1
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Kawatomi K, Morita Y, Katakura Y, Takegawa K, Berepiki A, Higuchi Y. Live cell imaging of β-tubulin mRNA reveals spatiotemporal expression dynamics in the filamentous fungus Aspergillus oryzae. Sci Rep 2024; 14:13797. [PMID: 38877139 PMCID: PMC11178776 DOI: 10.1038/s41598-024-64531-5] [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: 05/13/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
In filamentous fungi, microtubules are important for polar growth and morphological maintenance and serve as rails for intracellular trafficking. The molecular mechanisms associated with microtubules have been analyzed. However, little is known about when and where tubulin, a component of microtubules, is biosynthesized in multinuclear and multicellular filamentous fungi. In this study, we visualized microtubules based on the enhanced green fluorescence protein (EGFP)-labeled α-tubulin and β-tubulin mRNA tagged by the EGFP-mediated MS2 system in living yellow Koji mold Aspergillus oryzae cells in order to understand the spatiotemporal production mechanism of tubulin. We found that mRNA of btuA, encoding for β-tubulin, localized at dot-like structures through the apical, middle and basal regions of the hyphal cells. In addition, some btuA mRNA dots showed microtubule-dependent motor protein-like dynamics in the cells. Furthermore, it was found that btuA mRNA dots were decreased in the cytoplasm just before mitosis but increased immediately after mitosis, followed by a gradual decrease. In summary, the localization and abundance of β-tubulin mRNA is spatiotemporally regulated in living A. oryzae hyphal cells.
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Affiliation(s)
- Keishu Kawatomi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | - Yuki Morita
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | - Yoshinori Katakura
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | - Kaoru Takegawa
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | | | - Yujiro Higuchi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan.
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2
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Luzia L, Battjes J, Zwering E, Jansen D, Melkonian C, Teusink B. A fast method to distinguish between fermentative and respiratory metabolisms in single yeast cells. iScience 2024; 27:108767. [PMID: 38235328 PMCID: PMC10793178 DOI: 10.1016/j.isci.2023.108767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/27/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024] Open
Abstract
Saccharomyces cerevisiae adjusts its metabolism based on nutrient availability, typically transitioning from glucose fermentation to ethanol respiration as glucose becomes limiting. However, our understanding of the regulation of metabolism is largely based on population averages, whereas nutrient transitions may cause heterogeneous responses. Here we introduce iCRAFT, a method that couples the ATP Förster resonance energy transfer (FRET)-based biosensor yAT1.03 with Antimycin A to differentiate fermentative and respiratory metabolisms in individual yeast cells. Upon Antimycin A addition, respiratory cells experienced a sharp decrease of the normalized FRET ratio, while respiro-fermentative cells showed no response. Next, we tracked changes in metabolism during the diauxic shift of a glucose pre-grown culture. Following glucose exhaustion, the entire cell population experienced a progressive rise in cytosolic ATP produced via respiration, suggesting a gradual increase in respiratory capacity. Overall, iCRAFT is a robust tool to distinguish fermentation from respiration, offering a new single-cell opportunity to study yeast metabolism.
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Affiliation(s)
- Laura Luzia
- Systems Biology Lab, A-LIFE, Institute of Molecular and Life Sciences (AIMMS), VU Amsterdam, 1081HZ Amsterdam, the Netherlands
| | - Julius Battjes
- Systems Biology Lab, A-LIFE, Institute of Molecular and Life Sciences (AIMMS), VU Amsterdam, 1081HZ Amsterdam, the Netherlands
| | - Emile Zwering
- Systems Biology Lab, A-LIFE, Institute of Molecular and Life Sciences (AIMMS), VU Amsterdam, 1081HZ Amsterdam, the Netherlands
| | - Derek Jansen
- Systems Biology Lab, A-LIFE, Institute of Molecular and Life Sciences (AIMMS), VU Amsterdam, 1081HZ Amsterdam, the Netherlands
| | - Chrats Melkonian
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
- Bioinformatics Group, Wageningen University and Research, 6700AP Wageningen, the Netherlands
| | - Bas Teusink
- Systems Biology Lab, A-LIFE, Institute of Molecular and Life Sciences (AIMMS), VU Amsterdam, 1081HZ Amsterdam, the Netherlands
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3
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Gerber A, van Otterdijk S, Bruggeman FJ, Tutucci E. Understanding spatiotemporal coupling of gene expression using single molecule RNA imaging technologies. Transcription 2023; 14:105-126. [PMID: 37050882 PMCID: PMC10807504 DOI: 10.1080/21541264.2023.2199669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 04/14/2023] Open
Abstract
Across all kingdoms of life, gene regulatory mechanisms underlie cellular adaptation to ever-changing environments. Regulation of gene expression adjusts protein synthesis and, in turn, cellular growth. Messenger RNAs are key molecules in the process of gene expression. Our ability to quantitatively measure mRNA expression in single cells has improved tremendously over the past decades. This revealed an unexpected coordination between the steps that control the life of an mRNA, from transcription to degradation. Here, we provide an overview of the state-of-the-art imaging approaches for measurement and quantitative understanding of gene expression, starting from the early visualizations of single genes by electron microscopy to current fluorescence-based approaches in single cells, including live-cell RNA-imaging approaches to FISH-based spatial transcriptomics across model organisms. We also highlight how these methods have shaped our current understanding of the spatiotemporal coupling between transcriptional and post-transcriptional events in prokaryotes. We conclude by discussing future challenges of this multidisciplinary field.Abbreviations: mRNA: messenger RNA; rRNA: ribosomal rDNA; tRNA: transfer RNA; sRNA: small RNA; FISH: fluorescence in situ hybridization; RNP: ribonucleoprotein; smFISH: single RNA molecule FISH; smiFISH: single molecule inexpensive FISH; HCR-FISH: Hybridization Chain-Reaction-FISH; RCA: Rolling Circle Amplification; seqFISH: Sequential FISH; MERFISH: Multiplexed error robust FISH; UTR: Untranslated region; RBP: RNA binding protein; FP: fluorescent protein; eGFP: enhanced GFP, MCP: MS2 coat protein; PCP: PP7 coat protein; MB: Molecular beacons; sgRNA: single guide RNA.
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Affiliation(s)
- Alan Gerber
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Sander van Otterdijk
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank J. Bruggeman
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Evelina Tutucci
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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4
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Liang Y, Willey S, Chung YC, Lo YM, Miao S, Rundell S, Tu LC, Bong D. Intracellular RNA and DNA tracking by uridine-rich internal loop tagging with fluorogenic bPNA. Nat Commun 2023; 14:2987. [PMID: 37225690 DOI: 10.1038/s41467-023-38579-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
The most widely used method for intracellular RNA fluorescence labeling is MS2 labeling, which generally relies on the use of multiple protein labels targeted to multiple RNA (MS2) hairpin structures installed on the RNA of interest (ROI). While effective and conveniently applied in cell biology labs, the protein labels add significant mass to the bound RNA, which potentially impacts steric accessibility and native RNA biology. We have previously demonstrated that internal, genetically encoded, uridine-rich internal loops (URILs) comprised of four contiguous UU pairs (8 nt) in RNA may be targeted with minimal structural perturbation by triplex hybridization with 1 kD bifacial peptide nucleic acids (bPNAs). A URIL-targeting strategy for RNA and DNA tracking would avoid the use of cumbersome protein fusion labels and minimize structural alterations to the RNA of interest. Here we show that URIL-targeting fluorogenic bPNA probes in cell media can penetrate cell membranes and effectively label RNAs and RNPs in fixed and live cells. This method, which we call fluorogenic U-rich internal loop (FLURIL) tagging, was internally validated through the use of RNAs bearing both URIL and MS2 labeling sites. Notably, a direct comparison of CRISPR-dCas labeled genomic loci in live U2OS cells revealed that FLURIL-tagged gRNA yielded loci with signal to background up to 7X greater than loci targeted by guide RNA modified with an array of eight MS2 hairpins. Together, these data show that FLURIL tagging provides a versatile scope of intracellular RNA and DNA tracking while maintaining a light molecular footprint and compatibility with existing methods.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Sydney Willey
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Yu-Chieh Chung
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | - Yi-Meng Lo
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Li-Chun Tu
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA.
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA.
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
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5
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Chen W, Zhao X, Yang N, Li X. Single mRNA Imaging with Fluorogenic RNA Aptamers and Small-molecule Fluorophores. Angew Chem Int Ed Engl 2023; 62:e202209813. [PMID: 36420710 DOI: 10.1002/anie.202209813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/07/2022] [Accepted: 11/24/2022] [Indexed: 11/25/2022]
Abstract
Messenger RNA (mRNA) is the fundamental information transfer system in the cell. Tracking single mRNA from transcription to degradation with fluorescent probes provides spatiotemporal information in cells about how the genetic information is transferred from DNA to proteins. The traditional single mRNA imaging approach utilizes RNA hairpins (e.g. MS2) and tethered fluorescent protein as probes. As an exciting alternative, RNA aptamers: small-molecule fluorophores (SFs) systems have emerged as novel single mRNA imaging probes since 2019, exhibiting several advantages including fluorogenic ability and minimal perturbation. This review summarizes all five reported RNA aptamers: SFs systems for single mRNA imaging in living cells so far. It also discusses the challenges and provides prospects for single mRNA imaging applications. This review is expected to inspire researchers to develop RNA aptamers: SFs systems for studying gene expression at single-molecule resolution in cells.
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Affiliation(s)
- Wei Chen
- Institute of Cytology and Genetics, the Hengyang Key Laboratory of Cellular Stress Biology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.,Beijing Institutes of Life Science, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Science, Beijing, 100101, China
| | - Xiaoying Zhao
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, 100048, China
| | - Nanyang Yang
- Institute of Cytology and Genetics, the Hengyang Key Laboratory of Cellular Stress Biology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Xing Li
- Beijing Institutes of Life Science, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Science, Beijing, 100101, China
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6
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Bühler B, Schokolowski J, Benderoth A, Englert D, Grün F, Jäschke A, Sunbul M. Avidity-based bright and photostable light-up aptamers for single-molecule mRNA imaging. Nat Chem Biol 2023; 19:478-487. [PMID: 36658339 DOI: 10.1038/s41589-022-01228-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 11/17/2022] [Indexed: 01/21/2023]
Abstract
Fluorescent light-up aptamers (FLAPs) have emerged as valuable tools to visualize RNAs, but are mostly limited by their poor brightness, low photostability, and high fluorescence background in live cells. Exploiting the avidity concept, here we present two of the brightest FLAPs with the strongest aptamer-dye interaction, high fluorogenicity, and remarkable photostability. They consist of dimeric fluorophore-binding aptamers (biRhoBAST and biSiRA) embedded in an RNA scaffold and their bivalent fluorophore ligands (bivalent tetramethylrhodamine TMR2 and silicon rhodamine SiR2). Red fluorescent biRhoBAST-TMR2 and near-infrared fluorescent biSiRA-SiR2 are orthogonal to each other, facilitating simultaneous visualization of two different RNA species in live cells. One copy of biRhoBAST allows for simple and robust mRNA imaging with strikingly higher signal-to-background ratios than other FLAPs. Moreover, eight biRhoBAST repeats enable single-molecule mRNA imaging and tracking with minimal perturbation of their localization, translation, and degradation, demonstrating the potential of avidity-enhanced FLAPs for imaging RNA dynamics.
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Affiliation(s)
- Bastian Bühler
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Janin Schokolowski
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Anja Benderoth
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Daniel Englert
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Franziska Grün
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
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7
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Guo Y, Lee RE. Long-term imaging of individual mRNA molecules in living cells. CELL REPORTS METHODS 2022; 2:100226. [PMID: 35784652 PMCID: PMC9243547 DOI: 10.1016/j.crmeth.2022.100226] [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] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/10/2022] [Accepted: 05/04/2022] [Indexed: 12/04/2022]
Abstract
Single-cell imaging of individual mRNAs has revealed core mechanisms of the central dogma. However, most approaches require cell fixation or have limited sensitivity for live-cell applications. Here, we describe SunRISER (SunTag-based reporter for imaging signal-enriched mRNA), a computationally and experimentally optimized approach for unambiguous detection of single mRNA molecules in living cells. When viewed by epifluorescence microscopy, SunRISER-labeled mRNAs show strong signal to background and resistance to photobleaching, which together enable long-term mRNA imaging studies. SunRISER variants, using 8× and 10× stem-loop arrays, demonstrate effective mRNA detection while significantly reducing alterations to target mRNA sequences. We characterize SunRISER to observe mRNA inheritance during mitosis and find that stressors enhance diversity among post-mitotic sister cells. Taken together, SunRISER enables a glimpse into living cells to observe aspects of the central dogma and the role of mRNAs in rare and dynamical trafficking events.
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Affiliation(s)
- Yue Guo
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Robin E.C. Lee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Systems Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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8
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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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9
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Fang C, Li Y, Hu S, Wang H, Chen X, Zhu X. Self-Assembled Growing DNA Tree Mediated by Exosomes for Amplified Imaging of Messenger RNA in Living Cells. Anal Chem 2021; 93:8414-8422. [PMID: 34114453 DOI: 10.1021/acs.analchem.1c00211] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Sensitive, accurate, and nondestructive probing of endogenous messenger RNA (mRNA) in living cells places extremely high demands on nanocarriers and probes and is still a challenge. In the present study, we describe a target-triggered self-assembled DNA tree for amplified analysis of mRNA in intact living cells. The probes assembled into a DNA tree are transported into cells by exosomes, which is beneficial for reducing cell damage and realizing nondestructive analysis. The probes are l-configured single-stranded DNAs (LDNAs) that can resist the degradation of exonuclease and endonuclease, thus laying the foundation for accurate analysis. Under the induction of the target mRNA, the probes in the cells assemble into a small plantlet and eventually grow into a tree after a few rounds of self-cycling, achieving the exponential amplification of fluorescence signals. Compared with the signal amplification based on one-dimensional DNA trunk self-assembly, the three-dimensional DNA tree shows an excellent sensitivity both ex situ and in situ. In this way, favorable sensitivity, accuracy, and nondestructive analysis are integrated into one system. This DNA tree expands the analysis platform for analyzing more biomarkers on a genetic level in an intracellular, nondestructive, and hypersensitive manner and holds great potential in clinical diagnostic and research applications.
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Affiliation(s)
- Cheng Fang
- Department of Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai 200040, P. R. China
| | - Yuming Li
- Department of Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai 200040, P. R. China
| | - Song Hu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Hao Wang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Xiaoxia Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.,School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China.,Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
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10
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Abulfaraj AA, Hirt H, Rayapuram N. G3BPs in Plant Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:680710. [PMID: 34177995 PMCID: PMC8222905 DOI: 10.3389/fpls.2021.680710] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/14/2021] [Indexed: 05/24/2023]
Abstract
The sessile nature of plants enforces highly adaptable strategies to adapt to different environmental stresses. Plants respond to these stresses by a massive reprogramming of mRNA metabolism. Balancing of mRNA fates, including translation, sequestration, and decay is essential for plants to not only coordinate growth and development but also to combat biotic and abiotic environmental stresses. RNA stress granules (SGs) and processing bodies (P bodies) synchronize mRNA metabolism for optimum functioning of an organism. SGs are evolutionarily conserved cytoplasmic localized RNA-protein storage sites that are formed in response to adverse conditions, harboring mostly but not always translationally inactive mRNAs. SGs disassemble and release mRNAs into a translationally active form upon stress relief. RasGAP SH3 domain binding proteins (G3BPs or Rasputins) are "scaffolds" for the assembly and stability of SGs, which coordinate receptor mediated signal transduction with RNA metabolism. The role of G3BPs in the formation of SGs is well established in mammals, but G3BPs in plants are poorly characterized. In this review, we discuss recent findings of the dynamics and functions of plant G3BPs in response to environmental stresses and speculate on possible mechanisms such as transcription and post-translational modifications that might regulate the function of this important family of proteins.
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Affiliation(s)
- Aala A. Abulfaraj
- Department of Biological Sciences, Science and Arts College, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Heribert Hirt
- King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Max Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Naganand Rayapuram
- King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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11
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Tsuboi T, Viana MP, Xu F, Yu J, Chanchani R, Arceo XG, Tutucci E, Choi J, Chen YS, Singer RH, Rafelski SM, Zid BM. Mitochondrial volume fraction and translation duration impact mitochondrial mRNA localization and protein synthesis. eLife 2020; 9:e57814. [PMID: 32762840 PMCID: PMC7413667 DOI: 10.7554/elife.57814] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/23/2020] [Indexed: 12/31/2022] Open
Abstract
Mitochondria are dynamic organelles that must precisely control their protein composition according to cellular energy demand. Although nuclear-encoded mRNAs can be localized to the mitochondrial surface, the importance of this localization is unclear. As yeast switch to respiratory metabolism, there is an increase in the fraction of the cytoplasm that is mitochondrial. Our data point to this change in mitochondrial volume fraction increasing the localization of certain nuclear-encoded mRNAs to the surface of the mitochondria. We show that mitochondrial mRNA localization is necessary and sufficient to increase protein production to levels required during respiratory growth. Furthermore, we find that ribosome stalling impacts mRNA sensitivity to mitochondrial volume fraction and counterintuitively leads to enhanced protein synthesis by increasing mRNA localization to mitochondria. This points to a mechanism by which cells are able to use translation elongation and the geometric constraints of the cell to fine-tune organelle-specific gene expression through mRNA localization.
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Affiliation(s)
- Tatsuhisa Tsuboi
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaUnited States
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California IrvineIrvineUnited States
- Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoyaJapan
| | - Matheus P Viana
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California IrvineIrvineUnited States
| | - Fan Xu
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaUnited States
| | - Jingwen Yu
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaUnited States
| | - Raghav Chanchani
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaUnited States
| | - Ximena G Arceo
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaUnited States
| | - Evelina Tutucci
- Department of Anatomy and Structural Biology, Albert Einstein College of MedicineBronxUnited States
| | - Joonhyuk Choi
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaUnited States
| | - Yang S Chen
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaUnited States
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of MedicineBronxUnited States
- Gruss-Lipper Biophotonics Center, Albert Einstein College of MedicineBronxUnited States
- Department of Neuroscience, Albert Einstein College of MedicineBronxUnited States
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Susanne M Rafelski
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California IrvineIrvineUnited States
| | - Brian M Zid
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaUnited States
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12
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Maekiniemi A, Singer RH, Tutucci E. Single molecule mRNA fluorescent in situ hybridization combined with immunofluorescence in S. cerevisiae: Dataset and quantification. Data Brief 2020; 30:105511. [PMID: 32368581 PMCID: PMC7186551 DOI: 10.1016/j.dib.2020.105511] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/25/2020] [Accepted: 03/23/2020] [Indexed: 11/29/2022] Open
Abstract
Single-molecule fluorescent in situ hybridization (smFISH) has emerged as a powerful technique that allows one to localize and quantify the absolute number of mRNAs in single cells. In combination with immunofluorescence (IF), smFISH can be used to correlate the expression of an mRNA and a protein of interest in single cells. Here, we provide and quantify an smFISH-IF dataset in S. cerevisiae. We measured the expression of the cell cycle-controlled mRNA CLN2 and the cell cycle marker alpha-tubulin. The smFISH-IF protocol describing the dataset generation is published in the accompanying article "Simultaneous detection of mRNA and protein in S. cerevisiae by single-molecule FISH and Immunofluorescence" [1]. Here, we analyze the smFISH data using the freely available software FISH-quant [2]. The provided datasets are intended to assist scientists interested in setting up smFISH-IF protocol in their laboratory. Furthermore, scientists interested in the generation of imaging analysis tools for single-cell approaches may find the provided dataset useful. To this end, we provide the differential interference contrast (DIC) channel, as well as multicolor, raw Z-stacks for smFISH, IF and DAPI.
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Affiliation(s)
- Anna Maekiniemi
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Robert H. Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, United States
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, United States
- Janelia Research Campus of the HHMI, Ashburn, Virginia 20147, United States
| | - Evelina Tutucci
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
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13
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Live cell imaging and proteomic profiling of endogenous NEAT1 lncRNA by CRISPR/Cas9-mediated knock-in. Protein Cell 2020; 11:641-660. [PMID: 32458346 PMCID: PMC7452982 DOI: 10.1007/s13238-020-00706-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
Abstract
In mammalian cells, long noncoding RNAs (lncRNAs) form complexes with proteins to execute various biological functions such as gene transcription, RNA processing and other signaling activities. However, methods to track endogenous lncRNA dynamics in live cells and screen for lncRNA interacting proteins are limited. Here, we report the development of CERTIS (CRISPR-mediated Endogenous lncRNA Tracking and Immunoprecipitation System) to visualize and isolate endogenous lncRNA, by precisely inserting a 24-repeat MS2 tag into the distal end of lncRNA locus through the CRISPR/Cas9 technology. In this study, we show that CERTIS effectively labeled the paraspeckle lncRNA NEAT1 without disturbing its physiological properties and could monitor the endogenous expression variation of NEAT1. In addition, CERTIS displayed superior performance on both short- and long-term tracking of NEAT1 dynamics in live cells. We found that NEAT1 and paraspeckles were sensitive to topoisomerase I specific inhibitors. Moreover, RNA Immunoprecipitation (RIP) of the MS2-tagged NEAT1 lncRNA successfully revealed several new protein components of paraspeckle. Our results support CERTIS as a tool suitable to track both spatial and temporal lncRNA regulation in live cells as well as study the lncRNA-protein interactomes.
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14
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Vera M, Tutucci E, Singer RH. Imaging Single mRNA Molecules in Mammalian Cells Using an Optimized MS2-MCP System. Methods Mol Biol 2020; 2038:3-20. [PMID: 31407274 DOI: 10.1007/978-1-4939-9674-2_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Visualization of single mRNAs in their native cellular environment provides key information to study gene expression regulation. This fundamental biological question triggered the development of the MS2-MCP (MS2-Capsid Protein) system to tag mRNAs and image their life cycle using widefield fluorescence microscopy. The last two decades have evolved toward improving the qualitative and quantitative characteristics of the MS2-MCP system. Here, we provide a protocol to use the latest versions, MS2V6 and MS2V7, to tag and visualize mRNAs in mammalian cells in culture. The motivation behind engineering MS2V6 and MS2V7 was to overcome a degradation caveat observed in S. cerevisiae with the previous MS2-MCP systems. While for yeast we recommend the use of MS2V6, we found that for live-cell imaging experiments in mammalian cells, the MS2V7 has improved reporter properties.
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Affiliation(s)
- Maria Vera
- Department of Biochemistry, McGill University, Montreal, Canada
| | - Evelina Tutucci
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA. .,Janelia Research Campus of the HHMI, Ashburn, Virginia, USA.
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15
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Peña EJ, Heinlein M. Visualization of Transiently Expressed mRNA in Plants Using MS2. Methods Mol Biol 2020; 2166:103-120. [PMID: 32710405 DOI: 10.1007/978-1-0716-0712-1_6] [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: 12/17/2023]
Abstract
RNA transport and localization are evolutionarily conserved processes that allow protein translation to occur at specific subcellular sites and thereby having fundamental roles in the determination of cell fates, embryonic patterning, asymmetric cell division, and cell polarity. In addition to localizing RNA molecules to specific subcellular sites, plants have the ability to exchange RNA molecules between cells through plasmodesmata (PD). Plant RNA viruses hijack the mechanisms of intracellular and intercellular RNA transport to establish localized replication centers within infected cells and then to disseminate their infectious genomes between cells and throughout the plant organism with the help of their movement proteins (MP). In this chapter, we describe the transient expression of the tobacco mosaic virus movement protein (TMV-MP) and the application of the MS2 system for the in vivo labeling of the MP-encoding mRNA. The MS2 method is based on the binding of the bacteriophage coat protein (CP) to its origin of assembly (OAS) in the phage RNA. Thus, to label a specific mRNA in vivo, a tandem repetition of a 19-nucleotide-long stem-loop (SL) sequence derived from the MS2 OAS sequence (MSL) is transcriptionally fused to the RNA under investigation. The RNA is detected by the co-expression of fluorescent protein-tagged MS2 CP (MCP), which binds to each of the MSL elements. In providing a detailed protocol for the in vivo visualization of TMV-MP mRNA tagged with the MS2 system in Nicotiana benthamiana epidermal cells, we describe (1) the specific DNA constructs, (2) Agrobacterium tumefaciens-mediated transfection for their transient expression in plants, and (3) imaging conditions required to obtain high-quality mRNA imaging data.
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Affiliation(s)
- Eduardo José Peña
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata CONICET, Fac. Cs. Exactas, U.N.L.P, La Plata, Argentina
| | - Manfred Heinlein
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France.
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16
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Pichon X, Robert MC, Bertrand E, Singer RH, Tutucci E. New Generations of MS2 Variants and MCP Fusions to Detect Single mRNAs in Living Eukaryotic Cells. Methods Mol Biol 2020; 2166:121-144. [PMID: 32710406 DOI: 10.1007/978-1-0716-0712-1_7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Live imaging of single RNA from birth to death brought important advances in our understanding of the spatiotemporal regulation of gene expression. These studies have provided a comprehensive understanding of RNA metabolism by describing the process step by step. Most of these studies used for live imaging a genetically encoded RNA-tagging system fused to fluorescent proteins. One of the best characterized RNA-tagging systems is derived from the bacteriophage MS2 and it allows single RNA imaging in real-time and live cells. This system has been successfully used to track the different steps of mRNA processing in many living organisms. The recent development of optimized MS2 and MCP variants now allows the labeling of endogenous RNAs and their imaging without modifying their behavior. In this chapter, we discuss the improvements in detecting single mRNAs with different variants of MCP and fluorescent proteins that we tested in yeast and mammalian cells. Moreover, we describe protocols using MS2-MCP systems improved for real-time imaging of single mRNAs and transcription dynamics in S. cerevisiae and mammalian cells, respectively.
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Affiliation(s)
- Xavier Pichon
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France.,Equipe labélisée Ligue Nationale Contre le Cancer, Montpellier, France
| | - Marie-Cécile Robert
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France.,Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA.,Janelia Research Campus of the HHMI, Ashburn, VA, USA
| | - Evelina Tutucci
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA. .,Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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17
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Ben-Yishay R, Shav-Tal Y. The dynamic lifecycle of mRNA in the nucleus. Curr Opin Cell Biol 2019; 58:69-75. [PMID: 30889416 DOI: 10.1016/j.ceb.2019.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/16/2019] [Accepted: 02/20/2019] [Indexed: 12/15/2022]
Abstract
The mRNA molecule roams through the nucleus on its way out to the cytoplasm. mRNA encounters and is bound by many protein factors, from the moment it begins to emerge from RNA polymerase II and during its travel in the nucleoplasm, where it will come upon chromatin and nuclear bodies. Some of the protein factors that engage with the mRNA can process it, until finally reaching a mature state fit for export through the nuclear pore complex (NPC). Examining the lifecycle of mRNAs in living cells using mRNA tagging techniques opens a window into our understanding of the rules that drive the dynamics of gene expression from transcription to mRNA export.
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Affiliation(s)
- Rakefet Ben-Yishay
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel.
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18
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Lari A, Farzam F, Bensidoun P, Oeffinger M, Zenklusen D, Grunwald D, Montpetit B. Live-Cell Imaging of mRNP-NPC Interactions in Budding Yeast. Methods Mol Biol 2019; 2038:131-150. [PMID: 31407282 DOI: 10.1007/978-1-4939-9674-2_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Single-molecule resolution imaging has become an important tool in the study of cell biology. Aptamer-based approaches (e.g., MS2 and PP7) allow for detection of single RNA molecules in living cells and have been used to study various aspects of mRNA metabolism, including mRNP nuclear export. Here we outline an imaging protocol for the study of interactions between mRNPs and nuclear pore complexes (NPCs) in the yeast S. cerevisiae, including mRNP export. We describe in detail the steps that allow for high-resolution live-cell mRNP imaging and measurement of mRNP interactions with NPCs using simultaneous two-color imaging. Our protocol discusses yeast strain construction, choice of marker proteins to label the nuclear pore complex, as well as imaging conditions that allow high signal-to-noise data acquisition. Moreover, we describe various aspects of postacquisition image analysis for single molecule tracking and image registration allowing for the characterization of mRNP-NPC interactions.
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Affiliation(s)
- Azra Lari
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Farzin Farzam
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Pierre Bensidoun
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
| | - Marlene Oeffinger
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Canada.
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA.
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