1
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Su F, Chen S, Liu Y, Zhou J, Du Z, Luo X, Wen S, Jin D. Lanthanide Complex for Single-Molecule Fluorescent in Situ Hybridization and Background-Free Imaging. Anal Chem 2024; 96:4430-4436. [PMID: 38447029 DOI: 10.1021/acs.analchem.3c04530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Traditional single-molecule fluorescence in situ hybridization (smFISH) methods for RNA detection often face sensitivity challenges due to the low fluorescence intensity of the probe. Also, short-lived autofluorescence complicates obtaining clear signals from tissue sections. In response, we have developed an smFISH probe using highly grafted lanthanide complexes to address both concentration quenching and autofluorescence background. Our approach involves an oligo PCR incorporating azide-dUTP, enabling conjugation with lanthanide complexes. This method has proven to be stable, convenient, and cost-effective. Notably, for the mRNA detection in SKBR3 cells, the lanthanide probe group exhibited 2.5 times higher luminescence intensity and detected 3 times more signal points in cells compared with the Cy3 group. Furthermore, we successfully applied the probe to image HER2 mRNA molecules in breast cancer FFPE tissue sections, achieving a 2.7-fold improvement in sensitivity compared to Cy3-based probes. These results emphasize the potential of time-resolved smFISH as a highly sensitive method for nucleic acid detection, free of background fluorescence interference.
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Affiliation(s)
- Fei Su
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Sidney, NSW 2007, Australia
| | - Shiyu Chen
- UTS-SUStech Joint Research Centre for Biomedical Materials and Devices, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, P. R. China
| | - Yuanhua Liu
- UTS-SUStech Joint Research Centre for Biomedical Materials and Devices, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, P. R. China
| | - Jiajia Zhou
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Sidney, NSW 2007, Australia
| | - Zhongbo Du
- UTS-SUStech Joint Research Centre for Biomedical Materials and Devices, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, P. R. China
| | - Xiongjian Luo
- UTS-SUStech Joint Research Centre for Biomedical Materials and Devices, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, P. R. China
| | - Shihui Wen
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Sidney, NSW 2007, Australia
- Eastern Institute for Advanced Study, Eastern Institute of Technology, Ningbo, Zhejiang 315200, P. R. China
| | - Dayong Jin
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Sidney, NSW 2007, Australia
- Eastern Institute for Advanced Study, Eastern Institute of Technology, Ningbo, Zhejiang 315200, P. R. China
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2
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Vervaeke P, Borgos SE, Sanders NN, Combes F. Regulatory guidelines and preclinical tools to study the biodistribution of RNA therapeutics. Adv Drug Deliv Rev 2022; 184:114236. [PMID: 35351470 PMCID: PMC8957368 DOI: 10.1016/j.addr.2022.114236] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/09/2022] [Accepted: 03/23/2022] [Indexed: 12/27/2022]
Abstract
The success of the messenger RNA-based COVID-19 vaccines of Moderna and Pfizer/BioNTech marks the beginning of a new chapter in modern medicine. However, the rapid rise of mRNA therapeutics has resulted in a regulatory framework that is somewhat lagging. The current guidelines either do not apply, do not mention RNA therapeutics, or do not have widely accepted definitions. This review describes the guidelines for preclinical biodistribution studies of mRNA/siRNA therapeutics and highlights the relevant differences for mRNA vaccines. We also discuss the role of in vivo RNA imaging techniques and other assays to fulfill and/or complement the regulatory requirements. Specifically, quantitative whole-body autoradiography, microautoradiography, mass spectrometry-based assays, hybridization techniques (FISH, bDNA), PCR-based methods, in vivo fluorescence imaging, and in vivo bioluminescence imaging, are discussed. We conclude that this new and rapidly evolving class of medicines demands a multi-layered approach to fully understand its biodistribution and in vivo characteristics.
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Affiliation(s)
- P Vervaeke
- Laboratory of Gene Therapy, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium
| | - S E Borgos
- SINTEF Industry, Dept. of Biotechnology and Nanomedicine, Research Group Mass Spectrometry, Sem Sælands v. 2A, N-7034 Trondheim, Norway
| | - N N Sanders
- Laboratory of Gene Therapy, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium.
| | - F Combes
- SINTEF Industry, Dept. of Biotechnology and Nanomedicine, Research Group Mass Spectrometry, Sem Sælands v. 2A, N-7034 Trondheim, Norway.
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3
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Basyuk E, Rage F, Bertrand E. RNA transport from transcription to localized translation: a single molecule perspective. RNA Biol 2021; 18:1221-1237. [PMID: 33111627 PMCID: PMC8354613 DOI: 10.1080/15476286.2020.1842631] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/21/2022] Open
Abstract
Transport of mRNAs is an important step of gene expression, which brings the genetic message from the DNA in the nucleus to a precise cytoplasmic location in a regulated fashion. Perturbation of this process can lead to pathologies such as developmental and neurological disorders. In this review, we discuss recent advances in the field of mRNA transport made using single molecule fluorescent imaging approaches. We present an overview of these approaches in fixed and live cells and their input in understanding the key steps of mRNA journey: transport across the nucleoplasm, export through the nuclear pores and delivery to its final cytoplasmic location. This review puts a particular emphasis on the coupling of mRNA transport with translation, such as localization-dependent translational regulation and translation-dependent mRNA localization. We also highlight the recently discovered translation factories, and how cellular and viral RNAs can hijack membrane transport systems to travel in the cytoplasm.
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Affiliation(s)
- Eugenia Basyuk
- Institut de Génétique Humaine, CNRS-UMR9002, Univ Montpellier, Montpellier, France
- Present address: Laboratoire de Microbiologie Fondamentale et Pathogénicité, CNRS-UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Florence Rage
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR5535, Univ Montpellier, Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Humaine, CNRS-UMR9002, Univ Montpellier, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR5535, Univ Montpellier, Montpellier, France
- Equipe Labélisée Ligue Nationale Contre Le Cancer, Montpellier, France
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4
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Muniz L, Nicolas E, Trouche D. RNA polymerase II speed: a key player in controlling and adapting transcriptome composition. EMBO J 2021; 40:e105740. [PMID: 34254686 PMCID: PMC8327950 DOI: 10.15252/embj.2020105740] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 05/01/2021] [Accepted: 05/10/2021] [Indexed: 12/19/2022] Open
Abstract
RNA polymerase II (RNA Pol II) speed or elongation rate, i.e., the number of nucleotides synthesized per unit of time, is a major determinant of transcriptome composition. It controls co-transcriptional processes such as splicing, polyadenylation, and transcription termination, thus regulating the production of alternative splice variants, circular RNAs, alternatively polyadenylated transcripts, or read-through transcripts. RNA Pol II speed itself is regulated in response to intra- and extra-cellular stimuli and can in turn affect the transcriptome composition in response to these stimuli. Evidence points to a potentially important role of transcriptome composition modification through RNA Pol II speed regulation for adaptation of cells to a changing environment, thus pointing to a function of RNA Pol II speed regulation in cellular physiology. Analyzing RNA Pol II speed dynamics may therefore be central to fully understand the regulation of physiological processes, such as the development of multicellular organisms. Recent findings also raise the possibility that RNA Pol II speed deregulation can be detrimental and participate in disease progression. Here, we review initial and current approaches to measure RNA Pol II speed, as well as providing an overview of the factors controlling speed and the co-transcriptional processes which are affected. Finally, we discuss the role of RNA Pol II speed regulation in cell physiology.
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Affiliation(s)
- Lisa Muniz
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
| | - Estelle Nicolas
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
| | - Didier Trouche
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
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5
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Biswas J, Nunez L, Das S, Yoon YJ, Eliscovich C, Singer RH. Zipcode Binding Protein 1 (ZBP1; IGF2BP1): A Model for Sequence-Specific RNA Regulation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:1-10. [PMID: 32086331 DOI: 10.1101/sqb.2019.84.039396] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The fate of an RNA, from its localization, translation, and ultimate decay, is dictated by interactions with RNA binding proteins (RBPs). β-actin mRNA has functioned as the classic example of RNA localization in eukaryotic cells. Studies of β-actin mRNA over the past three decades have allowed understanding of how RBPs, such as ZBP1 (IGF2BP1), can control both RNA localization and translational status. Here, we summarize studies of β-actin mRNA and focus on how ZBP1 serves as a model for understanding interactions between RNA and their binding protein(s). Central to the study of RNA and RBPs were technological developments that occurred along the way. We conclude with a future outlook highlighting new technologies that may be used to address still unanswered questions about RBP-mediated regulation of mRNA during its life cycle, within the cell.
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Affiliation(s)
- Jeetayu Biswas
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Leti Nunez
- 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
| | - Young J Yoon
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Carolina Eliscovich
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Medicine, 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.,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147, USA
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6
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Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies. Nat Methods 2020; 17:193-200. [PMID: 31988518 DOI: 10.1038/s41592-019-0701-7] [Citation(s) in RCA: 200] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 12/09/2019] [Indexed: 12/19/2022]
Abstract
Identifying genes that display spatial expression patterns in spatially resolved transcriptomic studies is an important first step toward characterizing the spatial transcriptomic landscape of complex tissues. Here we present a statistical method, SPARK, for identifying spatial expression patterns of genes in data generated from various spatially resolved transcriptomic techniques. SPARK directly models spatial count data through generalized linear spatial models. It relies on recently developed statistical formulas for hypothesis testing, providing effective control of type I errors and yielding high statistical power. With a computationally efficient algorithm, which is based on penalized quasi-likelihood, SPARK is also scalable to datasets with tens of thousands of genes measured on tens of thousands of samples. Analyzing four published spatially resolved transcriptomic datasets using SPARK, we show it can be up to ten times more powerful than existing methods and disclose biological discoveries that otherwise cannot be revealed by existing approaches.
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7
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Into the basket and beyond: the journey of mRNA through the nuclear pore complex. Biochem J 2020; 477:23-44. [DOI: 10.1042/bcj20190132] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/28/2019] [Accepted: 12/10/2019] [Indexed: 02/06/2023]
Abstract
The genetic information encoded in nuclear mRNA destined to reach the cytoplasm requires the interaction of the mRNA molecule with the nuclear pore complex (NPC) for the process of mRNA export. Numerous proteins have important roles in the transport of mRNA out of the nucleus. The NPC embedded in the nuclear envelope is the port of exit for mRNA and is composed of ∼30 unique proteins, nucleoporins, forming the distinct structures of the nuclear basket, the pore channel and cytoplasmic filaments. Together, they serve as a rather stationary complex engaged in mRNA export, while a variety of soluble protein factors dynamically assemble on the mRNA and mediate the interactions of the mRNA with the NPC. mRNA export factors are recruited to and dissociate from the mRNA at the site of transcription on the gene, during the journey through the nucleoplasm and at the nuclear pore at the final stages of export. In this review, we present the current knowledge derived from biochemical, molecular, structural and imaging studies, to develop a high-resolution picture of the many events that culminate in the successful passage of the mRNA out of the nucleus.
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8
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Pichon X, Robert MC, Bertrand E, Singer RH, Tutucci E. New Generations of MS2 Variants and MCP Fusions to Detect Single mRNAs in Living Eukaryotic Cells. Methods Mol Biol 2020; 2166:121-144. [PMID: 32710406 DOI: 10.1007/978-1-0716-0712-1_7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Live imaging of single RNA from birth to death brought important advances in our understanding of the spatiotemporal regulation of gene expression. These studies have provided a comprehensive understanding of RNA metabolism by describing the process step by step. Most of these studies used for live imaging a genetically encoded RNA-tagging system fused to fluorescent proteins. One of the best characterized RNA-tagging systems is derived from the bacteriophage MS2 and it allows single RNA imaging in real-time and live cells. This system has been successfully used to track the different steps of mRNA processing in many living organisms. The recent development of optimized MS2 and MCP variants now allows the labeling of endogenous RNAs and their imaging without modifying their behavior. In this chapter, we discuss the improvements in detecting single mRNAs with different variants of MCP and fluorescent proteins that we tested in yeast and mammalian cells. Moreover, we describe protocols using MS2-MCP systems improved for real-time imaging of single mRNAs and transcription dynamics in S. cerevisiae and mammalian cells, respectively.
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Affiliation(s)
- Xavier Pichon
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France.,Equipe labélisée Ligue Nationale Contre le Cancer, Montpellier, France
| | - Marie-Cécile Robert
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France.,Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA.,Janelia Research Campus of the HHMI, Ashburn, VA, USA
| | - Evelina Tutucci
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA. .,Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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9
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Gille AS, Lapoujade C, Wolf JP, Fouchet P, Barraud-Lange V. Contribution of Single-Cell Transcriptomics to the Characterization of Human Spermatogonial Stem Cells: Toward an Application in Male Fertility Regenerative Medicine? Int J Mol Sci 2019; 20:ijms20225773. [PMID: 31744138 PMCID: PMC6888480 DOI: 10.3390/ijms20225773] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 01/15/2023] Open
Abstract
Ongoing progress in genomic technologies offers exciting tools that can help to resolve transcriptome and genome-wide DNA modifications at single-cell resolution. These methods can be used to characterize individual cells within complex tissue organizations and to highlight various molecular interactions. Here, we will discuss recent advances in the definition of spermatogonial stem cells (SSC) and their progenitors in humans using the single-cell transcriptome sequencing (scRNAseq) approach. Exploration of gene expression patterns allows one to investigate stem cell heterogeneity. It leads to tracing the spermatogenic developmental process and its underlying biology, which is highly influenced by the microenvironment. scRNAseq already represents a new diagnostic tool for the personalized investigation of male infertility. One may hope that a better understanding of SSC biology could facilitate the use of these cells in the context of fertility preservation of prepubertal children, as a key component of regenerative medicine.
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Affiliation(s)
- Anne-Sophie Gille
- UMRE008 Stabilité Génétique, Cellules Souches et Radiations, Laboratoire des Cellules Souches Germinales, IRCM, Université de Paris, Université Paris-Saclay, CEA, F-92260 Fontenay-aux-Roses, France; (C.L.); (P.F.)
- Team Genomic Epigenetic and Physiopathology of Reproduction, Department of Genetic, Development and Cancer, Cochin Institute, Inserm U1016, 22 rue Méchain, 75014 Paris, France; (J.-P.W.); (V.B.-L.)
- Correspondence:
| | - Clémentine Lapoujade
- UMRE008 Stabilité Génétique, Cellules Souches et Radiations, Laboratoire des Cellules Souches Germinales, IRCM, Université de Paris, Université Paris-Saclay, CEA, F-92260 Fontenay-aux-Roses, France; (C.L.); (P.F.)
| | - Jean-Philippe Wolf
- Team Genomic Epigenetic and Physiopathology of Reproduction, Department of Genetic, Development and Cancer, Cochin Institute, Inserm U1016, 22 rue Méchain, 75014 Paris, France; (J.-P.W.); (V.B.-L.)
- Sorbonne Paris Cité, Faculty of Medicine, University Paris Descartes, Assistance Publique-Hôpitaux de Paris, University Hospital Paris Centre, CHU Cochin, Laboratory of Histology Embryology Biology of Reproduction, 123 boulevard de Port Royal, 75014 Paris, France
| | - Pierre Fouchet
- UMRE008 Stabilité Génétique, Cellules Souches et Radiations, Laboratoire des Cellules Souches Germinales, IRCM, Université de Paris, Université Paris-Saclay, CEA, F-92260 Fontenay-aux-Roses, France; (C.L.); (P.F.)
| | - Virginie Barraud-Lange
- Team Genomic Epigenetic and Physiopathology of Reproduction, Department of Genetic, Development and Cancer, Cochin Institute, Inserm U1016, 22 rue Méchain, 75014 Paris, France; (J.-P.W.); (V.B.-L.)
- Sorbonne Paris Cité, Faculty of Medicine, University Paris Descartes, Assistance Publique-Hôpitaux de Paris, University Hospital Paris Centre, CHU Cochin, Laboratory of Histology Embryology Biology of Reproduction, 123 boulevard de Port Royal, 75014 Paris, France
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10
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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11
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Abstract
Numerous studies based on new single-cell and single-gene techniques show that individual genes can be transcribed in short bursts or pulses accompanied by changes in pulsing frequencies. Since so many examples of such discontinuous or fluctuating transcription have been found from prokaryotes to mammals, it now seems to be a common mode of gene expression. In this review we discuss the occurrence of the transcriptional fluctuations, the techniques used for their detection, their putative causes, kinetic characteristics, and probable physiological significance.
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Affiliation(s)
- Evgeny Smirnov
- a Institute of Biology and Medical Genetics , First Faculty of Medicine , Charles University and General University Hospital in Prague , Prague , Czech Republic
| | - Matúš Hornáček
- a Institute of Biology and Medical Genetics , First Faculty of Medicine , Charles University and General University Hospital in Prague , Prague , Czech Republic
| | - Tomáš Vacík
- a Institute of Biology and Medical Genetics , First Faculty of Medicine , Charles University and General University Hospital in Prague , Prague , Czech Republic
| | - Dušan Cmarko
- a Institute of Biology and Medical Genetics , First Faculty of Medicine , Charles University and General University Hospital in Prague , Prague , Czech Republic
| | - Ivan Raška
- a Institute of Biology and Medical Genetics , First Faculty of Medicine , Charles University and General University Hospital in Prague , Prague , Czech Republic
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12
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Blencowe M, Arneson D, Ding J, Chen YW, Saleem Z, Yang X. Network modeling of single-cell omics data: challenges, opportunities, and progresses. Emerg Top Life Sci 2019; 3:379-398. [PMID: 32270049 PMCID: PMC7141415 DOI: 10.1042/etls20180176] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/07/2019] [Accepted: 06/24/2019] [Indexed: 01/07/2023]
Abstract
Single-cell multi-omics technologies are rapidly evolving, prompting both methodological advances and biological discoveries at an unprecedented speed. Gene regulatory network modeling has been used as a powerful approach to elucidate the complex molecular interactions underlying biological processes and systems, yet its application in single-cell omics data modeling has been met with unique challenges and opportunities. In this review, we discuss these challenges and opportunities, and offer an overview of the recent development of network modeling approaches designed to capture dynamic networks, within-cell networks, and cell-cell interaction or communication networks. Finally, we outline the remaining gaps in single-cell gene network modeling and the outlooks of the field moving forward.
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Affiliation(s)
- Montgomery Blencowe
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
| | - Douglas Arneson
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
| | - Jessica Ding
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
| | - Yen-Wei Chen
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
- Molecular Toxicology Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
| | - Zara Saleem
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
- Molecular Toxicology Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
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13
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Latallo MJ, Livingston NM, Wu B. Translation imaging of single mRNAs in established cell lines and primary cultured neurons. Methods 2019; 162-163:12-22. [PMID: 30905747 DOI: 10.1016/j.ymeth.2019.03.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/17/2019] [Accepted: 03/20/2019] [Indexed: 12/28/2022] Open
Abstract
The central dogma of molecular biology reaches a crescendo at its final step: the translation of an mRNA into its corresponding protein product. This process is highly regulated both spatially and temporally, requiring techniques to interrogate the subcellular translational status of mRNAs in both living and fixed cells. Single-molecule imaging of nascent peptides (SINAPs) and related techniques allow us to study this fundamental process for single mRNAs in live cells. These techniques enable researchers to address previously intractable questions in the central dogma, such as the origin of stochastic translational control and the role of local translation in highly polarized cells. In this review, we present the methodology and the theoretical framework for conducting studies using SINAPs in both established cell lines and primary cultured neurons.
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Affiliation(s)
- Malgorzata J Latallo
- Johns Hopkins School of Medicine, Department of Biophysics and Biophysical Chemistry, 855 N Wolfe Street Ste. 454, Baltimore, MD 21205, USA; Johns Hopkins School of Medicine, Center for Cell Dynamics, Baltimore, USA
| | - Nathan M Livingston
- Johns Hopkins School of Medicine, Department of Biophysics and Biophysical Chemistry, 855 N Wolfe Street Ste. 454, Baltimore, MD 21205, USA; Johns Hopkins School of Medicine, Center for Cell Dynamics, Baltimore, USA
| | - Bin Wu
- Johns Hopkins School of Medicine, Department of Biophysics and Biophysical Chemistry, 855 N Wolfe Street Ste. 454, Baltimore, MD 21205, USA; Johns Hopkins School of Medicine, Center for Cell Dynamics, Baltimore, USA; Johns Hopkins School of Medicine, Solomon H. Snyder Department of Neuroscience, Baltimore, USA.
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14
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Wang F, Wang L, Zou X, Duan S, Li Z, Deng Z, Luo J, Lee SY, Chen S. Advances in CRISPR-Cas systems for RNA targeting, tracking and editing. Biotechnol Adv 2019; 37:708-729. [PMID: 30926472 DOI: 10.1016/j.biotechadv.2019.03.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 12/21/2022]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems, especially type II (Cas9) systems, have been widely used in gene/genome targeting. Modifications of Cas9 enable these systems to become platforms for precise DNA manipulations. However, the utilization of CRISPR-Cas systems in RNA targeting remains preliminary. The discovery of type VI CRISPR-Cas systems (Cas13) shed light on RNA-guided RNA targeting. Cas13d, the smallest Cas13 protein, with a length of only ~930 amino acids, is a promising platform for RNA targeting compatible with viral delivery systems. Much effort has also been made to develop Cas9, Cas13a and Cas13b applications for RNA-guided RNA targeting. The discovery of new RNA-targeting CRISPR-Cas systems as well as the development of RNA-targeting platforms with Cas9 and Cas13 will promote RNA-targeting technology substantially. Here, we review new advances in RNA-targeting CRISPR-Cas systems as well as advances in applications of these systems in RNA targeting, tracking and editing. We also compare these Cas protein-based technologies with traditional technologies for RNA targeting, tracking and editing. Finally, we discuss remaining questions and prospects for the future.
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Affiliation(s)
- Fei Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Xuan Zou
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology, Yuseong-gu, 34141 Daejeon, Republic of Korea
| | - Suling Duan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
| | - Zhiqiang Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
| | - Jie Luo
- Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology, Yuseong-gu, 34141 Daejeon, Republic of Korea.
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China.
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15
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Hughes SC, Simmonds AJ. Drosophila mRNA Localization During Later Development: Past, Present, and Future. Front Genet 2019; 10:135. [PMID: 30899273 PMCID: PMC6416162 DOI: 10.3389/fgene.2019.00135] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 02/11/2019] [Indexed: 12/12/2022] Open
Abstract
Multiple mechanisms tightly regulate mRNAs during their transcription, translation, and degradation. Of these, the physical localization of mRNAs to specific cytoplasmic regions is relatively easy to detect; however, linking localization to functional regulatory roles has been more difficult to establish. Historically, Drosophila melanogaster is a highly effective model to identify localized mRNAs and has helped identify roles for this process by regulating various cell activities. The majority of the well-characterized functional roles for localizing mRNAs to sub-regions of the cytoplasm have come from the Drosophila oocyte and early syncytial embryo. At present, relatively few functional roles have been established for mRNA localization within the relatively smaller, differentiated somatic cell lineages characteristic of later development, beginning with the cellular blastoderm, and the multiple cell lineages that make up the gastrulating embryo, larva, and adult. This review is divided into three parts—the first outlines past evidence for cytoplasmic mRNA localization affecting aspects of cellular activity post-blastoderm development in Drosophila. The majority of these known examples come from highly polarized cell lineages such as differentiating neurons. The second part considers the present state of affairs where we now know that many, if not most mRNAs are localized to discrete cytoplasmic regions in one or more somatic cell lineages of cellularized embryos, larvae or adults. Assuming that the phenomenon of cytoplasmic mRNA localization represents an underlying functional activity, and correlation with the encoded proteins suggests that mRNA localization is involved in far more than neuronal differentiation. Thus, it seems highly likely that past-identified examples represent only a small fraction of localization-based mRNA regulation in somatic cells. The last part highlights recent technological advances that now provide an opportunity for probing the role of mRNA localization in Drosophila, moving beyond cataloging the diversity of localized mRNAs to a similar understanding of how localization affects mRNA activity.
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Affiliation(s)
- Sarah C Hughes
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.,Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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16
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Abstract
RNA is the fundamental information transfer system in the cell. The ability to follow single messenger RNAs (mRNAs) from transcription to degradation with fluorescent probes gives quantitative information about how the information is transferred from DNA to proteins. This review focuses on the latest technological developments in the field of single-mRNA detection and their usage to study gene expression in both fixed and live cells. By describing the application of these imaging tools, we follow the journey of mRNA from transcription to decay in single cells, with single-molecule resolution. We review current theoretical models for describing transcription and translation that were generated by single-molecule and single-cell studies. These methods provide a basis to study how single-molecule interactions generate phenotypes, fundamentally changing our understating of gene expression regulation.
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Affiliation(s)
- Evelina Tutucci
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461;,
| | - Nathan M. Livingston
- Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
| | - Robert H. Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461;,
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461
- Cellular Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Bin Wu
- Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland 21205;,
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17
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Strell C, Hilscher MM, Laxman N, Svedlund J, Wu C, Yokota C, Nilsson M. Placing RNA in context and space - methods for spatially resolved transcriptomics. FEBS J 2018. [PMID: 29542254 DOI: 10.1111/febs.14435] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Single-cell transcriptomics provides us with completely new insights into the molecular diversity of different cell types and the different states they can adopt. The technique generates inventories of cells that constitute the building blocks of multicellular organisms. However, since the method requires isolation of discrete cells, information about the original location within tissue is lost. Therefore, it is not possible to draw detailed cellular maps of tissue architecture and their positioning in relation to other cells. In order to better understand the cellular and tissue function of multicellular organisms, we need to map the cells within their physiological, morphological, and anatomical context and space. In this review, we will summarize and compare the different methods of in situ RNA analysis and the most recent developments leading to more comprehensive and highly multiplexed spatially resolved transcriptomic approaches. We will discuss their highlights and advantages as well as their limitations and challenges and give an outlook on promising future applications and directions both within basic research as well as clinical integration.
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Affiliation(s)
- Carina Strell
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Markus M Hilscher
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Navya Laxman
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Jessica Svedlund
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Chenglin Wu
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Chika Yokota
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
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18
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Kocks C, Boltengagen A, Piwecka M, Rybak-Wolf A, Rajewsky N. Single-Molecule Fluorescence In Situ Hybridization (FISH) of Circular RNA CDR1as. Methods Mol Biol 2018; 1724:77-96. [PMID: 29322442 DOI: 10.1007/978-1-4939-7562-4_7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Individual mRNA molecules can be imaged in fixed cells by hybridization with multiple, singly labeled oligonucleotide probes, followed by computational identification of fluorescent signals. This approach, called single-molecule RNA fluorescence in situ hybridization (smRNA FISH), allows subcellular localization and absolute quantification of RNA molecules in individual cells. Here, we describe a simple smRNA FISH protocol for two-color imaging of a circular RNA, CDR1as, simultaneously with an unrelated messenger RNA. The protocol can be adapted to circRNAs that coexist with overlapping, noncircular mRNA isoforms produced from the same genetic locus.
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Affiliation(s)
- Christine Kocks
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
| | - Anastasiya Boltengagen
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Monika Piwecka
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Agnieszka Rybak-Wolf
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
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19
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Optimized FISH methods for visualizing RNA localization properties in Drosophila and human tissues and cultured cells. Methods 2017; 126:156-165. [DOI: 10.1016/j.ymeth.2017.06.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/20/2017] [Accepted: 06/24/2017] [Indexed: 11/24/2022] Open
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20
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Donlin-Asp PG, Rossoll W, Bassell GJ. Spatially and temporally regulating translation via mRNA-binding proteins in cellular and neuronal function. FEBS Lett 2017; 591:1508-1525. [PMID: 28295262 DOI: 10.1002/1873-3468.12621] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/02/2017] [Accepted: 03/03/2017] [Indexed: 12/20/2022]
Abstract
Coordinated regulation of mRNA localization and local translation are essential steps in cellular asymmetry and function. It is increasingly evident that mRNA-binding proteins play critical functions in controlling the fate of mRNA, including when and where translation occurs. In this review, we discuss the robust and complex roles that mRNA-binding proteins play in the regulation of local translation that impact cellular function in vertebrates. First, we discuss the role of local translation in cellular polarity and possible links to vertebrate development and patterning. Next, we discuss the expanding role for local protein synthesis in neuronal development and function, with special focus on how a number of neurological diseases have given us insight into the importance of translational regulation. Finally, we discuss the ever-increasing set of tools to study regulated translation and how these tools will be vital in pushing forward and addressing the outstanding questions in the field.
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Affiliation(s)
- Paul G Donlin-Asp
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Wilfried Rossoll
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA.,Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA.,Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
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21
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Techniques for Single-Molecule mRNA Imaging in Living Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 978:425-441. [DOI: 10.1007/978-3-319-53889-1_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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22
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Yao J. Imaging Transcriptional Regulation of Eukaryotic mRNA Genes: Advances and Outlook. J Mol Biol 2017; 429:14-31. [DOI: 10.1016/j.jmb.2016.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/03/2016] [Accepted: 11/10/2016] [Indexed: 01/07/2023]
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23
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Larkin JD, Cook PR. Super-resolution measurement of distance between transcription sites using RNA FISH with intronic probes. Methods 2016; 98:150-157. [PMID: 26564237 PMCID: PMC4819770 DOI: 10.1016/j.ymeth.2015.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/05/2015] [Accepted: 11/08/2015] [Indexed: 11/06/2022] Open
Abstract
Label intronic RNA using FISH to identify sites of transcription by RNA polymerase II. Low-tech microscopes are used to acquire images for super-resolution measurements. Distances between sites of transcription are determined with precision near 20 nm. Spatial-temporal relationships between active genes are studied with this method.
Nascent transcripts being copied from specific human genes can be detected using RNA FISH (fluorescence in situ hybridization) with intronic probes, and the distance between two different nascent transcripts is often measured when studying structure–function relationships. Such distance measurements are limited by the resolution of the light microscope. Here we describe methods for measuring these distances in cultured cells with a precision of a few tens of nanometers, using equipment found in most laboratories (i.e., a wide-field fluorescence microscope equipped with a charged-coupled-device camera). Using images of pairs of transcripts that are often co-transcribed, we discuss how selection of cell type, design of FISH probes, image acquisition, and image processing affect the precision that can be achieved.
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Affiliation(s)
- Joshua D Larkin
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Peter R Cook
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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24
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Coleman RA, Liu Z, Darzacq X, Tjian R, Singer RH, Lionnet T. Imaging Transcription: Past, Present, and Future. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2016; 80:1-8. [PMID: 26763984 DOI: 10.1101/sqb.2015.80.027201] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Transcription, the first step of gene expression, is exquisitely regulated in higher eukaryotes to ensure correct development and homeostasis. Traditional biochemical, genetic, and genomic approaches have proved successful at identifying factors, regulatory sequences, and potential pathways that modulate transcription. However, they typically only provide snapshots or population averages of the highly dynamic, stochastic biochemical processes involved in transcriptional regulation. Single-molecule live-cell imaging has, therefore, emerged as a complementary approach capable of circumventing these limitations. By observing sequences of molecular events in real time as they occur in their native context, imaging has the power to derive cause-and-effect relationships and quantitative kinetics to build predictive models of transcription. Ongoing progress in fluorescence imaging technology has brought new microscopes and labeling technologies that now make it possible to visualize and quantify the transcription process with single-molecule resolution in living cells and animals. Here we provide an overview of the evolution and current state of transcription imaging technologies. We discuss some of the important concepts they uncovered and present possible future developments that might solve long-standing questions in transcriptional regulation.
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Affiliation(s)
- Robert A Coleman
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Zhe Liu
- HHMI Janelia Research Campus, Ashburn, Virginia 20147
| | - Xavier Darzacq
- HHMI Janelia Research Campus, Ashburn, Virginia 20147 Department of MCB, LKS Biomedical and Health Sciences Center, CIRM Center of Excellence, University of California, Berkeley, California 94720
| | - Robert Tjian
- HHMI Janelia Research Campus, Ashburn, Virginia 20147 Department of MCB, LKS Biomedical and Health Sciences Center, CIRM Center of Excellence, University of California, Berkeley, California 94720
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461 HHMI Janelia Research Campus, Ashburn, Virginia 20147
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25
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Integrating single-molecule experiments and discrete stochastic models to understand heterogeneous gene transcription dynamics. Methods 2015; 85:12-21. [PMID: 26079925 DOI: 10.1016/j.ymeth.2015.06.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 06/06/2015] [Accepted: 06/08/2015] [Indexed: 11/21/2022] Open
Abstract
The production and degradation of RNA transcripts is inherently subject to biological noise that arises from small gene copy numbers in individual cells. As a result, cellular RNA levels can exhibit large fluctuations over time and from one cell to the next. This article presents a range of precise single-molecule experimental techniques, based upon RNA fluorescence in situ hybridization, which can be used to measure the fluctuations of RNA at the single-cell level. A class of models for gene activation and deactivation is postulated in order to capture complex stochastic effects of chromatin modifications or transcription factor interactions. A computational tool, known as the finite state projection approach, is introduced to accurately and efficiently analyze these models in order to predict how probability distributions of RNA change over time in response to changing environmental conditions. These single-molecule experiments, discrete stochastic models, and computational analyses are systematically integrated to identify models of gene regulation dynamics. To illustrate the power and generality of our integrated experimental and computational approach, we explore cases that include different models for three different RNA types (sRNA, mRNA and nascent RNA), three different experimental techniques and three different biological species (bacteria, yeast and human cells).
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26
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Promoter-Autonomous Functioning in a Controlled Environment using Single Molecule FISH. Sci Rep 2015; 5:9934. [PMID: 26017315 PMCID: PMC4446897 DOI: 10.1038/srep09934] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 03/11/2015] [Indexed: 11/09/2022] Open
Abstract
Transcription is a highly regulated biological process, initiated through the assembly of complexes at the promoter that contain both the general transcriptional machinery and promoter-specific factors. Despite the abundance of studies focusing on transcription, certain questions have remained unanswered. It is not clear how the transcriptional profile of a promoter is affected by genomic context. Also, there is no single cell method to directly compare transcriptional profiles independent of gene length and sequence. In this work, we employ a single genetic site for isolating the transcriptional kinetics of yeast promoters. Utilizing single molecule FISH, we directly compare the transcriptional activity of different promoters, considering both synthesis and cell-to-cell variability. With this approach, we provide evidence suggesting promoters autonomously encode their associated transcriptional profiles, independent of genomic locus, gene length and gene sequence.
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27
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Gutierrez N, Eromobor I, Petrie RJ, Vedula P, Cruz L, Rodriguez AJ. The β-actin mRNA zipcode regulates epithelial adherens junction assembly but not maintenance. RNA (NEW YORK, N.Y.) 2014; 20:689-701. [PMID: 24681968 PMCID: PMC3988570 DOI: 10.1261/rna.043208.113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 02/14/2014] [Indexed: 06/03/2023]
Abstract
Epithelial cell-cell contact stimulates actin cytoskeleton remodeling to down-regulate branched filament polymerization-driven lamellar protrusion and subsequently to assemble linear actin filaments required for E-cadherin anchoring during adherens junction complex assembly. In this manuscript, we demonstrate that de novo protein synthesis, the β-actin 3' UTR, and the β-actin mRNA zipcode are required for epithelial adherens junction complex assembly but not maintenance. Specifically, we demonstrate that perturbing cell-cell contact-localized β-actin monomer synthesis causes epithelial adherens junction assembly defects. Consequently, inhibiting β-actin mRNA zipcode/ZBP1 interactions with β-actin mRNA zipcode antisense oligonucleotides, to intentionally delocalize β-actin monomer synthesis, is sufficient to perturb adherens junction assembly following epithelial cell-cell contact. Additionally, we demonstrate active RhoA, the signal required to drive zipcode-mediated β-actin mRNA targeting, is localized at epithelial cell-cell contact sites in a β-actin mRNA zipcode-dependent manner. Moreover, chemically inhibiting Src kinase activity prevents the local stimulation of β-actin monomer synthesis at cell-cell contact sites while inhibiting epithelial adherens junction assembly. Together, these data demonstrate that epithelial cell-cell contact stimulates β-actin mRNA zipcode-mediated monomer synthesis to spatially regulate actin filament remodeling, thereby controlling adherens junction assembly to modulate cell and tissue adhesion.
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Affiliation(s)
- Natasha Gutierrez
- Department of Biological Sciences, Rutgers University Newark, Newark, New Jersey 07102, USA
| | - Itua Eromobor
- Department of Biological Sciences, Rutgers University Newark, Newark, New Jersey 07102, USA
| | - Ryan J. Petrie
- National Institutes of Health, National Institute of Dental and Craniofacial Research, Bethesda, Maryland 20892, USA
| | - Pavan Vedula
- Department of Biological Sciences, Rutgers University Newark, Newark, New Jersey 07102, USA
| | - Lissette Cruz
- Department of Biological Sciences, Rutgers University Newark, Newark, New Jersey 07102, USA
| | - Alexis J. Rodriguez
- Department of Biological Sciences, Rutgers University Newark, Newark, New Jersey 07102, USA
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28
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Pitchiaya S, Heinicke LA, Custer TC, Walter NG. Single molecule fluorescence approaches shed light on intracellular RNAs. Chem Rev 2014; 114:3224-65. [PMID: 24417544 PMCID: PMC3968247 DOI: 10.1021/cr400496q] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sethuramasundaram Pitchiaya
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Laurie A. Heinicke
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thomas C. Custer
- Program in Chemical Biology, University of Michigan,
Ann Arbor, MI 48109-1055, USA
| | - Nils G. Walter
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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29
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Local translation of TC10 is required for membrane expansion during axon outgrowth. Nat Commun 2014; 5:3506. [PMID: 24667291 PMCID: PMC3991842 DOI: 10.1038/ncomms4506] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 02/25/2014] [Indexed: 11/14/2022] Open
Abstract
The surface of developing axons expands in a process mediated by the exocyst complex. The spatial-temporal regulation of the exocyst is only partially understood. Here we report that stimulated membrane enlargement in dorsal root ganglion (DRG) axons is triggered by intra-axonal synthesis of TC10, a small GTPase required for exocyst function. Induced membrane expansion and axon outgrowth are inhibited after axon-specific knockdown of TC10 mRNA. To determine the relationship of intra-axonal TC10 synthesis with the previously described stimulus-induced translation of the cytoskeletal regulator Par3, we investigate the signaling pathways controlling their local translation in response to NGF. Phosphoinositide 3-kinase (PI3K)-dependent activation of the Rheb-mTOR pathway triggers the simultaneous local synthesis of TC10 and Par3. These results reveal the importance of local translation in the control of membrane dynamics and demonstrate that localized, mTOR-dependent protein synthesis triggers the simultaneous activation of parallel pathways.
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30
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Sinnamon JR, Czaplinski K. RNA detection in situ with FISH-STICs. RNA (NEW YORK, N.Y.) 2014; 20:260-266. [PMID: 24345395 PMCID: PMC3895277 DOI: 10.1261/rna.041905.113] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 10/31/2013] [Indexed: 06/03/2023]
Abstract
The ability to detect RNA molecules in situ has long had important applications for molecular biological studies. Enzyme or dye-labeled antisense in vitro runoff transcripts and synthetic oligodeoxynucleotides (ODN) both have a proven track record of success, but each of these also has scientific and practical drawbacks and limitations to its use. We devised a means to use commercially synthesized oligonucleotides as RNA-FISH probes without further modification and show that such probes work well for detection of RNA in cultured cells. This approach can bind a high concentration of fluorescent ODN to a short stretch of an RNA using commercial DNA synthesis outlets available to any laboratory. We call this approach for creating in situ hybridization probes Fluorescence In Situ Hybridization with Sequential Tethered and Intertwined ODN Complexes (FISH-STICs). We demonstrate that one FISH-STIC probe can detect mRNA molecules in culture, and that probe detection can be improved by the addition of multiple probes that can be easily adapted for robust mRNA quantification. Using FISH-STICs, we demonstrate a nonoverlapping distribution for β-actin and γ-actin mRNA in cultured fibroblasts, and the detection of neuron-specific transcripts within cultured primary hippocampal neurons.
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Affiliation(s)
- John R. Sinnamon
- Center for Nervous Systems Disorders, Centers for Molecular Medicine
- Program in Neuroscience, Department of Neurobiology and Behavior
| | - Kevin Czaplinski
- Center for Nervous Systems Disorders, Centers for Molecular Medicine
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11749, USA
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31
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Quantifying the transcriptional output of single alleles in single living mammalian cells. Nat Protoc 2013; 8:393-408. [PMID: 23424748 DOI: 10.1038/nprot.2013.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Transcription kinetics of actively transcribing genes in vivo have generally been measured using tandem gene arrays. However, tandem arrays do not reflect the endogenous state of genome organization in which genes appear as single alleles. Here we present a robust technique for the quantification of mRNA synthesis from a single allele in real time in single living mammalian cells. The protocol describes how to generate cell clones harboring an MS2-tagged allele and how to detect in vivo transcription from this tagged allele at high spatial and temporal resolution throughout the cell cycle. Quantification of nascent mRNAs produced from the single tagged allele is performed using RNA fluorescence in situ hybridization (FISH) and live-cell imaging. Subsequent analyses and data modeling detailed in the protocol include measurements of transcription rates of RNA polymerase II, determination of the number of polymerases recruited to the tagged allele and measurement of the spacing between polymerases. Generation of the cells containing the single tagged alleles should take up to 1 month; RNA FISH or live-cell imaging will require an additional week.
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Newhart A, Rafalska-Metcalf IU, Yang T, Joo LM, Powers SL, Kossenkov AV, Lopez-Jones M, Singer RH, Showe LC, Skordalakes E, Janicki SM. Single cell analysis of RNA-mediated histone H3.3 recruitment to a cytomegalovirus promoter-regulated transcription site. J Biol Chem 2013; 288:19882-99. [PMID: 23689370 DOI: 10.1074/jbc.m113.473181] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Unlike the core histones, which are incorporated into nucleosomes concomitant with DNA replication, histone H3.3 is synthesized throughout the cell cycle and utilized for replication-independent (RI) chromatin assembly. The RI incorporation of H3.3 into nucleosomes is highly conserved and occurs at both euchromatin and heterochromatin. However, neither the mechanism of H3.3 recruitment nor its essential function is well understood. Several different chaperones regulate H3.3 assembly at distinct sites. The H3.3 chaperone, Daxx, and the chromatin-remodeling factor, ATRX, are required for H3.3 incorporation and heterochromatic silencing at telomeres, pericentromeres, and the cytomegalovirus (CMV) promoter. By evaluating H3.3 dynamics at a CMV promoter-regulated transcription site in a genetic background in which RI chromatin assembly is blocked, we have been able to decipher the regulatory events upstream of RI nucleosomal deposition. We find that at the activated transcription site, H3.3 accumulates with sense and antisense RNA, suggesting that it is recruited through an RNA-mediated mechanism. Sense and antisense transcription also increases after H3.3 knockdown, suggesting that the RNA signal is amplified when chromatin assembly is blocked and attenuated by nucleosomal deposition. Additionally, we find that H3.3 is still recruited after Daxx knockdown, supporting a chaperone-independent recruitment mechanism. Sequences in the H3.3 N-terminal tail and αN helix mediate both its recruitment to RNA at the activated transcription site and its interaction with double-stranded RNA in vitro. Interestingly, the H3.3 gain-of-function pediatric glioblastoma mutations, G34R and K27M, differentially affect H3.3 affinity in these assays, suggesting that disruption of an RNA-mediated regulatory event could drive malignant transformation.
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Affiliation(s)
- Alyshia Newhart
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, Pennsylvania 19104, USA
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Jones KL, Karpala A, Hirst B, Jenkins K, Tizard M, Pereira CF, Leis A, Monaghan P, Hyatt A, Mak J. Visualising single molecules of HIV-1 and miRNA nucleic acids. BMC Cell Biol 2013; 14:21. [PMID: 23590669 PMCID: PMC3639109 DOI: 10.1186/1471-2121-14-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 04/12/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The scarcity of certain nucleic acid species and the small size of target sequences such as miRNA, impose a significant barrier to subcellular visualization and present a major challenge to cell biologists. Here, we offer a generic and highly sensitive visualization approach (oligo fluorescent in situ hybridization, O-FISH) that can be used to detect such nucleic acids using a single-oligonucleotide probe of 19-26 nucleotides in length. RESULTS We used O-FISH to visualize miR146a in human and avian cells. Furthermore, we reveal the sensitivity of O-FISH detection by using a HIV-1 model system to show that as little as 1-2 copies of nucleic acids can be detected in a single cell. We were able to discern newly synthesized viral cDNA and, moreover, observed that certain HIV RNA sequences are only transiently available for O-FISH detection. CONCLUSIONS Taken together, these results suggest that the O-FISH method can potentially be used for in situ probing of, as few as, 1-2 copies of nucleic acid and, additionally, to visualize small RNA such as miRNA. We further propose that the O-FISH method could be extended to understand viral function by probing newly transcribed viral intermediates; and discern the localisation of nucleic acids of interest. Additionally, interrogating the conformation and structure of a particular nucleic acid in situ might also be possible, based on the accessibility of a target sequence.
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Affiliation(s)
- Kate L Jones
- Centre for Virology, Burnet Institute, Melbourne, Australia
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34
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Trcek T, Sato H, Singer RH, Maquat LE. Temporal and spatial characterization of nonsense-mediated mRNA decay. Genes Dev 2013; 27:541-51. [PMID: 23431032 PMCID: PMC3605467 DOI: 10.1101/gad.209635.112] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 01/29/2013] [Indexed: 12/11/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is a quality control mechanism responsible for "surveying" mRNAs during translation and degrading those that harbor a premature termination codon (PTC). Currently the intracellular spatial location of NMD and the kinetics of its decay step in mammalian cells are under debate. To address these issues, we used single-RNA fluorescent in situ hybridization (FISH) and measured the NMD of PTC-containing β-globin mRNA in intact single cells after the induction of β-globin gene transcription. This approach preserves temporal and spatial information of the NMD process, both of which would be lost in an ensemble study. We determined that decay of the majority of PTC-containing β-globin mRNA occurs soon after its export into the cytoplasm, with a half-life of <1 min; the remainder is degraded with a half-life of >12 h, similar to the half-life of normal PTC-free β-globin mRNA, indicating that it had evaded NMD. Importantly, NMD does not occur within the nucleoplasm, thus countering the long-debated idea of nuclear degradation of PTC-containing transcripts. We provide a spatial and temporal model for the biphasic decay of NMD targets.
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Affiliation(s)
- Tatjana Trcek
- Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Hanae Sato
- Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Robert H. Singer
- Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Lynne E. Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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Tischler J, Surani MA. Investigating transcriptional states at single-cell-resolution. Curr Opin Biotechnol 2012; 24:69-78. [PMID: 23084076 DOI: 10.1016/j.copbio.2012.09.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/13/2012] [Accepted: 09/24/2012] [Indexed: 01/09/2023]
Abstract
Gene expression analysis at single-cell-resolution is a powerful tool for uncovering individual cell differences within heterogeneous cell populations and complex tissues, which can provide invaluable insights into the extent of gene expression variability. Multi-dimensional information of gene expression at the level of the individual cell can help to identify distinct and rare molecular cell 'states' within populations and aid in unravelling genetic regulatory circuits. Gene expression analysis at the single-cell-level will also enhance our understanding of the molecular basis of aberrant cell states and disease development and holds great promise for the advancement of personalized medicine. We present approaches that provide large-scale views of gene expression at the level of the individual cell.
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Affiliation(s)
- Julia Tischler
- The Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Cambridge CB2 1QN, United Kingdom
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36
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Eberwine J, Lovatt D, Buckley P, Dueck H, Francis C, Kim TK, Lee J, Lee M, Miyashiro K, Morris J, Peritz T, Schochet T, Spaethling J, Sul JY, Kim J. Quantitative biology of single neurons. J R Soc Interface 2012; 9:3165-83. [PMID: 22915636 PMCID: PMC3481569 DOI: 10.1098/rsif.2012.0417] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The building blocks of complex biological systems are single cells. Fundamental insights gained from single-cell analysis promise to provide the framework for understanding normal biological systems development as well as the limits on systems/cellular ability to respond to disease. The interplay of cells to create functional systems is not well understood. Until recently, the study of single cells has concentrated primarily on morphological and physiological characterization. With the application of new highly sensitive molecular and genomic technologies, the quantitative biochemistry of single cells is now accessible.
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Affiliation(s)
- James Eberwine
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, 36th and Hamilton Walk, Philadelphia, PA 19104, USA.
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37
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Trcek T, Larson DR, Moldón A, Query CC, Singer RH. Single-molecule mRNA decay measurements reveal promoter- regulated mRNA stability in yeast. Cell 2012; 147:1484-97. [PMID: 22196726 DOI: 10.1016/j.cell.2011.11.051] [Citation(s) in RCA: 198] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 07/27/2011] [Accepted: 11/22/2011] [Indexed: 12/29/2022]
Abstract
Messenger RNA decay measurements are typically performed on a population of cells. However, this approach cannot reveal sufficient complexity to provide information on mechanisms that may regulate mRNA degradation, possibly on short timescales. To address this deficiency, we measured cell cycle-regulated decay in single yeast cells using single-molecule FISH. We found that two genes responsible for mitotic progression, SWI5 and CLB2, exhibit a mitosis-dependent mRNA stability switch. Their transcripts are stable until mitosis, when a precipitous decay eliminates the mRNA complement, preventing carryover into the next cycle. Remarkably, the specificity and timing of decay is entirely regulated by their promoter, independent of specific cis mRNA sequences. The mitotic exit network protein Dbf2p binds to SWI5 and CLB2 mRNAs cotranscriptionally and regulates their decay. This work reveals the promoter-dependent control of mRNA stability, a regulatory mechanism that could be employed by a variety of mRNAs and organisms.
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Affiliation(s)
- Tatjana Trcek
- Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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38
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Trcek T, Chao JA, Larson DR, Park HY, Zenklusen D, Shenoy SM, Singer RH. Single-mRNA counting using fluorescent in situ hybridization in budding yeast. Nat Protoc 2012; 7:408-19. [PMID: 22301778 DOI: 10.1038/nprot.2011.451] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Fluorescent in situ hybridization (FISH) allows the quantification of single mRNAs in budding yeast using fluorescently labeled single-stranded DNA probes, a wide-field epifluorescence microscope and a spot-detection algorithm. Fixed yeast cells are attached to coverslips and hybridized with a mixture of FISH probes, each conjugated to several fluorescent dyes. Images of cells are acquired in 3D and maximally projected for single-molecule analysis. Diffraction-limited labeled mRNAs are observed as bright fluorescent spots and can be quantified using a spot-detection algorithm. FISH preserves the spatial distribution of cellular RNA distribution within the cell and the stochastic fluctuations in individual cells that can lead to phenotypic differences within a clonal population. This information, however, is lost if the RNA content is measured on a population of cells by using reverse transcriptase PCR, microarrays or high-throughput sequencing. The FISH procedure and image acquisition described here can be completed in 3 d.
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Affiliation(s)
- Tatjana Trcek
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, USA
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39
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High-resolution whole-mount in situ hybridization using Quantum Dot nanocrystals. J Biomed Biotechnol 2012; 2012:627602. [PMID: 22287835 PMCID: PMC3263632 DOI: 10.1155/2012/627602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 09/29/2011] [Accepted: 10/03/2011] [Indexed: 11/23/2022] Open
Abstract
The photostability and narrow emission spectra of nanometer-scale semiconductor crystallites (QDs) make them desirable candidates for whole-mount fluorescent in situ hybridization to detect mRNA transcripts in morphologically preserved intact embryos. We describe a method for direct QD labeling of modified oligonucleotide probes through streptavidin-biotin and antibody-mediated interactions (anti-FITC and anti-digoxigenin). To overcome permeability issues and allow QD conjugate penetration, embryos were treated with proteinase K. The use of QDs dramatically increased sensitivity of whole-mount in situ hybridization (WISH) in comparison with organic fluorophores and enabled fluorescent detection of specific transcripts within cells without the use of enzymatic amplification. Therefore, this method offers significant advantages both in terms of sensitivity, as well as resolution. Specifically, the use of QDs alleviates issues of photostability and limited brightness plaguing organic fluorophores and allows fluorescent imaging of cleared embryos. It also offers new imaging possibilities, including intracellular localization of mRNAs, simultaneous multiple-transcript detection, and visualization of mRNA expression patterns in 3D.
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40
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Ganesan S, Karr JE, Featherstone DE. Drosophila glutamate receptor mRNA expression and mRNP particles. RNA Biol 2011; 8:771-81. [PMID: 21743295 PMCID: PMC3256355 DOI: 10.4161/rna.8.5.16014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 03/31/2011] [Indexed: 02/07/2023] Open
Abstract
The processes controlling glutamate receptor expression early in synaptogenesis are poorly understood. Here, we examine glutamate receptor (GluR) subunit mRNA expression and localization in Drosophila embryonic/larval neuromuscular junctions (NMJs). We show that postsynaptic GluR subunit gene expression is triggered by contact from the presynaptic nerve, approximately halfway through embryogenesis. After contact, GluRIIA and GluRIIB mRNA abundance rises quickly approximately 20-fold, then falls within a few hours back to very low levels. Protein abundance, however, gradually increases throughout development. At the same time that mRNA levels decrease following their initial spike, GluRIIA, GluRIIB, and GluRIIC subunit mRNA aggregates become visible in the cytoplasm of postsynaptic muscle cells. These mRNA aggregates do not colocalize with eIF4E, but nevertheless presumably represent mRNP particles of unknown function. Multiplex FISH shows that different GluR subunit mRNAs are found in different mRNPs. GluRIIC mRNPs are most common, followed by GluRIIA and then GluRIIB mRNPs. GluR mRNP density is not increased near NMJs, for any subunit; if anything, GluR mRNP density is highest away from NMJs and near nuclei. These results reveal some of the earliest events in postsynaptic development and provide a foundation for future studies of GluR mRNA biology.
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Affiliation(s)
- Subhashree Ganesan
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
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41
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Abstract
High-throughput gene expression screens provide a quantitative picture of the average expression signature of biological samples. However, the analysis of spatial gene expression patterns with single-cell resolution requires quantitative in situ measurement techniques. Here we describe recent technological advances in RNA fluorescence in situ hybridization (FISH) techniques that facilitate detection of individual fluorescently labeled mRNA molecules of practically any endogenous gene. These methods, which are based on advances in probe design, imaging technology and image processing, enable the absolute measurement of transcript abundance in individual cells with single-molecule resolution.
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42
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Chubb JR, Liverpool TB. Bursts and pulses: insights from single cell studies into transcriptional mechanisms. Curr Opin Genet Dev 2010; 20:478-84. [PMID: 20638837 DOI: 10.1016/j.gde.2010.06.009] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/18/2010] [Accepted: 06/22/2010] [Indexed: 11/30/2022]
Abstract
With a developing appreciation of how noisy gene expression can be, and difficulties in deciphering conventional gene expression data into cell control mechanisms, it has become clear that single cell techniques for measuring transcription are necessary to illuminate basic cell regulation strategies. The resultant use of in situ hybridisation and live cell RNA visualisation approaches in single cells revealed transcription is not adequately reflected by the smooth, seamless process we tend to infer from standard measures of RNA level. When RNA production is measured in single cells, the process of transcription has been shown to occur in bursts, or pulses. This review will highlight the evidence for these phenomena, the proposed mechanisms underlying discontinuity, and the biological implications of such behaviour.
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Affiliation(s)
- Jonathan R Chubb
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.
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43
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Weil TT, Parton RM, Davis I. Making the message clear: visualizing mRNA localization. Trends Cell Biol 2010; 20:380-90. [PMID: 20444605 PMCID: PMC2902723 DOI: 10.1016/j.tcb.2010.03.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 03/26/2010] [Accepted: 03/30/2010] [Indexed: 11/28/2022]
Abstract
Localized mRNA provides spatial and temporal protein expression essential to cell development and physiology. To explore the mechanisms involved, considerable effort has been spent in establishing new and improved methods for visualizing mRNA. Here, we discuss how these techniques have extended our understanding of intracellular mRNA localization in a variety of organisms. In addition to increased ease and specificity of detection in fixed tissue, in situ hybridization methods now enable examination of mRNA distribution at the ultrastructural level with electron microscopy. Most significantly, methods for following the movement of mRNA in living cells are now in widespread use. These include the introduction of labeled transcripts by microinjection, hybridization based methods using labeled antisense probes and complementary transgenic methods for tagging endogenous mRNAs using bacteriophage components. These technical innovations are now being coupled with super-resolution light microscopy methods and promise to revolutionize our understanding of the dynamics and complexity of the molecular mechanism of mRNA localization.
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44
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Arvey A, Hermann A, Hsia CC, Ie E, Freund Y, McGinnis W. Minimizing off-target signals in RNA fluorescent in situ hybridization. Nucleic Acids Res 2010; 38:e115. [PMID: 20164092 PMCID: PMC2879521 DOI: 10.1093/nar/gkq042] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 12/11/2009] [Accepted: 01/17/2010] [Indexed: 12/19/2022] Open
Abstract
Fluorescent in situ hybridization (FISH) techniques are becoming extremely sensitive, to the point where individual RNA or DNA molecules can be detected with small probes. At this level of sensitivity, the elimination of 'off-target' hybridization is of crucial importance, but typical probes used for RNA and DNA FISH contain sequences repeated elsewhere in the genome. We find that very short (e.g. 20 nt) perfect repeated sequences within much longer probes (e.g. 350-1500 nt) can produce significant off-target signals. The extent of noise is surprising given the long length of the probes and the short length of non-specific regions. When we removed the small regions of repeated sequence from either short or long probes, we find that the signal-to-noise ratio is increased by orders of magnitude, putting us in a regime where fluorescent signals can be considered to be a quantitative measure of target transcript numbers. As the majority of genes in complex organisms contain repeated k-mers, we provide genome-wide annotations of k-mer-uniqueness at http://cbio.mskcc.org/ approximately aarvey/repeatmap.
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Affiliation(s)
- Aaron Arvey
- Computational and Systems Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, Department of Computer Sciences and Engineering, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 and Google Inc., Mountain View, CA 94043, USA
| | - Anita Hermann
- Computational and Systems Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, Department of Computer Sciences and Engineering, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 and Google Inc., Mountain View, CA 94043, USA
| | - Cheryl C. Hsia
- Computational and Systems Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, Department of Computer Sciences and Engineering, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 and Google Inc., Mountain View, CA 94043, USA
| | - Eugene Ie
- Computational and Systems Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, Department of Computer Sciences and Engineering, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 and Google Inc., Mountain View, CA 94043, USA
| | - Yoav Freund
- Computational and Systems Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, Department of Computer Sciences and Engineering, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 and Google Inc., Mountain View, CA 94043, USA
| | - William McGinnis
- Computational and Systems Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, Department of Computer Sciences and Engineering, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 and Google Inc., Mountain View, CA 94043, USA
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45
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Rates of in situ transcription and splicing in large human genes. Nat Struct Mol Biol 2009; 16:1128-33. [PMID: 19820712 PMCID: PMC2783620 DOI: 10.1038/nsmb.1666] [Citation(s) in RCA: 330] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 08/11/2009] [Indexed: 12/26/2022]
Abstract
Transcription and splicing must proceed over genomic distances of hundreds of kilobases in many human genes. However, the rates and mechanisms of these processes are poorly understood. We have used the compound 5,6-Dichlorobenzimidazole 1-b-D-ribofuranoside (DRB) that reversibly blocks gene transcription in vivo combined with quantitative RT-PCR to analyze the transcription and RNA processing of several long human genes. We found that the rate of RNA polymerase II transcription over long genomic distances is about 3.8 kb per minute and is nearly the same whether transcribing long introns or exon rich regions. We also determined that co-transcriptional pre-mRNA splicing of U2-dependent introns occurs within 5–10 minutes of synthesis irrespective of intron length between 1 kb and 240 kb. Similarly, U12-dependent introns were co-transcriptionally spliced within 10 minutes of synthesis confirming that these introns are spliced within the nuclear compartment. These results show that the expression of large genes is surprisingly rapid and efficient.
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46
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Hengst U, Deglincerti A, Kim HJ, Jeon NL, Jaffrey SR. Axonal elongation triggered by stimulus-induced local translation of a polarity complex protein. Nat Cell Biol 2009; 11:1024-30. [PMID: 19620967 PMCID: PMC2724225 DOI: 10.1038/ncb1916] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 04/23/2009] [Indexed: 12/11/2022]
Affiliation(s)
- Ulrich Hengst
- Department of Pharmacology, Weill Medical College, Cornell University, NY 10065, USA
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47
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Abstract
Over the past few decades, great strides have been made in anatomical imaging of disease that has led to their diagnosis with minimal invasion. Despite these advances, diseases such as cancer continue to take one human life every minute in the United States. Complimentary approaches that pertain directly to the genesis of the disease might contribute to its early diagnosis and subsequent management. In cancer, an array of molecular abnormalities leading to the modulations in expression of key proteins important in the cellular signaling pathways and cell proliferation has been identified. These specific disease fingerprints, biomarkers, are overexpressed on malignant cell surfaces or within the cytoplasm, and they provide unique targets that are promising for improving cancer diagnosis and therapy. We and others have designed, synthesized, and evaluated some novel probes specific for those oncogenes and oncogene product biomarkers for PET and SPECT molecular imaging of certain types of cancers. This article briefly describes this approach and gives specific examples that depict the ability of molecular imaging to detect occult lesions not detectable by current scintigraphic approaches. The article also outlines a few examples predicting other possible applications of targeting such specific probes not yet used.
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Affiliation(s)
- Mathew L Thakur
- Laboratories of Radiopharmaceutical Research and Molecular Imaging, Department of Radiology and Radiation Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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48
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Nitin N, Rhee WJ, Bao G. Translation inhibition reveals interaction of 2'-deoxy and 2'-O-methyl molecular beacons with mRNA targets in living cells. Nucleic Acids Res 2009; 37:4977-86. [PMID: 19528073 PMCID: PMC2731902 DOI: 10.1093/nar/gkp517] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Understanding the interaction between oligonucleotide probes and RNA targets in living cells is important for biological and clinical studies of gene expression in vivo. Here, we demonstrate that starvation of cells and translation inhibition by blocking the mTOR or PI-3 kinase pathway could significantly reduce the fluorescence signal from 2′-deoxy molecular beacons (MBs) targeting K-ras and GAPDH mRNAs in living cells. However, the intensity and localization of fluorescence signal from MBs targeting nontranslated 28S rRNA remained the same in normal and translation-inhibited cells. We also found that, in targeting K-ras and GAPDH mRNAs, the signal level from MBs with 2′-O-methyl backbone did not change when translation was repressed. Taken together, our findings suggest that MBs with DNA backbone hybridize preferentially with mRNAs in their translational state in living cells, whereas those with 2′-O-methyl chemistry tend to hybridize to mRNA targets in both translational and nontranslational states. This work may thus provide a significant insight into probe design for detection of RNA molecules in living cells and RNA biology.
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Affiliation(s)
- Nitin Nitin
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
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49
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Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods 2008; 5:877-9. [PMID: 18806792 PMCID: PMC3126653 DOI: 10.1038/nmeth.1253] [Citation(s) in RCA: 1436] [Impact Index Per Article: 89.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 08/25/2008] [Indexed: 02/01/2023]
Abstract
We describe a method for imaging individual mRNA molecules in fixed cells by probing each mRNA species with 48 or more short, singly labeled oligonucleotide probes. This makes each mRNA molecule visible as a computationally identifiable fluorescent spot via fluorescence microscopy. We demonstrate simultaneous detection of three mRNA species in single cells and mRNA detection in yeast, nematodes, fruit fly wing discs, mammalian cell lines and neurons.
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50
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Abstract
Although 30 years ago it was strongly suggested that some cytoplasmic ribosomes are bound to the surface of yeast mitochondria, the mechanisms and the raison d'être of this process are not understood. For instance, it is not perfectly known which of the several hundred nuclearly encoded genes have to be translated to the mitochondrial vicinity to guide the import of the corresponding proteins. One can take advantage of several modern methods to address a number of aspects of the site-specific translation process of messenger ribonucleic acid (mRNA) coding for proteins imported into mitochondria. Three complementary approaches are presented to analyze the spatial distribution of mRNAs coding for proteins imported into mitochondria. Starting from biochemical purifications of mitochondria-bound polysomes, we describe a genomewide approach to classify all the cellular mRNAs according to their physical proximity with mitochondria; we also present real-time quantitative reverse transcription polymerase chain reaction monitoring of mRNA distribution to provide a quantified description of this localization. Finally, a fluorescence microscopy approach on a single living cell is described to visualize the in vivo localization of mRNAs involved in mitochondria biogenesis.
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Affiliation(s)
- Mathilde Garcia
- Laboratoire de Génétique Moléculaire CNRS-ENS, Paris, France
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