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Eguchi M, Yoshimura H, Ozawa T. A Method for Bioluminescence-Based RNA Monitoring Using Split-Luciferase Reconstitution Techniques. Methods Mol Biol 2025; 2875:9-20. [PMID: 39535636 DOI: 10.1007/978-1-0716-4248-1_2] [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: 11/16/2024]
Abstract
A bioluminescence-based RNA monitoring method in living cells was developed using a split NanoLuc (NLuc) reconstitution technique. For specific recognition of a target RNA sequence, a mutant PUM-HD (mPUM) was used. The method was applied to β-actin mRNA in various cells, including primary cultures of rat hippocampal neurons. It allowed for continuous observation of intracellular localization distribution of the target mRNA in living cells, providing insights into various biological phenomena involving intracellular RNA localization and dynamics.
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Affiliation(s)
- Masatoshi Eguchi
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo, Japan
| | - Hideaki Yoshimura
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo, Japan.
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Eguchi M, Yoshimura H, Ueda Y, Ozawa T. Split Luciferase-Fragment Reconstitution for Unveiling RNA Localization and Dynamics in Live Cells. ACS Sens 2023; 8:4055-4063. [PMID: 37889477 DOI: 10.1021/acssensors.3c01080] [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: 10/28/2023]
Abstract
The intracellular distribution and dynamics of RNAs play pivotal roles in various physiological phenomena. The ability to monitor the amount and localization of endogenous RNAs in living cells allows for elucidating the mechanisms of various intracellular events. Protein-based fluorescent RNA probes are now widely used to visualize and analyze RNAs in living cells. However, continuously monitoring the temporal changes in RNA localization and dynamics in living cells is challenging. In this study, we developed a bioluminescent probe for spatiotemporal monitoring of RNAs in living cells by using a split-luciferase reconstitution technique. The probe consists of split fragments of a bioluminescent protein, NanoLuc, connected with RNA-binding protein domains generated from a custom-made mutation of a PUM-HD. The probe showed rapid luminescence intensity changes in response to an increase or decrease in the amount of a target RNA in vitro. In live-cell imaging, temporal alteration of the intracellular distribution of endogenous β-actin mRNA was visualized in response to extracellular stimulation. Furthermore, the application of the probe to the visualization of the specific localization of β-actin mRNA in primary hippocampal neurons was conducted. These results demonstrate the capability of the bioluminescent RNA probe to monitor the changes in localization, dynamics, and the amount of target RNA in living cells.
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Affiliation(s)
- Masatoshi Eguchi
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hideaki Yoshimura
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yoshibumi Ueda
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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ISOBE M, SUZUKI Y, SUGIURA H, SHIBATA M, OHSAKI Y, KAMETAKA S. Novel cell-based system to assay cell-cell fusion during myotube formation. Biomed Res 2022; 43:107-114. [DOI: 10.2220/biomedres.43.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Mari ISOBE
- Division of Biofunctional Sciences, Department of Integrated Health Sciences, Graduate School of Medicine, Nagoya University
| | - Yumika SUZUKI
- Division of Biofunctional Sciences, Department of Integrated Health Sciences, Graduate School of Medicine, Nagoya University
| | - Hideshi SUGIURA
- Division of Biofunctional Sciences, Department of Integrated Health Sciences, Graduate School of Medicine, Nagoya University
| | - Masahiro SHIBATA
- Division of Morphological Sciences, Kagoshima University Graduate School of Medical and Dental Sciences
| | - Yuki OHSAKI
- Department of Anatomy I, Sapporo Medical University School of Medicine
| | - Satoshi KAMETAKA
- Division of Biofunctional Sciences, Department of Integrated Health Sciences, Graduate School of Medicine, Nagoya University
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A Split-Luciferase-Based Cell Fusion Assay for Evaluating the Myogenesis-Promoting Effects of Bioactive Molecules. Methods Mol Biol 2021. [PMID: 34050464 DOI: 10.1007/978-1-0716-1258-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
A split-luciferase-based cell fusion assay enables high-throughput screening of myogenesis-promoting chemicals in chemical libraries. The assay consists of two C2C12 myoblast-derived cell lines (N- and C-cells), each of which stably expresses either an N- or C-terminal split-firefly luciferase (FLuc) fragment fused to a naturally split DnaE intein (N- and C-probes, respectively). The fusion of N- and C-cells during myogenesis induces bioluminescence (BL) in the cytosol due to a stable reconstitution of the split-FLuc. Thus, the myogenesis-promoting effects of a chemical compound can be determined through the enhanced BL intensity. Here, we describe the preparation of N- and C-cells and determination of the myogenesis-promoting effects of imatinib using a 96-well microplate-based assay.
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Littmann T, Ozawa T, Hoffmann C, Buschauer A, Bernhardt G. A split luciferase-based probe for quantitative proximal determination of Gα q signalling in live cells. Sci Rep 2018; 8:17179. [PMID: 30464299 PMCID: PMC6249299 DOI: 10.1038/s41598-018-35615-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/08/2018] [Indexed: 01/04/2023] Open
Abstract
The earlier an activation of a G protein-dependent signalling cascade at a G protein-coupled receptor (GPCR) is probed, the less amplificatory effects contribute to the measured signal. This is especially useful in case of a precise quantification of agonist efficacies, and is of paramount importance, when determining agonist bias in relation to the β-arrestin pathway. As most canonical assays with medium to high throughput rely on the quantification of second messengers, and assays affording more proximal readouts are often limited in throughput, we developed a technique with a proximal readout and sufficiently high throughput that can be used in live cells. Split luciferase complementation (SLC) was applied to assess the interaction of Gαq with its effector phospholipase C-β3. The resulting probe yielded an excellent Z' value of 0.7 and offers a broad and easy applicability to various Gαq-coupling GPCRs (hH1R, hM1,3,5R, hNTS1R), expressed in HEK293T cells, allowing the functional characterisation of agonists and antagonists. Furthermore, the developed sensor enabled imaging of live cells by luminescence microscopy, as demonstrated for the hM3R. The versatile SLC-based probe is broadly applicable e.g. to the screening and the pharmacological characterisation of GPCR ligands as well as to molecular imaging.
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Affiliation(s)
- Timo Littmann
- Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany.
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Carsten Hoffmann
- Institute of Molecular Cell Biology, University Hospital Jena, University of Jena, Hans-Knöll-Str. 2, D-07745, Jena, Germany
| | - Armin Buschauer
- Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany
| | - Günther Bernhardt
- Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany.
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Li Q, Yoshimura H, Komiya M, Tajiri K, Uesugi M, Hata Y, Ozawa T. A robust split-luciferase-based cell fusion screening for discovering myogenesis-promoting molecules. Analyst 2018; 143:3472-3480. [DOI: 10.1039/c8an00285a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Screening by the luciferase complementation-based cell fusion assay discovered two myogenesis-promoting chemicals.
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Affiliation(s)
- Qiaojing Li
- Department of Chemistry
- School of Science
- The University of Tokyo
- Tokyo 113-0033
- Japan
| | - Hideaki Yoshimura
- Department of Chemistry
- School of Science
- The University of Tokyo
- Tokyo 113-0033
- Japan
| | - Maki Komiya
- Department of Chemistry
- School of Science
- The University of Tokyo
- Tokyo 113-0033
- Japan
| | - Ken Tajiri
- Institute for Integrated Cell-Material Sciences (iCeMS)/Institute for Chemical Research (ICR)
- Kyoto University
- Kyoto 611-0011
- Japan
| | - Motonari Uesugi
- Institute for Integrated Cell-Material Sciences (iCeMS)/Institute for Chemical Research (ICR)
- Kyoto University
- Kyoto 611-0011
- Japan
| | - Yutaka Hata
- Graduate School of Medical and Dental Sciences
- Tokyo Medical and Dental University
- Tokyo 113-8510
- Japan
| | - Takeaki Ozawa
- Department of Chemistry
- School of Science
- The University of Tokyo
- Tokyo 113-0033
- Japan
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Yoshimura H, Ozawa T. Real-Time Fluorescence Imaging of Single-Molecule Endogenous Noncoding RNA in Living Cells. Methods Mol Biol 2018; 1649:337-347. [PMID: 29130208 DOI: 10.1007/978-1-4939-7213-5_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Visualizing RNA in living cells is increasingly important to facilitate accumulation of knowledge about the relation between specific RNA dynamics and physiological events. Single-molecule fluorescence imaging of target RNAs is an excellent approach to analyzing intracellular RNA motion, but it requires special techniques for probe design and microscope setup. Herein, we present a principle and protocol of an RNA visualization probe based on an RNA binding protein of the Pumilio homology domain (PUM-HD). We also describe the setup and operation of a microscope, and introduce an application to visualize telomeric repeats-containing RNA with telomeres and a telomere-related protein: hnRNPA1. This imaging technique is applicable to visualization of different RNAs, especially including repetitive sequences, in living cells.
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Affiliation(s)
- Hideaki Yoshimura
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
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Yoshimura H. Live Cell Imaging of Endogenous RNAs Using Pumilio Homology Domain Mutants: Principles and Applications. Biochemistry 2017; 57:200-208. [PMID: 29164876 DOI: 10.1021/acs.biochem.7b00983] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recently, dynamic changes in the location of RNA in space and time in living cells have become a target of interest in biology because of their essential roles in controlling physiological phenomena. To visualize RNA, methods for the fluorescent labeling of RNA in living cells have been developed. For RNA labeling, oligonucleotide-based RNA probes have mainly been used because of their high selectivity for target RNAs. By contrast, protein-based RNA probes have not been used widely because of their lack of design flexibility, although they have various potential advantages compared with nucleotide-based probes, such as controllability of intracellular localization, high detectability, and ease of introduction into cells and transgenic organisms in a cell type and tissue specific manner by genetic engineering techniques. This Perspective focuses on a possible approach to the development of protein-based RNA probes using Pumilio homology domain (PUM-HD) mutants. The PUM-HD is a domain of an RNA binding protein that allows custom-made modifications to recognize a given eight-base RNA sequence. PUM-HD-based RNA probes have been applied to visualize various RNAs in living cells. Here, the techniques and RNA imaging results obtained using the PUM-HD are introduced.
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Affiliation(s)
- Hideaki Yoshimura
- Department of Chemistry, School of Science, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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9
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Yoshimura H, Ozawa T. Monitoring of RNA Dynamics in Living Cells Using PUM-HD and Fluorescent Protein Reconstitution Technique. Methods Enzymol 2016; 572:65-85. [DOI: 10.1016/bs.mie.2016.03.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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