1
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Kannaiah S, Goldberger O, Alam N, Barnabas G, Pozniak Y, Nussbaum-Shochat A, Schueler-Furman O, Geiger T, Amster-Choder O. MinD-RNase E interplay controls localization of polar mRNAs in E. coli. EMBO J 2024; 43:637-662. [PMID: 38243117 PMCID: PMC10897333 DOI: 10.1038/s44318-023-00026-9] [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: 02/03/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024] Open
Abstract
The E. coli transcriptome at the cell's poles (polar transcriptome) is unique compared to the membrane and cytosol. Several factors have been suggested to mediate mRNA localization to the membrane, but the mechanism underlying polar localization of mRNAs remains unknown. Here, we combined a candidate system approach with proteomics to identify factors that mediate mRNAs localization to the cell poles. We identified the pole-to-pole oscillating protein MinD as an essential factor regulating polar mRNA localization, although it is not able to bind RNA directly. We demonstrate that RNase E, previously shown to interact with MinD, is required for proper localization of polar mRNAs. Using in silico modeling followed by experimental validation, the membrane-binding site in RNase E was found to mediate binding to MinD. Intriguingly, not only does MinD affect RNase E interaction with the membrane, but it also affects its mode of action and dynamics. Polar accumulation of RNase E in ΔminCDE cells resulted in destabilization and depletion of mRNAs from poles. Finally, we show that mislocalization of polar mRNAs may prevent polar localization of their protein products. Taken together, our findings show that the interplay between MinD and RNase E determines the composition of the polar transcriptome, thus assigning previously unknown roles for both proteins.
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Affiliation(s)
- Shanmugapriya Kannaiah
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, 63110, USA.
| | - Omer Goldberger
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
| | - Nawsad Alam
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Georgina Barnabas
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 6997801, Tel-Aviv, Israel
- Department of Pathology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Yair Pozniak
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 6997801, Tel-Aviv, Israel
| | - Anat Nussbaum-Shochat
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 6997801, Tel-Aviv, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, 76100001, Rehovot, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O.Box 12272, 91120, Jerusalem, Israel.
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2
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Patterson D. The scope and scale of the life sciences (‘Nature’s envelope’). RESEARCH IDEAS AND OUTCOMES 2022. [DOI: 10.3897/rio.8.e96132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The extension of biology with a more data-centric component offers new opportunities for discovery. To enable investigations that rely on third-party data, the infrastructure that retains data and allows their re-use should, arguably, enable transactions that relate to any and all biological processes. The assembly of such a service-oriented and enabling infrastructure is challenging. Part of the challenge is to factor in the scope and scale of biological processes. From this foundation can emerge an estimate of the number of discipline-specific centres which will gather data in their given area of interest and prepare them for a path that will lead to trusted, persistent data repositories which will make fit-for-purpose data available for re-use. A simple model is presented for the scope and scale of life sciences. It can accommodate all known processes conducted by or caused by any and all organisms. It is depicted on a grid, the axes of which are (x) the durations of the processes and (y) the sizes of participants involved. Both axes are presented in log10 scales, and the grid is divided into decadal blocks with ten fold increments of time and size. Processes range in duration from 10-17 seconds to 3.5 billion years or more, and the sizes of participants range from 10-15 to 1.3 107 metres. Examples are given to illustrate the diversity of biological processes and their often inexact character. About half of the blocks within the grid do not contain known processes. The blocks that include biological processes amount to ‘Nature’s envelope’, a valuable rhetorical device onto which subdisciplines and existing initiatives may be mapped, and from which can be derived some key requirements for a comprehensive data infrastructure.
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3
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Recent advance of RNA aptamers and DNAzymes for MicroRNA detection. Biosens Bioelectron 2022; 212:114423. [DOI: 10.1016/j.bios.2022.114423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/19/2022] [Accepted: 05/23/2022] [Indexed: 02/02/2023]
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4
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Wang Q, Xiao F, Su H, Liu H, Xu J, Tang H, Qin S, Fang Z, Lu Z, Wu J, Weng X, Zhou X. Inert Pepper aptamer-mediated endogenous mRNA recognition and imaging in living cells. Nucleic Acids Res 2022; 50:e84. [PMID: 35580055 PMCID: PMC9371900 DOI: 10.1093/nar/gkac368] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/01/2022] [Accepted: 05/12/2022] [Indexed: 02/06/2023] Open
Abstract
The development of RNA aptamers/fluorophores system is highly desirable for understanding the dynamic molecular biology of RNAs in vivo. Peppers-based imaging systems have been reported and applied for mRNA imaging in living cells. However, the need to insert corresponding RNA aptamer sequences into target RNAs and relatively low fluorescence signal limit its application in endogenous mRNA imaging. Herein, we remolded the original Pepper aptamer and developed a tandem array of inert Pepper (iPepper) fluorescence turn-on system. iPepper allows for efficient and selective imaging of diverse endogenous mRNA species in live cells with minimal agitation of the target mRNAs. We believe iPepper would significantly expand the applications of the aptamer/fluorophore system in endogenous mRNA imaging, and it has the potential to become a powerful tool for real-time studies in living cells and biological processing.
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Affiliation(s)
- Qi Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Feng Xiao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Haomiao Su
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China.,Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA
| | - Hui Liu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Jinglei Xu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Heng Tang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Shanshan Qin
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Zhentian Fang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Ziang Lu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Jian Wu
- School of Medicine, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China.,The Institute of Advanced Studies, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
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5
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Comparative studies on the binding interaction of two chiral Ru(II) polypyridyl complexes with triple- and double-helical forms of RNA. J Inorg Biochem 2020; 214:111301. [PMID: 33166867 DOI: 10.1016/j.jinorgbio.2020.111301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/12/2020] [Accepted: 10/25/2020] [Indexed: 12/27/2022]
Abstract
Two chiral Ru(II) polypyridyl complexes, Δ-[Ru(bpy)2(6-F-dppz)]2+ (Δ-1; bpy = 2,2'-bipyridine, 6-F-dppz = 6-fluorodipyrido[3,2-a:2',3'-c]phenazine) and Λ-[Ru(bpy)2(6-F-dppz)]2+ (Λ-1), have been synthesized and characterized as binders for the RNA poly(U)•poly(A)*poly(U) triplex and poly(A)•poly(U) duplex in this work. Analysis of the UV-Vis absorption spectra and fluorescence emission spectra indicates that the binding of intercalating Δ-1 with the triplex and duplex RNA is greater than that of Λ-1, while the binding affinities of the two enantiomers to triplex structure is stronger than that of duplex structure. Fluorescence titrations show that the two enantiomers can act as molecular "light switches" for triple- and double-helical RNA. Thermal denaturation studies revealed that that the two enantiomers are more stable to Watson-Crick base-paired double strand of the triplex than the Hoogsteen base-paired third strand, but their stability and selectivity are different. For Δ-enantiomer, the increase of the thermal stability of the Watson-Crick base-paired duplex (13 °C) is slightly stronger than of the Hoogsteen base-paired strand (10 °C), displaying no obvious selectivity. However, compared to the Hoogsteen base-paired strand (5 °C), the stability of the Λ-enantiomer to the Watson-Crick base-paired duplex (13 °C) is more significant, which has obvious selectivity. The overall increase in viscosity of the RNA-(Λ-1) system and its curve shape are similar to that of the RNA-(Δ-1) system, suggesting that the binding modes of two enantiomers with RNA are intercalation. The obtained results in this work may be useful for understanding the binding differences in chiral Ru(II) polypyridyl complexes toward RNA triplex and duplex.
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6
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Gu B. Light up the embryos: knock-in reporter generation for mouse developmental biology. Anim Reprod 2020; 17:e20200055. [PMID: 33029220 PMCID: PMC7534580 DOI: 10.1590/1984-3143-ar2020-0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Developmental biology seeks to understand the sophisticated regulated process through which a single cell – a fertilized egg – generates a highly organized organism. The most effective way to reveal the nature of these processes is to follow single cells and cell lineages in real-time. Recent advances in imaging equipment, fluorescent tags and computational tools have made long term multi-color imaging of cells and embryos possible. However, there is still one major challenging for achieving live imaging of mammalian embryos- the generation of embryos carrying reporters that recapitulate the endogenous expression pattern of marker genes. Recent developments of genome editing technology played important roles in enabling efficient generation of reporter mouse models. This mini review discusses recent developments of technologies for efficiently generate knock-in reporter mice and the application of these models in live imaging development. With these developments, we are starting to realize the long-sought promises of realtime analysis of mammalian development.
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Affiliation(s)
- Bin Gu
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Canada.,Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Michigan, USA.,Institute for Quantitative Health Science and Engineering, Michigan State University, Michigan, USA
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7
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Embryo-Based Large Fragment Knock-in in Mammals: Why, How and What's Next. Genes (Basel) 2020; 11:genes11020140. [PMID: 32013077 PMCID: PMC7073597 DOI: 10.3390/genes11020140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/24/2020] [Accepted: 01/26/2020] [Indexed: 02/08/2023] Open
Abstract
Endonuclease-mediated genome editing technologies, most notably CRISPR/Cas9, have revolutionized animal genetics by allowing for precise genome editing directly through embryo manipulations. As endonuclease-mediated model generation became commonplace, large fragment knock-in remained one of the most challenging types of genetic modification. Due to their unique value in biological and biomedical research, however, a diverse range of technological innovations have been developed to achieve efficient large fragment knock-in in mammalian animal model generation, with a particular focus on mice. Here, we first discuss some examples that illustrate the importance of large fragment knock-in animal models and then detail a subset of the recent technological advancements that have allowed for efficient large fragment knock-in. Finally, we envision the future development of even larger fragment knock-ins performed in even larger animal models, the next step in expanding the potential of large fragment knock-in in animal models.
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8
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Tang W, Zhu Z, Tan L. [Ru(bpy)2(7-CH3-dppz)](2+) and [Ru(phen)2(7-CH3-dppz)](2+) as metallointercalators that affect third-strand stabilization of the poly(U)˙poly(A)*poly(U) triplex. MOLECULAR BIOSYSTEMS 2017; 12:1478-85. [PMID: 26999574 DOI: 10.1039/c6mb00094k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Stable RNA triplexes play key roles in many biological processes. However, due to Hoogsteen base pairing, triplexes are thermodynamically less stable than the corresponding duplexes. To understand the factors effecting the stabilization of RNA triplexes by octahedral ruthenium(ii) complexes, two Ru(ii) complexes, [Ru(bpy)2(7-CH3-dppz)](2+) (Ru) and [Ru(phen)2(7-CH3-dppz)](2+) (Ru), have been synthesized and characterized in this work. The interactions of the two Ru(ii) complexes with the poly(U)˙poly(A)*poly(U) triplex are investigated by spectrophotometry, spectrofluorometry, circular dichroism as well as viscometry. The results demonstrate that the two complexes are able to enhance the stability of the RNA triplex and serve as molecular "light switches" for the triplex. However, Ru and Ru affecting the stabilization of the third strand are significantly weaker than that of the Watson-Crick base-paired duplex, suggesting that the binding of the two complexes with the triplex is favored by the Watson-Crick base-paired duplex to a large extent. In addition, considering the nature of Ru and Ru, we presume that their binding differences may be due to different ancillary ligand effects. This study further advances our knowledge on the interaction of RNA triple-stranded structures with metal complexes, particularly with Ru(ii) complexes.
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Affiliation(s)
- Wuzhi Tang
- College of Chemistry, Xiangtan University, Xiangtan 411105, P. R. China.
| | - Zhiyuan Zhu
- College of Chemistry, Xiangtan University, Xiangtan 411105, P. R. China.
| | - Lifeng Tan
- College of Chemistry, Xiangtan University, Xiangtan 411105, P. R. China. and Key Lab of Environmentally Friendly Chemistry and Application in Ministry of Education, Xiangtan University, Xiangtan 411105, P. R. China
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9
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Xia Y, Zhang R, Wang Z, Tian J, Chen X. Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes. Chem Soc Rev 2017; 46:2824-2843. [PMID: 28345687 PMCID: PMC5472208 DOI: 10.1039/c6cs00675b] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment. For each probe, we review its structure and imaging principle in detail. Finally, we summarize the application of mRNA and miRNA imaging probes in studying life processes as well as in detecting cancer. By correlating the structures and principles of various probes with their practical uses, we compare different RNA imaging probes and offer guidance for better utilization of the current imaging probes and the future design of higher-performance RNA imaging probes.
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Affiliation(s)
- Yuqiong Xia
- Engineering Research Center of Molecular-imaging and Neuro-imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China.
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10
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Lampasona AA, Czaplinski K. RNA voyeurism: A coming of age story. Methods 2016; 98:10-17. [DOI: 10.1016/j.ymeth.2015.11.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 10/22/2022] Open
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11
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Abstract
Localization of mRNA plays a crucial role in a variety of neuronal processes including synaptogenesis, axonal guidance, and long-term plasticity. Recent advances in fluorescence imaging and RNA labeling techniques allow us to visualize how individual mRNA molecules are dynamically regulated inside live neurons and brain tissues. Here, we describe key methods in imaging mRNA dynamics, including preparation of neuron culture and brain slices from transgenic mice expressing GFP-labeled mRNA, high-resolution detection of single molecules, live tissue imaging, and analysis of mRNA transport.
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Affiliation(s)
- Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, University 1 Gwanak-ro, Gwanak-gu, Seoul, 151-747, South Korea.
| | - Minho Song
- Department of Physics and Astronomy, Seoul National University, University 1 Gwanak-ro, Gwanak-gu, Seoul, 151-747, South Korea
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12
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Guet D, Burns LT, Maji S, Boulanger J, Hersen P, Wente SR, Salamero J, Dargemont C. Combining Spinach-tagged RNA and gene localization to image gene expression in live yeast. Nat Commun 2015; 6:8882. [PMID: 26582123 PMCID: PMC4673486 DOI: 10.1038/ncomms9882] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/13/2015] [Indexed: 11/14/2022] Open
Abstract
Although many factors required for the formation of export-competent mRNPs have been described, an integrative view of the spatiotemporal coordinated cascade leading mRNPs from their site of transcription to their site of nuclear exit, at a single cell level, is still partially missing due to technological limitations. Here we report that the RNA Spinach aptamer is a powerful tool for mRNA imaging in live S. cerevisiae with high spatial-temporal resolution and no perturbation of the mRNA biogenesis properties. Dedicated image processing workflows are developed to allow detection of very low abundance of transcripts, accurate quantitative dynamic studies, as well as to provide a localization precision close to 100 nm at consistent time scales. Combining these approaches has provided a state-of-the-art analysis of the osmotic shock response in live yeast by localizing induced transcription factors, target gene loci and corresponding transcripts. Measuring single-cell mRNA dynamics is critical to understand gene expression. Here, using RNA Spinach technique to detect very low abundant mRNAs, Guet et al. report an analysis of the osmotic shock response in live yeast by localizing induced transcription factors, target gene loci and corresponding transcripts.
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Affiliation(s)
- David Guet
- Univ Paris Diderot, Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, Hôpital St Louis, 1 Avenue Claude Vellefaux, 75475 Paris Cedex 10, 75475, France
| | - Laura T Burns
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 205 Kirkland Hall, Nashville, Tennessee 37232-8240, USA
| | - Suman Maji
- Univ Paris Diderot, Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, Hôpital St Louis, 1 Avenue Claude Vellefaux, 75475 Paris Cedex 10, 75475, France
| | - Jérôme Boulanger
- Team-Space Time Imaging of Endomembranes and Organelles Dynamics, UMR144 CNRS, Univ Pierre et Marie Curie, Institut Curie, 12 rue Lhomond, Paris 75005, France
| | - Pascal Hersen
- Univ Paris Diderot, Sorbonne Paris Cité, CNRS UMR7057, Laboratoire Matière et Systèmes Complexes, 10 rue Alice Domon et Léonie Duquet, Paris 75013, France
| | - Susan R Wente
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 205 Kirkland Hall, Nashville, Tennessee 37232-8240, USA
| | - Jean Salamero
- Team-Space Time Imaging of Endomembranes and Organelles Dynamics, UMR144 CNRS, Univ Pierre et Marie Curie, Institut Curie, 12 rue Lhomond, Paris 75005, France.,PICT-IBiSA Imaging Core Facility, Institut Curie, 12 rue Lhomond, Paris 75005, France
| | - Catherine Dargemont
- Univ Paris Diderot, Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, Hôpital St Louis, 1 Avenue Claude Vellefaux, 75475 Paris Cedex 10, 75475, France
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13
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Abstract
The spectrum of RNA functions in the cell continues to widen and new types of RNA molecules continue to be discovered. However, methods to access and manipulate endogenous RNAs in live cells are limited. Here we describe a universal technique for labeling natural RNAs in live cells with the probes synthesized by the cell. The method is based on fluorescent protein complementation in combination with a split aptamer approach. Two RNA probes containing split aptamer sequences flanked with the antisense RNA target sequences are assembled on the target RNA to form a fluorescent ribonucleoprotein (RNP) complex. The mechanism of complex formation ensures highly sensitive RNA detection allowing visualization of endogenous bacterial mRNAs. We demonstrate the great potential of this method by detecting chromosomally low-level expressed unmodified bacterial mRNA in living bacterial cells. This method holds promise to become a broadly used tool in basic research, and eventually in diagnostics and therapeutics.
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Affiliation(s)
- Irina Smolina
- Department of Biomedical Engineering, Boston University, Boston, MA, 01225, USA,
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14
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Kim JS, Park YS, Nam HG, Park JW. Imaging a specific mRNA in pollen with atomic force microscopy. RSC Adv 2015. [DOI: 10.1039/c5ra00199d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Distribution of ammonium transporter mRNA in a sectioned pollen is studied at the higher resolution, and localization of the mRNA in the nucleus of the sperm cells is observed.
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Affiliation(s)
- Jung Sook Kim
- Department of Chemistry
- Pohang University of Science and Technology
- Pohang 790–784
- Republic of Korea
| | - Yu Shin Park
- Center for Core Research Facilities
- DGIST
- Daegu 711–873
- Republic of Korea
| | - Hong Gil Nam
- Center for Plant Aging Research
- Institute for Basic Science (IBS)
- Daegu 711–873
- Republic of Korea
- Department of New Biology
| | - Joon Won Park
- Department of Chemistry
- Pohang University of Science and Technology
- Pohang 790–784
- Republic of Korea
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15
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Real-time imaging of the epithelial-mesenchymal transition using microRNA-200a sequence-based molecular beacon-conjugated magnetic nanoparticles. PLoS One 2014; 9:e102164. [PMID: 25048580 PMCID: PMC4105468 DOI: 10.1371/journal.pone.0102164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/16/2014] [Indexed: 12/30/2022] Open
Abstract
The epithelial-mesenchymal transition (EMT) plays important roles in tumor progression to metastasis. Thus, the development of an imaging probe that can monitor transient periods of the EMT process in live cells is required for a better understanding of metastatic process. Inspired by the fact that the mRNA expression levels of zinc finger E-box-binding homeobox 1 (ZEB1) increase when cells adopt mesenchyme characteristics and that microRNA-200a (miR-200a) can bind to ZEB1 mRNA, we conjugated molecular beacon (MB) mimicking mature miR-200a to magnetic nanoparticles (miR-200a-MB-MNPs) and devised an imaging method to observe transitional changes in the cells during EMT. Transforming growth factor-β1 treated epithelial cells and breast cancer cell lines representing both epithelial and mesenchymal phenotypes were used for the validation of miR-200a-MB-MNPs as an EMT imaging probe. The real-time imaging of live cells acquired with the induction of EMT revealed an increase in fluorescence signals by miR-200a-MB-MNPs, cell morphology alterations, and the loss of cell-cell adhesion. Our results suggest that miR-200a-MB-MNPs can be used as an imaging probe for the real-time monitoring of the EMT process in live cells.
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Abstract
Live imaging of developmental gene expression in Drosophila embryos opens up exciting new prospects for understanding gene regulation during development.
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17
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McConnell AJ, Song H, Barton JK. Luminescence of [Ru(bpy)2(dppz)]2+ bound to RNA mismatches. Inorg Chem 2013; 52:10131-6. [PMID: 23968195 DOI: 10.1021/ic401531r] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The luminescence of rac-[Ru(bpy)2(dppz)](2+) (bpy = 2,2'-bipyridine and dppz = dipyrido[3,2-a:2',3'-c]phenazine) was explored in the presence of RNA oligonucleotides containing a single RNA mismatch (CA and GG) in order to develop a probe for RNA mismatches. While there is minimal luminescence of [Ru(bpy)2(dppz)](2+) in the presence of matched RNA due to weak binding, the luminescence is significantly enhanced in the presence of a single CA mismatch. The luminescence differential between CA mismatched and matched RNA is substantially higher compared to the DNA analogue, and therefore, [Ru(bpy)2(dppz)](2+) appears to be also a sensitive light switch probe for a CA mismatch in duplex RNA. Although the luminescence intensity is lower in the presence of RNA than DNA, Förster resonance energy transfer (FRET) between the donor ruthenium complex and FRET acceptor SYTO 61 is successfully exploited to amplify the luminescence in the presence of the mismatch. Luminescence and quenching studies with sodium iodide suggest that [Ru(bpy)2(dppz)](2+) binds to these mismatches via metalloinsertion from the minor groove. This work provides further evidence that metalloinsertion is a general binding mode of octahedral metal complexes to thermodynamically destabilized mismatches not only in DNA but also in RNA.
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Affiliation(s)
- Anna J McConnell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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18
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Genetic encoding of fluorescent RNA ensures a bright future for visualizing nucleic acid dynamics. Trends Biotechnol 2012; 30:621-6. [PMID: 23127753 DOI: 10.1016/j.tibtech.2012.09.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 09/19/2012] [Indexed: 11/22/2022]
Abstract
Recently RNA localization has been appreciated as an essential post-transcriptional mechanism to program local proteome composition and function. Although RNA has been visualized using diverse techniques, the use of the bacteriophage MS2 method to encode genetically fluorescent RNA has revolutionized the study of RNA dynamics in living cells. Here, I highlight the strength of MS2 compared to other techniques, and how further evolution of this system will enable the visualization of RNA in the context of complex live-cell dynamics. Although the generation of MS2-fluorescence resonance energy transfer (FRET) and MS2-bifluorescence complementation (BiFC) will require further development, it has the potential to increase significantly the signal-to-noise ratio, which is the major obstacle to rapid live-cell imaging of RNA.
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19
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Wu B, Chao JA, Singer RH. Fluorescence fluctuation spectroscopy enables quantitative imaging of single mRNAs in living cells. Biophys J 2012; 102:2936-44. [PMID: 22735544 DOI: 10.1016/j.bpj.2012.05.017] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 05/01/2012] [Accepted: 05/07/2012] [Indexed: 01/12/2023] Open
Abstract
Imaging mRNA with single-molecule sensitivity in live cells has become an indispensable tool for quantitatively studying RNA biology. The MS2 system has been extensively used due to its unique simplicity and sensitivity. However, the levels of the coat protein needed for consistent labeling of mRNAs limits the sensitivity and quantitation of this technology. Here, we applied fluorescence fluctuation spectroscopy to quantitatively characterize and enhance the MS2 system. Surprisingly, we found that a high fluorescence background resulted from inefficient dimerization of fluorescent protein (FP)-labeled MS2 coat protein (MCP). To mitigate this problem, we used a single-chain tandem dimer of MCP (tdMCP) that significantly increased the uniformity and sensitivity of mRNA labeling. Furthermore, we characterized the PP7 coat protein and the binding to its respective RNA stem loop. We conclude that the PP7 system performs better for RNA labeling. Finally, we used these improvements to study endogenous β-actin mRNA, which has 24xMS2 binding sites inserted into the 3' untranslated region. The tdMCP-FP allowed uniform RNA labeling and provided quantitative measurements of endogenous mRNA concentration and diffusion. This work provides a foundation for quantitative spectroscopy and imaging of single mRNAs directly in live cells.
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Affiliation(s)
- Bin Wu
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, USA
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20
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Wen F, Zhou R, Shen A, Choi A, Uribe D, Shi J. The tumor suppressive role of eIF3f and its function in translation inhibition and rRNA degradation. PLoS One 2012; 7:e34194. [PMID: 22457825 PMCID: PMC3311619 DOI: 10.1371/journal.pone.0034194] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Accepted: 02/28/2012] [Indexed: 12/22/2022] Open
Abstract
Deregulated translation plays an important role in human cancer. We previously reported decreased eukaryotic initiation factor 3 subunit f (eIF3f) expression in pancreatic cancer. Whether decreased eIF3f expression can transform normal epithelial cells is not known. In our current study, we found evidence that stable knockdown of eIF3f in normal human pancreatic ductal epithelial cells increased cell size, nuclear pleomorphism, cytokinesis defects, cell proliferation, clonogenicity, apoptotic resistance, migration, and formation of 3-dimensional irregular masses. Our findings support the tumor suppressive role of eIF3f in pancreatic cancer. Mechanistically, we found that eIF3f inhibited both cap-dependent and cap-independent translation. An increase in the ribosomal RNA (rRNA) level was suggested to promote the generation of cancer. The regulatory mechanism of rRNA degradation in mammals is not well understood. We demonstrated here that eIF3f promotes rRNA degradation through direct interaction with heterogeneous nuclear ribonucleoprotein (hnRNP) K. We showed that hnRNP K is required for maintaining rRNA stability: under stress conditions, eIF3f dissociates hnRNP K from rRNA, thereby preventing it from protecting rRNA from degradation. We also demonstrated that rRNA degradation occurred in non-P body, non-stress granule cytoplasmic foci that contain eIF3f. Our findings established a new mechanism of rRNA decay regulation mediated by hnRNP K/eIF3f and suggest that the tumor suppressive function of eIF3f may link to impaired rRNA degradation and translation.
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Affiliation(s)
- Fushi Wen
- Department of Pathology, Department of Surgery, The University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, United States of America
| | - Renyuan Zhou
- Department of Urology, Fifth People's Hospital of Shanghai, Shanghai, People's Republic of China
| | - Alex Shen
- Department of Pathology, Department of Surgery, The University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, United States of America
| | - Andrew Choi
- Department of Pathology, Department of Surgery, The University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, United States of America
| | - Diana Uribe
- Department of Pathology, Department of Surgery, The University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, United States of America
| | - Jiaqi Shi
- Department of Pathology, Department of Surgery, The University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
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21
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A genetic in vivo system to detect asymmetrically distributed RNA. EMBO Rep 2011; 12:1167-74. [PMID: 21921935 DOI: 10.1038/embor.2011.178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 08/10/2011] [Accepted: 08/15/2011] [Indexed: 11/08/2022] Open
Abstract
Many RNAs show polarized or otherwise non-random subcellular distributions. To create a method for genome-wide genetic screens for RNAs with asymmetric subcellular distributions, we have combined methods for gene tagging and live imaging of messenger RNA (mRNA). A pilot screen in a highly polarized, differentiated cell in the Drosophila larva, the branched terminal cell of the tracheal system, demonstrates the feasibility of the method for identifying new asymmetrically localized mRNAs in vivo.
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22
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Andou T, Endoh T, Mie M, Kobatake E. Direct detection of RNAs in living cells using peptide-inserted Renilla luciferase. Analyst 2011; 136:2446-9. [PMID: 21541389 DOI: 10.1039/c1an15130d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In this study, non-engineered RNAs were detected in living cells using bioluminescence. Two types of probe were utilized: a peptide inserted RLuc (PI-RLuc) probe and a split-RNA probe. Incorporation of the PI-RLuc and split-RNA probes enabled the direct detection of RNA introduced into living cells.
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Affiliation(s)
- Takashi Andou
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan
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23
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Murata A, Sato SI, Kawazoe Y, Uesugi M. Small-molecule fluorescent probes for specific RNA targets. Chem Commun (Camb) 2011; 47:4712-4. [PMID: 21412566 DOI: 10.1039/c1cc10393h] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A method was developed that uses small molecules as fluorescent probes to detect specific mRNAs. In this approach, the fluorescence of fluorophore-quencher conjugates is restored by the binding of an mRNA aptamer tag to the quencher segment of the molecules. The method allows real-time detection of mRNA transcripts in vitro.
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Affiliation(s)
- Asako Murata
- Institute for Integrated Cell-Material Sciences, Kyoto University Gokasho, Uji, Kyoto 611-0011, Japan
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24
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Urbinati CR, Long RM. Techniques for following the movement of single RNAs in living cells. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:601-9. [PMID: 21957047 DOI: 10.1002/wrna.83] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The ability to investigate gene expression has evolved from static approaches that analyze a population of cells to dynamic approaches that analyze individual living cells. During the last decade, a number of different fluorescent methods have been developed for monitoring the dynamics of single RNAs in living cells. Spatial-temporal analyses of single RNAs in living cells have provided novel insight into nuclear transport, RNA localization, and decay. Technical advances with these approaches allow for single molecule detection, providing an unprecedented view of RNA movement. In this article, we discuss the methods for observing single RNAs in living cells, highlighting the advantages and limitations of each method.
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Affiliation(s)
- Carl R Urbinati
- Department of Biology, Loyola Marymount University, Los Angeles, CA, USA
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25
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Belaya K, St Johnston D. Using the mRNA-MS2/MS2CP-FP system to study mRNA transport during Drosophila oogenesis. Methods Mol Biol 2011; 714:265-283. [PMID: 21431747 DOI: 10.1007/978-1-61779-005-8_17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Asymmetric mRNA localisation to specific compartments of the cell is a fundamental mechanism of -spatial and temporal regulation of gene expression. It is used by a variety of organisms and cell types to achieve different cellular functions. However, the mechanisms of mRNA localisation are not well understood. An important advance in this field has been the development of techniques that allow the visualisation of mRNA movements in living cells in real time. In this paper, we describe one approach to visualising mRNA localisation in vivo, in which RNAs containing MS2 binding sites are labelled by the MS2 coat protein fused to fluorescent reporters. We discuss the use of this mRNA-MS2/MS2CP-FP system to study mRNA localisation during Drosophila oogenesis, and provide a detailed explanation of the steps required for this approach, including the design of the mRNA-MS2 and MS2CP-FP constructs, the preparation of fly oocytes for imaging, the optimal microscope configurations for live cell imaging, and strategies for image processing and analysis.
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26
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Rifkin SA. Identifying fluorescently labeled single molecules in image stacks using machine learning. Methods Mol Biol 2011; 772:329-348. [PMID: 22065448 DOI: 10.1007/978-1-61779-228-1_20] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In the past several years, a host of new technologies have made it possible to visualize single molecules within cells and organisms (Raj et al., Nat Methods 5:877-879, 2008; Paré et al., Curr Biol 19:2037-2042, 2009; Lu and Tsourkas, Nucleic Acids Res 37:e100, 2009; Femino et al., Science 280:585-590, 1998; Rodriguez et al., Semin Cell Dev Biol 18:202-208, 2007; Betzig et al., Science 313:1642-1645, 2006; Rust et al., Nat Methods 3:793-796, 2006; Fusco et al., Curr Biol 13:161-167, 2003). Many of these are based on fluorescence, either fluorescent proteins or fluorescent dyes coupled to a molecule of interest. In many applications, the fluorescent signal is limited to a few pixels, which poses a classic signal processing problem: how can actual signal be distinguished from background noise? In this chapter, I present a MATLAB (MathWorks (2010) MATLAB. Retrieved from http://www.mathworks.com) software suite designed to work with these single-molecule visualization technologies (Rifkin (2010) spotFinding Suite. http://www.biology.ucsd.edu/labs/rifkin/software.html). It takes images or image stacks from a fluorescence microscope as input and outputs locations of the molecules. Although the software was developed for the specific application of identifying single mRNA transcripts in fixed specimens, it is more general than this and can be used and/or customized for other applications that produce localized signals embedded in a potentially noisy background. The analysis pipeline consists of the following steps: (a) create a gold-standard dataset, (b) train a machine-learning algorithm to classify image features as signal or noise depending upon user defined statistics, (c) run the machine-learning algorithm on a new dataset to identify mRNA locations, and (d) visually inspect and correct the results.
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Affiliation(s)
- Scott A Rifkin
- Division of Biological Sciences, Section of Ecology, Behavior and Evolution, University of California, San Diego, CA, USA.
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27
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Østergaard ME, Cheguru P, Papasani MR, Hill RA, Hrdlicka PJ. Glowing Locked Nucleic Acids: Brightly Fluorescent Probes for Detection of Nucleic Acids in Cells. J Am Chem Soc 2010; 132:14221-8. [DOI: 10.1021/ja1057295] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Michael E. Østergaard
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, Department of Animal Veterinary Science, University of Idaho, Moscow, Idaho 83844-2330, and Biological Applications of Nanotechnology (BANTech) Center, University of Idaho, Moscow, Idaho 83844
| | - Pallavi Cheguru
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, Department of Animal Veterinary Science, University of Idaho, Moscow, Idaho 83844-2330, and Biological Applications of Nanotechnology (BANTech) Center, University of Idaho, Moscow, Idaho 83844
| | - Madhusudhan R. Papasani
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, Department of Animal Veterinary Science, University of Idaho, Moscow, Idaho 83844-2330, and Biological Applications of Nanotechnology (BANTech) Center, University of Idaho, Moscow, Idaho 83844
| | - Rodney A. Hill
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, Department of Animal Veterinary Science, University of Idaho, Moscow, Idaho 83844-2330, and Biological Applications of Nanotechnology (BANTech) Center, University of Idaho, Moscow, Idaho 83844
| | - Patrick J. Hrdlicka
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, Department of Animal Veterinary Science, University of Idaho, Moscow, Idaho 83844-2330, and Biological Applications of Nanotechnology (BANTech) Center, University of Idaho, Moscow, Idaho 83844
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28
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Chudakov DM, Matz MV, Lukyanov S, Lukyanov KA. Fluorescent proteins and their applications in imaging living cells and tissues. Physiol Rev 2010; 90:1103-63. [PMID: 20664080 DOI: 10.1152/physrev.00038.2009] [Citation(s) in RCA: 939] [Impact Index Per Article: 67.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Green fluorescent protein (GFP) from the jellyfish Aequorea victoria and its homologs from diverse marine animals are widely used as universal genetically encoded fluorescent labels. Many laboratories have focused their efforts on identification and development of fluorescent proteins with novel characteristics and enhanced properties, resulting in a powerful toolkit for visualization of structural organization and dynamic processes in living cells and organisms. The diversity of currently available fluorescent proteins covers nearly the entire visible spectrum, providing numerous alternative possibilities for multicolor labeling and studies of protein interactions. Photoactivatable fluorescent proteins enable tracking of photolabeled molecules and cells in space and time and can also be used for super-resolution imaging. Genetically encoded sensors make it possible to monitor the activity of enzymes and the concentrations of various analytes. Fast-maturing fluorescent proteins, cell clocks, and timers further expand the options for real time studies in living tissues. Here we focus on the structure, evolution, and function of GFP-like proteins and their numerous applications for in vivo imaging, with particular attention to recent techniques.
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29
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Jourdren L, Delaveau T, Marquenet E, Jacq C, Garcia M. CORSEN, a new software dedicated to microscope-based 3D distance measurements: mRNA-mitochondria distance, from single-cell to population analyses. RNA (NEW YORK, N.Y.) 2010; 16:1301-1307. [PMID: 20494971 PMCID: PMC2885679 DOI: 10.1261/rna.1996810] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Accepted: 04/13/2010] [Indexed: 05/29/2023]
Abstract
Recent improvements in microscopy technology allow detection of single molecules of RNA, but tools for large-scale automatic analyses of particle distributions are lacking. An increasing number of imaging studies emphasize the importance of mRNA localization in the definition of cell territory or the biogenesis of cell compartments. CORSEN is a new tool dedicated to three-dimensional (3D) distance measurements from imaging experiments especially developed to access the minimal distance between RNA molecules and cellular compartment markers. CORSEN includes a 3D segmentation algorithm allowing the extraction and the characterization of the cellular objects to be processed--surface determination, aggregate decomposition--for minimal distance calculations. CORSEN's main contribution lies in exploratory statistical analysis, cell population characterization, and high-throughput assays that are made possible by the implementation of a batch process analysis. We highlighted CORSEN's utility for the study of relative positions of mRNA molecules and mitochondria: CORSEN clearly discriminates mRNA localized to the vicinity of mitochondria from those that are translated on free cytoplasmic polysomes. Moreover, it quantifies the cell-to-cell variations of mRNA localization and emphasizes the necessity for statistical approaches. This method can be extended to assess the evolution of the distance between specific mRNAs and other cellular structures in different cellular contexts. CORSEN was designed for the biologist community with the concern to provide an easy-to-use and highly flexible tool that can be applied for diverse distance quantification issues.
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Affiliation(s)
- Laurent Jourdren
- 1Institute of Biology of the Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 75230 Paris Cedex 05, France
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30
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Fang H, Shen Y, Taylor JS. Native mRNA antisense-accessible sites library for the selection of antisense oligonucleotides, PNAs, and siRNAs. RNA (NEW YORK, N.Y.) 2010; 16:1429-1435. [PMID: 20498459 PMCID: PMC2885691 DOI: 10.1261/rna.1940610] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 04/01/2010] [Indexed: 05/29/2023]
Abstract
A procedure for rapidly generating a library of antisense-accessible sites on native mRNAs (mRNA antisense-accessible sites library [MASL]) is described that involves reverse transcription of whole cell mRNA extracts with a random oligodeoxynucleotide primer followed by mRNA-specific polymerase chain reaction (PCR). Antisense phosphorothioate oligodeoxynucleotides (ODNs), peptide nucleic acids (PNAs), and small interfering RNAs (siRNAs) can then be identified by screening against the antisense-accessible sites. The utility of this methodology is demonstrated for the identification of more effective inhibitors of inducible nitric oxide synthase (iNOS) induction than have previously been reported. This method may also be useful for constraining folding calculations of native mRNAs and for designing mRNA imaging probes.
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Affiliation(s)
- Huafeng Fang
- Department of Chemistry, Washington University, St Louis, Missouri 63130, USA
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31
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Chen AK, Behlke MA, Tsourkas A. Sub-cellular trafficking and functionality of 2'-O-methyl and 2'-O-methyl-phosphorothioate molecular beacons. Nucleic Acids Res 2010; 37:e149. [PMID: 19820111 PMCID: PMC2794186 DOI: 10.1093/nar/gkp837] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Molecular beacons (MBs) have shown great potential for the imaging of RNAs within single living cells; however, the ability to perform accurate measurements of RNA expression can be hampered by false-positives resulting from nonspecific interactions and/or nuclease degradation. These false-positives could potentially be avoided by introducing chemically modified oligonucleotides into the MB design. In this study, fluorescence microscopy experiments were performed to elucidate the subcellular trafficking, false-positive signal generation, and functionality of 2′-O-methyl (2Me) and 2′-O-methyl-phosphorothioate (2MePS) MBs. The 2Me MBs exhibited rapid nuclear sequestration and a gradual increase in fluorescence over time, with nearly 50% of the MBs being opened nonspecifically within 24 h. In contrast, the 2MePS MBs elicited an instantaneous increase in false-positives, corresponding to ∼5–10% of the MBs being open, but little increase was observed over the next 24 h. Moreover, trafficking to the nucleus was slower. After 24 h, both MBs were localized in the nucleus and lysosomal compartments, but only the 2MePS MBs were still functional. When the MBs were retained in the cytoplasm, via conjugation to NeutrAvidin, a significant reduction in false-positives and improvement in functionality was observed. Overall, these results have significant implications for the design and applications of MBs for intracellular RNA measurement.
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Affiliation(s)
- Antony K Chen
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104 and Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
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32
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Abstract
Asymmetric distribution of mRNA is a prevalent phenomenon observed in diverse cell types. The posttranscriptional movement and localization of mRNA provides an important mechanism to target certain proteins to specific cytoplasmic regions of their function. Recent technical advances have enabled real-time visualization of single mRNA molecules in living cells. Studies analyzing the motion of individual mRNAs have shed light on the complex RNA transport system. This chapter presents an overview of general approaches for single particle tracking and some methodologies that are used for single mRNA detection.
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Affiliation(s)
- Hye Yoon Park
- Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, USA
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33
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Ikeda S, Kubota T, Yuki M, Okamoto A. Exciton-controlled hybridization-sensitive fluorescent probes: multicolor detection of nucleic acids. Angew Chem Int Ed Engl 2009; 48:6480-4. [PMID: 19637175 DOI: 10.1002/anie.200902000] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Shuji Ikeda
- Advanced Science Institute, RIKEN, Wako, Saitama 351-0198, Japan
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34
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Huranová M, Jablonski JA, Benda A, Hof M, Stanek D, Caputi M. In vivo detection of RNA-binding protein interactions with cognate RNA sequences by fluorescence resonance energy transfer. RNA (NEW YORK, N.Y.) 2009; 15:2063-2071. [PMID: 19767419 PMCID: PMC2764471 DOI: 10.1261/rna.1678209] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 08/12/2009] [Indexed: 05/28/2023]
Abstract
Expression of the nascent RNA transcript is regulated by its interaction with a number of proteins. The misregulation of such interactions can often result in impaired cellular functions that can lead to cancer and a number of diseases. Thus, our understanding of RNA-protein interactions within the cellular context is essential for the development of novel diagnostic and therapeutic tools. While there are many in vitro methods that analyze RNA-protein interactions in vivo approaches are scarce. Here we established a method based on fluorescence resonance energy transfer (FRET), which we term RNA-binding mediated FRET (RB-FRET), which determines RNA-protein interaction inside cells and tested it on hnRNP H protein binding to its cognate RNA. Using two different approaches, we provide evidence that RB-FRET is sensitive enough to detect specific RNA-protein interactions in the cell, providing a powerful tool to study spatial and temporal localization of specific RNA-protein complexes.
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Affiliation(s)
- Martina Huranová
- Department of RNA Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, CZ-14220 Prague 4, Czech Republic
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35
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Kubota T, Ikeda S, Yanagisawa H, Yuki M, Okamoto A. Hybridization-sensitive fluorescent probe for long-term monitoring of intracellular RNA. Bioconjug Chem 2009; 20:1256-61. [PMID: 19441821 DOI: 10.1021/bc900120a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Nuclease-resistant hybridization probes for long-term intracellular RNA imaging were synthesized. Newly designed probes with a 2'-O-MeRNA structure showed high resistance against nucleases, which is in contrast to the low resistance of DNA probes. These modified probes retained the function on the on-off switching of fluorescence emission in sensitive response to RNA recognition, based on the mechanism of interdye excitonic interaction, and functioned effectively for the long-term monitoring of RNA-stained living cells.
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Affiliation(s)
- Takeshi Kubota
- Advanced Science Institute, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-1098, Japan
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36
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Ikeda S, Kubota T, Yuki M, Okamoto A. Exciton-Controlled Hybridization-Sensitive Fluorescent Probes: Multicolor Detection of Nucleic Acids. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902000] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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37
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Schifferer M, Griesbeck O. Application of aptamers and autofluorescent proteins for RNA visualization. Integr Biol (Camb) 2009; 1:499-505. [PMID: 20023764 DOI: 10.1039/b906870h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The repertoire of RNAs transcribed and processed within living cells is of extraordinary complexity. With new types of RNA being identified, the need for tools to investigate the spatio-temporal aspects of processing and trafficking of these molecules has become more evident. To visualize RNA in living cells, autofluorescent proteins (AFPs) appear as a promising alternative to synthetic fluorescent compound based labels. While current fluorescent protein-based RNA labelings have provided many new insights into the biology of RNA regulation, further improvements and adaptations are desirable to make AFP labels as valuable in the RNA world as they have proven to be for protein tagging. This article reviews the achievements and existing challenges in engineering AFPs as efficient RNA tags for high resolution fluorescence microscopy in living cells.
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38
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Abstract
Powerful methods now allow the imaging of specific mRNAs in living cells. These methods enlist fluorescent proteins to illuminate mRNAs, use labeled oligonucleotide probes and exploit aptamers that render organic dyes fluorescent. The intracellular dynamics of mRNA synthesis, transport and localization can be analyzed at higher temporal resolution with these methods than has been possible with traditional fixed-cell or biochemical approaches. These methods have also been adopted to visualize and track single mRNA molecules in real time. This review explores the promises and limitations of these methods.
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39
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Furukawa K, Abe H, Hibino K, Sako Y, Tsuneda S, Ito Y. Reduction-Triggered Fluorescent Amplification Probe for the Detection of Endogenous RNAs in Living Human Cells. Bioconjug Chem 2009; 20:1026-36. [DOI: 10.1021/bc900040t] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kazuhiro Furukawa
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroshi Abe
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kayo Hibino
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yasushi Sako
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Satoshi Tsuneda
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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40
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Pei R, Rothman J, Xie Y, Stojanovic MN. Light-up properties of complexes between thiazole orange-small molecule conjugates and aptamers. Nucleic Acids Res 2009; 37:e59. [PMID: 19293274 PMCID: PMC2677889 DOI: 10.1093/nar/gkp154] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The full understanding of dynamics of cellular processes hinges on the development of efficient and non-invasive labels for intracellular RNA species. Light-up aptamers binding fluorogenic ligands show promise as specific labels for RNA species containing those aptamers. Herein, we took advantage of existing, non-light-up aptamers against small molecules and demonstrated a new class of light-up probes in vitro. We synthesized two conjugates of thiazole orange dye to small molecules (GMP and AMP) and characterized in vitro their interactions with corresponding RNA aptamers. The conjugates preserved specific binding to aptamers while showing several 100-fold increase in fluorescence of the dye (the ‘light-up’ property). In the presence of free small molecules, conjugates can be displaced from aptamers serving also as fluorescent sensors. Our in vitro results provide the proof-of-concept that the small-molecule conjugates with light-up properties can serve as a general approach to label RNA sequences containing aptamers.
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Affiliation(s)
- Renjun Pei
- Division of Experimental Therapeutics, Department of Medicine, Columbia University, New York, NY 10032, USA.
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41
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Bhalla AD, Gudikote JP, Wang J, Chan WK, Chang YF, Olivas OR, Wilkinson MF. Nonsense codons trigger an RNA partitioning shift. J Biol Chem 2009; 284:4062-72. [PMID: 19091751 PMCID: PMC2640978 DOI: 10.1074/jbc.m805193200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Revised: 11/24/2008] [Indexed: 11/06/2022] Open
Abstract
T-cell receptor-beta (TCRbeta) genes naturally acquire premature termination codons (PTCs) as a result of programmed gene rearrangements. PTC-bearing TCRbeta transcripts are dramatically down-regulated to protect T-cells from the deleterious effects of the truncated proteins that would otherwise be produced. Here we provide evidence that two responses collaborate to elicit this dramatic down-regulation. One is rapid mRNA decay triggered by the nonsense-mediated decay (NMD) RNA surveillance pathway. We demonstrate that this occurs in highly purified nuclei lacking detectable levels of three different cytoplasmic markers, but containing an outer nuclear membrane marker, suggesting that decay occurs either in the nucleoplasm or at the outer nuclear membrane. The second response is a dramatic partitioning shift in the nuclear fraction-to-cytoplasmic fraction mRNA ratio that results in few TCRbeta transcripts escaping to the cytoplasmic fraction of cells. Analysis of TCRbeta mRNA kinetics after either transcriptional repression or induction suggested that this nonsense codon-induced partitioning shift (NIPS) response is not the result of cytoplasmic NMD but instead reflects retention of PTC(+) TCRbeta mRNA in the nuclear fraction of cells. We identified TCRbeta sequences crucial for NIPS but found that NIPS is not exclusively a property of TCRbeta transcripts, and we identified non-TCRbeta sequences that elicit NIPS. RNA interference experiments indicated that NIPS depends on the NMD factors UPF1 and eIF4AIII but not the NMD factor UPF3B. We propose that NIPS collaborates with NMD to retain and degrade a subset of PTC(+) transcripts at the outer nuclear membrane and/or within the nucleoplasm.
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MESH Headings
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Codon, Nonsense/genetics
- Codon, Nonsense/metabolism
- DEAD-box RNA Helicases/genetics
- DEAD-box RNA Helicases/metabolism
- Down-Regulation/physiology
- Eukaryotic Initiation Factor-4A
- Gene Rearrangement, beta-Chain T-Cell Antigen Receptor/physiology
- HeLa Cells
- Humans
- Kinetics
- Pol1 Transcription Initiation Complex Proteins/genetics
- Pol1 Transcription Initiation Complex Proteins/metabolism
- RNA Interference
- RNA Stability/physiology
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/biosynthesis
- Receptors, Antigen, T-Cell, alpha-beta/genetics
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Affiliation(s)
- Angela D Bhalla
- Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030-4009, USA
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42
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Lorenz M. Visualizing protein-RNA interactions inside cells by fluorescence resonance energy transfer. RNA (NEW YORK, N.Y.) 2009; 15:97-103. [PMID: 19033374 PMCID: PMC2612761 DOI: 10.1261/rna.1307809] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Accepted: 10/17/2008] [Indexed: 05/24/2023]
Abstract
Approaches for studying protein-protein interactions in living cells have been broadly developed, but the temporal and spatial association of proteins with nucleic acids has been less explored. Here, we report a novel approach to study and visualize the association of an RNA-binding protein with its native RNA target in situ by fluorescence resonance energy transfer (FRET). The RNA-binding protein is tagged with a yellow variant of GFP and the RNA stained with SytoxOrange. RNA binding results in a decrease of the fluorescence lifetime of YFP due to FRET, which can be measured by fluorescence lifetime imaging microscopy (FLIM). With this method we analyzed the RNA binding of the alternative splicing repressors PTB and Raver1 and could show an RNA-specific FRET signal. Interestingly, PTB and Raver1 were bound to RNAs all over the nucleus, as expected, but additionally interacted with RNAs in the perinucleolar compartment (PNC), where only noncoding Pol III transcripts are present.
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Affiliation(s)
- Mike Lorenz
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
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43
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Hogg JR, Collins K. Structured non-coding RNAs and the RNP Renaissance. Curr Opin Chem Biol 2008; 12:684-9. [PMID: 18950732 DOI: 10.1016/j.cbpa.2008.09.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Revised: 09/10/2008] [Accepted: 09/20/2008] [Indexed: 11/15/2022]
Abstract
Non-protein-coding (nc) RNAs are diverse in their modes of synthesis, processing, assembly, and function. The inventory of transcripts known or suspected to serve their biological roles as RNA has increased dramatically in recent years. Although studies of ncRNA function are only beginning to match the pace of ncRNA discovery, some principles are emerging. Here we focus on a framework for understanding functions of ncRNAs that have evolved in a protein-rich cellular environment, as distinct from ncRNAs that arose originally in the ancestral RNA World. The folding and function of ncRNAs in the context of ribonucleoprotein (RNP) complexes provide myriad opportunities for ncRNA gain of function, leading to a modern-day RNP Renaissance.
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Affiliation(s)
- J Robert Hogg
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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44
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Lange S, Katayama Y, Schmid M, Burkacky O, Bruchle C, Lamb DC, Jansen RP. Simultaneous Transport of Different Localized mRNA Species Revealed by Live-Cell Imaging. Traffic 2008; 9:1256-67. [DOI: 10.1111/j.1600-0854.2008.00763.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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45
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Chen J, Lovell JF, Lo PC, Stefflova K, Niedre M, Wilson BC, Zheng G. A tumor mRNA-triggered photodynamic molecular beacon based on oligonucleotide hairpin control of singlet oxygen production. Photochem Photobiol Sci 2008; 7:775-81. [PMID: 18597024 DOI: 10.1039/b800653a] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We report a new class of photodynamic molecular beacon (PMB) with tumor specific mRNA-triggered control of singlet oxygen ((1)O(2)) production. The beacon contains a single-stranded oligonucleotide linker that forms a stem-loop structure (hairpin) in which the sequence is an antisense oligonucleotide (AS-ON) complementary to a target mRNA. The stem is formed by the annealing of two complementary arm sequences that are on either side of the loop sequence. A photosensitizer molecule (PS) is attached to the end of one arm and a quencher (Q) is similarly attached to the other end. The conformationally-restricted hairpin forces Q to efficiently silence the photoreactivity of PS. In the presence of target mRNA, the hairpin opens and the PS is no longer silenced. Upon irradiating with light, the PS then emits fluorescence and generates cytotoxic (1)O(2). To show proof of concept, we have synthesized a c-raf-1 mRNA-triggered PMB using pyropheophorbide (Pyro) as PS, carotenoid as Q and c-raf-1 mRNA-targeted AS-ON as the loop sequence. We show that the (1)O(2) production of Pyro is quenched in its native state by 15-fold and is restored 9-fold by the addition of the target RNA. Comparing this to our recently reported self-folding peptide linker-based PMB, the hairpin effect results in an enhanced (1)O(2) quenching efficiency that decreases the residual (1)O(2) production by over 3-fold, thus providing enhanced control of (1)O(2) production upon target-linker interactions. When incubated with c-raf-1 expressing MDA-MB-231 cancer cells, the PMB displayed efficient cellular uptake and subsequently effective PDT activation in targeted cells.
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Affiliation(s)
- Juan Chen
- Division of Biophysics and Bioimaging, Ontario Cancer Institute, Toronto, Ontario M5G 1L7, Canada.
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46
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Tripathi T, Chowdhury D. Interacting RNA polymerase motors on a DNA track: effects of traffic congestion and intrinsic noise on RNA synthesis. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 77:011921. [PMID: 18351890 DOI: 10.1103/physreve.77.011921] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Indexed: 05/26/2023]
Abstract
RNA polymerase (RNAP) is an enzyme that synthesizes a messenger RNA (mRNA) strand which is complementary to a single-stranded DNA template. From the perspective of physicists, an RNAP is a molecular motor that utilizes chemical energy input to move along the track formed by DNA. In many circumstances, which are described in this paper, a large number of RNAPs move simultaneously along the same track; we refer to such collective movements of the RNAPs as RNAP traffic. Here we develop a theoretical model for RNAP traffic by incorporating the steric interactions between RNAPs as well as the mechanochemical cycle of individual RNAPs during the elongation of the mRNA. By a combination of analytical and numerical techniques, we calculate the rates of mRNA synthesis and the average density profile of the RNAPs on the DNA track. We also introduce, and compute, two different measures of fluctuations in the synthesis of RNA. Analyzing these fluctuations, we show how the level of intrinsic noise in mRNA synthesis depends on the concentrations of the RNAPs as well as on those of some of the reactants and the products of the enzymatic reactions catalyzed by RNAP. We suggest appropriate experimental systems and techniques for testing our theoretical predictions.
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Affiliation(s)
- Tripti Tripathi
- Physics Department, Indian Institute of Technology, Kanpur 208016, India
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47
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Reining in RNA. Workshop on intracellular RNA localization and localized translation. EMBO Rep 2007; 9:22-6. [PMID: 18084187 DOI: 10.1038/sj.embor.7401140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Accepted: 11/19/2007] [Indexed: 12/14/2022] Open
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