1
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Kiebler MA, Bauer KE. RNA granules in flux: dynamics to balance physiology and pathology. Nat Rev Neurosci 2024:10.1038/s41583-024-00859-1. [PMID: 39367081 DOI: 10.1038/s41583-024-00859-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2024] [Indexed: 10/06/2024]
Abstract
The life cycle of an mRNA is a complex process that is tightly regulated by interactions between the mRNA and RNA-binding proteins, forming molecular machines known as RNA granules. Various types of these membrane-less organelles form inside cells, including neurons, and contribute critically to various physiological processes. RNA granules are constantly in flux, change dynamically and adapt to their local environment, depending on their intracellular localization. The discovery that RNA condensates can form by liquid-liquid phase separation expanded our understanding of how compartments may be generated in the cell. Since then, a plethora of new functions have been proposed for distinct condensates in cells that await their validation in vivo. The finding that dysregulation of RNA granules (for example, stress granules) is likely to affect neurodevelopmental and neurodegenerative diseases further boosted interest in this topic. RNA granules have various physiological functions in neurons and in the brain that we would like to focus on. We outline examples of state-of-the-art experiments including timelapse microscopy in neurons to unravel the precise functions of various types of RNA granule. Finally, we distinguish physiologically occurring RNA condensation from aberrant aggregation, induced by artificial RNA overexpression, and present visual examples to discriminate both forms in neurons.
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Affiliation(s)
- Michael A Kiebler
- Biomedical Center (BMC), Department of Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany.
| | - Karl E Bauer
- Biomedical Center (BMC), Department of Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
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2
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Espadas I, Wingfield JL, Nakahata Y, Chanda K, Grinman E, Ghosh I, Bauer KE, Raveendra B, Kiebler MA, Yasuda R, Rangaraju V, Puthanveettil S. Synaptically-targeted long non-coding RNA SLAMR promotes structural plasticity by increasing translation and CaMKII activity. Nat Commun 2024; 15:2694. [PMID: 38538603 PMCID: PMC10973417 DOI: 10.1038/s41467-024-46972-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) play crucial roles in maintaining cell homeostasis and function. However, it remains largely unknown whether and how neuronal activity impacts the transcriptional regulation of lncRNAs, or if this leads to synapse-related changes and contributes to the formation of long-term memories. Here, we report the identification of a lncRNA, SLAMR, which becomes enriched in CA1-hippocampal neurons upon contextual fear conditioning but not in CA3 neurons. SLAMR is transported along dendrites via the molecular motor KIF5C and is recruited to the synapse upon stimulation. Loss of function of SLAMR reduces dendritic complexity and impairs activity-dependent changes in spine structural plasticity and translation. Gain of function of SLAMR, in contrast, enhances dendritic complexity, spine density, and translation. Analyses of the SLAMR interactome reveal its association with CaMKIIα protein through a 220-nucleotide element also involved in SLAMR transport. A CaMKII reporter reveals a basal reduction in CaMKII activity with SLAMR loss-of-function. Furthermore, the selective loss of SLAMR function in CA1 disrupts the consolidation of fear memory in male mice, without affecting their acquisition, recall, or extinction, or spatial memory. Together, these results provide new molecular and functional insight into activity-dependent changes at the synapse and consolidation of contextual fear.
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Affiliation(s)
- Isabel Espadas
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Jenna L Wingfield
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | | | - Kaushik Chanda
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Eddie Grinman
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Ilika Ghosh
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
| | - Karl E Bauer
- Biomedical Center, Department for Cell Biology, Ludwig-Maximilians-University of Munich, Medical Faculty, 82152, Planegg-Martinsried, Germany
| | - Bindu Raveendra
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Michael A Kiebler
- Biomedical Center, Department for Cell Biology, Ludwig-Maximilians-University of Munich, Medical Faculty, 82152, Planegg-Martinsried, Germany
| | - Ryohei Yasuda
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
| | | | - Sathyanarayanan Puthanveettil
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA.
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3
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Peng Y, Shu L, Deng X, Huang X, Mo X, Du F, Tang Z. Live-Cell Imaging of Endogenous RNA with a Genetically Encoded Fluorogenic Allosteric Aptamer. Anal Chem 2023; 95:13762-13768. [PMID: 37661353 DOI: 10.1021/acs.analchem.2c05724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Imaging and tracking tools for natural cellular RNA with improved biocompatibility, specificity, and sensitivity are critical to understanding RNA function and providing insights into disease therapeutics. We developed a new genetically encoded sensor using fluorogenic allosteric aptamer (FaApt) for the sensitive imaging of the localization and dynamics of RNA targets in live cells. Target RNAs can be specifically recognized with our sensor by forming perfectly complementary duplexes, which in turn can induce allosteric structural changes of the sensor to refold the native conformation of fluorogenic RNA aptamers. We demonstrated the ability of the sensor to monitor the effect of tumor necrosis factor and small-molecule inhibitor on the expression abundance of CXCL1 and survivin mRNA in human cancer cells, respectively. The asymmetrical distribution of endogenous Squint mRNA was confirmed in developing zebrafish embryos through microinjection of FaApt probes. This study provides an effective molecular tool for sensitive imaging and tracking endogenous RNA in living cells. Due to the high specificity and small size of our sensor system, it is expected to be applied to early diagnosis of RNA marker-related diseases and real-time evaluation of the treatment process.
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Affiliation(s)
- Yan Peng
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Linjuan Shu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 6100141, P. R. China
| | - Xiongfei Deng
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xin Huang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Xianming Mo
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 6100141, P. R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
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4
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Espadas I, Wingfield J, Grinman E, Ghosh I, Chanda K, Nakahata Y, Bauer K, Raveendra B, Kiebler M, Yasuda R, Rangaraju V, Puthanveettil S. SLAMR, a synaptically targeted lncRNA, facilitates the consolidation of contextual fear memory. RESEARCH SQUARE 2023:rs.3.rs-2489387. [PMID: 36993323 PMCID: PMC10055528 DOI: 10.21203/rs.3.rs-2489387/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
LncRNAs are involved in critical processes for cell homeostasis and function. However, it remains largely unknown whether and how the transcriptional regulation of long noncoding RNAs results in activity-dependent changes at the synapse and facilitate formation of long-term memories. Here, we report the identification of a novel lncRNA, SLAMR, that becomes enriched in CA1- but not in CA3-hippocampal neurons upon contextual fear conditioning. SLAMR is transported to dendrites via the molecular motor KIF5C and recruited to the synapse in response to stimulation. Loss of function of SLAMR reduced dendritic complexity and impaired activity dependent changes in spine structural plasticity. Interestingly, gain of function of SLAMR enhanced dendritic complexity, and spine density through enhanced translation. Analyses of the SLAMR interactome revealed its association with CaMKIIα protein through a 220-nucleotide element and its modulation of CaMKIIα activity. Furthermore, loss-of-function of SLAMR in CA1 selectively impairs consolidation but neither acquisition, recall, nor extinction of fear memory and spatial memory. Together, these results establish a new mechanism for activity dependent changes at the synapse and consolidation of contextual fear.
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Affiliation(s)
- Isabel Espadas
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Jenna Wingfield
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Eddie Grinman
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Ilika Ghosh
- Max Planck Florida Institute, Jupiter, FL, USA
| | - Kaushik Chanda
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | | | - Karl Bauer
- Biomedical Center (BMC), Department for Cell Biology, Medical Faculty, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Bindu Raveendra
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Michael Kiebler
- Biomedical Center (BMC), Department for Cell Biology, Medical Faculty, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | | | | | - Sathyanarayanan Puthanveettil
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
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Hees JT, Harbauer AB. Live-Cell Imaging of RNA Transport in Axons of Cultured Primary Neurons. Methods Mol Biol 2022; 2431:225-237. [PMID: 35412279 DOI: 10.1007/978-1-0716-1990-2_11] [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
The use of fluorescent proteins has revolutionized the study of protein localization and transport. However, the visualization of other molecules and specifically RNA during live-cell imaging remains challenging. In this chapter, we provide guidance to the available methods, their advantages and drawbacks as well as provide a detailed protocol for the detection of RNA transport using the MS2/PP7-split-Venus system for background-free RNA imaging.
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Affiliation(s)
- J Tabitha Hees
- Max Planck Institute for Neurobiology, Martinsried, Germany
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6
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Sun NH, Chen DY, Ye LP, Sheng G, Gong JJ, Chen BH, Lu YM, Han F. CRISPR-Sunspot: Imaging of endogenous low-abundance RNA at the single-molecule level in live cells. Theranostics 2020; 10:10993-11012. [PMID: 33042266 PMCID: PMC7532675 DOI: 10.7150/thno.43094] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 08/21/2020] [Indexed: 12/23/2022] Open
Abstract
CRISPR/Cas-based mRNA imaging has been developed to labeling of high-abundance mRNAs. A lack of non-genetically encoded mRNA-tagged imaging tools has limited our ability to explore the functional distributions of endogenous low-abundance mRNAs in cells. Here, we developed a CRISPR-Sunspot method based on the SunTag signal amplification system that allows efficient imaging of low-abundance mRNAs with CRISPR/Cas9. Methods: We created a stable TRE3G-dCas9-EGFP cell line and generated an Inducible dCas9-EGFP imaging system for assessment of two factors, sgRNA and dCas9, which influence imaging quality. Based on SunTag system, we established a CRISPR-Sunspot imaging system for amplifying signals from single-molecule mRNA in live cells. CRISPR-Sunspot was used to track co-localization of Camk2a mRNA with regulatory protein Xlr3b in neurons. CRISPR-Sunspot combined with CRISPRa was used to determine elevated mRNA molecules. Results: Our results showed that manipulating the expression of fluorescent proteins and sgRNA increased the efficiency of RNA imaging in cells. CRISPR-Sunspot could target endogenous mRNAs in the cytoplasm and amplified signals from single-molecule mRNA. Furthermore, CRISPR-Sunspot was also applied to visualize mRNA distributions with its regulating proteins in neurons. CRISPR-Sunspot detected the co-localization of Camk2a mRNA with overexpressed Xlr3b proteins in the neuronal dendrites. Moreover, we also manipulated CRISPR-Sunspot to detect transcriptional activation of target gene such as HBG1 in live cells. Conclusion: Our findings suggest that CRISPR-Sunspot is a novel applicable imaging tool for visualizing the distributions of low-abundance mRNAs in cells. This study provides a novel strategy to unravel the molecular mechanisms of diseases caused by aberrant mRNA molecules.
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Affiliation(s)
- Ning-He Sun
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Drug Target and Drug Discovery Center, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
- Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dan-Yang Chen
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Drug Target and Drug Discovery Center, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
- Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lu-Peng Ye
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Gang Sheng
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Drug Target and Drug Discovery Center, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Jun-Jie Gong
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Drug Target and Drug Discovery Center, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Bao-Hui Chen
- Department of Cell Biology, School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Ying-Mei Lu
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
| | - Feng Han
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Drug Target and Drug Discovery Center, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
- Center for Global Health of Nanjing Medical University, Nanjing, 211166, China
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7
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Corradi E, Dalla Costa I, Gavoci A, Iyer A, Roccuzzo M, Otto TA, Oliani E, Bridi S, Strohbuecker S, Santos-Rodriguez G, Valdembri D, Serini G, Abreu-Goodger C, Baudet ML. Axonal precursor miRNAs hitchhike on endosomes and locally regulate the development of neural circuits. EMBO J 2020; 39:e102513. [PMID: 32073171 PMCID: PMC7073465 DOI: 10.15252/embj.2019102513] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 12/24/2019] [Accepted: 01/17/2020] [Indexed: 12/22/2022] Open
Abstract
Various species of non‐coding RNAs (ncRNAs) are enriched in specific subcellular compartments, but the mechanisms orchestrating their localization and their local functions remain largely unknown. We investigated both aspects using the elongating retinal ganglion cell axon and its tip, the growth cone, as models. We reveal that specific endogenous precursor microRNAs (pre‐miRNAs) are actively trafficked to distal axons by hitchhiking primarily on late endosomes/lysosomes. Upon exposure to the axon guidance cue semaphorin 3A (Sema3A), pre‐miRNAs are processed specifically within axons into newly generated miRNAs, one of which, in turn, silences the basal translation of tubulin beta 3 class III (TUBB3), but not amyloid beta precursor protein (APP). At the organismal level, these mature miRNAs are required for growth cone steering and a fully functional visual system. Overall, our results uncover a novel mode of ncRNA transport from one cytosolic compartment to another within polarized cells. They also reveal that newly generated miRNAs are critical components of a ncRNA‐based signaling pathway that transduces environmental signals into the structural remodeling of subcellular compartments.
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Affiliation(s)
- Eloina Corradi
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Irene Dalla Costa
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Antoneta Gavoci
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Archana Iyer
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Michela Roccuzzo
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Tegan A Otto
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Eleonora Oliani
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Simone Bridi
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Stephanie Strohbuecker
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | | | - Donatella Valdembri
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy.,Department of Oncology, University of Torino School of Medicine, Candiolo, Italy
| | - Guido Serini
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy.,Department of Oncology, University of Torino School of Medicine, Candiolo, Italy
| | | | - Marie-Laure Baudet
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
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Wang Z, Liu W, Fan C, Chen N. Visualizing mRNA in live mammalian cells. Methods 2019; 161:16-23. [DOI: 10.1016/j.ymeth.2019.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 03/10/2019] [Accepted: 03/12/2019] [Indexed: 01/06/2023] Open
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9
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Lipshitz HD, Claycomb JM, Smibert CA. Post-transcriptional regulation of gene expression. Methods 2017; 126:1-2. [DOI: 10.1016/j.ymeth.2017.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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