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Ying Y, Mao S, Krueger CJ, Chen AK. Live-Cell Imaging of Long Noncoding RNAs Using Molecular Beacons. Methods Mol Biol 2020; 2038:21-33. [PMID: 31407275 DOI: 10.1007/978-1-4939-9674-2_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Long noncoding RNAs (lncRNAs) are a family of non-protein-coding RNA transcripts greater than 200 nucleotides in length that have been regarded as crucial modulators of gene expression in various biological and disease contexts, but mechanisms underlying such regulation still remains largely elusive. In addition to cell lysate-based approaches that have proven invaluable for studies of lncRNAs, live-imaging methods can add value by providing more in-depth information on lncRNA dynamics and localizations at the single-molecule level. Recently, we have developed a versatile imaging approach based on molecular beacons (MBs), which are a class of fluorogenic oligonucleotide-based probes with the capacity to convert RNA target hybridization into a measurable fluorescence signal. In this chapter, we describe the detailed protocol of using MBs to illuminate lncRNA transcripts at the single-molecule level in living cells.
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Affiliation(s)
- Yachen Ying
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Shiqi Mao
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Christopher J Krueger
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China.
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Mao S, Ying Y, Wu X, Krueger CJ, Chen AK. CRISPR/dual-FRET molecular beacon for sensitive live-cell imaging of non-repetitive genomic loci. Nucleic Acids Res 2019; 47:e131. [PMID: 31504824 PMCID: PMC6847002 DOI: 10.1093/nar/gkz752] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/15/2019] [Accepted: 08/21/2019] [Indexed: 01/19/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based genomic imaging systems predominantly rely on fluorescent protein reporters, which lack the optical properties essential for sensitive dynamic imaging. Here, we modified the CRISPR single-guide RNA (sgRNA) to carry two distinct molecular beacons (MBs) that can undergo fluorescence resonance energy transfer (FRET) and demonstrated that the resulting system, CRISPR/dual-FRET MB, enables dynamic imaging of non-repetitive genomic loci with only three unique sgRNAs.
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Affiliation(s)
- Shiqi Mao
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Yachen Ying
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Xiaotian Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Christopher J Krueger
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
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Chen M, Mao S, Wu X, Ma Z, Yang Y, Krueger CJ, Chen AK. Single-Molecule Analysis of RNA Dynamics in Living Cells Using Molecular Beacons. Methods Mol Biol 2019; 1870:23-39. [PMID: 30539544 DOI: 10.1007/978-1-4939-8808-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Over the past decade, emerging evidence has indicated that long intergenic noncoding RNAs (lincRNAs), a class of RNA transcripts greater than 200 nt in length, function as key regulators of gene expression in cellular physiology and pathogenesis. Greater understanding of lincRNA activities, particularly in the context of subcellular localization and dynamic regulation at the single-molecule level, is expected to provide in-depth understanding of molecular mechanisms that regulate cell behavior and disease evolution. We have recently developed a fluorescence-imaging approach to investigate RNA dynamics in living cells at the single-molecule level. This approach entails the use of molecular beacons (MBs), which are a class of stem-loop forming oligonculeotide-based probes that emit detectable fluorescence upon binding to target sequence, and tandem repeats of MB target sequences integrated to the target RNA sequence. Binding of the MBs to the tandem repeats could illuminate the target RNA as a bright spot when imaged by conventional fluorescence microscopy, making the MB-based imaging approach a versatile tool for RNA analysis across laboratories. In this chapter, we describe the development of the MB-based approach and its application for imaging single NEAT1 lincRNA transcripts in living cells.
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Affiliation(s)
- Mingming Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Shiqi Mao
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Xiaotian Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Zhao Ma
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Yantao Yang
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Christopher J Krueger
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China.
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Dynamics and regulation of nuclear import and nuclear movements of HIV-1 complexes. PLoS Pathog 2017; 13:e1006570. [PMID: 28827840 PMCID: PMC5578721 DOI: 10.1371/journal.ppat.1006570] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/31/2017] [Accepted: 08/05/2017] [Indexed: 11/19/2022] Open
Abstract
The dynamics and regulation of HIV-1 nuclear import and its intranuclear movements after import have not been studied. To elucidate these essential HIV-1 post-entry events, we labeled viral complexes with two fluorescently tagged virion-incorporated proteins (APOBEC3F or integrase), and analyzed the HIV-1 dynamics of nuclear envelope (NE) docking, nuclear import, and intranuclear movements in living cells. We observed that HIV-1 complexes exhibit unusually long NE residence times (1.5±1.6 hrs) compared to most cellular cargos, which are imported into the nuclei within milliseconds. Furthermore, nuclear import requires HIV-1 capsid (CA) and nuclear pore protein Nup358, and results in significant loss of CA, indicating that one of the viral core uncoating steps occurs during nuclear import. Our results showed that the CA-Cyclophilin A interaction regulates the dynamics of nuclear import by delaying the time of NE docking as well as transport through the nuclear pore, but blocking reverse transcription has no effect on the kinetics of nuclear import. We also visualized the translocation of viral complexes docked at the NE into the nucleus and analyzed their nuclear movements and determined that viral complexes exhibited a brief fast phase (<9 min), followed by a long slow phase lasting several hours. A comparison of the movement of viral complexes to those of proviral transcription sites supports the hypothesis that HIV-1 complexes quickly tether to chromatin at or near their sites of integration in both wild-type cells and cells in which LEDGF/p75 was deleted using CRISPR/cas9, indicating that the tethering interactions do not require LEDGF/p75. These studies provide novel insights into the dynamics of viral complex-NE association, regulation of nuclear import, viral core uncoating, and intranuclear movements that precede integration site selection. Although nuclear import of HIV-1 is essential for viral replication, many aspects of this process are currently unknown. Here, we defined the dynamics of HIV-1 nuclear envelope (NE) docking, nuclear import and its relationship to viral core uncoating, and intranuclear movements. We observed that HIV-1 complexes exhibit an unusually long residence time at the NE (∼1.5 hrs) compared to other cellular and viral cargos, and that HIV-1 capsid (CA) and host nuclear pore protein Nup358 are required for NE docking and nuclear import. Soon after import, the viral complexes exhibit a brief fast phase of movement, followed by a long slow phase, during which their movement is similar to that of integrated proviruses, suggesting that they rapidly become tethered to chromatin through interactions that do not require LEDGF/p75. Importantly, we found that NE association and nuclear import is regulated by the CA-cyclophilin A interaction, but not reverse transcription, and that one of the viral core uncoating steps, characterized by substantial loss of CA, occurs concurrently with nuclear import.
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Structurally responsive oligonucleotide-based single-probe lateral-flow test for detection of miRNA-21 mimics. Anal Bioanal Chem 2015; 408:1475-85. [DOI: 10.1007/s00216-015-9250-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/26/2015] [Accepted: 12/03/2015] [Indexed: 10/22/2022]
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Song Y, Zhang X, Huang L, Behlke MA, Tsourkas A. Real-time imaging of single engineered RNA transcripts in living cells using ratiometric bimolecular beacons. J Vis Exp 2014:e51544. [PMID: 25146531 DOI: 10.3791/51544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The growing realization that both the temporal and spatial regulation of gene expression can have important consequences on cell function has led to the development of diverse techniques to visualize individual RNA transcripts in single living cells. One promising technique that has recently been described utilizes an oligonucleotide-based optical probe, ratiometric bimolecular beacon (RBMB), to detect RNA transcripts that were engineered to contain at least four tandem repeats of the RBMB target sequence in the 3'-untranslated region. RBMBs are specifically designed to emit a bright fluorescent signal upon hybridization to complementary RNA, but otherwise remain quenched. The use of a synthetic probe in this approach allows photostable, red-shifted, and highly emissive organic dyes to be used for imaging. Binding of multiple RBMBs to the engineered RNA transcripts results in discrete fluorescence spots when viewed under a wide-field fluorescent microscope. Consequently, the movement of individual RNA transcripts can be readily visualized in real-time by taking a time series of fluorescent images. Here we describe the preparation and purification of RBMBs, delivery into cells by microporation and live-cell imaging of single RNA transcripts.
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Affiliation(s)
- Yang Song
- Department of Bioengineering, University of Pennsylvania
| | - Xuemei Zhang
- Department of Bioengineering, University of Pennsylvania
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Göhring J, Fulcher N, Schilcher K, Barta A, Jacak J. Suitable transfection methods for single particle tracing in plant suspension cells. PLANT METHODS 2014; 10:15. [PMID: 24991230 PMCID: PMC4076440 DOI: 10.1186/1746-4811-10-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 05/15/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND A multitude of different imaging systems are already available to image genetically altered RNA species; however, only a few of these techniques are actually suitable to visualize endogenous RNA. One possibility is to use fluorescently-labelled and hybridization-sensitive probes. In order to yield more information about the exact localization and movement of a single RNA molecule, it is necessary to image such probes with highly sensitive microscope setups. More challenges arise if such experiments are conducted in plant cells due to their high autofluorescence and demanding transfection procedures. RESULTS Here, we report in planta imaging of single RNA molecules using fluorescently labeled molecular beacons. We tested three different transfection protocols in order to identify optimal conditions for transfection of fluorescent DNA probes and their subsequent detection at the single molecule level. CONCLUSIONS We found that an optimized heat shock protocol provided a vastly improved transfection method for small DNA molecules which were used for subsequent single RNA molecule detection in living plant suspension cells.
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Affiliation(s)
- Janett Göhring
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, Vienna, Austria
| | - Nick Fulcher
- Gregor Mendel Institute, Dr. Bohrgasse 3, Vienna, Austria
| | - Kurt Schilcher
- Upper Austria University of Applied Sciences, Campus Linz, Linz, 4020, Austria
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, Vienna, Austria
| | - Jaroslaw Jacak
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, Vienna, Austria
- Upper Austria University of Applied Sciences, Campus Linz, Linz, 4020, Austria
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Zhang X, Zajac AL, Huang L, Behlke MA, Tsourkas A. Imaging the directed transport of single engineered RNA transcripts in real-time using ratiometric bimolecular beacons. PLoS One 2014; 9:e85813. [PMID: 24454933 PMCID: PMC3893274 DOI: 10.1371/journal.pone.0085813] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 12/02/2013] [Indexed: 11/26/2022] Open
Abstract
The relationship between RNA expression and cell function can often be difficult to decipher due to the presence of both temporal and sub-cellular processing of RNA. These intricacies of RNA regulation can often be overlooked when only acquiring global measurements of RNA expression. This has led to development of several tools that allow for the real-time imaging of individual engineered RNA transcripts in living cells. Here, we describe a new technique that utilizes an oligonucleotide-based probe, ratiometric bimolecular beacon (RBMB), to image RNA transcripts that were engineered to contain 96-tandem repeats of the RBMB target sequence in the 3′-untranslated region. Binding of RBMBs to the target RNA resulted in discrete bright fluorescent spots, representing individual transcripts, that could be imaged in real-time. Since RBMBs are a synthetic probe, the use of photostable, bright, and red-shifted fluorophores led to a high signal-to-background. RNA motion was readily characterized by both mean squared displacement and moment scaling spectrum analyses. These analyses revealed clear examples of directed, Brownian, and subdiffusive movements.
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Affiliation(s)
- Xuemei Zhang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Allison L. Zajac
- Cell Biology and Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lingyan Huang
- Integrated DNA Technologies, Inc., Coralville, Iowa, United States of America
| | - Mark A. Behlke
- Integrated DNA Technologies, Inc., Coralville, Iowa, United States of America
| | - Andrew Tsourkas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Hensel Z, Xiao J. Single-molecule methods for studying gene regulation in vivo. Pflugers Arch 2013; 465:383-95. [PMID: 23430319 PMCID: PMC3595547 DOI: 10.1007/s00424-013-1243-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 01/30/2013] [Accepted: 01/31/2013] [Indexed: 01/25/2023]
Abstract
The recent emergence of new experimental tools employing sensitive fluorescence detection in vivo has made it possible to visualize various aspects of gene regulation at the single-molecule level in the native, intracellular context. In this review, we will first describe general considerations for in vivo, single-molecule fluorescence detection of DNA, mRNA, and protein molecules involved in gene regulation. We will then give an overview of the rapidly evolving suite of molecular tools available for observing gene regulation in vivo and discuss new insights they have brought into gene regulation.
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Affiliation(s)
- Zach Hensel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21211, USA
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Abstract
Cellular life can be described as a dynamic equilibrium of a highly complex network of interacting molecules. For this reason, it is no longer sufficient to “only” know the identity of the participants in a cellular process, but questions such as where, when, and for how long also have to be addressed to understand the mechanism being investigated. Additionally, ensemble measurements may not sufficiently describe individual steps of molecular mobility, spatial-temporal resolution, kinetic parameters, and geographical mapping. It is vital to investigate where individual steps exactly occur to enhance our understanding of the living cell. The nucleus, home too many highly complex multi-order processes, such as replication, transcription, splicing, etc., provides a complicated, heterogeneous landscape. Its dynamics were studied to a new level of detail by fluorescence correlation spectroscopy (FCS). Single-molecule tracking, while still in its infancy in cell biology, is becoming a more and more attractive method to deduce key elements of this organelle. Here we discuss the potential of tracking single RNAs and proteins in the nucleus. Their dynamics, localization, and interaction rates will be vital to our understanding of cellular life. To demonstrate this, we provide a review of the HIV life cycle, which is an extremely elegant balance of nuclear and cytoplasmic functions and provides an opportunity to study mechanisms deeply integrated within the structure of the nucleus. In summary, we aim to present a specific, dynamic view of nuclear cellular life based on single molecule and FCS data and provide a prospective for the future.
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