151
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Visualizing the life of mRNA in T cells. Biochem Soc Trans 2017; 45:563-570. [PMID: 28408496 DOI: 10.1042/bst20170003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/23/2017] [Accepted: 02/27/2017] [Indexed: 12/15/2022]
Abstract
T cells release ample amounts of cytokines during infection. This property is critical to prevent pathogen spreading and persistence. Nevertheless, whereas rapid and ample cytokine production supports the clearance of pathogens, the production must be restricted in time and location to prevent detrimental effects of chronic inflammation and immunopathology. Transcriptional and post-transcriptional processes determine the levels of cytokine production. How these regulatory mechanisms are interconnected, and how they regulate the magnitude of protein production in primary T cells is to date not well studied. Here, we highlight recent advances in the field that boost our understanding of the regulatory processes of cytokine production of T cells, with a focus on transcription, mRNA stability, localization and translation.
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152
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Vera M, Biswas J, Senecal A, Singer RH, Park HY. Single-Cell and Single-Molecule Analysis of Gene Expression Regulation. Annu Rev Genet 2017; 50:267-291. [PMID: 27893965 DOI: 10.1146/annurev-genet-120215-034854] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent advancements in single-cell and single-molecule imaging technologies have resolved biological processes in time and space that are fundamental to understanding the regulation of gene expression. Observations of single-molecule events in their cellular context have revealed highly dynamic aspects of transcriptional and post-transcriptional control in eukaryotic cells. This approach can relate transcription with mRNA abundance and lifetimes. Another key aspect of single-cell analysis is the cell-to-cell variability among populations of cells. Definition of heterogeneity has revealed stochastic processes, determined characteristics of under-represented cell types or transitional states, and integrated cellular behaviors in the context of multicellular organisms. In this review, we discuss novel aspects of gene expression of eukaryotic cells and multicellular organisms revealed by the latest advances in single-cell and single-molecule imaging technology.
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Affiliation(s)
- Maria Vera
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461; , , ,
| | - Jeetayu Biswas
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461; , , ,
| | - Adrien Senecal
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461; , , ,
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461; , , , .,Janelia Research Campus of the HHMI, Ashburn, Virginia 20147
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Korea; .,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Korea
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153
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Hochberg H, Brody Y, Shav-Tal Y. Measuring transcription dynamics in living cells using a photobleaching approach. Methods 2017; 120:58-64. [PMID: 28434903 DOI: 10.1016/j.ymeth.2017.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/02/2017] [Accepted: 04/14/2017] [Indexed: 11/28/2022] Open
Abstract
The transcriptional kinetics of RNA polymerase II, the enzyme responsible for mRNA transcription in the nucleoplasm, can be modulated by a variety of factors. It is therefore important to establish experimental systems that will enable the readout of transcription kinetics of specific genes as they occur in real time within individual cells. This can be performed by implementing fluorescent tagging of the mRNA under live-cell conditions. This chapter describes how to generate fluorescently tagged genes and mRNA, and how a photobleaching approach can produce information on mRNA transcription kinetics.
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Affiliation(s)
- Hodaya Hochberg
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Yehuda Brody
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel.
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154
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Pilaz LJ, Silver DL. Moving messages in the developing brain-emerging roles for mRNA transport and local translation in neural stem cells. FEBS Lett 2017; 591:1526-1539. [PMID: 28304078 DOI: 10.1002/1873-3468.12626] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/06/2017] [Accepted: 03/11/2017] [Indexed: 11/10/2022]
Abstract
The mammalian cerebral cortex is a complex brain structure integral to our higher cognition. During embryonic cortical development, radial glial progenitors (RGCs) produce neurons and serve as physical structures for migrating neurons. Recent discoveries highlight new roles for RNA localization and local translation in RGCs, both at the cell body and at distal structures called basal endfeet. By implementing technologies from the field of RNA research to brain development, investigators can manipulate RNA-binding proteins as well as visualize single-molecule RNAs, live movement of mRNAs and their binding proteins, and translation. Going forward, these studies establish a framework for investigating how post-transcriptional RNA regulation helps shape RGC function and triggers neurodevelopmental diseases.
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Affiliation(s)
- Louis-Jan Pilaz
- Department of Molecular Genetics and Microbiology, Regeneration Next, Duke University Medical Center, Durham, NC, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Regeneration Next, Duke University Medical Center, Durham, NC, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.,Department of Neurobiology, Duke University Medical Center, Durham, NC, USA.,Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC, USA
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155
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Fernández-Moya SM, Ehses J, Kiebler MA. The alternative life of RNA-sequencing meets single molecule approaches. FEBS Lett 2017; 591:1455-1470. [PMID: 28369835 DOI: 10.1002/1873-3468.12639] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 03/15/2017] [Accepted: 03/24/2017] [Indexed: 12/31/2022]
Abstract
The central dogma of RNA processing has started to totter. Single genes produce a variety of mRNA isoforms by mRNA modification, alternative polyadenylation (APA), and splicing. Different isoforms, even those that code for the identical protein, may differ in function or spatiotemporal expression. One option of how this can be achieved is by the selective recruitment of trans-acting factors to the 3'-untranslated region of a given isoform. Recent innovations in high-throughput RNA-sequencing methods allow deep insight into global RNA regulation, whereas novel imaging-based technologies enable researchers to explore single RNA molecules during different stages of development, in different tissues and different compartments of the cell. Resolving the dynamic function of ribonucleoprotein particles in splicing, APA, or RNA modification will enable us to understand their contribution to pathological conditions.
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Affiliation(s)
| | - Janina Ehses
- BioMedical Center, Ludwig Maximilians University, Planegg-Martinsried, Germany
| | - Michael A Kiebler
- BioMedical Center, Ludwig Maximilians University, Planegg-Martinsried, Germany
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156
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Imaging Translational and Post-Translational Gene Regulatory Dynamics in Living Cells with Antibody-Based Probes. Trends Genet 2017; 33:322-335. [PMID: 28359585 DOI: 10.1016/j.tig.2017.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/25/2017] [Accepted: 02/28/2017] [Indexed: 12/17/2022]
Abstract
Antibody derivatives, such as antibody fragments (Fabs) and single-chain variable fragments (scFvs), are now being used to image traditionally hard-to-see protein subpopulations, including nascent polypeptides being translated and post-translationally modified proteins. This has allowed researchers to directly image and quantify, for the first time, translation initiation and elongation kinetics with single-transcript resolution and the temporal ordering and kinetics of post-translational histone and RNA polymerase II modifications. Here, we review these developments and discuss the strengths and weaknesses of live-cell imaging with antibody-based probes. Further development of these probes will increase their versatility and open new avenues of research for dissecting complex gene regulatory dynamics.
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157
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Eliscovich C, Singer RH. RNP transport in cell biology: the long and winding road. Curr Opin Cell Biol 2017; 45:38-46. [PMID: 28258033 DOI: 10.1016/j.ceb.2017.02.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/17/2017] [Accepted: 02/08/2017] [Indexed: 01/08/2023]
Abstract
Regulation of gene expression is key determinant to cell structure and function. RNA localization, where specific mRNAs are transported to subcellular regions and then translated, is highly conserved in eukaryotes ranging from yeast to extremely specialized and polarized cells such as neurons. Messenger RNA and associated proteins (mRNP) move from the site of transcription in the nucleus to their final destination in the cytoplasm both passively through diffusion and actively via directed transport. Dysfunction of RNA localization, transport and translation machinery can lead to pathology. Single-molecule live-cell imaging techniques have revealed unique features of this journey with unprecedented resolution. In this review, we highlight key recent findings that have been made using these approaches and possible implications for spatial control of gene function.
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Affiliation(s)
- Carolina Eliscovich
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States; Current address: Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States; Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, United States; Janelia Research Campus of the HHMI, Ashburn, VA, 20147, United States.
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158
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Pocock GM, Zimdars LL, Yuan M, Eliceiri KW, Ahlquist P, Sherer NM. Diverse activities of viral cis-acting RNA regulatory elements revealed using multicolor, long-term, single-cell imaging. Mol Biol Cell 2017; 28:476-487. [PMID: 27903772 PMCID: PMC5341730 DOI: 10.1091/mbc.e16-08-0612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 02/06/2023] Open
Abstract
Cis-acting RNA structural elements govern crucial aspects of viral gene expression. How these structures and other posttranscriptional signals affect RNA trafficking and translation in the context of single cells is poorly understood. Herein we describe a multicolor, long-term (>24 h) imaging strategy for measuring integrated aspects of viral RNA regulatory control in individual cells. We apply this strategy to demonstrate differential mRNA trafficking behaviors governed by RNA elements derived from three retroviruses (HIV-1, murine leukemia virus, and Mason-Pfizer monkey virus), two hepadnaviruses (hepatitis B virus and woodchuck hepatitis virus), and an intron-retaining transcript encoded by the cellular NXF1 gene. Striking behaviors include "burst" RNA nuclear export dynamics regulated by HIV-1's Rev response element and the viral Rev protein; transient aggregations of RNAs into discrete foci at or near the nuclear membrane triggered by multiple elements; and a novel, pulsiform RNA export activity regulated by the hepadnaviral posttranscriptional regulatory element. We incorporate single-cell tracking and a data-mining algorithm into our approach to obtain RNA element-specific, high-resolution gene expression signatures. Together these imaging assays constitute a tractable, systems-based platform for studying otherwise difficult to access spatiotemporal features of viral and cellular gene regulation.
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MESH Headings
- Active Transport, Cell Nucleus/physiology
- Cell Nucleus/metabolism
- Gene Expression Regulation, Viral
- Gene Products, rev/metabolism
- Genes, env/physiology
- HIV-1
- Mason-Pfizer monkey virus
- Molecular Imaging/methods
- RNA Processing, Post-Transcriptional/physiology
- RNA, Messenger/metabolism
- RNA, Viral
- Regulatory Sequences, Nucleic Acid/genetics
- Regulatory Sequences, Nucleic Acid/physiology
- Regulatory Sequences, Ribonucleic Acid/genetics
- Regulatory Sequences, Ribonucleic Acid/physiology
- Single-Cell Analysis/methods
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Affiliation(s)
- Ginger M Pocock
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53706
| | - Laraine L Zimdars
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
| | - Ming Yuan
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53706
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706
| | - Kevin W Eliceiri
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53706
- Laboratory for Optical and Computational Instrumentation and Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706
| | - Paul Ahlquist
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53706
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI 53706
| | - Nathan M Sherer
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
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159
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Konopka G. Cognitive genomics: Linking genes to behavior in the human brain. Netw Neurosci 2017; 1:3-13. [PMID: 29601049 PMCID: PMC5846799 DOI: 10.1162/netn_a_00003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/19/2016] [Indexed: 11/05/2022] Open
Abstract
Correlations of genetic variation in DNA with functional brain activity have already provided a starting point for delving into human cognitive mechanisms. However, these analyses do not provide the specific genes driving the associations, which are complicated by intergenic localization as well as tissue-specific epigenetics and expression. The use of brain-derived expression datasets could build upon the foundation of these initial genetic insights and yield genes and molecular pathways for testing new hypotheses regarding the molecular bases of human brain development, cognition, and disease. Thus, coupling these human brain gene expression data with measurements of brain activity may provide genes with critical roles in brain function. However, these brain gene expression datasets have their own set of caveats, most notably a reliance on postmortem tissue. In this perspective, I summarize and examine the progress that has been made in this realm to date, and discuss the various frontiers remaining, such as the inclusion of cell-type-specific information, additional physiological measurements, and genomic data from patient cohorts.
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Affiliation(s)
- Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
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160
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Heinrich S, Derrer CP, Lari A, Weis K, Montpetit B. Temporal and spatial regulation of mRNA export: Single particle RNA-imaging provides new tools and insights. Bioessays 2017; 39. [PMID: 28052353 DOI: 10.1002/bies.201600124] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The transport of messenger RNAs (mRNAs) from the nucleus to cytoplasm is an essential step in the gene expression program of all eukaryotes. Recent technological advances in the areas of RNA-labeling, microscopy, and sequencing are leading to novel insights about mRNA biogenesis and export. This includes quantitative single molecule imaging (SMI) of RNA molecules in live cells, which is providing knowledge of the spatial and temporal dynamics of the export process. As this information becomes available, it leads to new questions, the reinterpretation of previous findings, and revised models of mRNA export. In this review, we will briefly highlight some of these recent findings and discuss how live cell SMI approaches may be used to further our current understanding of mRNA export and gene expression.
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Affiliation(s)
| | | | - Azra Lari
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Karsten Weis
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Canada.,Department of Viticulture and Enology, University of California, Davis, CA, USA
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161
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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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162
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Lee BH, Bae SW, Shim JJ, Park SY, Park HY. Imaging Single-mRNA Localization and Translation in Live Neurons. Mol Cells 2016; 39:841-846. [PMID: 28030897 PMCID: PMC5223100 DOI: 10.14348/molcells.2016.0277] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 01/18/2023] Open
Abstract
Local protein synthesis mediates precise spatio-temporal regulation of gene expression for neuronal functions such as long-term plasticity, axon guidance and regeneration. To reveal the underlying mechanisms of local translation, it is crucial to understand mRNA transport, localization and translation in live neurons. Among various techniques for mRNA analysis, fluorescence microscopy has been widely used as the most direct method to study localization of mRNA. Live-cell imaging of single RNA molecules is particularly advantageous to dissect the highly heterogeneous and dynamic nature of messenger ribonucleoprotein (mRNP) complexes in neurons. Here, we review recent advances in the study of mRNA localization and translation in live neurons using novel techniques for single-RNA imaging.
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Affiliation(s)
- Byung Hun Lee
- Department of Physics and Astronomy, Seoul National University, Seoul 08826,
Korea
| | - Seong-Woo Bae
- Department of Physics and Astronomy, Seoul National University, Seoul 08826,
Korea
| | - Jaeyoun Jay Shim
- Department of Physics and Astronomy, Seoul National University, Seoul 08826,
Korea
| | - Sung Young Park
- Center for RNA Research, Institute for Basic Science, Seoul 08826,
Korea
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul 08826,
Korea
- The Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826,
Korea
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163
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Schieweck R, Popper B, Kiebler MA. Co-Translational Folding: A Novel Modulator of Local Protein Expression in Mammalian Neurons? Trends Genet 2016; 32:788-800. [DOI: 10.1016/j.tig.2016.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/04/2016] [Accepted: 10/11/2016] [Indexed: 01/15/2023]
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164
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Bright photoactivatable fluorophores for single-molecule imaging. Nat Methods 2016; 13:985-988. [PMID: 27776112 DOI: 10.1038/nmeth.4034] [Citation(s) in RCA: 248] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 09/20/2016] [Indexed: 12/23/2022]
Abstract
Small-molecule fluorophores are important tools for advanced imaging experiments. We previously reported a general method to improve small, cell-permeable fluorophores which resulted in the azetidine-containing 'Janelia Fluor' (JF) dyes. Here, we refine and extend the utility of these dyes by synthesizing photoactivatable derivatives that are compatible with live-cell labeling strategies. Once activated, these derived compounds retain the superior brightness and photostability of the JF dyes, enabling improved single-particle tracking and facile localization microscopy experiments.
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165
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Seeing is Believing: Tracking Translation Dynamics In Vivo. Trends Biochem Sci 2016; 41:818-821. [DOI: 10.1016/j.tibs.2016.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 07/22/2016] [Accepted: 07/27/2016] [Indexed: 11/21/2022]
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166
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Rate control in yeast protein synthesis at the population and single-cell levels. Biochem Soc Trans 2016; 43:1266-70. [PMID: 26614671 DOI: 10.1042/bst20150169] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Yeast commits approximately 76% of its energy budget to protein synthesis and the efficiency and control of this process are accordingly critical to organism growth and fitness. We now have detailed genetic, biochemical and biophysical knowledge of the components of the eukaryotic translation machinery. However, these kinds of information do not, in themselves, give us a satisfactory picture of how the overall system is controlled. This is where quantitative system analysis can enable a step-change in our understanding of biological resource management and how this relates to cell physiology and evolution. An important aspect of this more system-oriented approach to translational control is the inherent heterogeneity of cell populations that is generated by gene expression noise. In this short review, we address the fact that, although the vast majority of our knowledge of the translation machinery is based on experimental analysis of samples that each contain hundreds of millions of cells, in reality every cell is unique in terms of its composition and control properties. We have entered a new era in which research into the heterogeneity of cell systems promises to provide answers to many (previously unanswerable) questions about cell physiology and evolution.
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167
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Ma L, Rajshekhar G, Wang R, Bhaduri B, Sridharan S, Mir M, Chakraborty A, Iyer R, Prasanth S, Millet L, Gillette MU, Popescu G. Phase correlation imaging of unlabeled cell dynamics. Sci Rep 2016; 6:32702. [PMID: 27615512 PMCID: PMC5018886 DOI: 10.1038/srep32702] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/05/2016] [Indexed: 12/30/2022] Open
Abstract
We present phase correlation imaging (PCI) as a novel approach to study cell dynamics in a spatially-resolved manner. PCI relies on quantitative phase imaging time-lapse data and, as such, functions in label-free mode, without the limitations associated with exogenous markers. The correlation time map outputted in PCI informs on the dynamics of the intracellular mass transport. Specifically, we show that PCI can extract quantitatively the diffusion coefficient map associated with live cells, as well as standard Brownian particles. Due to its high sensitivity to mass transport, PCI can be applied to studying the integrity of actin polymerization dynamics. Our results indicate that the cyto-D treatment blocking the actin polymerization has a dominant effect at the large spatial scales, in the region surrounding the cell. We found that PCI can distinguish between senescent and quiescent cells, which is extremely difficult without using specific markers currently. We anticipate that PCI will be used alongside established, fluorescence-based techniques to enable valuable new studies of cell function.
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Affiliation(s)
- Lihong Ma
- Quantitative Light Imaging Laboratory, Department of Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Institute of Information Optics, Zhejiang Normal University, Jinhua, Zhejiang, 321004, China
| | - Gannavarpu Rajshekhar
- Quantitative Light Imaging Laboratory, Department of Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ru Wang
- Quantitative Light Imaging Laboratory, Department of Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Basanta Bhaduri
- Quantitative Light Imaging Laboratory, Department of Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Shamira Sridharan
- Quantitative Light Imaging Laboratory, Department of Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Mustafa Mir
- Quantitative Light Imaging Laboratory, Department of Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Arindam Chakraborty
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Rajashekar Iyer
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Supriya Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Larry Millet
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Biological and Nanoscale Systems Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Martha U. Gillette
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Neuroscience Program, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign IL 61801, USA
| | - Gabriel Popescu
- Quantitative Light Imaging Laboratory, Department of Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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168
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Pichon X, Bastide A, Safieddine A, Chouaib R, Samacoits A, Basyuk E, Peter M, Mueller F, Bertrand E. Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells. J Cell Biol 2016; 214:769-81. [PMID: 27597760 PMCID: PMC5021097 DOI: 10.1083/jcb.201605024] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 08/16/2016] [Indexed: 12/13/2022] Open
Abstract
Pichon et al. describe a method to visualize translation of single endogenous mRNPs in live cells and provide evidence for specialized translation factories, as well as measurements of translation elongation rate, ribosome loading, and movements of single polysomes. Translation is an essential step in gene expression. In this study, we used an improved SunTag system to label nascent proteins and image translation of single messenger ribonucleoproteins (mRNPs) in human cells. Using a dedicated reporter RNA, we observe that translation of single mRNPs stochastically turns on and off while they diffuse through the cytoplasm. We further measure a ribosome density of 1.3 per kilobase and an elongation rate of 13–18 amino acids per second. Tagging the endogenous POLR2A gene revealed similar elongation rates and ribosomal densities and that nearly all messenger RNAs (mRNAs) are engaged in translation. Remarkably, tagging of the heavy chain of dynein 1 (DYNC1H1) shows this mRNA accumulates in foci containing three to seven RNA molecules. These foci are translation sites and thus represent specialized translation factories. We also observe that DYNC1H1 polysomes are actively transported by motors, which may deliver the mature protein at appropriate cellular locations. The SunTag should be broadly applicable to study translational regulation in live single cells.
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Affiliation(s)
- Xavier Pichon
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Amandine Bastide
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Adham Safieddine
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Racha Chouaib
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Aubin Samacoits
- Unité Imagerie et Modélisation, Institut Pasteur, UMR3691, Centre National de la Recherche Scientifique, 75015 Paris, France
| | - Eugenia Basyuk
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Marion Peter
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
| | - Florian Mueller
- Unité Imagerie et Modélisation, Institut Pasteur, UMR3691, Centre National de la Recherche Scientifique, 75015 Paris, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS, 34293 Montpellier Cedex 5, France; Université de Montpellier, 34090 Montpellier, France
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169
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Carrell ST, Carrell EM, Auerbach D, Pandey SK, Bennett CF, Dirksen RT, Thornton CA. Dmpk gene deletion or antisense knockdown does not compromise cardiac or skeletal muscle function in mice. Hum Mol Genet 2016; 25:4328-4338. [PMID: 27522499 DOI: 10.1093/hmg/ddw266] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 11/13/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a genetic disorder in which dominant-active DM protein kinase (DMPK) transcripts accumulate in nuclear foci, leading to abnormal regulation of RNA processing. A leading approach to treat DM1 uses DMPK-targeting antisense oligonucleotides (ASOs) to reduce levels of toxic RNA. However, basal levels of DMPK protein are reduced by half in DM1 patients. This raises concern that intolerance for further DMPK loss may limit ASO therapy, especially since mice with Dmpk gene deletion reportedly show cardiac defects and skeletal myopathy. We re-examined cardiac and muscle function in mice with Dmpk gene deletion, and studied post-maturity knockdown using Dmpk-targeting ASOs in mice with heterozygous deletion. Contrary to previous reports, we found no effect of Dmpk gene deletion on cardiac or muscle function, when studied on two genetic backgrounds. In heterozygous knockouts, the administration of ASOs reduced Dmpk expression in cardiac and skeletal muscle by > 90%, yet survival, electrocardiogram intervals, cardiac ejection fraction and muscle strength remained normal. The imposition of cardiac stress by pressure overload, or muscle stress by myotonia, did not unmask a requirement for DMPK. Our results support the feasibility and safety of using ASOs for post-transcriptional silencing of DMPK in muscle and heart.
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Affiliation(s)
| | | | | | | | | | | | - Charles A Thornton
- Department of Neurology, University of Rochester, Rochester, New York, NY, USA and
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170
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Where are things inside a bacterial cell? Curr Opin Microbiol 2016; 33:83-90. [PMID: 27450542 DOI: 10.1016/j.mib.2016.07.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/21/2016] [Accepted: 07/06/2016] [Indexed: 01/13/2023]
Abstract
Bacterial cells are intricately organized, despite the lack of membrane-bounded organelles. The extremely crowded cytoplasm promotes macromolecular self-assembly and formation of distinct subcellular structures, which perform specialized functions. For example, the cell poles act as hubs for signal transduction complexes, thus providing a platform for the coordination of optimal cellular responses to environmental cues. Distribution of macromolecules is mostly mediated via specialized transport machineries, including the MreB cytoskeleton. Recent evidence shows that RNAs also specifically localize within bacterial cells, raising the possibility that gene expression is spatially organized. Here we review the current understanding of where things are in bacterial cells and discuss emerging questions that need to be addressed in the future.
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171
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Liu C, Liu YL, Perillo EP, Dunn AK, Yeh HC. Single-Molecule Tracking and Its Application in Biomolecular Binding Detection. IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS : A PUBLICATION OF THE IEEE LASERS AND ELECTRO-OPTICS SOCIETY 2016; 22:6804013. [PMID: 27660404 PMCID: PMC5028128 DOI: 10.1109/jstqe.2016.2568160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
In the past two decades significant advances have been made in single-molecule detection, which enables the direct observation of single biomolecules at work in real time and under physiological conditions. In particular, the development of single-molecule tracking (SMT) microscopy allows us to monitor the motion paths of individual biomolecules in living systems, unveiling the localization dynamics and transport modalities of the biomolecules that support the development of life. Beyond the capabilities of traditional camera-based tracking techniques, state-of-the-art SMT microscopies developed in recent years can record fluorescence lifetime while tracking a single molecule in the 3D space. This multiparameter detection capability can open the door to a wide range of investigations at the cellular or tissue level, including identification of molecular interaction hotspots and characterization of association/dissociation kinetics between molecules. In this review, we discuss various SMT techniques developed to date, with an emphasis on our recent development of the next generation 3D tracking system that not only achieves ultrahigh spatiotemporal resolution but also provides sufficient working depth suitable for live animal imaging. We also discuss the challenges that current SMT techniques are facing and the potential strategies to tackle those challenges.
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Affiliation(s)
- Cong Liu
- University of Texas at Austin, Austin, TX 78703 USA
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172
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Ben-Yishay R, Ashkenazy AJ, Shav-Tal Y. Dynamic Encounters of Genes and Transcripts with the Nuclear Pore. Trends Genet 2016; 32:419-431. [DOI: 10.1016/j.tig.2016.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 04/20/2016] [Indexed: 01/04/2023]
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173
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Ramanathan A, Robb GB, Chan SH. mRNA capping: biological functions and applications. Nucleic Acids Res 2016; 44:7511-26. [PMID: 27317694 PMCID: PMC5027499 DOI: 10.1093/nar/gkw551] [Citation(s) in RCA: 456] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/03/2016] [Indexed: 12/19/2022] Open
Abstract
The 5′ m7G cap is an evolutionarily conserved modification of eukaryotic mRNA. Decades of research have established that the m7G cap serves as a unique molecular module that recruits cellular proteins and mediates cap-related biological functions such as pre-mRNA processing, nuclear export and cap-dependent protein synthesis. Only recently has the role of the cap 2′O methylation as an identifier of self RNA in the innate immune system against foreign RNA has become clear. The discovery of the cytoplasmic capping machinery suggests a novel level of control network. These new findings underscore the importance of a proper cap structure in the synthesis of functional messenger RNA. In this review, we will summarize the current knowledge of the biological roles of mRNA caps in eukaryotic cells. We will also discuss different means that viruses and their host cells use to cap their RNA and the application of these capping machineries to synthesize functional mRNA. Novel applications of RNA capping enzymes in the discovery of new RNA species and sequencing the microbiome transcriptome will also be discussed. We will end with a summary of novel findings in RNA capping and the questions these findings pose.
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Affiliation(s)
- Anand Ramanathan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - G Brett Robb
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Siu-Hong Chan
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
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174
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Abstract
Septins are highly conserved cytoskeletal proteins involved in a variety of biological processes such as cell polarization and cytokinesis. In humans, functional defects in these proteins have been linked to cancer and neuronal diseases. In recent years, substantial progress has been made in studying the structure of septin subunits and the formation of defined heteromeric building blocks. These are assembled into higher-order structures at distinct subcellular sites. An important microscopic approach in studying septin assembly and dynamics is the use of septins tagged with fluorescent proteins. This revealed, eg, that septins form rings during cytokinesis and that septins build extended filaments partially colocalizing with actin cables and microtubules. Here, we describe extensive live cell imaging of septins in the model microorganism Ustilago maydis. We present techniques to study dynamic localization of protein and septin mRNA on shuttling endosomes as well as colocalization of proteins at these highly motile units. Moreover, FLIM-FRET experiments for analyzing local protein interactions are presented. Importantly, these imaging approaches transfer well to other fungal and animal model systems for in vivo analysis of septin dynamics.
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175
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Trcek T, Lionnet T, Shroff H, Lehmann R. mRNA quantification using single-molecule FISH in Drosophila embryos. Nat Protoc 2016; 12:1326-1348. [PMID: 28594816 DOI: 10.1038/nprot.2017.030] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Spatial information is critical to the interrogation of developmental and tissue-level regulation of gene expression. However, this information is usually lost when global mRNA levels from tissues are measured using reverse transcriptase PCR, microarray analysis or high-throughput sequencing. By contrast, single-molecule fluorescence in situ hybridization (smFISH) preserves the spatial information of the cellular mRNA content with subcellular resolution within tissues. Here we describe an smFISH protocol that allows for the quantification of single mRNAs in Drosophila embryos, using commercially available smFISH probes (e.g., short fluorescently labeled DNA oligonucleotides) in combination with wide-field epifluorescence, confocal or instant structured illumination microscopy (iSIM, a super-resolution imaging approach) and a spot-detection algorithm. Fixed Drosophila embryos are hybridized in solution with a mixture of smFISH probes, mounted onto coverslips and imaged in 3D. Individual fluorescently labeled mRNAs are then localized within tissues and counted using spot-detection software to generate quantitative, spatially resolved gene expression data sets. With minimum guidance, a graduate student can successfully implement this protocol. The smFISH procedure described here can be completed in 4-5 d.
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Affiliation(s)
- Tatjana Trcek
- Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, New York, USA
| | - Timothée Lionnet
- Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Ruth Lehmann
- Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, New York, USA
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176
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Morisaki T, Lyon K, DeLuca KF, DeLuca JG, English BP, Zhang Z, Lavis LD, Grimm JB, Viswanathan S, Looger LL, Lionnet T, Stasevich TJ. Real-time quantification of single RNA translation dynamics in living cells. Science 2016; 352:1425-9. [PMID: 27313040 DOI: 10.1126/science.aaf0899] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/28/2016] [Indexed: 12/14/2022]
Abstract
Although messenger RNA (mRNA) translation is a fundamental biological process, it has never been imaged in real time in vivo with single-molecule precision. To achieve this, we developed nascent chain tracking (NCT), a technique that uses multi-epitope tags and antibody-based fluorescent probes to quantify protein synthesis dynamics at the single-mRNA level. NCT reveals an elongation rate of ~10 amino acids per second, with initiation occurring stochastically every ~30 seconds. Polysomes contain ~1 ribosome every 200 to 900 nucleotides and are globular rather than elongated in shape. By developing multicolor probes, we showed that most polysomes act independently; however, a small fraction (~5%) form complexes in which two distinct mRNAs can be translated simultaneously. The sensitivity and versatility of NCT make it a powerful new tool for quantifying mRNA translation kinetics.
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Affiliation(s)
- Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
| | - Kenneth Lyon
- Department of Biochemistry and Molecular Biology and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
| | - Keith F DeLuca
- Department of Biochemistry and Molecular Biology and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
| | - Jennifer G DeLuca
- Department of Biochemistry and Molecular Biology and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
| | - Brian P English
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Zhengjian Zhang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Sarada Viswanathan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Timothee Lionnet
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
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177
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Wang C, Han B, Zhou R, Zhuang X. Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells. Cell 2016; 165:990-1001. [PMID: 27153499 PMCID: PMC4905760 DOI: 10.1016/j.cell.2016.04.040] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/07/2016] [Accepted: 04/15/2016] [Indexed: 10/21/2022]
Abstract
Translation is under tight spatial and temporal controls to ensure protein production in the right time and place in cells. Methods that allow real-time, high-resolution visualization of translation in live cells are essential for understanding the spatiotemporal dynamics of translation regulation. Based on multivalent fluorescence amplification of the nascent polypeptide signal, we develop a method to image translation on individual mRNA molecules in real time in live cells, allowing direct visualization of translation events at the translation sites. Using this approach, we monitor transient changes of translation dynamics in responses to environmental stresses, capture distinct mobilities of individual polysomes in different subcellular compartments, and detect 3' UTR-dependent local translation and active transport of polysomes in dendrites of primary neurons.
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Affiliation(s)
- Chong Wang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Boran Han
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Ruobo Zhou
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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178
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Wu B, Eliscovich C, Yoon YJ, Singer RH. Translation dynamics of single mRNAs in live cells and neurons. Science 2016; 352:1430-5. [PMID: 27313041 DOI: 10.1126/science.aaf1084] [Citation(s) in RCA: 321] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/28/2016] [Indexed: 12/17/2022]
Abstract
Translation is the fundamental biological process converting mRNA information into proteins. Single-molecule imaging in live cells has illuminated the dynamics of RNA transcription; however, it is not yet applicable to translation. Here, we report single-molecule imaging of nascent peptides (SINAPS) to assess translation in live cells. The approach provides direct readout of initiation, elongation, and location of translation. We show that mRNAs coding for endoplasmic reticulum (ER) proteins are translated when they encounter the ER membrane. Single-molecule fluorescence recovery after photobleaching provides direct measurement of elongation speed (5 amino acids per second). In primary neurons, mRNAs are translated in proximal dendrites but repressed in distal dendrites and display "bursting" translation. This technology provides a tool with which to address the spatiotemporal translation mechanism of single mRNAs in living cells.
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Affiliation(s)
- Bin Wu
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA. Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Carolina Eliscovich
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Young J Yoon
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA. Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA. Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA. Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA. Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA 20147, USA.
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179
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Yan X, Hoek TA, Vale RD, Tanenbaum ME. Dynamics of Translation of Single mRNA Molecules In Vivo. Cell 2016; 165:976-89. [PMID: 27153498 PMCID: PMC4889334 DOI: 10.1016/j.cell.2016.04.034] [Citation(s) in RCA: 291] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/04/2016] [Accepted: 04/11/2016] [Indexed: 11/16/2022]
Abstract
Regulation of mRNA translation, the process by which ribosomes decode mRNAs into polypeptides, is used to tune cellular protein levels. Currently, methods for observing the complete process of translation from single mRNAs in vivo are unavailable. Here, we report the long-term (>1 hr) imaging of single mRNAs undergoing hundreds of rounds of translation in live cells, enabling quantitative measurements of ribosome initiation, elongation, and stalling. This approach reveals a surprising heterogeneity in the translation of individual mRNAs within the same cell, including rapid and reversible transitions between a translating and non-translating state. Applying this method to the cell-cycle gene Emi1, we find strong overall repression of translation initiation by specific 5' UTR sequences, but individual mRNA molecules in the same cell can exhibit dramatically different translational efficiencies. The ability to observe translation of single mRNA molecules in live cells provides a powerful tool to study translation regulation.
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Affiliation(s)
- Xiaowei Yan
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158-2517, USA
| | - Tim A Hoek
- Hubrecht Institute, The Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht 3584CT, the Netherlands
| | - Ronald D Vale
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158-2517, USA
| | - Marvin E Tanenbaum
- Hubrecht Institute, The Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht 3584CT, the Netherlands.
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180
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Halstead JM, Wilbertz JH, Wippich F, Lionnet T, Ephrussi A, Chao JA. TRICK: A Single-Molecule Method for Imaging the First Round of Translation in Living Cells and Animals. Methods Enzymol 2016; 572:123-57. [PMID: 27241753 DOI: 10.1016/bs.mie.2016.02.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
The life of an mRNA is dynamic within a cell. The development of quantitative fluorescent microscopy techniques to image single molecules of RNA has allowed many aspects of the mRNA lifecycle to be directly observed in living cells. Recent advances in live-cell multicolor RNA imaging, however, have now made it possible to investigate RNA metabolism in greater detail. In this chapter, we present an overview of the design and implementation of the translating RNA imaging by coat protein knockoff RNA biosensor, which allows untranslated mRNAs to be distinguished from ones that have undergone a round of translation. The methods required for establishing this system in mammalian cell lines and Drosophila melanogaster oocytes are described here, but the principles may be applied to any experimental system.
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Affiliation(s)
- J M Halstead
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - J H Wilbertz
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - F Wippich
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - T Lionnet
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA, United States
| | - A Ephrussi
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - J A Chao
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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181
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Battich N, Stoeger T, Pelkmans L. Control of Transcript Variability in Single Mammalian Cells. Cell 2016; 163:1596-610. [PMID: 26687353 DOI: 10.1016/j.cell.2015.11.018] [Citation(s) in RCA: 229] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 10/08/2015] [Accepted: 11/04/2015] [Indexed: 11/17/2022]
Abstract
A central question in biology is whether variability between genetically identical cells exposed to the same culture conditions is largely stochastic or deterministic. Using image-based transcriptomics in millions of single human cells, we find that while variability of cytoplasmic transcript abundance is large, it is for most genes minimally stochastic and can be predicted with multivariate models of the phenotypic state and population context of single cells. Computational multiplexing of these predictive signatures across hundreds of genes revealed a complex regulatory system that controls the observed variability of transcript abundance between individual cells. Mathematical modeling and experimental validation show that nuclear retention and transport of transcripts between the nucleus and the cytoplasm is central to buffering stochastic transcriptional fluctuations in mammalian gene expression. Our work indicates that cellular compartmentalization confines transcriptional noise to the nucleus, thereby preventing it from interfering with the control of single-cell transcript abundance in the cytoplasm.
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Affiliation(s)
- Nico Battich
- Faculty of Sciences, Institute of Molecular Life Sciences, University of Zurich, 8006 Zurich, Switzerland; Systems Biology PhD Program, Life Science Zurich Graduate School, ETH Zurich and University of Zurich, 8057 Zurich, Switzerland
| | - Thomas Stoeger
- Faculty of Sciences, Institute of Molecular Life Sciences, University of Zurich, 8006 Zurich, Switzerland; Systems Biology PhD Program, Life Science Zurich Graduate School, ETH Zurich and University of Zurich, 8057 Zurich, Switzerland
| | - Lucas Pelkmans
- Faculty of Sciences, Institute of Molecular Life Sciences, University of Zurich, 8006 Zurich, Switzerland.
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182
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Abstract
Recent live-cell microscopy techniques now allow the visualization in multiple colors of RNAs as they are transcribed on genes of interest. Following the number of nascent RNAs over time at a single locus reveals complex fluctuations originating from the underlying transcriptional kinetics. We present here a technique based on concepts from signal theory-called fluctuation analysis-to analyze and interpret multicolor transcriptional time traces and extract the temporal signatures of the underlying mechanisms. The principle is to generate, from the time traces, a set of functions called correlation functions. We explain how to compute these functions practically from a set of experimental traces and how to interpret them through different theoretical and computational means. We also present the major difficulties and pitfalls one might encounter with this technique. This approach is capable of extracting mechanistic information hidden in transcriptional fluctuations at multiple timescales and has broad applications for understanding transcriptional kinetics.
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183
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Hellens RP, Brown CM, Chisnall MAW, Waterhouse PM, Macknight RC. The Emerging World of Small ORFs. TRENDS IN PLANT SCIENCE 2016; 21:317-328. [PMID: 26684391 DOI: 10.1016/j.tplants.2015.11.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/23/2015] [Accepted: 11/05/2015] [Indexed: 05/10/2023]
Abstract
Small open reading frames (sORFs) are an often overlooked feature of plant genomes. Initially found in plant viral RNAs and considered an interesting curiosity, an increasing number of these sORFs have been shown to encode functional peptides or play a regulatory role. The recent discovery that many of these sORFs initiate with start codons other than AUG, together with the identification of functional small peptides encoded in supposedly noncoding primary miRNA transcripts (pri-miRs), has drastically increased the number of potentially functional sORFs within the genome. Here we review how advances in technology, notably ribosome profiling (RP) assays, are complementing bioinformatics and proteogenomic methods to provide powerful ways to identify these elusive features of plant genomes, and highlight the regulatory roles sORFs can play.
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Affiliation(s)
- Roger P Hellens
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia
| | - Chris M Brown
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Matthew A W Chisnall
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter M Waterhouse
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia
| | - Richard C Macknight
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand; New Zealand Institute for Plant and Food Research Ltd.
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184
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Abbaszadeh EK, Gavis ER. Fixed and live visualization of RNAs in Drosophila oocytes and embryos. Methods 2016; 98:34-41. [PMID: 26827935 PMCID: PMC4808400 DOI: 10.1016/j.ymeth.2016.01.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 01/23/2016] [Accepted: 01/27/2016] [Indexed: 12/21/2022] Open
Abstract
The ability to visualize RNA in situ is essential to dissect mechanisms for the temporal and spatial regulation of gene expression that drives development. Although considerable attention has been focused on transcriptional control, studies in model organisms like Drosophila have highlighted the importance of post-transcriptional mechanisms - most notably intracellular mRNA localization - in the formation and patterning of the body axes, specification of cell fates, and polarized cell functions. Our understanding of both types of regulation has been greatly advanced by technological innovations that enable a combination of highly quantitative and dynamic analysis of RNA. This review presents two methods, single molecule fluorescence in situ hybridization for high resolution quantitative RNA detection in fixed Drosophila oocytes and embryos and genetically encoded fluorescent RNA labeling for detection in live cells.
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Affiliation(s)
- Evan K Abbaszadeh
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
| | - Elizabeth R Gavis
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States.
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185
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Lampasona AA, Czaplinski K. RNA voyeurism: A coming of age story. Methods 2016; 98:10-17. [DOI: 10.1016/j.ymeth.2015.11.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 10/22/2022] Open
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186
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Hogstrom LJ, Guo SM, Murugadoss K, Bathe M. Advancing multiscale structural mapping of the brain through fluorescence imaging and analysis across length scales. Interface Focus 2016; 6:20150081. [PMID: 26855758 DOI: 10.1098/rsfs.2015.0081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Brain function emerges from hierarchical neuronal structure that spans orders of magnitude in length scale, from the nanometre-scale organization of synaptic proteins to the macroscopic wiring of neuronal circuits. Because the synaptic electrochemical signal transmission that drives brain function ultimately relies on the organization of neuronal circuits, understanding brain function requires an understanding of the principles that determine hierarchical neuronal structure in living or intact organisms. Recent advances in fluorescence imaging now enable quantitative characterization of neuronal structure across length scales, ranging from single-molecule localization using super-resolution imaging to whole-brain imaging using light-sheet microscopy on cleared samples. These tools, together with correlative electron microscopy and magnetic resonance imaging at the nanoscopic and macroscopic scales, respectively, now facilitate our ability to probe brain structure across its full range of length scales with cellular and molecular specificity. As these imaging datasets become increasingly accessible to researchers, novel statistical and computational frameworks will play an increasing role in efforts to relate hierarchical brain structure to its function. In this perspective, we discuss several prominent experimental advances that are ushering in a new era of quantitative fluorescence-based imaging in neuroscience along with novel computational and statistical strategies that are helping to distil our understanding of complex brain structure.
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Affiliation(s)
- L J Hogstrom
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue, Building 16, Room 255, Cambridge, MA 02139 , USA
| | - S M Guo
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue, Building 16, Room 255, Cambridge, MA 02139 , USA
| | - K Murugadoss
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue, Building 16, Room 255, Cambridge, MA 02139 , USA
| | - M Bathe
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue, Building 16, Room 255, Cambridge, MA 02139 , USA
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187
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Bensidoun P, Raymond P, Oeffinger M, Zenklusen D. Imaging single mRNAs to study dynamics of mRNA export in the yeast Saccharomyces cerevisiae. Methods 2016; 98:104-114. [PMID: 26784711 DOI: 10.1016/j.ymeth.2016.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 01/08/2023] Open
Abstract
Regulation of mRNA and protein expression occurs at many levels, initiated at transcription and followed by mRNA processing, export, localization, translation and mRNA degradation. The ability to study mRNAs in living cells has become a critical tool to study and analyze how the various steps of the gene expression pathway are carried out. Here we describe a detailed protocol for real time fluorescent RNA imaging using the PP7 bacteriophage coat protein, which allows mRNA detection with high spatial and temporal resolution in the yeast Saccharomyces cerevisiae, and can be applied to study various stages of mRNA metabolism. We describe the different parameters required for quantitative single molecule imaging in yeast, including strategies for genomic integration, expression of a PP7 coat protein GFP fusion protein, microscope setup and analysis strategies. We illustrate the method's use by analyzing the behavior of nuclear mRNA in yeast and the role of the nuclear basket in mRNA export.
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Affiliation(s)
- Pierre Bensidoun
- Département de Biochimieet médecine moléculaire, Faculté de médecine, Université de Montréal, Montréal, Québec H3C 3J7, Canada; Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
| | - Pascal Raymond
- Département de Biochimieet médecine moléculaire, Faculté de médecine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Marlene Oeffinger
- Département de Biochimieet médecine moléculaire, Faculté de médecine, Université de Montréal, Montréal, Québec H3C 3J7, Canada; Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada; Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
| | - Daniel Zenklusen
- Département de Biochimieet médecine moléculaire, Faculté de médecine, Université de Montréal, Montréal, Québec H3C 3J7, Canada.
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188
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Katz ZB, English BP, Lionnet T, Yoon YJ, Monnier N, Ovryn B, Bathe M, Singer RH. Mapping translation 'hot-spots' in live cells by tracking single molecules of mRNA and ribosomes. eLife 2016; 5. [PMID: 26760529 PMCID: PMC4764586 DOI: 10.7554/elife.10415] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 12/29/2015] [Indexed: 11/13/2022] Open
Abstract
Messenger RNA localization is important for cell motility by local protein translation. However, while single mRNAs can be imaged and their movements tracked in single cells, it has not yet been possible to determine whether these mRNAs are actively translating. Therefore, we imaged single β-actin mRNAs tagged with MS2 stem loops colocalizing with labeled ribosomes to determine when polysomes formed. A dataset of tracking information consisting of thousands of trajectories per cell demonstrated that mRNAs co-moving with ribosomes have significantly different diffusion properties from non-translating mRNAs that were exposed to translation inhibitors. These data indicate that ribosome load changes mRNA movement and therefore highly translating mRNAs move slower. Importantly, β-actin mRNA near focal adhesions exhibited sub-diffusive corralled movement characteristic of increased translation. This method can identify where ribosomes become engaged for local protein production and how spatial regulation of mRNA-protein interactions mediates cell directionality.
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Affiliation(s)
- Zachary B Katz
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, United States.,Salk Institute for Biological Studies, La Jolla, United States
| | - Brian P English
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, United States.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Timothée Lionnet
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Young J Yoon
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, United States
| | - Nilah Monnier
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Ben Ovryn
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, United States.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
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189
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Proteostasis and RNA Binding Proteins in Synaptic Plasticity and in the Pathogenesis of Neuropsychiatric Disorders. Neural Plast 2016; 2016:3857934. [PMID: 26904297 PMCID: PMC4745388 DOI: 10.1155/2016/3857934] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/30/2015] [Indexed: 12/30/2022] Open
Abstract
Decades of research have demonstrated that rapid alterations in protein abundance are required for synaptic plasticity, a cellular correlate for learning and memory. Control of protein abundance, known as proteostasis, is achieved across a complex neuronal morphology that includes a tortuous axon as well as an extensive dendritic arbor supporting thousands of individual synaptic compartments. To regulate the spatiotemporal synthesis of proteins, neurons must efficiently coordinate the transport and metabolism of mRNAs. Among multiple levels of regulation, transacting RNA binding proteins (RBPs) control proteostasis by binding to mRNAs and mediating their transport and translation in response to synaptic activity. In addition to synthesis, protein degradation must be carefully balanced for optimal proteostasis, as deviations resulting in excess or insufficient abundance of key synaptic factors produce pathologies. As such, mutations in components of the proteasomal or translational machinery, including RBPs, have been linked to the pathogenesis of neurological disorders such as Fragile X Syndrome (FXS), Fragile X Tremor Ataxia Syndrome (FXTAS), and Autism Spectrum Disorders (ASD). In this review, we summarize recent scientific findings, highlight ongoing questions, and link basic molecular mechanisms to the pathogenesis of common neuropsychiatric disorders.
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190
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Bergeman J, Caillier A, Houle F, Gagné LM, Huot MÉ. Localized translation regulates cell adhesion and transendothelial migration. J Cell Sci 2016; 129:4105-4117. [DOI: 10.1242/jcs.191320] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/08/2016] [Indexed: 12/31/2022] Open
Abstract
By progressing through the epithelial to mesenchymal transition (EMT), cancer cells gain the ability to leave the primary tumor site and invade surrounding tissues. These metastatic cancers cells can further increase their plasticity by adopting an amoeboid-like morphology, by undergoing mesenchymal to amoeboid transition (MAT). We found that adhering cells producing spreading initiation centers (SIC), a transient structure localized above nascent adhesion complexes, share common biological and morphological characteristics associated with amoeboid cells. Meanwhile, spreading cells seem to return to a mesenchymal-like morphology. Thus, our results indicate that SIC-induced adhesion recapitulate events associated with amoeboid to mesenchymal transition (AMT). We found that polyadenylated RNAs were enriched within SIC and blocking their translation decreased adhesion potential of metastatic cells that progressed through EMT. These results point to a novel checkpoint regulating cell adhesion and allowing metastatic cells to alter adhesion strength in order to modulate their dissemination.
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Affiliation(s)
- Jonathan Bergeman
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, Canada, G1R 3S3
| | - Alexia Caillier
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, Canada, G1R 3S3
| | - François Houle
- CRCHU de Québec: Hôtel-Dieu de Québec; Québec, Canada, G1R 3S3
| | - Laurence M. Gagné
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, Canada, G1R 3S3
| | - Marc-Étienne Huot
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, Canada, G1R 3S3
- CRCHU de Québec: Hôtel-Dieu de Québec; Québec, Canada, G1R 3S3
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191
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Chu Z, Li L, Liu G, Jin W. A novel membrane with heterogeneously functionalized nanocrystal layers performing blood separation and sensing synchronously. Chem Commun (Camb) 2016; 52:12706-12709. [DOI: 10.1039/c6cc05334c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel membrane can synchronously perform blood separation and sensing for serum extraction and analysis of various physiological indexes.
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Affiliation(s)
- Zhenyu Chu
- State Key Laboratory of Materials-Oriented Chemical Engineering
- Jiangsu National Synergetic Innovation Center for Advanced Materials
- College of Chemical Engineering
- Nanjing Tech University
- Nanjing 210009
| | - Linlin Li
- State Key Laboratory of Materials-Oriented Chemical Engineering
- Jiangsu National Synergetic Innovation Center for Advanced Materials
- College of Chemical Engineering
- Nanjing Tech University
- Nanjing 210009
| | - Gongping Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering
- Jiangsu National Synergetic Innovation Center for Advanced Materials
- College of Chemical Engineering
- Nanjing Tech University
- Nanjing 210009
| | - Wanqin Jin
- State Key Laboratory of Materials-Oriented Chemical Engineering
- Jiangsu National Synergetic Innovation Center for Advanced Materials
- College of Chemical Engineering
- Nanjing Tech University
- Nanjing 210009
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192
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Li S, Xu L, Ma W, Wu X, Sun M, Kuang H, Wang L, Kotov NA, Xu C. Dual-Mode Ultrasensitive Quantification of MicroRNA in Living Cells by Chiroplasmonic Nanopyramids Self-Assembled from Gold and Upconversion Nanoparticles. J Am Chem Soc 2015; 138:306-12. [DOI: 10.1021/jacs.5b10309] [Citation(s) in RCA: 345] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Si Li
- State
Key Lab of Food Science and Technology, International Joint Research
Laboratory for Biointerface and Biodetection, School of Food Science
and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Liguang Xu
- State
Key Lab of Food Science and Technology, International Joint Research
Laboratory for Biointerface and Biodetection, School of Food Science
and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Wei Ma
- State
Key Lab of Food Science and Technology, International Joint Research
Laboratory for Biointerface and Biodetection, School of Food Science
and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Xiaoling Wu
- State
Key Lab of Food Science and Technology, International Joint Research
Laboratory for Biointerface and Biodetection, School of Food Science
and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Maozhong Sun
- State
Key Lab of Food Science and Technology, International Joint Research
Laboratory for Biointerface and Biodetection, School of Food Science
and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Hua Kuang
- State
Key Lab of Food Science and Technology, International Joint Research
Laboratory for Biointerface and Biodetection, School of Food Science
and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Libing Wang
- State
Key Lab of Food Science and Technology, International Joint Research
Laboratory for Biointerface and Biodetection, School of Food Science
and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Nicholas A. Kotov
- Department
of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2136, United States
| | - Chuanlai Xu
- State
Key Lab of Food Science and Technology, International Joint Research
Laboratory for Biointerface and Biodetection, School of Food Science
and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
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193
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Methods for studying RNA localization in bacteria. Methods 2015; 98:99-103. [PMID: 26707207 DOI: 10.1016/j.ymeth.2015.12.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/13/2015] [Accepted: 12/15/2015] [Indexed: 11/24/2022] Open
Abstract
The subcellular localization of RNA transcripts provides important insights into biological processes. Hence, understanding the mechanisms underlying RNA targeting is a high priority aim of modern cell biology. The advancements in imaging techniques, such as in situ hybridization and live-cell imaging, coupled with the evolution in optical microscopy led to the discovery that bacterial RNAs, despite the lack of nucleus, are specifically localized. Here we describe the methods used to study RNA localization in bacteria and their applications and discuss their advantages and limitations.
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194
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Mardakheh FK, Paul A, Kümper S, Sadok A, Paterson H, Mccarthy A, Yuan Y, Marshall CJ. Global Analysis of mRNA, Translation, and Protein Localization: Local Translation Is a Key Regulator of Cell Protrusions. Dev Cell 2015; 35:344-57. [PMID: 26555054 PMCID: PMC4643311 DOI: 10.1016/j.devcel.2015.10.005] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 08/23/2015] [Accepted: 10/08/2015] [Indexed: 12/12/2022]
Abstract
Polarization of cells into a protrusive front and a retracting cell body is the hallmark of mesenchymal-like cell migration. Many mRNAs are localized to protrusions, but it is unclear to what degree mRNA localization contributes toward protrusion formation. We performed global quantitative analysis of the distributions of mRNAs, proteins, and translation rates between protrusions and the cell body by RNA sequencing (RNA-seq) and quantitative proteomics. Our results reveal local translation as a key determinant of protein localization to protrusions. Accordingly, inhibition of local translation destabilizes protrusions and inhibits mesenchymal-like morphology. Interestingly, many mRNAs localized to protrusions are translationally repressed. Specific cis-regulatory elements within mRNA UTRs define whether mRNAs are locally translated or repressed. Finally, RNAi screening of RNA-binding proteins (RBPs) enriched in protrusions revealed trans-regulators of localized translation that are functionally important for protrusions. We propose that by deciphering the localized mRNA UTR code, these proteins regulate protrusion stability and mesenchymal-like morphology.
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Affiliation(s)
- Faraz K Mardakheh
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
| | - Angela Paul
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Sandra Kümper
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Amine Sadok
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Hugh Paterson
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Afshan Mccarthy
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Yinyin Yuan
- Division of Molecular Pathology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Christopher J Marshall
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
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195
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Translation in the mammalian oocyte in space and time. Cell Tissue Res 2015; 363:69-84. [PMID: 26340983 DOI: 10.1007/s00441-015-2269-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 08/03/2015] [Indexed: 02/07/2023]
Abstract
A hallmark of oocyte development in mammals is the dependence on the translation and utilization of stored RNA and proteins rather than the de novo transcription of genes in order to sustain meiotic progression and early embryo development. In the absence of transcription, the completion of meiosis and early embryo development in mammals relies significantly on maternally synthesized RNAs. Post-transcriptional control of gene expression at the translational level has emerged as an important cellular function in normal development. Therefore, the regulation of gene expression in oocytes is controlled almost exclusively at the level of mRNA and protein stabilization and protein synthesis. This current review is focused on the recently emerged findings on RNA distribution related to the temporal and spatial translational control of the meiotic progression of the mammalian oocyte.
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196
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Lu YJ, Deng Q, Hu DP, Wang ZY, Huang BH, Du ZY, Fang YX, Wong WL, Zhang K, Chow CF. A molecular fluorescent dye for specific staining and imaging of RNA in live cells: a novel ligand integration from classical thiazole orange and styryl compounds. Chem Commun (Camb) 2015; 51:15241-4. [PMID: 26329127 DOI: 10.1039/c5cc05551b] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A new RNA-selective fluorescent dye integrated with a thiazole orange and a p-(methylthio)styryl moiety shows better nucleolus RNA staining and imaging performance in live cells than the commercial stains. It also exhibits excellent photostability, cell tolerance, and counterstain compatibility with 4',6-diamidino-2-phenylindole for specific RNA-DNA colocalization in bioassays.
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Affiliation(s)
- Yu-Jing Lu
- Institute of Natural Medicine and Green Chemistry, School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, P. R. China.
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197
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Abdi K, Singh NJ. Making many from few: IL-12p40 as a model for the combinatorial assembly of heterodimeric cytokines. Cytokine 2015; 76:53-7. [PMID: 26242928 DOI: 10.1016/j.cyto.2015.07.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 07/28/2015] [Accepted: 07/29/2015] [Indexed: 12/20/2022]
Abstract
How dendritic cells (DCs) gather information from the local milieu at a site of infection or injury and communicate this to influence adaptive immunity is not well understood. We and others have reported that soon after microbial encounter, DCs secrete the p40 subunit of IL-12, by itself, in a monomeric form. Based on recent data that this p40 monomer subsequently associates with p35 released from other cells to generate functional IL-12, we proposed that p40 can function as a DC-derived probe which samples the composition of the local milieu by looking for other binding partners. In this opinion, we discuss how such a sampling function might generate an elaborate combinatorial "code" of heterodimeric cytokines, capable of conveying location-specific information to cells downstream of DC activation, including NK and T cells.
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Affiliation(s)
- Kaveh Abdi
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Twinbrook II 12441 Parklawn Dr., Rockville, MD 20852, United States
| | - Nevil J Singh
- Department of Microbiology & Immunology, University of Maryland School of Medicine, 685 W Baltimore St, HSF1, Room 380, Baltimore, MD 21201, United States.
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198
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A TRICK for studying translation. Nat Methods 2015. [DOI: 10.1038/nmeth.3381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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199
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Affiliation(s)
- Maximilian W Popp
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA, Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA, Center for RNA Biology, University of Rochester, Rochester, NY, USA.
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200
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Spille JH, Kubitscheck U. Labelling and imaging of single endogenous messenger RNA particles in vivo. J Cell Sci 2015; 128:3695-706. [DOI: 10.1242/jcs.166728] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
ABSTRACT
RNA molecules carry out widely diverse functions in numerous different physiological processes in living cells. The RNA life cycle from transcription, through the processing of nascent RNA, to the regulatory function of non-coding RNA and cytoplasmic translation of messenger RNA has been studied extensively using biochemical and molecular biology techniques. In this Commentary, we highlight how single molecule imaging and particle tracking can yield further insight into the dynamics of RNA particles in living cells. In the past few years, a variety of bright and photo-stable labelling techniques have been developed to generate sufficient contrast for imaging of single endogenous RNAs in vivo. New imaging modalities allow determination of not only lateral but also axial positions with high precision within the cellular context, and across a wide range of specimen from yeast and bacteria to cultured cells, and even multicellular organisms or live animals. A whole range of methods to locate and track single particles, and to analyze trajectory data are available to yield detailed information about the kinetics of all parts of the RNA life cycle. Although the concepts presented are applicable to all types of RNA, we showcase here the wealth of information gained from in vivo imaging of single particles by discussing studies investigating dynamics of intranuclear trafficking, nuclear pore transport and cytoplasmic transport of endogenous messenger RNA.
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Affiliation(s)
- Jan-Hendrik Spille
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegeler Str. 12, Bonn 53115, Germany
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegeler Str. 12, Bonn 53115, Germany
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