1
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Johansson TB, Davtyan R, Valderas-Gutiérrez J, Gonzalez Rodriguez A, Agnarsson B, Munita R, Fioretos T, Lilljebjörn H, Linke H, Höök F, Prinz CN. Sub-Nanomolar Detection of Oligonucleotides Using Molecular Beacons Immobilized on Lightguiding Nanowires. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:453. [PMID: 38470783 DOI: 10.3390/nano14050453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024]
Abstract
The detection of oligonucleotides is a central step in many biomedical investigations. The most commonly used methods for detecting oligonucleotides often require concentration and amplification before detection. Therefore, developing detection methods with a direct read-out would be beneficial. Although commonly used for the detection of amplified oligonucleotides, fluorescent molecular beacons have been proposed for such direct detection. However, the reported limits of detection using molecular beacons are relatively high, ranging from 100 nM to a few µM, primarily limited by the beacon fluorescence background. In this study, we enhanced the relative signal contrast between hybridized and non-hybridized states of the beacons by immobilizing them on lightguiding nanowires. Upon hybridization to a complementary oligonucleotide, the fluorescence from the surface-bound beacon becomes coupled in the lightguiding nanowire core and is re-emitted at the nanowire tip in a narrower cone of light compared with the standard 4π emission. Prior knowledge of the nanowire positions allows for the continuous monitoring of fluorescence signals from each nanowire, which effectively facilitates the discrimination of signals arising from hybridization events against background signals. This resulted in improved signal-to-background and signal-to-noise ratios, which allowed for the direct detection of oligonucleotides at a concentration as low as 0.1 nM.
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Affiliation(s)
- Therese B Johansson
- Division of Solid State Physics, Lund University, 221 00 Lund, Sweden
- NanoLund, Lund University, 221 00 Lund, Sweden
| | - Rubina Davtyan
- Division of Solid State Physics, Lund University, 221 00 Lund, Sweden
- NanoLund, Lund University, 221 00 Lund, Sweden
| | - Julia Valderas-Gutiérrez
- Division of Solid State Physics, Lund University, 221 00 Lund, Sweden
- NanoLund, Lund University, 221 00 Lund, Sweden
| | | | - Björn Agnarsson
- Division of Nano and Biophysics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Roberto Munita
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund University, 221 00 Lund, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 00 Lund, Sweden
| | - Henrik Lilljebjörn
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 00 Lund, Sweden
| | - Heiner Linke
- Division of Solid State Physics, Lund University, 221 00 Lund, Sweden
- NanoLund, Lund University, 221 00 Lund, Sweden
| | - Fredrik Höök
- NanoLund, Lund University, 221 00 Lund, Sweden
- Division of Nano and Biophysics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Christelle N Prinz
- Division of Solid State Physics, Lund University, 221 00 Lund, Sweden
- NanoLund, Lund University, 221 00 Lund, Sweden
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2
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Lu S, Hou Y, Zhang XE, Gao Y. Live cell imaging of DNA and RNA with fluorescent signal amplification and background reduction techniques. Front Cell Dev Biol 2023; 11:1216232. [PMID: 37342234 PMCID: PMC10277805 DOI: 10.3389/fcell.2023.1216232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
Illuminating DNA and RNA dynamics in live cell can elucidate their life cycle and related biochemical activities. Various protocols have been developed for labeling the regions of interest in DNA and RNA molecules with different types of fluorescent probes. For example, CRISPR-based techniques have been extensively used for imaging genomic loci. However, some DNA and RNA molecules can still be difficult to tag and observe dynamically, such as genomic loci in non-repetitive regions. In this review, we will discuss the toolbox of techniques and methodologies that have been developed for imaging DNA and RNA. We will also introduce optimized systems that provide enhanced signal intensity or low background fluorescence for those difficult-to-tag molecules. These strategies can provide new insights for researchers when designing and using techniques to visualize DNA or RNA molecules.
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Affiliation(s)
- Song Lu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Yu Hou
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
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3
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Arnould B, Quillin AL, Heemstra JM. Tracking the Message: Applying Single Molecule Localization Microscopy to Cellular RNA Imaging. Chembiochem 2023; 24:e202300049. [PMID: 36857087 PMCID: PMC10192057 DOI: 10.1002/cbic.202300049] [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: 01/20/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/02/2023]
Abstract
RNA function is increasingly appreciated to be more complex than merely communicating between DNA sequence and protein structure. RNA localization has emerged as a key contributor to the intricate roles RNA plays in the cell, and the link between dysregulated spatiotemporal localization and disease warrants an exploration beyond sequence and structure. However, the tools needed to visualize RNA with precise resolution are lacking in comparison to methods available for studying proteins. In the past decade, many techniques have been developed for imaging RNA, and in parallel super resolution and single-molecule techniques have enabled imaging of single molecules in cells. Of these methods, single molecule localization microscopy (SMLM) has shown significant promise for probing RNA localization. In this review, we highlight current approaches that allow super resolution imaging of specific RNA transcripts and summarize challenges and future opportunities for developing innovative RNA labeling methods that leverage the power of SMLM.
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Affiliation(s)
- Benoît Arnould
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alexandria L Quillin
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jennifer M Heemstra
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
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4
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Kim SH, Li ITS. Super-Resolution Tension PAINT Imaging with a Molecular Beacon. Angew Chem Int Ed Engl 2023; 62:e202217028. [PMID: 36534951 DOI: 10.1002/anie.202217028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/23/2022]
Abstract
DNA-PAINT enabled super-resolution imaging through the transient binding of fluorescently-labelled single-stranded DNA (ssDNA) imagers to target ssDNA. However, its performance is constrained by imager background fluorescence, resulting in relatively long image acquisition and potential artifacts. We designed a molecular beacon (MB) as the PAINT imager. Unbound MB in solution reduces the background fluorescence due to its natively quenched state. They are fluorogenic upon binding to target DNA to create individual fluorescence events. We demonstrate that MB-PAINT provides localization precision similar to traditional linear imager DNA-PAINT. We also show that MB-PAINT is ideally suited for fast super-resolution imaging of molecular tension probes in living cells, eliminating the potential of artifacts from free-diffusing imagers in traditional DNA-PAINT at the cell-substrate interface.
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Affiliation(s)
- Seong Ho Kim
- Department of Chemistry, The University of British Columbia, Kelowna, BC V1V 1V7, Canada
| | - Isaac T S Li
- Department of Chemistry, The University of British Columbia, Kelowna, BC V1V 1V7, Canada
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5
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Sun P, Zou W. Research progress of live-cell RNA imaging techniques. Zhejiang Da Xue Xue Bao Yi Xue Ban 2022; 51:362-372. [PMID: 36207827 PMCID: PMC9511491 DOI: 10.3724/zdxbyxb-2022-0017] [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] [Received: 01/23/2022] [Accepted: 04/12/2022] [Indexed: 06/16/2023]
Abstract
RNA molecules play diverse roles in many physiological and pathological processes as they interact with various nucleic acids and proteins. The various biological processes of RNA are highly dynamic. Tracking RNA dynamics in living cells is crucial for a better understanding of the spatiotemporal control of gene expression and the regulatory roles of RNA. Genetically encoded RNA-tagging systems include MS2/MCP, PP7/PCP, boxB/λN22 and CRISPR-Cas. The MS2/MCP system is the most widely applied, and it has the advantages of stable binding and high signal-to-noise ratio, while the realization of RNA imaging requires gene editing of the target RNA, which may change the characteristics of the target RNA. Recently developed CRISPR-dCas13 system does not require RNA modification, but the uncertainty in CRISPR RNA (crRNA) efficiency and low signal-to-noise ratio are its limitations. Fluorescent dye-based RNA-tagging systems include molecular beacons and fluorophore-binding aptamers. The molecular beacons have high specificity and high signal-to-noise ratio; Mango and Peppers outperform the other RNA-tagging system in signal-to-noise, but they also need gene editing. Live-cell RNA imaging allows us to visualize critical steps of RNA activities, including transcription, splicing, transport, translation (for message RNA only) and subcellular localization. It will contribute to studying biological processes such as cell differentiation and the transcriptional regulation mechanism when cells adapt to the external environment, and it improves our understanding of the pathogenic mechanism of various diseases caused by abnormal RNA behavior and helps to find potential therapeutic targets. This review provides an overview of current progress of live-cell RNA imaging techniques and highlights their major strengths and limitations.
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Affiliation(s)
- Pingping Sun
- 1. The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, Zhejiang Province, China
- 2. Institute of Translational Medicine, Zhejiang University, Hangzhou 310058, China
| | - Wei Zou
- 1. The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, Zhejiang Province, China
- 2. Institute of Translational Medicine, Zhejiang University, Hangzhou 310058, China
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Liu J, Yang LZ, Chen LL. Understanding lncRNA-protein assemblies with imaging and single-molecule approaches. Curr Opin Genet Dev 2021; 72:128-137. [PMID: 34933201 DOI: 10.1016/j.gde.2021.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 11/24/2022]
Abstract
Long non-coding RNAs (lncRNAs) associate with RNA-binding proteins (RBPs) to form lncRNA-protein complexes that act in a wide range of biological processes. Understanding the molecular mechanism of how a lncRNA-protein complex is assembled and regulated is key for their cellular functions. In this mini-review, we outline molecular methods used to identify lncRNA-protein interactions from large-scale to individual levels using bulk cells as well as those recently developed imaging and single-molecule approaches that are capable of visualizing RNA-protein assemblies in single cells and in real-time. Focusing on the latter group of approaches, we discuss their applications and limitations, which nevertheless have enabled quantification and comprehensive dissection of RNA-protein interactions possible.
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Affiliation(s)
- Jiaquan Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| | - Liang-Zhong Yang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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7
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Abstract
The imaging of chromatin, genomic loci, RNAs, and proteins is very important to study their localization, interaction, and coordinated regulation. Recently, several clustered regularly interspaced short palindromic repeats (CRISPR) based imaging methods have been established. The refurbished tool kits utilizing deactivated Cas9 (dCas9) and dCas13 have been established to develop applications of CRISPR-Cas technology beyond genome editing. Here, we review recent advancements in CRISPR-based methods that enable efficient imaging and visualization of chromatin, genomic loci, RNAs, and proteins. RNA aptamers, Pumilio, SuperNova tagging system, molecular beacons, halotag, bimolecular fluorescence complementation, RNA-guided endonuclease in situ labeling, and oligonucleotide-based imaging methods utilizing fluorescent proteins, organic dyes, or quantum dots have been developed to achieve improved fluorescence and signal-to-noise ratio for the imaging of chromatin or genomic loci. RNA-guided RNA targeting CRISPR systems (CRISPR/dCas13) and gene knock-in strategies based on CRISPR/Cas9 mediated site-specific cleavage and DNA repair mechanisms have been employed for efficient RNA and protein imaging, respectively. A few CRISPR-Cas-based methods to investigate the coordinated regulation of DNA-protein, DNA-RNA, or RNA-protein interactions for understanding chromatin dynamics, transcription, and protein function are also available. Overall, the CRISPR-based methods offer a significant improvement in elucidating chromatin organization and dynamics, RNA visualization, and protein imaging. The current and future advancements in CRISPR-based imaging techniques can revolutionize genome biology research for various applications.
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Affiliation(s)
- Vikram Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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A Miniaturized Platform for Multiplexed Drug Response Imaging in Live Tumors. Cancers (Basel) 2021; 13:cancers13040653. [PMID: 33562152 PMCID: PMC7915324 DOI: 10.3390/cancers13040653] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary We have developed an implantable microdevice that is placed into a live tumor, and can directly image how effective various chemotherapy drugs are at inducing cell death, without having to remove or process the tumor tissue. Currently drug optimization is performed by assessing tumor shrinkage after treating a patient with systemic doses of a chemotherapy agent; this only evaluates a single treatment at a time and typically takes weeks-months before an optimal treatment strategy is found (if found at all) for a specific patient. In contrast, using the technology presented here, a personalized cancer treatment strategy can potentially be optimized and tailored to a specific patient’s tumor characteristics within several hours, without requiring surgical tissue removal or prolonged trials of potentially ineffective chemotherapies. Abstract By observing the activity of anti-cancer agents directly in tumors, there is potential to greatly expand our understanding of drug response and develop more personalized cancer treatments. Implantable microdevices (IMD) have been recently developed to deliver microdoses of chemotherapeutic agents locally into confined regions of live tumors; the tissue can be subsequently removed and analyzed to evaluate drug response. This method has the potential to rapidly screen multiple drugs, but requires surgical tissue removal and only evaluates drug response at a single timepoint when the tissue is excised. Here, we describe a “lab-in-a-tumor” implantable microdevice (LIT-IMD) platform to image cell-death drug response within a live tumor, without requiring surgical resection or tissue processing. The LIT-IMD is inserted into a live tumor and delivers multiple drug microdoses into spatially discrete locations. In parallel, it locally delivers microdose levels of a fluorescent cell-death assay, which diffuses into drug-exposed tissues and accumulates at sites of cell death. An integrated miniaturized fluorescence imaging probe images each region to evaluate drug-induced cell death. We demonstrate ability to evaluate multi-drug response over 8 h using murine tumor models and show correlation with gold-standard conventional fluorescence microscopy and histopathology. This is the first demonstration of a fully integrated platform for evaluating multiple chemotherapy responses in situ. This approach could enable a more complete understanding of drug activity in live tumors, and could expand the utility of drug-response measurements to a wide range of settings where surgery is not feasible.
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9
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Mao S, Ying Y, Wu R, Chen AK. Recent Advances in the Molecular Beacon Technology for Live-Cell Single-Molecule Imaging. iScience 2020; 23:101801. [PMID: 33299972 PMCID: PMC7702005 DOI: 10.1016/j.isci.2020.101801] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids, aside from being best known as the carrier of genetic information, are versatile biomaterials for constructing nanoscopic devices for biointerfacing, owing to their unique properties such as specific base pairing and predictable structure. For live-cell analysis of native RNA transcripts, the most widely used nucleic acid-based nanodevice has been the molecular beacon (MB), a class of stem-loop-forming probes that is activated to fluoresce upon hybridization with target RNA. Here, we overview efforts that have been made in developing MB-based bioassays for sensitive intracellular analysis, particularly at the single-molecule level. We also describe challenges that are currently limiting the widespread use of MBs and provide possible solutions. With continued refinement of MBs in terms of labeling specificity and detection accuracy, accompanied by new development in imaging platforms with unprecedented sensitivity, the application of MBs is envisioned to expand in various biological research fields.
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Affiliation(s)
- Shiqi Mao
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Yachen Ying
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Ruonan Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Antony K. Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
- Corresponding author
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10
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Bejugam PR, Das A, Panda AC. Seeing Is Believing: Visualizing Circular RNAs. Noncoding RNA 2020; 6:E45. [PMID: 33187156 PMCID: PMC7712394 DOI: 10.3390/ncrna6040045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023] Open
Abstract
Advancement in the RNA sequencing techniques has discovered hundreds of thousands of circular RNAs (circRNAs) in humans. However, the physiological function of most of the identified circRNAs remains unexplored. Recent studies have established that spliceosomal machinery and RNA-binding proteins modulate circRNA biogenesis. Furthermore, circRNAs have been implicated in regulating crucial cellular processes by interacting with various proteins and microRNAs. However, there are several challenges in understanding the mechanism of circRNA biogenesis, transport, and their interaction with cellular factors to regulate cellular events because of their low abundance and sequence similarity with linear RNA. Addressing these challenges requires systematic studies that directly visualize the circRNAs in cells at single-molecule resolution along with the molecular regulators. In this review, we present the design, benefits, and weaknesses of RNA imaging techniques such as single-molecule RNA fluorescence in situ hybridization and BaseScope in fixed cells and fluorescent RNA aptamers in live-cell imaging of circRNAs. Furthermore, we propose the potential use of molecular beacons, multiply labeled tetravalent RNA imaging probes, and Cas-derived systems to visualize circRNAs.
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Affiliation(s)
- Pruthvi Raj Bejugam
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India; (P.R.B.); (A.D.)
| | - Aniruddha Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India; (P.R.B.); (A.D.)
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Amaresh Chandra Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India; (P.R.B.); (A.D.)
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11
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Kapdi AR, Bhilare S, Kori S, Shet H, Balaram G, Mahendar K, Sanghvi YS. Scale-Up of a Heck Alkenylation Reaction: Application to the Synthesis of an Amino-Modifier Nucleoside ‘Ruth Linker’. SYNTHESIS-STUTTGART 2020. [DOI: 10.1055/s-0040-1707260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AbstractRuth linker is a C5 pyrimidine modified nucleoside analogue widely utilized for the incorporation of a primary amine in a synthetic oligonucleotide. The increasing demand for non-radioactive labeling, detection of biomolecules, and assembly of COVID-19 test kits has triggered a need for scale-up of Ruth linker. Herein, an efficient protocol involving a palladium-catalyzed Heck alkenylation is described. The synthesis has been optimized with a goal of low catalyst concentration, column-free isolation, high product purity, reproducibility, and shorter reaction time. The scalability and utility of the process have been demonstrated successfully on a 100 g scale (starting material). Additionally, for scale-up of the Heck alkenylation protocol, 7-phospha-1,3,5-triaza-adamantanebutane sulfonate (PTABS) as the coordinating caged phosphine ligand was also synthesized on a multigram scale after careful optimization of the conditions.
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Affiliation(s)
- Anant R. Kapdi
- Department of Chemistry, Institute of Chemical Technology
| | | | - Santosh Kori
- Department of Chemistry, Institute of Chemical Technology
- Institute of Chemical Technology-Indian Oil Odisha Campus, IIT Kharagpur Extension Centre
| | - Harshita Shet
- Department of Chemistry, Institute of Chemical Technology
- Institute of Chemical Technology-Indian Oil Odisha Campus, IIT Kharagpur Extension Centre
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12
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Sun NH, Chen DY, Ye LP, Sheng G, Gong JJ, Chen BH, Lu YM, Han F. CRISPR-Sunspot: Imaging of endogenous low-abundance RNA at the single-molecule level in live cells. Theranostics 2020; 10:10993-11012. [PMID: 33042266 PMCID: PMC7532675 DOI: 10.7150/thno.43094] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 08/21/2020] [Indexed: 12/23/2022] Open
Abstract
CRISPR/Cas-based mRNA imaging has been developed to labeling of high-abundance mRNAs. A lack of non-genetically encoded mRNA-tagged imaging tools has limited our ability to explore the functional distributions of endogenous low-abundance mRNAs in cells. Here, we developed a CRISPR-Sunspot method based on the SunTag signal amplification system that allows efficient imaging of low-abundance mRNAs with CRISPR/Cas9. Methods: We created a stable TRE3G-dCas9-EGFP cell line and generated an Inducible dCas9-EGFP imaging system for assessment of two factors, sgRNA and dCas9, which influence imaging quality. Based on SunTag system, we established a CRISPR-Sunspot imaging system for amplifying signals from single-molecule mRNA in live cells. CRISPR-Sunspot was used to track co-localization of Camk2a mRNA with regulatory protein Xlr3b in neurons. CRISPR-Sunspot combined with CRISPRa was used to determine elevated mRNA molecules. Results: Our results showed that manipulating the expression of fluorescent proteins and sgRNA increased the efficiency of RNA imaging in cells. CRISPR-Sunspot could target endogenous mRNAs in the cytoplasm and amplified signals from single-molecule mRNA. Furthermore, CRISPR-Sunspot was also applied to visualize mRNA distributions with its regulating proteins in neurons. CRISPR-Sunspot detected the co-localization of Camk2a mRNA with overexpressed Xlr3b proteins in the neuronal dendrites. Moreover, we also manipulated CRISPR-Sunspot to detect transcriptional activation of target gene such as HBG1 in live cells. Conclusion: Our findings suggest that CRISPR-Sunspot is a novel applicable imaging tool for visualizing the distributions of low-abundance mRNAs in cells. This study provides a novel strategy to unravel the molecular mechanisms of diseases caused by aberrant mRNA molecules.
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Affiliation(s)
- Ning-He Sun
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Drug Target and Drug Discovery Center, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
- Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dan-Yang Chen
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Drug Target and Drug Discovery Center, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
- Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lu-Peng Ye
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Gang Sheng
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Drug Target and Drug Discovery Center, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Jun-Jie Gong
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Drug Target and Drug Discovery Center, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Bao-Hui Chen
- Department of Cell Biology, School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Ying-Mei Lu
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
| | - Feng Han
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, Drug Target and Drug Discovery Center, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
- Center for Global Health of Nanjing Medical University, Nanjing, 211166, China
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13
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Ebrahimi SB, Samanta D, Mirkin CA. DNA-Based Nanostructures for Live-Cell Analysis. J Am Chem Soc 2020; 142:11343-11356. [DOI: 10.1021/jacs.0c04978] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Moutsiopoulou A, Broyles D, Joda H, Dikici E, Kaur A, Kaifer A, Daunert S, Deo SK. Bioluminescent Protein-Inhibitor Pair in the Design of a Molecular Aptamer Beacon Biosensing System. Anal Chem 2020; 92:7393-7398. [PMID: 32410446 PMCID: PMC7955708 DOI: 10.1021/acs.analchem.0c00518] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although bioluminescent molecular beacons designed around resonance quenchers have shown higher signal-to-noise ratios and increased sensitivity compared with fluorescent beacon systems, bioluminescence quenching is still comparatively inefficient. A more elegant solution to inefficient quenching can be realized by designing a competitive inhibitor that is structurally very similar to the native substrate, resulting in essentially complete substrate exclusion. In this work, we designed a conjugated anti-interferon-γ (IFN-γ) molecular aptamer beacon (MAB) attached to a bioluminescent protein, Gaussia luciferase (GLuc), and an inhibitor molecule with a similar structure to the native substrate coelenterazine. To prove that a MAB can be more sensitive and have a better signal-to-noise ratio, a bioluminescence-based assay was developed against IFN-γ and provided an optimized, physiologically relevant detection limit of 1.0 nM. We believe that this inhibitor approach may provide a simple alternative strategy to standard resonance quenching in the development of high-performance molecular beacon-based biosensing systems.
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Affiliation(s)
- Angeliki Moutsiopoulou
- University of Miami, Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, Miami, Florida 33136, United States
- University of Miami, Department of Chemistry, Coral Gables, Florida 33146, United States
| | - David Broyles
- University of Miami, Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, Miami, Florida 33136, United States
| | - Hamdi Joda
- University of Miami, Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, Miami, Florida 33136, United States
| | - Emre Dikici
- University of Miami, Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, Miami, Florida 33136, United States
| | - Avinash Kaur
- University of Miami, Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, Miami, Florida 33136, United States
| | - Angel Kaifer
- University of Miami, Department of Chemistry, Coral Gables, Florida 33146, United States
| | - Sylvia Daunert
- University of Miami, Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, Miami, Florida 33136, United States
- Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute of the University of Miami, Miami, Florida 33136, United States
- University of Miami Clinical and Translational Science Institute, Miami, Florida 33136, United States
| | - Sapna K Deo
- University of Miami, Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, Miami, Florida 33136, United States
- Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute of the University of Miami, Miami, Florida 33136, United States
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15
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Fazal FM, Chang HY. Subcellular Spatial Transcriptomes: Emerging Frontier for Understanding Gene Regulation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:31-45. [PMID: 32482897 PMCID: PMC7426137 DOI: 10.1101/sqb.2019.84.040352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNAs are trafficked and localized with exquisite precision inside the cell. Studies of candidate messenger RNAs have shown the vital importance of RNA subcellular location in development and cellular function. New sequencing- and imaging-based methods are providing complementary insights into subcellular localization of RNAs transcriptome-wide. APEX-seq and ribosome profiling as well as proximity-labeling approaches have revealed thousands of transcript isoforms are localized to distinct cytotopic locations, including locations that defy biochemical fractionation and hence were missed by prior studies. Sequences in the 3' and 5' untranslated regions (UTRs) serve as "zip codes" to direct transcripts to particular locales, and it is clear that intronic and retrotransposable sequences within transcripts have been co-opted by cells to control localization. Molecular motors, nuclear-to-cytosol RNA export, liquid-liquid phase separation, RNA modifications, and RNA structure dynamically shape the subcellular transcriptome. Location-based RNA regulation continues to pose new mysteries for the field, yet promises to reveal insights into fundamental cell biology and disease mechanisms.
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Affiliation(s)
- Furqan M Fazal
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA
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16
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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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17
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Samanta D, Ebrahimi SB, Mirkin CA. Nucleic-Acid Structures as Intracellular Probes for Live Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1901743. [PMID: 31271253 PMCID: PMC6942251 DOI: 10.1002/adma.201901743] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/08/2019] [Indexed: 05/02/2023]
Abstract
The chemical composition of cells at the molecular level determines their growth, differentiation, structure, and function. Probing this composition is powerful because it provides invaluable insight into chemical processes inside cells and in certain cases allows disease diagnosis based on molecular profiles. However, many techniques analyze fixed cells or lysates of bulk populations, in which information about dynamics and cellular heterogeneity is lost. Recently, nucleic-acid-based probes have emerged as a promising platform for the detection of a wide variety of intracellular analytes in live cells with single-cell resolution. Recent advances in this field are described and common strategies for probe design, types of targets that can be identified, current limitations, and future directions are discussed.
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Affiliation(s)
- Devleena Samanta
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Sasha B Ebrahimi
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Chad A Mirkin
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
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18
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Sato H, Das S, Singer RH, Vera M. Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression. Annu Rev Biochem 2020; 89:159-187. [PMID: 32176523 DOI: 10.1146/annurev-biochem-011520-104955] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This review focuses on imaging DNA and single RNA molecules in living cells to define eukaryotic functional organization and dynamic processes. The latest advances in technologies to visualize individual DNA loci and RNAs in real time are discussed. Single-molecule fluorescence microscopy provides the spatial and temporal resolution to reveal mechanisms regulating fundamental cell functions. Novel insights into the regulation of nuclear architecture, transcription, posttranscriptional RNA processing, and RNA localization provided by multicolor fluorescence microscopy are reviewed. A perspective on the future use of live imaging technologies and overcoming their current limitations is provided.
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Affiliation(s)
- Hanae Sato
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , ,
| | - Sulagna Das
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , ,
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , , .,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Maria Vera
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , , .,Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada;
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19
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Delivering Molecular Beacons via an Electroporation-Based Approach Enables Live-Cell Imaging of Single RNA Transcripts and Genomic Loci. Methods Mol Biol 2020; 2106:241-252. [PMID: 31889262 DOI: 10.1007/978-1-0716-0231-7_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Molecular beacons (MBs) are synthetic oligonucleotide probes that are designed to fluoresce upon hybridization to complementary nucleic acid targets. In contrast to genetically encoded probes that can be readily introduced into cells via standard transfection procedures, using MBs to obtain reliable intracellular measurements entails a reliable delivery method that maximizes MB entry while minimizing cell damage. One promising approach is microporation, a microliter volume electroporation-based method that exhibits reduced harmful events as compared with traditional electroporation methods. In this chapter, we describe in detail microporation steps for MB delivery that we have utilized over the past several years, followed by examples demonstrating successful MB-based imaging of specific RNA transcripts and genomic loci at the single-molecule level.
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20
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Detection of Extracellular Vesicle RNA Using Molecular Beacons. iScience 2019; 23:100782. [PMID: 31958756 PMCID: PMC6992906 DOI: 10.1016/j.isci.2019.100782] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 12/02/2019] [Accepted: 12/12/2019] [Indexed: 01/22/2023] Open
Abstract
Extracellular vesicles (EVs) have recently emerged as intercellular conveyors of biological information and disease biomarkers. Identification and characterization of RNA species in single EVs are currently challenging. Molecular beacons (MBs) represent an attractive means for detecting specific RNA molecules. Coupling the MBs to cell-penetrating peptides (CPPs) provides a fast, effective, and membrane-type agnostic means to deliver MBs across the plasma membrane and into the cytosol. Here, we generated RBCs-derived EVs by complement activation and tested the ability of MBs coupled with CPP to detect miRNAs from RBC-EVs. Our results showed that RBC and RBC-EVs miRNA-451a can be detected using MB-CPP, and the respective fluorescence levels can be measured by nano-flow cytometry. MB-based detection of RNA via nano-flow cytometry creates a powerful new analytical framework in which a simple addition of a reagent allows profiling of specific RNA species present within certain EV subsets.
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21
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Yang LZ, Wang Y, Li SQ, Yao RW, Luan PF, Wu H, Carmichael GG, Chen LL. Dynamic Imaging of RNA in Living Cells by CRISPR-Cas13 Systems. Mol Cell 2019; 76:981-997.e7. [PMID: 31757757 DOI: 10.1016/j.molcel.2019.10.024] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/25/2019] [Accepted: 10/15/2019] [Indexed: 12/26/2022]
Abstract
Visualizing the location and dynamics of RNAs in live cells is key to understanding their function. Here, we identify two endonuclease-deficient, single-component programmable RNA-guided and RNA-targeting Cas13 RNases (dCas13s) that allow robust real-time imaging and tracking of RNAs in live cells, even when using single 20- to 27-nt-long guide RNAs. Compared to the aptamer-based MS2-MCP strategy, an optimized dCas13 system is user friendly, does not require genetic manipulation, and achieves comparable RNA-labeling efficiency. We demonstrate that the dCas13 system is capable of labeling NEAT1, SatIII, MUC4, and GCN4 RNAs and allows the study of paraspeckle-associated NEAT1 dynamics. Applying orthogonal dCas13 proteins or combining dCas13 and MS2-MCP allows dual-color imaging of RNAs in single cells. Further combination of dCas13 and dCas9 systems allows simultaneous visualization of genomic DNA and RNA transcripts in living cells.
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Affiliation(s)
- Liang-Zhong Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yang Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Si-Qi Li
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Run-Wen Yao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Peng-Fei Luan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Huang Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Gordon G Carmichael
- Department of Genetics and Developmental Biology, University of Connecticut Stem Cell Institute, University of Connecticut Health Center, Farmington, CT 06030-3301, USA
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.
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22
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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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23
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Anhäuser L, Hüwel S, Zobel T, Rentmeister A. Multiple covalent fluorescence labeling of eukaryotic mRNA at the poly(A) tail enhances translation and can be performed in living cells. Nucleic Acids Res 2019; 47:e42. [PMID: 30726958 PMCID: PMC6468298 DOI: 10.1093/nar/gkz084] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/24/2019] [Accepted: 01/31/2019] [Indexed: 12/22/2022] Open
Abstract
Post-transcriptional regulation of gene expression occurs by multiple mechanisms, including subcellular localization of mRNA and alteration of the poly(A) tail length. These mechanisms play crucial roles in the dynamics of cell polarization and embryonic development. Furthermore, mRNAs are emerging therapeutics and chemical alterations to increase their translational efficiency are highly sought after. We show that yeast poly(A) polymerase can be used to install multiple azido-modified adenosine nucleotides to luciferase and eGFP-mRNAs. These mRNAs can be efficiently reacted in a bioorthogonal click reaction with fluorescent reporters without degradation and without sequence alterations in their coding or untranslated regions. Importantly, the modifications in the poly(A) tail impact positively on the translational efficiency of reporter-mRNAs in vitro and in cells. Therefore, covalent fluorescent labeling at the poly(A) tail presents a new way to increase the amount of reporter protein from exogenous mRNA and to label genetically unaltered and translationally active mRNAs.
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Affiliation(s)
- Lea Anhäuser
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany
| | - Sabine Hüwel
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany
| | - Thomas Zobel
- Cells-in-Motion Cluster of Excellence (EXC1003-CiM), University of Münster, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany.,Cells-in-Motion Cluster of Excellence (EXC1003-CiM), University of Münster, Germany
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24
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Kim SH, Vieira M, Shim JY, Choi H, Park HY. Recent progress in single-molecule studies of mRNA localization in vivo. RNA Biol 2019; 16:1108-1118. [PMID: 30336727 PMCID: PMC6693552 DOI: 10.1080/15476286.2018.1536592] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/28/2018] [Accepted: 10/08/2018] [Indexed: 12/26/2022] Open
Abstract
From biogenesis to degradation, mRNA goes through diverse types of regulation and interaction with other biomolecules. Uneven distribution of mRNA transcripts and the diverse isoforms and modifications of mRNA make us wonder how cells manage the complexity and keep the functional integrity for the normal development of cells and organisms. Single-molecule microscopy tools have expanded the scope of RNA research with unprecedented spatiotemporal resolution. In this review, we highlight the recent progress in the methods for labeling mRNA targets and analyzing the quantitative information from fluorescence images of single mRNA molecules. In particular, the MS2 system and its various applications are the main focus of this article. We also review how recent studies have addressed biological questions related to the significance of mRNA localization in vivo. Efforts to visualize the dynamics of single mRNA molecules in live cells will push forward our knowledge on the nature of heterogeneity in RNA sequence, structure, and distribution as well as their molecular function and coordinated interaction with RNA binding proteins.
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Affiliation(s)
- Songhee H. Kim
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Melissa Vieira
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul, Korea
| | - Jae Youn Shim
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
| | - Hongyoung Choi
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul, Korea
- Institute of Applied Physics, Seoul National University, Seoul, Korea
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25
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Wu X, Mao S, Yang Y, Rushdi MN, Krueger CJ, Chen AK. A CRISPR/molecular beacon hybrid system for live-cell genomic imaging. Nucleic Acids Res 2019; 46:e80. [PMID: 29718399 PMCID: PMC6061827 DOI: 10.1093/nar/gky304] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/12/2018] [Indexed: 12/20/2022] Open
Abstract
The clustered regularly interspersed short palindromic repeat (CRISPR) gene-editing system has been repurposed for live-cell genomic imaging, but existing approaches rely on fluorescent protein reporters, making sensitive and continuous imaging difficult. Here, we present a fluorophore-based live-cell genomic imaging system that consists of a nuclease-deactivated mutant of the Cas9 protein (dCas9), a molecular beacon (MB), and an engineered single-guide RNA (sgRNA) harboring a unique MB target sequence (sgRNA-MTS), termed CRISPR/MB. Specifically, dCas9 and sgRNA-MTS are first co-expressed to target a specific locus in cells, followed by delivery of MBs that can then hybridize to MTS to illuminate the target locus. We demonstrated the feasibility of this approach for quantifying genomic loci, for monitoring chromatin dynamics, and for dual-color imaging when using two orthogonal MB/MTS pairs. With flexibility in selecting different combinations of fluorophore/quencher pairs and MB/MTS sequences, our CRISPR/MB hybrid system could be a promising platform for investigating chromatin activities.
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Affiliation(s)
- Xiaotian Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.,School of Life Sciences, Peking University, Beijing 100871, China
| | - Shiqi Mao
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Yantao Yang
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Muaz N Rushdi
- 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
| | - 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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26
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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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27
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Single-molecule analysis of endogenous β-actin mRNA trafficking reveals a mechanism for compartmentalized mRNA localization in axons. Proc Natl Acad Sci U S A 2018; 115:E9697-E9706. [PMID: 30254174 PMCID: PMC6187124 DOI: 10.1073/pnas.1806189115] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
De novo protein synthesis in neuronal axons plays important roles in neural circuit formation, maintenance, and disease. Key to the selectivity of axonal protein synthesis is whether an mRNA is present at the right place to be translated, but the mechanisms behind axonal mRNA localization remain poorly understood. In this work, we quantitatively analyze the link between axonal β-actin mRNA trafficking and its localization patterns. By developing a single-molecule approach to live-image β-actin mRNAs in axons, we explore the biophysical drivers behind β-actin mRNA motion and uncover a mechanism for generating increased density at the axon tip by differences in motor protein-driven transport speeds. These results provide mechanistic insight into the control of local translation through mRNA trafficking. During embryonic nervous system assembly, mRNA localization is precisely regulated in growing axons, affording subcellular autonomy by allowing controlled protein expression in space and time. Different sets of mRNAs exhibit different localization patterns across the axon. However, little is known about how mRNAs move in axons or how these patterns are generated. Here, we couple molecular beacon technology with highly inclined and laminated optical sheet microscopy to image single molecules of identified endogenous mRNA in growing axons. By combining quantitative single-molecule imaging with biophysical motion models, we show that β-actin mRNA travels mainly as single copies and exhibits different motion-type frequencies in different axonal subcompartments. We find that β-actin mRNA density is fourfold enriched in the growth cone central domain compared with the axon shaft and that a modicum of directed transport is vital for delivery of mRNA to the axon tip. Through mathematical modeling we further demonstrate that directional differences in motor-driven mRNA transport speeds are sufficient to generate β-actin mRNA enrichment at the growth cone. Our results provide insight into how mRNAs are trafficked in axons and a mechanism for generating different mRNA densities across axonal subcompartments.
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28
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Tutucci E, Vera M, Singer RH. Single-mRNA detection in living S. cerevisiae using a re-engineered MS2 system. Nat Protoc 2018; 13:2268-2296. [DOI: 10.1038/s41596-018-0037-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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29
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Jefcoate CR, Lee J. Cholesterol signaling in single cells: lessons from STAR and sm-FISH. J Mol Endocrinol 2018; 60:R213-R235. [PMID: 29691317 PMCID: PMC6324173 DOI: 10.1530/jme-17-0281] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 03/06/2018] [Indexed: 12/11/2022]
Abstract
Cholesterol is an important regulator of cell signaling, both through direct impacts on cell membranes and through oxy-metabolites that activate specific receptors (steroids, hydroxy-cholesterols, bile acids). Cholesterol moves slowly through and between cell membranes with the assistance of specific binding proteins and transfer processes. The prototype cholesterol regulator is the Steroidogenesis Acute Regulatory (STAR), which moves cholesterol into mitochondria, where steroid synthesis is initiated by cytochrome P450 11A1 in multiple endocrine cell types. CYP27A1 generates hydroxyl cholesterol metabolites that activate LXR nuclear receptors to control cholesterol homeostatic and transport mechanisms. LXR regulation of cholesterol transport and storage as cholesterol ester droplets is shared by both steroid-producing cells and macrophage. This cholesterol signaling is crucial to brain neuron regulation by astrocytes and microglial macrophage, mediated by ApoE and sensitive to disruption by β-amyloid plaques. sm-FISH delivers appreciable insights into signaling in single cells, by resolving single RNA molecules as mRNA and by quantifying pre-mRNA at gene loci. sm-FISH has been applied to problems in physiology, embryo development and cancer biology, where single cell features have critical impacts. sm-FISH identifies novel features of STAR transcription in adrenal and testis cells, including asymmetric expression at individual gene loci, delayed splicing and 1:1 association of mRNA with mitochondria. This may represent a functional unit for the translation-dependent cholesterol transfer directed by STAR, which integrates into mitochondrial fusion dynamics. Similar cholesterol dynamics repeat with different players in the cycling of cholesterol between astrocytes and neurons in the brain, which may be abnormal in neurodegenerative diseases.
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Affiliation(s)
- Colin R Jefcoate
- Department of Cell and Regenerative Biology and the Endocrinology and Reproductive Physiology ProgramUniversity of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Jinwoo Lee
- Department of Cell and Regenerative Biology and the Endocrinology and Reproductive Physiology ProgramUniversity of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
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30
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He D, Wong KW, Dong Z, Li HW. Recent progress in live cell mRNA/microRNA imaging probes based on smart and versatile nanomaterials. J Mater Chem B 2018; 6:7773-7793. [DOI: 10.1039/c8tb02285b] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We summarize the recent progress in live cell mRNA/miRNA imaging probes based on various versatile nanomaterials, describing their structures and their working principles of bio-imaging applications.
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Affiliation(s)
- Dinggeng He
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
- State Key Laboratory of Developmental Biology of Freshwater Fish
| | - Ka-Wang Wong
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Zhenzhen Dong
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Hung-Wing Li
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
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Ando H, Hirose M, Kurosawa G, Impey S, Mikoshiba K. Time-lapse imaging of microRNA activity reveals the kinetics of microRNA activation in single living cells. Sci Rep 2017; 7:12642. [PMID: 28974737 PMCID: PMC5626736 DOI: 10.1038/s41598-017-12879-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/15/2017] [Indexed: 01/11/2023] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that play critical roles in the post-transcriptional regulation of gene expression. Although the molecular mechanisms of the biogenesis and activation of miRNA have been extensively studied, the details of their kinetics within individual living cells remain largely unknown. We developed a novel method for time-lapse imaging of the rapid dynamics of miRNA activity in living cells using destabilized fluorescent proteins (dsFPs). Real-time monitoring of dsFP-based miRNA sensors revealed the duration necessary for miRNA biogenesis to occur, from primary miRNA transcription to mature miRNA activation, at single-cell resolution. Mathematical modeling, which included the decay kinetics of the fluorescence of the miRNA sensors, demonstrated that miRNAs induce translational repression depending on their complementarity with targets. We also developed a dual-color imaging system, and demonstrated that miR-9-5p and miR-9-3p were produced and activated from a common hairpin precursor with similar kinetics, in single cells. Furthermore, a dsFP-based miR-132 sensor revealed the rapid kinetics of miR-132 activation in cortical neurons under physiological conditions. The timescale of miRNA biogenesis and activation is much shorter than the median half-lives of the proteome, suggesting that the degradation rates of miRNA target proteins are the dominant rate-limiting factors for miRNA-mediated gene silencing.
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Affiliation(s)
- Hideaki Ando
- Laboratory for Developmental Neurobiology, RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan.
| | - Matsumi Hirose
- Laboratory for Developmental Neurobiology, RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
| | - Gen Kurosawa
- Theoretical Biology Laboratory, RIKEN, Wako, Saitama, 351-0198, Japan
| | - Soren Impey
- Oregon Stem Cell Center, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Katsuhiko Mikoshiba
- Laboratory for Developmental Neurobiology, RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
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Ma Z, Wu X, Krueger CJ, Chen AK. Engineering Novel Molecular Beacon Constructs to Study Intracellular RNA Dynamics and Localization. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:279-286. [PMID: 28942262 PMCID: PMC5673673 DOI: 10.1016/j.gpb.2017.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 04/08/2017] [Accepted: 04/17/2017] [Indexed: 11/25/2022]
Abstract
With numerous advancements in novel biochemical techniques, our knowledge of the role of RNAs in the regulation of cellular physiology and pathology has grown significantly over the past several decades. Nevertheless, detailed information regarding RNA processing, trafficking, and localization in living cells has been lacking due to technical limitations in imaging single RNA transcripts in living cells with high spatial and temporal resolution. In this review, we discuss techniques that have shown great promise for single RNA imaging, followed by highlights in our recent work in the development of molecular beacons (MBs), a class of nanoscale oligonucleotide-probes, for detecting individual RNA transcripts in living cells. With further refinement of MB design and development of more sophisticated fluorescence microscopy techniques, we envision that MB-based approaches could promote new discoveries of RNA functions and activities.
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Affiliation(s)
- Zhao Ma
- 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
| | - 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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