northwestern UniversityEvanstonUnited States
| | | | - Yevgenia Kozorovitskiy
- Department of Neurobiology, Northwestern UniversityEvanstonUnited States
- The Chemistry of Life Processes Institute, Northwestern UniversityEvanstonUnited States
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25
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Schmitd LB, Perez-Pacheco C, Bellile EL, Wu W, Casper K, Mierzwa M, Rozek LS, Wolf GT, Taylor JM, D'Silva NJ. Spatial and Transcriptomic Analysis of Perineural Invasion in Oral Cancer. Clin Cancer Res 2022; 28:3557-3572. [PMID: 35819260 PMCID: PMC9560986 DOI: 10.1158/1078-0432.ccr-21-4543] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/25/2022] [Accepted: 05/24/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE Perineural invasion (PNI), a common occurrence in oral squamous cell carcinomas, is associated with poor survival. Consequently, these tumors are treated aggressively. However, diagnostic criteria of PNI vary and its role as an independent predictor of prognosis has not been established. To address these knowledge gaps, we investigated spatial and transcriptomic profiles of PNI-positive and PNI-negative nerves. EXPERIMENTAL DESIGN Tissue sections from 142 patients were stained with S100 and cytokeratin antibodies. Nerves were identified in two distinct areas: tumor bulk and margin. Nerve diameter and nerve-to-tumor distance were assessed; survival analyses were performed. Spatial transcriptomic analysis of nerves at varying distances from tumor was performed with NanoString GeoMx Digital Spatial Profiler Transcriptomic Atlas. RESULTS PNI is an independent predictor of poor prognosis among patients with metastasis-free lymph nodes. Patients with close nerve-tumor distance have poor outcomes even if diagnosed as PNI negative using current criteria. Patients with large nerve(s) in the tumor bulk survive poorly, suggesting that even PNI-negative nerves facilitate tumor progression. Diagnostic criteria were supported by spatial transcriptomic analyses of >18,000 genes; nerves in proximity to cancer exhibit stress and growth response changes that diminish with increasing nerve-tumor distance. These findings were validated in vitro and in human tissue. CONCLUSIONS This is the first study in human cancer with high-throughput gene expression analysis in nerves with striking correlations between transcriptomic profile and clinical outcomes. Our work illuminates nerve-cancer interactions suggesting that cancer-induced injury modulates neuritogenesis, and supports reclassification of PNI based on nerve-tumor distance rather than current subjective criteria.
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Affiliation(s)
- Ligia B. Schmitd
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan
| | - Cindy Perez-Pacheco
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan
| | - Emily L. Bellile
- Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Weisheng Wu
- Bioinformatics Core, University of Michigan, Ann Arbor, Michigan
| | - Keith Casper
- Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Michelle Mierzwa
- Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Laura S. Rozek
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Gregory T. Wolf
- Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Jeremy M.G. Taylor
- Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan
- Radiation Oncology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Nisha J. D'Silva
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan
- Pathology, University of Michigan Medical School, Ann Arbor, Michigan
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
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26
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Triantopoulou N, Vidaki M. Local mRNA translation and cytoskeletal reorganization: Mechanisms that tune neuronal responses. Front Mol Neurosci 2022; 15:949096. [PMID: 35979146 PMCID: PMC9376447 DOI: 10.3389/fnmol.2022.949096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/07/2022] [Indexed: 12/31/2022] Open
Abstract
Neurons are highly polarized cells with significantly long axonal and dendritic extensions that can reach distances up to hundreds of centimeters away from the cell bodies in higher vertebrates. Their successful formation, maintenance, and proper function highly depend on the coordination of intricate molecular networks that allow axons and dendrites to quickly process information, and respond to a continuous and diverse cascade of environmental stimuli, often without enough time for communication with the soma. Two seemingly unrelated processes, essential for these rapid responses, and thus neuronal homeostasis and plasticity, are local mRNA translation and cytoskeletal reorganization. The axonal cytoskeleton is characterized by high stability and great plasticity; two contradictory attributes that emerge from the powerful cytoskeletal rearrangement dynamics. Cytoskeletal reorganization is crucial during nervous system development and in adulthood, ensuring the establishment of proper neuronal shape and polarity, as well as regulating intracellular transport and synaptic functions. Local mRNA translation is another mechanism with a well-established role in the developing and adult nervous system. It is pivotal for axonal guidance and arborization, synaptic formation, and function and seems to be a key player in processes activated after neuronal damage. Perturbations in the regulatory pathways of local translation and cytoskeletal reorganization contribute to various pathologies with diverse clinical manifestations, ranging from intellectual disabilities (ID) to autism spectrum disorders (ASD) and schizophrenia (SCZ). Despite the fact that both processes are essential for the orchestration of pathways critical for proper axonal and dendritic function, the interplay between them remains elusive. Here we review our current knowledge on the molecular mechanisms and specific interaction networks that regulate and potentially coordinate these interconnected processes.
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Affiliation(s)
- Nikoletta Triantopoulou
- Division of Basic Sciences, Medical School, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (IMBB-FORTH), Heraklion, Greece
| | - Marina Vidaki
- Division of Basic Sciences, Medical School, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (IMBB-FORTH), Heraklion, Greece
- *Correspondence: Marina Vidaki,
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27
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Soumbasis A, Eldeeb MA. A molecular dialogue between local translation and mitochondria: powering mitophagy in axons. Mol Biol Rep 2022; 49:9013-9016. [PMID: 35902447 DOI: 10.1007/s11033-022-07708-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/11/2022] [Accepted: 06/14/2022] [Indexed: 11/27/2022]
Abstract
Mitochondrial quality control is a key element of neuronal health and viability. When left untouched, defective mitochondria can initiate neuronal degeneration. Cytosolic proteins PINK1 and Parkin comprise one key pathway responsible for clearing damaged mitochondria. Neurons, however, pose a unique challenge to this process because proteins need to be abundantly available at locations distant from the cell body. Recent study has confirmed that local translation of PINK1 in axons and dendrites is the solution. Pink1 transcripts are tethered to mitochondria via SYNJ2a and active translation, then subsequently co-transported to distal locations. Once arriving in the neuron's periphery, local translation of PINK1 can facilitate mitophagy and ultimately sustain mitochondrial health.
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Affiliation(s)
- Andrea Soumbasis
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Mohamed A Eldeeb
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada.
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28
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Jin LQ, Zhou Y, Li YS, Zhang G, Hu J, Selzer ME. Transcriptomes of Injured Lamprey Axon Tips: Single-Cell RNA-Seq Suggests Differential Involvement of MAPK Signaling Pathways in Axon Retraction and Regeneration after Spinal Cord Injury. Cells 2022; 11:cells11152320. [PMID: 35954164 PMCID: PMC9367414 DOI: 10.3390/cells11152320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 02/01/2023] Open
Abstract
Axotomy in the CNS activates retrograde signals that can trigger regeneration or cell death. Whether these outcomes use different injury signals is not known. Local protein synthesis in axon tips plays an important role in axon retraction and regeneration. Microarray and RNA-seq studies on cultured mammalian embryonic or early postnatal peripheral neurons showed that axon growth cones contain hundreds to thousands of mRNAs. In the lamprey, identified reticulospinal neurons vary in the probability that their axons will regenerate after axotomy. The bad regenerators undergo early severe axon retraction and very delayed apoptosis. We micro-aspirated axoplasms from 10 growing, 9 static and 5 retracting axon tips of spinal cord transected lampreys and performed single-cell RNA-seq, analyzing the results bioinformatically. Genes were identified that were upregulated selectively in growing (n = 38), static (20) or retracting tips (18). Among them, map3k2, csnk1e and gtf2h were expressed in growing tips, mapk8(1) was expressed in static tips and prkcq was expressed in retracting tips. Venn diagrams revealed more than 40 components of MAPK signaling pathways, including jnk and p38 isoforms, which were differentially distributed in growing, static and/or retracting tips. Real-time q-PCR and immunohistochemistry verified the colocalization of map3k2 and csnk1e in growing axon tips. Thus, differentially regulated MAPK and circadian rhythm signaling pathways may be involved in activating either programs for axon regeneration or axon retraction and apoptosis.
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Affiliation(s)
- Li-Qing Jin
- Shriners Hospitals Pediatric Research Center, The Lewis Katz School of Medicine (LKSOM) at Temple University, Philadelphia, PA 19140, USA; (G.Z.); (J.H.)
- Department of Neural Sciences, Lewis Katz School of Medicine (LKSOM), 3500 North Broad Street, Philadelphia, PA 19140, USA
- Correspondence: (L.-Q.J.); (M.E.S.)
| | - Yan Zhou
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, PA 19111, USA;
| | - Yue-Sheng Li
- DNA Sequence & Genomics Core Facility at the NHLBI, Bethesda, MD 20892, USA;
| | - Guixin Zhang
- Shriners Hospitals Pediatric Research Center, The Lewis Katz School of Medicine (LKSOM) at Temple University, Philadelphia, PA 19140, USA; (G.Z.); (J.H.)
- Department of Neural Sciences, Lewis Katz School of Medicine (LKSOM), 3500 North Broad Street, Philadelphia, PA 19140, USA
| | - Jianli Hu
- Shriners Hospitals Pediatric Research Center, The Lewis Katz School of Medicine (LKSOM) at Temple University, Philadelphia, PA 19140, USA; (G.Z.); (J.H.)
- Department of Neural Sciences, Lewis Katz School of Medicine (LKSOM), 3500 North Broad Street, Philadelphia, PA 19140, USA
| | - Michael E. Selzer
- Shriners Hospitals Pediatric Research Center, The Lewis Katz School of Medicine (LKSOM) at Temple University, Philadelphia, PA 19140, USA; (G.Z.); (J.H.)
- Department of Neural Sciences, Lewis Katz School of Medicine (LKSOM), 3500 North Broad Street, Philadelphia, PA 19140, USA
- Department of Neurology, Lewis Katz School of Medicine (LKSOM), 3500 North Broad Street, Philadelphia, PA 19140, USA
- Correspondence: (L.-Q.J.); (M.E.S.)
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29
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Lo HYG, Engel KL, Goering R, Li Y, Spitale RC, Taliaferro JM. Halo-seq: An RNA Proximity Labeling Method for the Isolation and Analysis of Subcellular RNA Populations. Curr Protoc 2022; 2:e424. [PMID: 35532287 PMCID: PMC9097300 DOI: 10.1002/cpz1.424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The subcellular localization of specific RNA molecules promotes localized cellular activity across a variety of species and cell types. The misregulation of this RNA targeting can result in developmental defects, and mutations in proteins that regulate this process are associated with multiple diseases. For the vast majority of localized RNAs, however, the mechanisms that underlie their subcellular targeting are unknown, partly due to the difficulty associated with profiling and quantifying subcellular RNA populations. To address this challenge, we developed Halo-seq, a proximity labeling technique that can label and profile local RNA content at virtually any subcellular location. Halo-seq relies on a HaloTag fusion protein localized to a subcellular space of interest. Through the use of a radical-producing Halo ligand, RNAs that are near the HaloTag fusion are specifically labeled with spatial and temporal control. Labeled RNA is then specifically biotinylated in vitro via a click reaction, facilitating its purification from a bulk RNA sample using streptavidin beads. The content of the biotinylated RNA is then profiled using high-throughput sequencing. In this article, we describe the experimental and computational procedures for Halo-seq, including important benchmark and quality control steps. By allowing the flexible profiling of a variety of subcellular RNA populations, we envision Halo-seq facilitating the discovery and further study of RNA localization regulatory mechanisms. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Visualization of HaloTag fusion protein localization Basic Protocol 2: In situ copper-catalyzed cycloaddition of fluorophore via click reaction Basic Protocol 3: In vivo RNA alkynylation and extraction of total RNA Basic Protocol 4: In vitro copper-catalyzed cycloaddition of biotin via click reaction Basic Protocol 5: Assessment of RNA biotinylation by RNA dot blot Basic Protocol 6: Enrichment of biotinylated RNA using streptavidin beads and preparation of RNA-seq library Basic Protocol 7: Computational analysis of Halo-seq data.
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Affiliation(s)
- Hei-Yong G Lo
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado.,RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Krysta L Engel
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Raeann Goering
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado.,RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Ying Li
- Department of Chemistry, University of Hong Kong, Hong Kong
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California.,Department of Chemistry, University of California Irvine, Irvine, California
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado.,RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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30
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Harbauer AB, Hees JT, Wanderoy S, Segura I, Gibbs W, Cheng Y, Ordonez M, Cai Z, Cartoni R, Ashrafi G, Wang C, Perocchi F, He Z, Schwarz TL. Neuronal mitochondria transport Pink1 mRNA via synaptojanin 2 to support local mitophagy. Neuron 2022; 110:1516-1531.e9. [PMID: 35216662 PMCID: PMC9081165 DOI: 10.1016/j.neuron.2022.01.035] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 06/25/2021] [Accepted: 01/28/2022] [Indexed: 01/18/2023]
Abstract
PTEN-induced kinase 1 (PINK1) is a short-lived protein required for the removal of damaged mitochondria through Parkin translocation and mitophagy. Because the short half-life of PINK1 limits its ability to be trafficked into neurites, local translation is required for this mitophagy pathway to be active far from the soma. The Pink1 transcript is associated and cotransported with neuronal mitochondria. In concert with translation, the mitochondrial outer membrane proteins synaptojanin 2 binding protein (SYNJ2BP) and synaptojanin 2 (SYNJ2) are required for tethering Pink1 mRNA to mitochondria via an RNA-binding domain in SYNJ2. This neuron-specific adaptation for the local translation of PINK1 provides distal mitochondria with a continuous supply of PINK1 for the activation of mitophagy.
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Affiliation(s)
- Angelika B Harbauer
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA; Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany; Institute of Neuronal Cell Biology, Technical University of Munich, Biedersteiner Straße 29, 80802 Munich, Germany; Munich Cluster of Systems Neurology, Feodor-Lynen-Straße 17, 81377 Munich, Germany.
| | - J Tabitha Hees
- Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Simone Wanderoy
- Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Inmaculada Segura
- Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany; Ludwig-Maximilians-Universität München, Department of Cellular Physiology Biomedical Center Munich - BMC, Großhaderner Str. 9, 82152 Martinsried, Germany
| | - Whitney Gibbs
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Yiming Cheng
- Munich Cluster of Systems Neurology, Feodor-Lynen-Straße 17, 81377 Munich, Germany; Institute for Diabetes and Obesity, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Munich, Germany
| | - Martha Ordonez
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Zerong Cai
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Romain Cartoni
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Ghazaleh Ashrafi
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Chen Wang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Fabiana Perocchi
- Institute of Neuronal Cell Biology, Technical University of Munich, Biedersteiner Straße 29, 80802 Munich, Germany; Munich Cluster of Systems Neurology, Feodor-Lynen-Straße 17, 81377 Munich, Germany; Institute for Diabetes and Obesity, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Munich, Germany
| | - Zhigang He
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas L Schwarz
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.
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31
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Nedozralova H, Basnet N, Ibiricu I, Bodakuntla S, Biertümpfel C, Mizuno N. In situ cryo-electron tomography reveals local cellular machineries for axon branch development. J Biophys Biochem Cytol 2022; 221:213057. [PMID: 35262630 PMCID: PMC8916118 DOI: 10.1083/jcb.202106086] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 11/23/2021] [Accepted: 01/31/2022] [Indexed: 01/02/2023] Open
Abstract
Neurons are highly polarized cells forming an intricate network of dendrites and axons. They are shaped by the dynamic reorganization of cytoskeleton components and cellular organelles. Axon branching allows the formation of new paths and increases circuit complexity. However, our understanding of branch formation is sparse due to the lack of direct in-depth observations. Using in situ cellular cryo-electron tomography on primary mouse neurons, we directly visualized the remodeling of organelles and cytoskeleton structures at axon branches. Strikingly, branched areas functioned as hotspots concentrating organelles to support dynamic activities. Unaligned actin filaments assembled at the base of premature branches accompanied by filopodia-like protrusions. Microtubules and ER comigrated into preformed branches to support outgrowth together with accumulating compact, ∼500-nm mitochondria and locally clustered ribosomes. We obtained a roadmap of events supporting the hypothesis of local protein synthesis selectively taking place at axon branches, allowing them to serve as unique control hubs for axon development and downstream neural network formation.
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Affiliation(s)
- Hana Nedozralova
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany.,Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Nirakar Basnet
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Iosune Ibiricu
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Satish Bodakuntla
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Christian Biertümpfel
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Naoko Mizuno
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD.,National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD
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32
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Taliaferro JM. Transcriptome-scale methods for uncovering subcellular RNA localization mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119202. [PMID: 34998919 PMCID: PMC9035289 DOI: 10.1016/j.bbamcr.2021.119202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/03/2021] [Accepted: 12/17/2021] [Indexed: 12/21/2022]
Abstract
Across a variety of systems, thousands of RNAs are localized to specific subcellular locations. However, for the vast majority of these RNAs, the mechanisms that underlie their transport are unknown. Historically, these mechanisms were uncovered for a single transcript at a time by laboriously testing the ability of RNA fragments to direct transcript localization. Recently developed methods profile the content of subcellular transcriptomes using high-throughput sequencing, allowing the analysis of the localization of thousands of transcripts at once. By identifying commonalities shared among multiple localized transcripts, these methods have the potential to rapidly expand our understanding of RNA localization mechanisms.
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Affiliation(s)
- J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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33
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Engmann AK, Hatch JJ, Nanda P, Veeraraghavan P, Ozkan A, Poulopoulos A, Murphy AJ, Macklis JD. Neuronal subtype-specific growth cone and soma purification from mammalian CNS via fractionation and fluorescent sorting for subcellular analyses and spatial mapping of local transcriptomes and proteomes. Nat Protoc 2022; 17:222-251. [PMID: 35022617 PMCID: PMC9751848 DOI: 10.1038/s41596-021-00638-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 09/24/2021] [Indexed: 11/09/2022]
Abstract
During neuronal development, growth cones (GCs) of projection neurons navigate complex extracellular environments to reach distant targets, thereby generating extraordinarily complex circuitry. These dynamic structures located at the tips of axonal projections respond to substrate-bound as well as diffusible guidance cues in a neuronal subtype- and stage-specific manner to construct highly specific and functional circuitry. In vitro studies of the past decade indicate that subcellular localization of specific molecular machinery in GCs underlies the precise navigational control that occurs during circuit 'wiring'. Our laboratory has recently developed integrated experimental and analytical approaches enabling high-depth, quantitative proteomic and transcriptomic investigation of subtype- and stage-specific GC molecular machinery directly from the rodent central nervous system (CNS) in vivo. By using these approaches, a pure population of GCs and paired somata can be isolated from any neuronal subtype of the CNS that can be fluorescently labeled. GCs are dissociated from parent axons using fluid shear forces, and a bulk GC fraction is isolated by buoyancy ultracentrifugation. Subtype-specific GCs and somata are purified by recently developed fluorescent small particle sorting and established FACS of neurons and are suitable for downstream analyses of proteins and RNAs, including small RNAs. The isolation of subtype-specific GCs and parent somata takes ~3 h, plus sorting time, and ~1-2 h for subsequent extraction of molecular contents. RNA library preparation and sequencing can take several days to weeks, depending on the turnaround time of the core facility involved.
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Affiliation(s)
- Anne K Engmann
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - John J Hatch
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Prakruti Nanda
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Priya Veeraraghavan
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Abdulkadir Ozkan
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Alexandros Poulopoulos
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alexander J Murphy
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
- Takeda Pharmaceutical Company Limited, Cambridge, MA, USA
| | - Jeffrey D Macklis
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA.
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34
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Arora A, Goering R, Lo HYG, Lo J, Moffatt C, Taliaferro JM. The Role of Alternative Polyadenylation in the Regulation of Subcellular RNA Localization. Front Genet 2022; 12:818668. [PMID: 35096024 PMCID: PMC8795681 DOI: 10.3389/fgene.2021.818668] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Abstract
Alternative polyadenylation (APA) is a widespread and conserved regulatory mechanism that generates diverse 3' ends on mRNA. APA patterns are often tissue specific and play an important role in cellular processes such as cell proliferation, differentiation, and response to stress. Many APA sites are found in 3' UTRs, generating mRNA isoforms with different 3' UTR contents. These alternate 3' UTR isoforms can change how the transcript is regulated, affecting its stability and translation. Since the subcellular localization of a transcript is often regulated by 3' UTR sequences, this implies that APA can also change transcript location. However, this connection between APA and RNA localization has only recently been explored. In this review, we discuss the role of APA in mRNA localization across distinct subcellular compartments. We also discuss current challenges and future advancements that will aid our understanding of how APA affects RNA localization and molecular mechanisms that drive these processes.
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Affiliation(s)
- Ankita Arora
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Raeann Goering
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Hei Yong G. Lo
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Joelle Lo
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Charlie Moffatt
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - J. Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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35
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Koppers M, Holt CE. Receptor-Ribosome Coupling: A Link Between Extrinsic Signals and mRNA Translation in Neuronal Compartments. Annu Rev Neurosci 2022; 45:41-61. [DOI: 10.1146/annurev-neuro-083021-110015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Axons receive extracellular signals that help to guide growth and synapse formation during development and to maintain neuronal function and survival during maturity. These signals relay information via cell surface receptors that can initiate local intracellular signaling at the site of binding, including local messenger RNA (mRNA) translation. Direct coupling of translational machinery to receptors provides an attractive way to activate this local mRNA translation and change the local proteome with high spatiotemporal resolution. Here, we first discuss the increasing evidence that different external stimuli trigger translation of specific subsets of mRNAs in axons via receptors and thus play a prominent role in various processes in both developing and mature neurons. We then discuss the receptor-mediated molecular mechanisms that regulate local mRNA translational with a focus on direct receptor-ribosome coupling. We advance the idea that receptor-ribosome coupling provides several advantages over other translational regulation mechanisms and is a common mechanism in cell communication. Expected final online publication date for the Annual Review of Neuroscience, Volume 45 is July 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Max Koppers
- Department of Biology, Division of Cell Biology, Neurobiology and Biophysics, Utrecht University, Utrecht, The Netherlands
| | - Christine E. Holt
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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36
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Arora A, Goering R, Velez PT, Taliaferro JM. Visualization and Quantification of Subcellular RNA Localization Using Single-Molecule RNA Fluorescence In Situ Hybridization. Methods Mol Biol 2022; 2404:247-266. [PMID: 34694613 PMCID: PMC9038117 DOI: 10.1007/978-1-0716-1851-6_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Advancements in imaging technologies, especially approaches that allow the imaging of single RNA molecules, have opened new avenues to understand RNA regulation, from synthesis to decay with high spatial and temporal resolution. Here, we describe a protocol for single-molecule fluorescent in situ hybridization (smFISH) using three different approaches for synthesizing the fluorescent probes. The three approaches described are commercially available probes, single-molecule inexpensive FISH (smiFISH), and in-house enzymatically labeled probes. These approaches offer technical and economic flexibility to meet the specific needs of an experiment. In addition, we provide a protocol to perform automated smFISH spot detection using the software FISH-quant.
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Affiliation(s)
- 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,RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Pedro Tirado Velez
- RNA Bioscience Initiative, 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,Address correspondence to:
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37
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Gupta P, Shinde A, Illath K, Kar S, Nagai M, Tseng FG, Santra TS. Microfluidic platforms for single neuron analysis. Mater Today Bio 2022; 13:100222. [PMID: 35243297 PMCID: PMC8866890 DOI: 10.1016/j.mtbio.2022.100222] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/05/2022] [Accepted: 02/14/2022] [Indexed: 11/29/2022]
Abstract
Single-neuron actions are the basis of brain function, as clinical sequelae, neuronal dysfunction or failure for most of the central nervous system (CNS) diseases and injuries can be identified via tracing single-neurons. The bulk analysis methods tend to miscue critical information by assessing the population-averaged outcomes. However, its primary requisite in neuroscience to analyze single-neurons and to understand dynamic interplay of neurons and their environment. Microfluidic systems enable precise control over nano-to femto-liter volumes via adjusting device geometry, surface characteristics, and flow-dynamics, thus facilitating a well-defined micro-environment with spatio-temporal control for single-neuron analysis. The microfluidic platform not only offers a comprehensive landscape to study brain cell diversity at the level of transcriptome, genome, and/or epigenome of individual cells but also has a substantial role in deciphering complex dynamics of brain development and brain-related disorders. In this review, we highlight recent advances of microfluidic devices for single-neuron analysis, i.e., single-neuron trapping, single-neuron dynamics, single-neuron proteomics, single-neuron transcriptomics, drug delivery at the single-neuron level, single axon guidance, and single-neuron differentiation. Moreover, we also emphasize limitations and future challenges of single-neuron analysis by focusing on key performances of throughput and multiparametric activity analysis on microfluidic platforms.
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38
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Medioni C, Vijayakumar J, Ephrussi A, Besse F. High-Resolution Live Imaging of Axonal RNP Granules in Drosophila Pupal Brain Explants. Methods Mol Biol 2022; 2431:451-462. [PMID: 35412292 DOI: 10.1007/978-1-0716-1990-2_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Dynamic and local adjustments of the axonal proteome are observed in response to extracellular cues and achieved via translation of axonally localized mRNAs. To be localized, these mRNAs must be recognized by RNA binding proteins and packaged into higher-order ribonucleoprotein (RNP) granules transported along axonal microtubules via molecular motors. Axonal recruitment of RNP granules is not constitutive, but rather regulated by external signals such as developmental cues, through pathways yet to be identified. The Drosophila brain represents an excellent model system where to study the transport of RNP granules as it is triggered in specific populations of neurons undergoing remodeling during metamorphosis. Here, we describe a protocol enabling live imaging of axonal RNP granule transport with high spatiotemporal resolution in Drosophila maturing brains. In this protocol, pupal brains expressing endogenous or ectopic fluorescent RNP components are dissected, mounted in a customized imaging chamber, and imaged with an inverted confocal microscope equipped with sensitive detectors. Axonal RNP granules are then individually tracked for further analysis of their trajectories. This protocol is rapid (less than 1 hour to prepare brains for imaging) and is easy to handle and to implement.
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Affiliation(s)
- Caroline Medioni
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, France
| | - Jeshlee Vijayakumar
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, France
| | - Anne Ephrussi
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Florence Besse
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, France.
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39
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Landínez-Macías M, Urwyler O. The Fine Art of Writing a Message: RNA Metabolism in the Shaping and Remodeling of the Nervous System. Front Mol Neurosci 2021; 14:755686. [PMID: 34916907 PMCID: PMC8670310 DOI: 10.3389/fnmol.2021.755686] [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: 08/09/2021] [Accepted: 10/18/2021] [Indexed: 01/25/2023] Open
Abstract
Neuronal morphogenesis, integration into circuits, and remodeling of synaptic connections occur in temporally and spatially defined steps. Accordingly, the expression of proteins and specific protein isoforms that contribute to these processes must be controlled quantitatively in time and space. A wide variety of post-transcriptional regulatory mechanisms, which act on pre-mRNA and mRNA molecules contribute to this control. They are thereby critically involved in physiological and pathophysiological nervous system development, function, and maintenance. Here, we review recent findings on how mRNA metabolism contributes to neuronal development, from neural stem cell maintenance to synapse specification, with a particular focus on axon growth, guidance, branching, and synapse formation. We emphasize the role of RNA-binding proteins, and highlight their emerging roles in the poorly understood molecular processes of RNA editing, alternative polyadenylation, and temporal control of splicing, while also discussing alternative splicing, RNA localization, and local translation. We illustrate with the example of the evolutionary conserved Musashi protein family how individual RNA-binding proteins are, on the one hand, acting in different processes of RNA metabolism, and, on the other hand, impacting multiple steps in neuronal development and circuit formation. Finally, we provide links to diseases that have been associated with the malfunction of RNA-binding proteins and disrupted post-transcriptional regulation.
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Affiliation(s)
- María Landínez-Macías
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Molecular Life Sciences Program, Life Science Zurich Graduate School, University of Zurich and Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Olivier Urwyler
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Molecular Life Sciences Program, Life Science Zurich Graduate School, University of Zurich and Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.,Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland
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40
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Carmona A, Chen S, Domart F, Choquet D, Ortega R. Imaging the structural organization of chemical elements in growth cones of developing hippocampal neurons. Metallomics 2021; 14:6462920. [PMID: 34910190 DOI: 10.1093/mtomcs/mfab073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/06/2021] [Indexed: 11/14/2022]
Abstract
During neurodevelopment, neurons form growth cones, F-actin rich extensions located at the distal end of the neurites. Growth cones allow dendrites and axons to build synaptic connections through a process of neurite guidance whose mechanisms have not been fully elucidated. Calcium is an important element in this process by inducing F-actin reorganization. We hypothesized that other biologically active elements might be involved in the growth cone-mediated neurite guidance mechanisms. We performed super resolution and confocal microscopy of F-actin, followed by synchrotron X-ray fluorescence microscopy of phosphorous, sulfur, chlorine, potassium, calcium, iron and zinc on growth cones from primary rat hippocampal neurons. We identified two main patterns of element organization. First, active growth cones presenting an asymmetric distribution of Ca co-localized with the cytoskeleton protein F-actin. In active growth cones, we found that the distributions of P, S, Cl, K and Zn are correlated with Ca. This correlation is lost in the second pattern, quiescent growth cones, exhibiting a spread elemental distribution. These results suggest that Ca is not the only element required in the F-actin rich active regions of growth cones. In addition, highly concentrated Fe spots of sub-micrometer size were observed in calcium-rich areas of active growth cones. These results reveal the need for biological active elements in growth cones during neural development and may help explain why early life deficiencies of elements, such as Fe or Zn, induce learning and memory deficits in children.
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Affiliation(s)
| | - Si Chen
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Florelle Domart
- Univ. Bordeaux, CNRS, CENBG, UMR 5797, 33170 Gradignan, France.,Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, 33000 Bordeaux, France
| | - Daniel Choquet
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, 33000 Bordeaux, France.,Univ. Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, 33000 Bordeaux, France
| | - Richard Ortega
- Univ. Bordeaux, CNRS, CENBG, UMR 5797, 33170 Gradignan, France
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41
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Engel KL, Lo HYG, Goering R, Li Y, Spitale RC, Taliaferro JM. Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq. Nucleic Acids Res 2021; 50:e24. [PMID: 34875090 PMCID: PMC8887463 DOI: 10.1093/nar/gkab1185] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/26/2021] [Accepted: 11/16/2021] [Indexed: 12/22/2022] Open
Abstract
Thousands of RNA species display nonuniform distribution within cells. However, quantification of the spatial patterns adopted by individual RNAs remains difficult, in part by a lack of quantitative tools for subcellular transcriptome analysis. In this study, we describe an RNA proximity labeling method that facilitates the quantification of subcellular RNA populations with high spatial specificity. This method, termed Halo-seq, pairs a light-activatable, radical generating small molecule with highly efficient Click chemistry to efficiently label and purify spatially defined RNA samples. We compared Halo-seq with previously reported similar methods and found that Halo-seq displayed a higher efficiency of RNA labeling, indicating that it is well suited to the investigation of small, precisely localized RNA populations. We then used Halo-seq to quantify nuclear, nucleolar and cytoplasmic transcriptomes, characterize their dynamic nature following perturbation, and identify RNA sequence features associated with their composition. Specifically, we found that RNAs containing AU-rich elements are relatively enriched in the nucleus. This enrichment becomes stronger upon treatment with the nuclear export inhibitor leptomycin B, both expanding the role of HuR in RNA export and generating a comprehensive set of transcripts whose export from the nucleus depends on HuR.
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Affiliation(s)
- Krysta L Engel
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Hei-Yong G Lo
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Raeann Goering
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ying Li
- Department of Chemistry, Hong Kong University
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA.,Department of Chemistry, University of California Irvine, Irvine, CA, USA
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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42
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Li L, Yu J, Ji SJ. Axonal mRNA localization and translation: local events with broad roles. Cell Mol Life Sci 2021; 78:7379-7395. [PMID: 34698881 PMCID: PMC11072051 DOI: 10.1007/s00018-021-03995-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/17/2021] [Accepted: 10/14/2021] [Indexed: 12/19/2022]
Abstract
Messenger RNA (mRNA) can be transported and targeted to different subcellular compartments and locally translated. Local translation is an evolutionally conserved mechanism that in mammals, provides an important tool to exquisitely regulate the subcellular proteome in different cell types, including neurons. Local translation in axons is involved in processes such as neuronal development, function, plasticity, and diseases. Here, we summarize the current progress on axonal mRNA transport and translation. We focus on the regulatory mechanisms governing how mRNAs are transported to axons and how they are locally translated in axons. We discuss the roles of axonally synthesized proteins, which either function locally in axons, or are retrogradely trafficked back to soma to achieve neuron-wide gene regulation. We also examine local translation in neurological diseases. Finally, we give a critical perspective on the remaining questions that could be answered to uncover the fundamental rules governing local translation, and discuss how this could lead to new therapeutic targets for neurological diseases.
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Affiliation(s)
- Lichao Li
- School of Life Sciences, Department of Biology, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Brain Research Center, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China
| | - Jun Yu
- School of Life Sciences, Department of Biology, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Brain Research Center, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China
| | - Sheng-Jian Ji
- School of Life Sciences, Department of Biology, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Brain Research Center, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China.
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43
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Mesquita-Ribeiro R, Fort RS, Rathbone A, Farias J, Lucci C, James V, Sotelo-Silveira J, Duhagon MA, Dajas-Bailador F. Distinct small non-coding RNA landscape in the axons and released extracellular vesicles of developing primary cortical neurons and the axoplasm of adult nerves. RNA Biol 2021; 18:832-855. [PMID: 34882524 PMCID: PMC8782166 DOI: 10.1080/15476286.2021.2000792] [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] [Indexed: 12/13/2022] Open
Abstract
Neurons have highlighted the needs for decentralized gene expression and specific RNA function in somato-dendritic and axonal compartments, as well as in intercellular communication via extracellular vesicles (EVs). Despite advances in miRNA biology, the identity and regulatory capacity of other small non-coding RNAs (sncRNAs) in neuronal models and local subdomains has been largely unexplored.We identified a highly complex and differentially localized content of sncRNAs in axons and EVs during early neuronal development of cortical primary neurons and in adult axons in vivo. This content goes far beyond miRNAs and includes most known sncRNAs and precisely processed fragments from tRNAs, sno/snRNAs, Y RNAs and vtRNAs. Although miRNAs are the major sncRNA biotype in whole-cell samples, their relative abundance is significantly decreased in axons and neuronal EVs, where specific tRNA fragments (tRFs and tRHs/tiRNAs) mainly derived from tRNAs Gly-GCC, Val-CAC and Val-AAC predominate. Notably, although 5'-tRHs compose the great majority of tRNA-derived fragments observed in vitro, a shift to 3'-tRNAs is observed in mature axons in vivo.The existence of these complex sncRNA populations that are specific to distinct neuronal subdomains and selectively incorporated into EVs, equip neurons with key molecular tools for spatiotemporal functional control and cell-to-cell communication.
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Affiliation(s)
| | - Rafael Sebastián Fort
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Alex Rathbone
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Joaquina Farias
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.,Polo de Desarrollo Universitario "Espacio de Biología Vegetal del Noreste", Centro Universitario Regional Noreste, UdelaR, Uruguay
| | - Cristiano Lucci
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Victoria James
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Jose Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Maria Ana Duhagon
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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44
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Fusco CM, Desch K, Dörrbaum AR, Wang M, Staab A, Chan ICW, Vail E, Villeri V, Langer JD, Schuman EM. Neuronal ribosomes exhibit dynamic and context-dependent exchange of ribosomal proteins. Nat Commun 2021; 12:6127. [PMID: 34675203 PMCID: PMC8531293 DOI: 10.1038/s41467-021-26365-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022] Open
Abstract
Owing to their morphological complexity and dense network connections, neurons modify their proteomes locally, using mRNAs and ribosomes present in the neuropil (tissue enriched for dendrites and axons). Although ribosome biogenesis largely takes place in the nucleus and perinuclear region, neuronal ribosomal protein (RP) mRNAs have been frequently detected remotely, in dendrites and axons. Here, using imaging and ribosome profiling, we directly detected the RP mRNAs and their translation in the neuropil. Combining brief metabolic labeling with mass spectrometry, we found that a group of RPs rapidly associated with translating ribosomes in the cytoplasm and that this incorporation was independent of canonical ribosome biogenesis. Moreover, the incorporation probability of some RPs was regulated by location (neurites vs. cell bodies) and changes in the cellular environment (following oxidative stress). Our results suggest new mechanisms for the local activation, repair and/or specialization of the translational machinery within neuronal processes, potentially allowing neuronal synapses a rapid means to regulate local protein synthesis.
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Affiliation(s)
- Claudia M. Fusco
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Kristina Desch
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Aline R. Dörrbaum
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,Present Address: MOS, Center for Mass Spectrometry and Optical Spectroscopy, Mannheim, Germany
| | - Mantian Wang
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,grid.508836.0Present Address: Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - Anja Staab
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Ivy C. W. Chan
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,grid.424247.30000 0004 0438 0426Present Address: German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Eleanor Vail
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Veronica Villeri
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,grid.412041.20000 0001 2106 639XPresent Address: Department of Neuroscience, University of Bordeaux, Bordeaux, France
| | - Julian D. Langer
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,grid.419494.50000 0001 1018 9466Max Planck Institute for Biophysics, Frankfurt, Germany
| | - Erin M. Schuman
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
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45
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Matthews J, Surey S, Grover LM, Logan A, Ahmed Z. Thermosensitive collagen/fibrinogen gels loaded with decorin suppress lesion site cavitation and promote functional recovery after spinal cord injury. Sci Rep 2021; 11:18124. [PMID: 34518601 PMCID: PMC8438067 DOI: 10.1038/s41598-021-97604-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/27/2021] [Indexed: 11/10/2022] Open
Abstract
The treatment of spinal cord injury (SCI) is a complex challenge in regenerative medicine, complicated by the low intrinsic capacity of CNS neurons to regenerate their axons and the heterogeneity in size, shape and extent of human injuries. For example, some contusion injuries do not compromise the dura mater and in such cases implantation of preformed scaffolds or drug delivery systems may cause further damage. Injectable in situ thermosensitive scaffolds are therefore a less invasive alternative. In this study, we report the development of a novel, flowable, thermosensitive, injectable drug delivery system comprising bovine collagen (BC) and fibrinogen (FB) that forms a solid BC/FB gel (Gel) immediately upon exposure to physiological conditions and can be used to deliver reparative drugs, such as the naturally occurring anti-inflammatory, anti-scarring agent Decorin, into adult rat spinal cord lesion sites. In dorsal column lesions of adult rats treated with the Gel + Decorin, cavitation was completely suppressed and instead lesion sites became filled with injury-responsive cells and extracellular matrix materials, including collagen and laminin. Decorin increased the intrinsic potential of dorsal root ganglion neurons (DRGN) by increasing their expression of regeneration associated genes (RAGs), enhanced local axon regeneration/sprouting, as evidenced both histologically and by improved electrophysiological, locomotor and sensory function recovery. These results suggest that this drug formulated, injectable hydrogel has the potential to be further studied and translated into the clinic.
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Affiliation(s)
- Jacob Matthews
- Neuroscience and Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Sarina Surey
- Neuroscience and Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Liam M Grover
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ann Logan
- Warwick Medical School, Biomedical Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Zubair Ahmed
- Neuroscience and Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK. .,Centre for Trauma Sciences Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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46
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Giandomenico SL, Alvarez-Castelao B, Schuman EM. Proteostatic regulation in neuronal compartments. Trends Neurosci 2021; 45:41-52. [PMID: 34489114 DOI: 10.1016/j.tins.2021.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/16/2021] [Accepted: 08/05/2021] [Indexed: 12/16/2022]
Abstract
Neurons continuously adapt to external cues and challenges, including stimulation, plasticity-inducing signals and aging. These adaptations are critical for neuronal physiology and extended survival. Proteostasis is the process by which cells adjust their protein content to achieve the specific protein repertoire necessary for cellular function. Due to their complex morphology and polarized nature, neurons possess unique proteostatic requirements. Proteostatic control in axons and dendrites must be implemented through regulation of protein synthesis and degradation in a decentralized fashion, but at the same time, it requires integration, at least in part, in the soma. Here, we discuss current understanding of neuronal proteostasis, as well as open questions and future directions requiring further exploration.
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Affiliation(s)
| | - Beatriz Alvarez-Castelao
- Department of Biochemistry and Molecular Biology, Veterinary School, Complutense University of Madrid, Madrid, Spain
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
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47
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Agrawal M, Welshhans K. Local Translation Across Neural Development: A Focus on Radial Glial Cells, Axons, and Synaptogenesis. Front Mol Neurosci 2021; 14:717170. [PMID: 34434089 PMCID: PMC8380849 DOI: 10.3389/fnmol.2021.717170] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
In the past two decades, significant progress has been made in our understanding of mRNA localization and translation at distal sites in axons and dendrites. The existing literature shows that local translation is regulated in a temporally and spatially restricted manner and is critical throughout embryonic and post-embryonic life. Here, recent key findings about mRNA localization and local translation across the various stages of neural development, including neurogenesis, axon development, and synaptogenesis, are reviewed. In the early stages of development, mRNAs are localized and locally translated in the endfeet of radial glial cells, but much is still unexplored about their functional significance. Recent in vitro and in vivo studies have provided new information about the specific mechanisms regulating local translation during axon development, including growth cone guidance and axon branching. Later in development, localization and translation of mRNAs help mediate the major structural and functional changes that occur in the axon during synaptogenesis. Clinically, changes in local translation across all stages of neural development have important implications for understanding the etiology of several neurological disorders. Herein, local translation and mechanisms regulating this process across developmental stages are compared and discussed in the context of function and dysfunction.
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Affiliation(s)
- Manasi Agrawal
- School of Biomedical Sciences, Kent State University, Kent, OH, United States
| | - Kristy Welshhans
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
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48
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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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49
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Norris K, Hopes T, Aspden JL. Ribosome heterogeneity and specialization in development. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1644. [PMID: 33565275 PMCID: PMC8647923 DOI: 10.1002/wrna.1644] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/13/2022]
Abstract
Regulation of protein synthesis is a vital step in controlling gene expression, especially during development. Over the last 10 years, it has become clear that rather than being homogeneous machines responsible for mRNA translation, ribosomes are highly heterogeneous and can play an active part in translational regulation. These "specialized ribosomes" comprise of specific protein and/or rRNA components, which are required for the translation of particular mRNAs. However, while there is extensive evidence for ribosome heterogeneity, support for specialized functions is limited. Recent work in a variety of developmental model organisms has shed some light on the biological relevance of ribosome heterogeneity. Tissue-specific expression of ribosomal components along with phenotypic analysis of ribosomal gene mutations indicate that ribosome heterogeneity and potentially specialization are common in key development processes like embryogenesis, spermatogenesis, oogenesis, body patterning, and neurogenesis. Several examples of ribosome specialization have now been proposed but strong links between ribosome heterogeneity, translation of specific mRNAs by defined mechanisms, and role of these translation events remain elusive. Furthermore, several studies have indicated that heterogeneous ribosome populations are a product of tissue-specific expression rather than specialized function and that ribosomal protein phenotypes are the result of extra-ribosomal function or overall reduced ribosome levels. Many important questions still need to be addressed in order to determine the functional importance of ribosome heterogeneity to development and disease, which is likely to vary across systems. It will be essential to dissect these issues to fully understand diseases caused by disruptions to ribosomal composition, such as ribosomopathies. This article is categorized under: Translation > Translation Regulation Translation > Ribosome Structure/Function RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Karl Norris
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
| | - Tayah Hopes
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
| | - Julie Louise Aspden
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
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Di Paolo A, Garat J, Eastman G, Farias J, Dajas-Bailador F, Smircich P, Sotelo-Silveira JR. Functional Genomics of Axons and Synapses to Understand Neurodegenerative Diseases. Front Cell Neurosci 2021; 15:686722. [PMID: 34248504 PMCID: PMC8267896 DOI: 10.3389/fncel.2021.686722] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/02/2021] [Indexed: 01/02/2023] Open
Abstract
Functional genomics studies through transcriptomics, translatomics and proteomics have become increasingly important tools to understand the molecular basis of biological systems in the last decade. In most cases, when these approaches are applied to the nervous system, they are centered in cell bodies or somatodendritic compartments, as these are easier to isolate and, at least in vitro, contain most of the mRNA and proteins present in all neuronal compartments. However, key functional processes and many neuronal disorders are initiated by changes occurring far away from cell bodies, particularly in axons (axopathologies) and synapses (synaptopathies). Both neuronal compartments contain specific RNAs and proteins, which are known to vary depending on their anatomical distribution, developmental stage and function, and thus form the complex network of molecular pathways required for neuron connectivity. Modifications in these components due to metabolic, environmental, and/or genetic issues could trigger or exacerbate a neuronal disease. For this reason, detailed profiling and functional understanding of the precise changes in these compartments may thus yield new insights into the still intractable molecular basis of most neuronal disorders. In the case of synaptic dysfunctions or synaptopathies, they contribute to dozens of diseases in the human brain including neurodevelopmental (i.e., autism, Down syndrome, and epilepsy) as well as neurodegenerative disorders (i.e., Alzheimer's and Parkinson's diseases). Histological, biochemical, cellular, and general molecular biology techniques have been key in understanding these pathologies. Now, the growing number of omics approaches can add significant extra information at a high and wide resolution level and, used effectively, can lead to novel and insightful interpretations of the biological processes at play. This review describes current approaches that use transcriptomics, translatomics and proteomic related methods to analyze the axon and presynaptic elements, focusing on the relationship that axon and synapses have with neurodegenerative diseases.
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Affiliation(s)
- Andres Di Paolo
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Departamento de Proteínas y Ácidos Nucleicos, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Joaquin Garat
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Guillermo Eastman
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Joaquina Farias
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Polo de Desarrollo Universitario “Espacio de Biología Vegetal del Noreste”, Centro Universitario Regional Noreste, Universidad de la República (UdelaR), Tacuarembó, Uruguay
| | - Federico Dajas-Bailador
- School of Life Sciences, Medical School Building, University of Nottingham, Nottingham, United Kingdom
| | - Pablo Smircich
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - José Roberto Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
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