1
|
Patange S, Ball DA, Karpova TS, Larson DR. Towards a 'Spot On' Understanding of Transcription in the Nucleus. J Mol Biol 2021; 433:167016. [PMID: 33951451 PMCID: PMC8184600 DOI: 10.1016/j.jmb.2021.167016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/16/2021] [Accepted: 04/22/2021] [Indexed: 11/29/2022]
Abstract
Regulation of transcription by RNA Polymerase II (RNAPII) is a rapidly evolving area of research. Technological developments in microscopy have revealed insight into the dynamics, structure, and localization of transcription components within single cells. A frequent observation in many studies is the appearance of 'spots' in cell nuclei associated with the transcription process. In this review we highlight studies that characterize the temporal and spatial characteristics of these spots, examine possible pitfalls in interpreting these kind of imaging data, and outline directions where single-cell imaging may advance in ways to further our understanding of transcription regulation.
Collapse
Affiliation(s)
- Simona Patange
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - David A Ball
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Tatiana S Karpova
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States.
| |
Collapse
|
2
|
Back to the Future: Genetically Encoded Fluorescent Proteins as Inert Tracers of the Intracellular Environment. Int J Mol Sci 2020; 21:ijms21114164. [PMID: 32545175 PMCID: PMC7312867 DOI: 10.3390/ijms21114164] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 01/08/2023] Open
Abstract
Over the past decades, the discovery and development of genetically encoded fluorescent proteins (FPs) has brought a revolution into our ability to study biologic phenomena directly within living matter. First, FPs enabled fluorescence-labeling of a variety of molecules of interest to study their localization, interactions and dynamic behavior at various scales-from cells to whole organisms/animals. Then, rationally engineered FP-based sensors facilitated the measurement of physicochemical parameters of living matter-especially at the intracellular level, such as ion concentration, temperature, viscosity, pressure, etc. In addition, FPs were exploited as inert tracers of the intracellular environment in which they are expressed. This oft-neglected role is made possible by two distinctive features of FPs: (i) the quite null, unspecific interactions of their characteristic β-barrel structure with the molecular components of the cellular environment; and (ii) their compatibility with the use of time-resolved fluorescence-based optical microscopy techniques. This review seeks to highlight the potential of such unique combinations of properties and report on the most significative and original applications (and related advancements of knowledge) produced to date. It is envisioned that the use of FPs as inert tracers of living matter structural organization holds a potential for several lines of further development in the next future, discussed in the last section of the review, which in turn can lead to new breakthroughs in bioimaging.
Collapse
|
3
|
Donovan BT, Huynh A, Ball DA, Patel HP, Poirier MG, Larson DR, Ferguson ML, Lenstra TL. Live-cell imaging reveals the interplay between transcription factors, nucleosomes, and bursting. EMBO J 2019; 38:embj.2018100809. [PMID: 31101674 DOI: 10.15252/embj.2018100809] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 04/12/2019] [Accepted: 04/25/2019] [Indexed: 12/19/2022] Open
Abstract
Transcription factors show rapid and reversible binding to chromatin in living cells, and transcription occurs in sporadic bursts, but how these phenomena are related is unknown. Using a combination of in vitro and in vivo single-molecule imaging approaches, we directly correlated binding of the Gal4 transcription factor with the transcriptional bursting kinetics of the Gal4 target genes GAL3 and GAL10 in living yeast cells. We find that Gal4 dwell time sets the transcriptional burst size. Gal4 dwell time depends on the affinity of the binding site and is reduced by orders of magnitude by nucleosomes. Using a novel imaging platform called orbital tracking, we simultaneously tracked transcription factor binding and transcription at one locus, revealing the timing and correlation between Gal4 binding and transcription. Collectively, our data support a model in which multiple RNA polymerases initiate transcription during one burst as long as the transcription factor is bound to DNA, and bursts terminate upon transcription factor dissociation.
Collapse
Affiliation(s)
- Benjamin T Donovan
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Anh Huynh
- Department of Physics, Boise State University, Boise, ID, USA
| | - David A Ball
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Heta P Patel
- Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michael G Poirier
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA.,Departments of Physics, Chemistry & Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Matthew L Ferguson
- Department of Physics, Boise State University, Boise, ID, USA .,Biomolecular Sciences, Boise State University, Boise, ID, USA
| | - Tineke L Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| |
Collapse
|
4
|
Ruba A, Luo W, Yang W. Application of High-speed Super-resolution SPEED Microscopy in Live Primary Cilium. J Vis Exp 2018. [PMID: 29364223 DOI: 10.3791/56475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The primary cilium is a microtubule-based protrusion on the surface of many eukaryotic cells and contains a unique complement of proteins that function critically in cell motility and signaling. Since cilia are incapable of synthesizing their own protein, nearly 200 unique ciliary proteins need to be trafficked between the cytosol and primary cilia. However, it is still a technical challenge to map three-dimensional (3D) locations of transport pathways for these proteins in live primary cilia due to the limitations of currently existing techniques. To conquer the challenge, recently we have developed and employed a high-speed virtual 3D super-resolution microscopy, termed single-point edge-excitation sub-diffraction (SPEED) microscopy, to determine the 3D spatial location of transport pathways for both cytosolic and membrane proteins in primary cilia of live cells. In this article, we will demonstrate the detailed setup of SPEED microscopy, the preparation of cells expressing fluorescence-protein-labeled ciliary proteins, the real-time single-molecule tracking of individual proteins in live cilium and the achievement of 3D spatial probability density maps of transport routes for ciliary proteins.
Collapse
Affiliation(s)
| | - Wangxi Luo
- Department of Biology, Temple University
| | | |
Collapse
|
5
|
Mapping the Dynamics of the Glucocorticoid Receptor within the Nuclear Landscape. Sci Rep 2017; 7:6219. [PMID: 28740156 PMCID: PMC5524710 DOI: 10.1038/s41598-017-06676-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/15/2017] [Indexed: 12/28/2022] Open
Abstract
The distribution of the transcription machinery among different sub-nuclear domains raises the question on how the architecture of the nucleus modulates the transcriptional response. Here, we used fluorescence fluctuation analyses to quantitatively explore the organization of the glucocorticoid receptor (GR) in the interphase nucleus of living cells. We found that this ligand-activated transcription factor diffuses within the nucleus and dynamically interacts with bodies enriched in the coregulator NCoA-2, DNA-dependent foci and chromatin targets. The distribution of the receptor among the nuclear compartments depends on NCoA-2 and the conformation of the receptor as assessed with synthetic ligands and GR mutants with impaired transcriptional abilities. Our results suggest that the partition of the receptor in different nuclear reservoirs ultimately regulates the concentration of receptor available for the interaction with specific targets, and thus has an impact on transcription regulation.
Collapse
|
6
|
Porcaro F, Miao Y, Kota R, Haun J, Polzonetti G, Battocchio C, Gratton E. Fluctuation Spectroscopy Analysis of Glucose Capped Gold Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:13409-13417. [PMID: 27935716 PMCID: PMC5470844 DOI: 10.1021/acs.langmuir.6b02545] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this work, we report the synthesis and biophysical studies carried out on a new kind of biocompatible and very stable gold nanoparticle (GNP) stabilized with glucose through a PEG linker (AuNP-PEG-Glu). The synthetic path was optimized to obtain nanoparticles of controlled sizes. ζ-potential and dynamic light scattering measurements allowed assessment of the nanodimension, dispersity, surface charge, and stability of our GNPs. Confocal microscopy demonstrated qualitatively that glucose molecules are successfully bonded to GNP surfaces. For our study, we selected nanoparticles with diameter in a range that maximizes the internalization efficiency in cells (40 nm). A detailed investigation about the biophysical proprieties of AuNP-PEG-Glu was carried out by means of fluorescence correlation spectroscopy (FCS) and orbital tracking techniques. This work gives new insights about the uptake mechanism of gold nanoparticles capped with glucose molecules.
Collapse
Affiliation(s)
- F. Porcaro
- Roma Tre University, Dept. of Sciences, Via della Vasca Navale 79, 00146 - Rome (Italy)
| | - Y. Miao
- Haun Laboratory for Nanoengineering and Molecular Medicine, Biomedical Engineering Department, University of California, Irvine, USA
| | - R. Kota
- Haun Laboratory for Nanoengineering and Molecular Medicine, Biomedical Engineering Department, University of California, Irvine, USA
| | - J. Haun
- Haun Laboratory for Nanoengineering and Molecular Medicine, Biomedical Engineering Department, University of California, Irvine, USA
| | - G. Polzonetti
- Roma Tre University, Dept. of Sciences, Via della Vasca Navale 79, 00146 - Rome (Italy)
| | - C Battocchio
- Roma Tre University, Dept. of Sciences, Via della Vasca Navale 79, 00146 - Rome (Italy)
| | - E. Gratton
- Laboratory for Fluorescence Dynamics, Biomedical Engineering Department, University of California, Irvine, USA
| |
Collapse
|
7
|
Annibale P, Dvornikov A, Gratton E. Electrically tunable lens speeds up 3D orbital tracking. BIOMEDICAL OPTICS EXPRESS 2015; 6:2181-90. [PMID: 26114037 PMCID: PMC4473752 DOI: 10.1364/boe.6.002181] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/13/2015] [Accepted: 05/18/2015] [Indexed: 05/12/2023]
Abstract
3D orbital particle tracking is a versatile and effective microscopy technique that allows following fast moving fluorescent objects within living cells and reconstructing complex 3D shapes using laser scanning microscopes. We demonstrated notable improvements in the range, speed and accuracy of 3D orbital particle tracking by replacing commonly used piezoelectric stages with Electrically Tunable Lens (ETL) that eliminates mechanical movement of objective lenses. This allowed tracking and reconstructing shape of structures extending 500 microns in the axial direction. Using the ETL, we tracked at high speed fluorescently labeled genomic loci within the nucleus of living cells with unprecedented temporal resolution of 8ms using a 1.42NA oil-immersion objective. The presented technology is cost effective and allows easy upgrade of scanning microscopes for fast 3D orbital tracking.
Collapse
Affiliation(s)
- Paolo Annibale
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine USA
- Authors contributed equally to this work
| | - Alexander Dvornikov
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine USA
- Authors contributed equally to this work
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine USA
| |
Collapse
|
8
|
Anzalone A, Gabriel M, Estrada LC, Gratton E. Spectral properties of single gold nanoparticles in close proximity to biological fluorophores excited by 2-photon excitation. PLoS One 2015; 10:e0124975. [PMID: 25909648 PMCID: PMC4409109 DOI: 10.1371/journal.pone.0124975] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/19/2015] [Indexed: 11/29/2022] Open
Abstract
Metallic nanoparticles (NPs) are able to modify the excitation and emission rates (plasmonic enhancement) of fluorescent molecules in their close proximity. In this work, we measured the emission spectra of 20 nm Gold Nanoparticles (AuNPs) fixed on a glass surface submerged in a solution of different fluorophores using a spectral camera and 2-photon excitation. While on the glass surface, we observed the presence in the emission at least 3 components: i) second harmonic signal (SHG), ii) a broad emission from AuNPS and iii) fluorescence arising from fluorophores nearby. When on the glass surface, we found that the 3 spectral components have different relative intensities when the incident direction of linear polarization was changed indicating different physical origins for these components. Then we measured by fluctuation correlation spectroscopy (FCS) the scattering and fluorescence signal of the particles alone and in a solution of 100 nM EGFP using the spectral camera or measuring the scattering and fluorescence from the particles. We observed occasional fluorescence bursts when in the suspension we added fluorescent proteins. The spectrum of these burst was devoid of the SHG and of the broad emission in contrast to the signal collected from the gold nanoparticles on the glass surface. Instead we found that the spectrum during the burst corresponded closely to the spectrum of the fluorescent protein. An additional control was obtained by measuring the cross-correlation between the reflection from the particles and the fluorescence arising from EGFP both excited at 488 nm. We found a very weak cross-correlation between the AuNPs and the fluorescence confirming that the burst originate from a few particles with a fluorescence signal.
Collapse
Affiliation(s)
- Andrea Anzalone
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, California, United States of America
| | - Manuela Gabriel
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, California, United States of America
| | - Laura C. Estrada
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, California, United States of America
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, California, United States of America
- Centre for Bioactive Discovery in Health and Ageing, School of Science & Technology, University of New England, Armidale, Australia
- * E-mail:
| |
Collapse
|