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Yoshida S, Schmid W, Vo N, Calabrase W, Kisley L. Computationally-efficient spatiotemporal correlation analysis super-resolves anomalous diffusion. OPTICS EXPRESS 2021; 29:7616-7629. [PMID: 33726259 DOI: 10.1364/oe.416465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
Anomalous diffusion dynamics in confined nanoenvironments govern the macroscale properties and interactions of many biophysical and material systems. Currently, it is difficult to quantitatively link the nanoscale structure of porous media to anomalous diffusion within them. Fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI) has been shown to extract nanoscale structure and Brownian diffusion dynamics within gels, liquid crystals, and polymers, but has limitations which hinder its wider application to more diverse, biophysically-relevant datasets. Here, we parallelize the least-squares curve fitting step on a GPU improving computation times by up to a factor of 40, implement anomalous diffusion and two-component Brownian diffusion models, and make fcsSOFI more accessible by packaging it in a user-friendly GUI. We apply fcsSOFI to simulations of the protein fibrinogen diffusing in polyacrylamide of varying matrix densities and super-resolve locations where slower, anomalous diffusion occurs within smaller, confined pores. The improvements to fcsSOFI in speed, scope, and usability will allow for the wider adoption of super-resolution correlation analysis to diverse research topics.
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2
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Revealing Plasma Membrane Nano-Domains with Diffusion Analysis Methods. MEMBRANES 2020; 10:membranes10110314. [PMID: 33138102 PMCID: PMC7693849 DOI: 10.3390/membranes10110314] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 12/18/2022]
Abstract
Nano-domains are sub-light-diffraction-sized heterogeneous areas in the plasma membrane of cells, which are involved in cell signalling and membrane trafficking. Throughout the last thirty years, these nano-domains have been researched extensively and have been the subject of multiple theories and models: the lipid raft theory, the fence model, and the protein oligomerization theory. Strong evidence exists for all of these, and consequently they were combined into a hierarchal model. Measurements of protein and lipid diffusion coefficients and patterns have been instrumental in plasma membrane research and by extension in nano-domain research. This has led to the development of multiple methodologies that can measure diffusion and confinement parameters including single particle tracking, fluorescence correlation spectroscopy, image correlation spectroscopy and fluorescence recovery after photobleaching. Here we review the performance and strengths of these methods in the context of their use in identification and characterization of plasma membrane nano-domains.
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3
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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.
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4
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Wong M, Newton LR, Hartmann J, Hennrich ML, Wachsmuth M, Ronchi P, Guzmán-Herrera A, Schwab Y, Gavin AC, Gilmour D. Dynamic Buffering of Extracellular Chemokine by a Dedicated Scavenger Pathway Enables Robust Adaptation during Directed Tissue Migration. Dev Cell 2020; 52:492-508.e10. [PMID: 32059773 DOI: 10.1016/j.devcel.2020.01.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/22/2019] [Accepted: 01/13/2020] [Indexed: 01/16/2023]
Abstract
How tissues migrate robustly through changing guidance landscapes is poorly understood. Here, quantitative imaging is combined with inducible perturbation experiments to investigate the mechanisms that ensure robust tissue migration in vivo. We show that tissues exposed to acute "chemokine floods" halt transiently before they perfectly adapt, i.e., return to the baseline migration behavior in the continued presence of elevated chemokine levels. A chemokine-triggered phosphorylation of the atypical chemokine receptor Cxcr7b reroutes it from constitutive ubiquitination-regulated degradation to plasma membrane recycling, thus coupling scavenging capacity to extracellular chemokine levels. Finally, tissues expressing phosphorylation-deficient Cxcr7b migrate normally in the presence of physiological chemokine levels but show delayed recovery when challenged with elevated chemokine concentrations. This work establishes that adaptation to chemokine fluctuations can be "outsourced" from canonical GPCR signaling to an autonomously acting scavenger receptor that both senses and dynamically buffers chemokine levels to increase the robustness of tissue migration.
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Affiliation(s)
- Mie Wong
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Lionel R Newton
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jonas Hartmann
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Marco L Hennrich
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Malte Wachsmuth
- Luxendo GmbH, Kurfürsten-Anlage 58, 69115 Heidelberg, Germany
| | - Paolo Ronchi
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Alejandra Guzmán-Herrera
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany; Electron Microscopy Core Facility, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Anne-Claude Gavin
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany; Department for Cell Physiology and Metabolism, University of Geneva, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Darren Gilmour
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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5
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Longfils M, Smisdom N, Ameloot M, Rudemo M, Lemmens V, Fernández GS, Röding M, Lorén N, Hendrix J, Särkkä A. Raster Image Correlation Spectroscopy Performance Evaluation. Biophys J 2019; 117:1900-1914. [PMID: 31668746 PMCID: PMC7018992 DOI: 10.1016/j.bpj.2019.09.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/28/2019] [Accepted: 09/30/2019] [Indexed: 01/02/2023] Open
Abstract
Raster image correlation spectroscopy (RICS) is a fluorescence image analysis method for extracting the mobility, concentration, and stoichiometry of diffusing fluorescent molecules from confocal image stacks. The method works by calculating a spatial correlation function for each image and analyzing the average of those by model fitting. Rules of thumb exist for RICS image acquisitioning, yet a rigorous theoretical approach to predict the accuracy and precision of the recovered parameters has been lacking. We outline explicit expressions to reveal the dependence of RICS results on experimental parameters. In terms of imaging settings, we observed that a twofold decrease of the pixel size, e.g., from 100 to 50 nm, decreases the error on the translational diffusion constant (D) between three- and fivefold. For D = 1 μm2 s-1, a typical value for intracellular measurements, ∼25-fold lower mean-squared relative error was obtained when the optimal scan speed was used, although more drastic improvements were observed for other values of D. We proposed a slightly modified RICS calculation that allows correcting for the significant bias of the autocorrelation function at small (≪50 × 50 pixels) sizes of the region of interest. In terms of sample properties, at molecular brightness E = 100 kHz and higher, RICS data quality was sufficient using as little as 20 images, whereas the optimal number of frames for lower E scaled pro rata. RICS data quality was constant over the nM-μM concentration range. We developed a bootstrap-based confidence interval of D that outperformed the classical least-squares approach in terms of coverage probability of the true value of D. We validated the theory via in vitro experiments of enhanced green fluorescent protein at different buffer viscosities. Finally, we outline robust practical guidelines and provide free software to simulate the parameter effects on recovery of the diffusion coefficient.
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Affiliation(s)
- Marco Longfils
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden.
| | - Nick Smisdom
- Stadius Centre for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, Leuven, Belgium; Advanced Optical Microscopy Centre, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Marcel Ameloot
- Advanced Optical Microscopy Centre, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Mats Rudemo
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - Veerle Lemmens
- Advanced Optical Microscopy Centre, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium; Dynamic Bioimaging Lab, Hasselt University, Diepenbeek, Belgium; Molecular Imaging and Photonics, Chemistry Department, KU Leuven, Heverlee, Belgium
| | | | | | - Niklas Lorén
- RISE Bioscience and Materials, Gothenburg, Sweden; Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Jelle Hendrix
- Advanced Optical Microscopy Centre, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium; Dynamic Bioimaging Lab, Hasselt University, Diepenbeek, Belgium.
| | - Aila Särkkä
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
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6
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Di Bona M, Mancini MA, Mazza D, Vicidomini G, Diaspro A, Lanzanò L. Measuring Mobility in Chromatin by Intensity-Sorted FCS. Biophys J 2019; 116:987-999. [PMID: 30819566 PMCID: PMC6428914 DOI: 10.1016/j.bpj.2019.02.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/14/2019] [Accepted: 02/08/2019] [Indexed: 12/12/2022] Open
Abstract
The architectural organization of chromatin can play an important role in genome regulation by affecting the mobility of molecules within its surroundings via binding interactions and molecular crowding. The diffusion of molecules at specific locations in the nucleus can be studied by fluorescence correlation spectroscopy (FCS), a well-established technique based on the analysis of fluorescence intensity fluctuations detected in a confocal observation volume. However, detecting subtle variations of mobility between different chromatin regions remains challenging with currently available FCS methods. Here, we introduce a method that samples multiple positions by slowly scanning the FCS observation volume across the nucleus. Analyzing the data in short time segments, we preserve the high temporal resolution of single-point FCS while probing different nuclear regions in the same cell. Using the intensity level of the probe (or a DNA marker) as a reference, we efficiently sort the FCS segments into different populations and obtain average correlation functions that are associated to different chromatin regions. This sorting and averaging strategy renders the method statistically robust while preserving the observation of intranuclear variations of mobility. Using this approach, we quantified diffusion of monomeric GFP in high versus low chromatin density regions. We found that GFP mobility was reduced in heterochromatin, especially within perinucleolar heterochromatin. Moreover, we found that modulation of chromatin compaction by ATP depletion, or treatment with solutions of different osmolarity, differentially affected the ratio of diffusion in both regions. Then, we used the approach to probe the mobility of estrogen receptor-α in the vicinity of an integrated multicopy prolactin gene array. Finally, we discussed the coupling of this method with stimulated emission depletion FCS for performing FCS at subdiffraction spatial scales.
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Affiliation(s)
- Melody Di Bona
- Nanoscopy and Nikon Imaging Center, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Physics, University of Genoa, Genoa, Italy
| | - Michael A Mancini
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Davide Mazza
- Experimental Imaging Center Ospedale San Raffaele, Milano, Italy; The European Center for Nanomedicine, Milano, Italy
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Alberto Diaspro
- Nanoscopy and Nikon Imaging Center, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Physics, University of Genoa, Genoa, Italy.
| | - Luca Lanzanò
- Nanoscopy and Nikon Imaging Center, Istituto Italiano di Tecnologia, Genoa, Italy.
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7
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Scipioni L, Lanzanó L, Diaspro A, Gratton E. Comprehensive correlation analysis for super-resolution dynamic fingerprinting of cellular compartments using the Zeiss Airyscan detector. Nat Commun 2018; 9:5120. [PMID: 30504919 PMCID: PMC6269422 DOI: 10.1038/s41467-018-07513-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/29/2018] [Indexed: 11/08/2022] Open
Abstract
The availability of the Airyscan detector in the Zeiss LSM 880 has made possible the development of a new concept in fluctuation correlation spectroscopy using super-resolution. The Airyscan unit acquires data simultaneously on 32 detectors arranged in a hexagonal array. This detector opens up the possibility to use fluctuation methods based on time correlation at single points or at a number of points simultaneously, as well as methods based on spatial correlation in the area covered by the detector. Given the frame rate of this detector, millions of frames can be acquired in seconds, providing a robust statistical basis for fluctuation data. We apply the comprehensive analysis to the molecular fluctuations of free GFP diffusing in live cells at different subcellular compartments to show that at the nanoscale different cell environments can be distinguished by the comprehensive fluctuation analysis.
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Affiliation(s)
- L Scipioni
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, 92697, CA, USA
| | - L Lanzanó
- Nanoscopy, Istituto Italiano di Tecnologia, Genoa, 16163, Italy
| | - A Diaspro
- Nanoscopy, Istituto Italiano di Tecnologia, Genoa, 16163, Italy
- Nikon Imaging Center, Istituto Italiano di Tecnologia, Genoa, 16163, Italy
| | - E Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, 92697, CA, USA.
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8
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Scipioni L, Di Bona M, Vicidomini G, Diaspro A, Lanzanò L. Local raster image correlation spectroscopy generates high-resolution intracellular diffusion maps. Commun Biol 2018; 1:10. [PMID: 30271897 PMCID: PMC6053083 DOI: 10.1038/s42003-017-0010-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/15/2017] [Indexed: 01/01/2023] Open
Abstract
Raster image correlation spectroscopy (RICS) is a powerful method for measuring molecular diffusion in live cells directly from images acquired on a laser scanning microscope. However, RICS only provides single average diffusion coefficients from regions with a lateral size on the order of few micrometers, which means that its spatial resolution is mainly limited to the cellular level. Here we introduce the local RICS (L-RICS), an easy-to-use tool that generates high resolution maps of diffusion coefficients from images acquired on a laser scanning microscope. As an application we show diffusion maps of a green fluorescent protein (GFP) within the nucleus and within the nucleolus of live cells at an effective spatial resolution of 500 nm. We find not only that diffusion in the nucleolus is slowed down compared to diffusion in the nucleoplasm, but also that diffusion in the nucleolus is highly heterogeneous. Lorenzo Scipioni et al. present Local Raster Image Correlation Spectroscopy (L-RICS), a method for generating sub-micrometer diffusion maps. They apply L-RICS to GFP in live cells and find that diffusion coefficients differ between the nucleus and nucleolus and are highly heterogeneous within compartments.
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Affiliation(s)
- Lorenzo Scipioni
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.,Department of Informatics, Bioengineering, Robotics and Systems Engineering, University of Genoa, Via All'Opera Pia, 13, 16145, Genoa, Italy
| | - Melody Di Bona
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.,Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Alberto Diaspro
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.,Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy.,Nikon Imaging Center, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Luca Lanzanò
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.
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9
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Hodges C, Kafle RP, Hoff JD, Meiners JC. Fluorescence Correlation Spectroscopy with Photobleaching Correction in Slowly Diffusing Systems. J Fluoresc 2018; 28:505-511. [PMID: 29368157 DOI: 10.1007/s10895-018-2210-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 01/15/2018] [Indexed: 12/23/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a powerful tool to quantitatively study the diffusion of fluorescently labeled molecules. It allows in principle important questions of macromolecular transport and supramolecular aggregation in living cells to be addressed. However, the crowded environment inside the cells slows diffusion and limits the reservoir of labeled molecules, causing artifacts that arise especially from photobleaching and limit the utility of FCS in these applications. We present a method to compute the time correlation function from weighted photon arrival times, which compensates computationally during the data analysis for the effect of photobleaching. We demonstrate the performance of this method using numerical simulations and experimental data from model solutions. Using this technique, we obtain correlation functions in which the effect of photobleaching has been removed and in turn recover quantitatively accurate mean-square displacements of the fluorophores, especially when deviations from an ideal Gaussian excitation volume are accounted for by using a reference calibration correlation function. This allows quantitative FCS studies of transport processes in challenging environments with substantial photobleaching like in living cells in the future.
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Affiliation(s)
- Cameron Hodges
- Department of Biophysics, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 4809-1055, USA
| | - Rudra P Kafle
- Department of Biophysics, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 4809-1055, USA.,Department of Physics, Worcester Polytechnic Institute, 100 Institute Rd., Worcester, MA, 01609-2280, USA
| | - J Damon Hoff
- Department of Biophysics, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 4809-1055, USA
| | - Jens-Christian Meiners
- Department of Biophysics, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 4809-1055, USA. .,Department of Physics, University of Michigan, 450 Church St., Ann Arbor, MI, 48109-1120, USA.
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10
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Hodges C, Meiners JC. Fluorescence Correlation Spectroscopy on Genomic DNA in Living Cells. Methods Mol Biol 2018; 1814:415-424. [PMID: 29956247 DOI: 10.1007/978-1-4939-8591-3_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) is a powerful technique used to measure diffusion, fluctuations, and other transport processes in biomolecular systems. It is, however, prone to artifacts and subject to considerable experimental difficulties when applied to living cells. In this chapter, we provide protocols to conduct quantitative FCS measurements on DNA inside living eukaryotic and prokaryotic cells. We discuss sample preparation, dye selection and characterization, FCS data acquisition, and data analysis, including a method to com pensate for photobleaching to obtain quantitatively meaningful spectra.
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Affiliation(s)
- Cameron Hodges
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
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11
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Malacrida L, Hedde PN, Ranjit S, Cardarelli F, Gratton E. Visualization of barriers and obstacles to molecular diffusion in live cells by spatial pair-cross-correlation in two dimensions. BIOMEDICAL OPTICS EXPRESS 2018; 9:303-321. [PMID: 29359105 PMCID: PMC5772584 DOI: 10.1364/boe.9.000303] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/09/2017] [Accepted: 12/11/2017] [Indexed: 05/09/2023]
Abstract
Despite recent advances in optical super-resolution, we lack a method that can visualize the path followed by diffusing molecules in the cytoplasm or in the nucleus of cells. Fluorescence correlation spectroscopy (FCS) provides molecular dynamics at the single molecule level by averaging the behavior of many molecules over time at a single spot, thus achieving very good statistics but at only one point in the cell. Earlier image-based methods including raster-scan and spatiotemporal image correlation need spatial averaging over relatively large areas, thus compromising spatial resolution. Here, we use spatial pair-cross-correlation in two dimensions (2D-pCF) to obtain relatively high resolution images of molecular diffusion dynamics and transport in live cells. The 2D-pCF method measures the time for a particle to go from one location to another by cross-correlating the intensity fluctuations at specific points in an image. Hence, a visual map of the average path followed by molecules is created.
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Affiliation(s)
- Leonel Malacrida
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, USA
- Área de Investigación Respiratoria, Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Uruguay
- LM and PNH contributed equally to this work
| | - Per Niklas Hedde
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, USA
- LM and PNH contributed equally to this work
| | - Suman Ranjit
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, USA
| | - Francesco Cardarelli
- Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, USA
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12
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Longfils M, Röding M, Altskär A, Schuster E, Lorén N, Särkkä A, Rudemo M. Single particle raster image analysis of diffusion for particle mixtures. J Microsc 2017; 269:269-281. [PMID: 28862754 DOI: 10.1111/jmi.12625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/09/2017] [Indexed: 11/26/2022]
Abstract
Recently we complemented the raster image correlation spectroscopy (RICS) method of analysing raster images via estimation of the image correlation function with the method single particle raster image analysis (SPRIA). In SPRIA, individual particles are identified and the diffusion coefficient of each particle is estimated by a maximum likelihood method. In this paper, we extend the SPRIA method to analyse mixtures of particles with a finite set of diffusion coefficients in a homogeneous medium. In examples with simulated and experimental data with two and three different diffusion coefficients, we show that SPRIA gives accurate estimates of the diffusion coefficients and their proportions. A simple technique for finding the number of different diffusion coefficients is also suggested. Further, we study the use of RICS for mixtures with two different diffusion coefficents and investigate, by plotting level curves of the correlation function, how large the quotient between diffusion coefficients needs to be in order to allow discrimination between models with one and two diffusion coefficients. We also describe a minor correction (compared to published papers) of the RICS autocorrelation function.
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Affiliation(s)
- M Longfils
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - M Röding
- RISE Bioscience and Materials, Gothenburg, Sweden
| | - A Altskär
- RISE Bioscience and Materials, Gothenburg, Sweden
| | - E Schuster
- RISE Bioscience and Materials, Gothenburg, Sweden
| | - N Lorén
- RISE Bioscience and Materials, Gothenburg, Sweden
| | - A Särkkä
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - M Rudemo
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
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13
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Spatiotemporal Fluorescence Correlation Spectroscopy of Inert Tracers: A Journey Within Cells, One Molecule at a Time. PERSPECTIVES ON FLUORESCENCE 2016. [DOI: 10.1007/4243_2016_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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14
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Raster image cross-correlation analysis for spatiotemporal visualization of intracellular degradation activities against exogenous DNAs. Sci Rep 2015; 5:14428. [PMID: 26400011 PMCID: PMC4585853 DOI: 10.1038/srep14428] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 08/28/2015] [Indexed: 11/09/2022] Open
Abstract
Reducing intracellular DNA degradation is critical to enhance the efficiency of gene therapy. Exogenous DNA incorporation into cells is strictly blocked by the defense machinery of intracellular nuclease activity. Raster image correlation spectroscopy (RICS) and raster image cross-correlation spectroscopy (cross-correlation RICS; ccRICS) are image-based correlation methods. These powerful tools allow the study of spatiotemporal molecular dynamics. Here we performed spatiotemporal ccRICS analyses of fluorescent DNA and directly monitored the process of exogenous DNA degradation in living cell cytoplasm. Such direct monitors of DNA degradation allow us to determine the fate of the exogenous DNA in living cells. On comparing the process in living cells, our study shows that cytoplasmic nuclease activity differs between cell lines; therefore, we propose that the difference of nuclease activity in cytoplasm dictates a different resistance to exogenous DNA incorporation. New insight on efficient gene delivery can be provided with our study.
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15
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Probing short-range protein Brownian motion in the cytoplasm of living cells. Nat Commun 2014; 5:5891. [PMID: 25532887 PMCID: PMC4281647 DOI: 10.1038/ncomms6891] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 11/18/2014] [Indexed: 12/02/2022] Open
Abstract
The translational motion of molecules in cells deviates from what is observed in dilute solutions. Theoretical models provide explanations for this effect but with predictions that drastically depend on the nanoscale organization assumed for macromolecular crowding agents. A conclusive test of the nature of the translational motion in cells is missing owing to the lack of techniques capable of probing crowding with the required temporal and spatial resolution. Here we show that fluorescence-fluctuation analysis of raster scans at variable timescales can provide this information. By using green fluorescent proteins in cells, we measure protein motion at the unprecedented timescale of 1 μs, unveiling unobstructed Brownian motion from 25 to 100 nm, and partially suppressed diffusion above 100 nm. Furthermore, experiments on model systems attribute this effect to the presence of relatively immobile structures rather than to diffusing crowding agents. We discuss the implications of these results for intracellular processes. Models for protein diffusion in cells assume a large macromolecular crowding effect. Here Di Rienzo et al. visualize GFP diffusion at the millisecond timescale to observe unobstructed Brownian motion in mammalian cells for distances up to 100 nm, revealing minimal influence of macromolecular crowding.
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Weidemann T, Mücksch J, Schwille P. Fluorescence fluctuation microscopy: a diversified arsenal of methods to investigate molecular dynamics inside cells. Curr Opin Struct Biol 2014; 28:69-76. [DOI: 10.1016/j.sbi.2014.07.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/11/2014] [Indexed: 11/26/2022]
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Recent applications of fluorescence correlation spectroscopy in live systems. FEBS Lett 2014; 588:3571-84. [PMID: 24726724 DOI: 10.1016/j.febslet.2014.03.056] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 03/29/2014] [Accepted: 03/31/2014] [Indexed: 11/20/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a widely used technique in biophysics and has helped address many questions in the life sciences. It provides important advantages compared to other fluorescence and biophysical methods. Its single molecule sensitivity allows measuring proteins within biological samples at physiological concentrations without the need of overexpression. It provides quantitative data on concentrations, diffusion coefficients, molecular transport and interactions even in live organisms. And its reliance on simple fluorescence intensity and its fluctuations makes it widely applicable. In this review we focus on applications of FCS in live samples, with an emphasis on work in the last 5 years, in the hope to provide an overview of the present capabilities of FCS to address biologically relevant questions.
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Bag N, Wohland T. Imaging fluorescence fluctuation spectroscopy: new tools for quantitative bioimaging. Annu Rev Phys Chem 2013; 65:225-48. [PMID: 24328446 DOI: 10.1146/annurev-physchem-040513-103641] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fluorescence fluctuation spectroscopy (FFS) techniques provide information at the single-molecule level with excellent time resolution. Usually applied at a single spot in a sample, they have been recently extended into imaging formats, referred to as imaging FFS. They provide spatial information at the optical diffraction limit and temporal information in the microsecond to millisecond range. This review provides an overview of the different modalities in which imaging FFS techniques have been implemented and discusses present imaging FFS capabilities and limitations. A combination of imaging FFS and nanoscopy would allow one to record information with the detailed spatial information of nanoscopy, which is ∼20 nm and limited only by fluorophore size and labeling density, and the time resolution of imaging FFS, limited by the fluorescence lifetime. This combination would provide new insights into biological events by providing spatiotemporal resolution at unprecedented levels.
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Affiliation(s)
- Nirmalya Bag
- Departments of Biological Sciences and Chemistry, and NUS Center for Bio-Imaging Sciences (CBIS), National University of Singapore, 117557 Singapore; ,
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Erdel F, Rippe K. Quantifying transient binding of ISWI chromatin remodelers in living cells by pixel-wise photobleaching profile evolution analysis. Proc Natl Acad Sci U S A 2012; 109:E3221-30. [PMID: 23129662 PMCID: PMC3511136 DOI: 10.1073/pnas.1209579109] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Interactions between nuclear proteins and chromatin frequently occur on the time scale of seconds and below. These transient binding events are important for the fast identification of target sites as concluded from our previous analysis of the human chromatin remodelers Snf2H and Snf2L from the imitation switch (ISWI) family. Both ATP-driven molecular motor proteins are able to translocate nucleosomes along the DNA and appear to exert this activity only on a small number of nucleosomes to which they bind more tightly. For mechanistic studies, one needs to distinguish such translocation reactions or other long-lived interactions associated with conformational changes and/or ATP hydrolysis from nonproductive chromatin sampling during target search. These processes can be separated by measuring the duration of nucleosome binding with subsecond time resolution. To reach this goal, we have developed a fluorescence bleaching technique termed pixel-wise photobleaching profile evolution analysis (3PEA). It exploits the inherent time structure of confocal microscopy images and yields millisecond resolution. 3PEA represents a generally applicable approach to quantitate transient chromatin interactions in the 2- to 500-ms time regime within only ∼1 s needed for a measurement. The green autofluorescent protein (GFP)-tagged Snf2H and Snf2L and the inactive Snf2L+13 splice variant were studied by 3PEA in comparison to the isolated GFP or red autofluorescent protein and a GFP pentamer. Our results reveal that the residence time for transient chromatin binding of Snf2H and Snf2L is <2 ms, and strongly support the view that ISWI-type remodelers are only rarely active in unperturbed cells during G1 phase.
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Affiliation(s)
- Fabian Erdel
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, 69120 Heidelberg, Germany
| | - Karsten Rippe
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, 69120 Heidelberg, Germany
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Kloster-Landsberg M, Herbomel G, Wang I, Derouard J, Vourc'h C, Usson Y, Souchier C, Delon A. Cellular response to heat shock studied by multiconfocal fluorescence correlation spectroscopy. Biophys J 2012; 103:1110-9. [PMID: 22995483 PMCID: PMC3446677 DOI: 10.1016/j.bpj.2012.07.041] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 07/21/2012] [Accepted: 07/27/2012] [Indexed: 10/27/2022] Open
Abstract
Heat shock triggers a transient and ubiquitous response, the function of which is to protect cells against stress-induced damage. The heat-shock response is controlled by a key transcription factor known as heat shock factor 1 (HSF1). We have developed a multiconfocal fluorescence correlation spectroscopy setup to measure the dynamics of HSF1 during the course of the heat-shock response. The system combines a spatial light modulator, to address several points of interest, and an electron-multiplying charge-coupled camera for fast multiconfocal recording of the photon streams. Autocorrelation curves with a temporal resolution of 14 μs were analyzed before and after heat shock on eGFP and HSF1-eGFP-expressing cells. Evaluation of the dynamic parameters of a diffusion-and-binding model showed a slower HSF1 diffusion after heat shock. It is also observed that the dissociation rate decreases after heat shock, whereas the association rate is not affected. In addition, thanks to the multiconfocal fluorescence correlation spectroscopy system, up to five spots could be simultaneously located in each cell nucleus. This made it possible to quantify the intracellular variability of the diffusion constant of HSF1, which is higher than that of inert eGFP molecules and increases after heat shock. This finding is consistent with the fact that heat-shock response is associated with an increase of HSF1 interactions with DNA and cannot be explained even partially by heat-induced modifications of nuclear organization.
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Affiliation(s)
- Meike Kloster-Landsberg
- University of Grenoble I/Centre National de la Recherche Scientifique, Laboratoire Interdisciplinaire de Physique, Grenoble, France
| | - Gaëtan Herbomel
- University of Grenoble I/Institut National de la Santé et de la Recherche Médicale, Institut Albert Bonniot, U823 team 10, Grenoble, France
| | - Irène Wang
- University of Grenoble I/Centre National de la Recherche Scientifique, Laboratoire Interdisciplinaire de Physique, Grenoble, France
| | - Jacques Derouard
- University of Grenoble I/Centre National de la Recherche Scientifique, Laboratoire Interdisciplinaire de Physique, Grenoble, France
| | - Claire Vourc'h
- University of Grenoble I/Institut National de la Santé et de la Recherche Médicale, Institut Albert Bonniot, U823 team 10, Grenoble, France
| | - Yves Usson
- University of Grenoble I/Centre National de la Recherche Scientifique, Laboratoire TIMC-IMAG, Grenoble, France
| | - Catherine Souchier
- University of Grenoble I/Institut National de la Santé et de la Recherche Médicale, Institut Albert Bonniot, U823 team 10, Grenoble, France
| | - Antoine Delon
- University of Grenoble I/Centre National de la Recherche Scientifique, Laboratoire Interdisciplinaire de Physique, Grenoble, France
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Hamrang Z, Pluen A, Zindy E, Clarke D. Raster Image Correlation Spectroscopy As a Novel Tool for the Quantitative Assessment of Protein Diffusional Behaviour in Solution. J Pharm Sci 2012; 101:2082-93. [DOI: 10.1002/jps.23105] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 01/27/2012] [Accepted: 02/16/2012] [Indexed: 01/12/2023]
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Analysis of molecular movement reveals latticelike obstructions to diffusion in heart muscle cells. Biophys J 2012; 102:739-48. [PMID: 22385844 DOI: 10.1016/j.bpj.2012.01.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Revised: 01/03/2012] [Accepted: 01/13/2012] [Indexed: 01/10/2023] Open
Abstract
Intracellular diffusion in muscle cells is known to be restricted. Although characteristics and localization of these restrictions is yet to be elucidated, it has been established that ischemia-reperfusion injury reduces the overall diffusion restriction. Here we apply an extended version of raster image correlation spectroscopy to determine directional anisotropy and coefficients of diffusion in rat cardiomyocytes. Our experimental results indicate that diffusion of a smaller molecule (1127 MW fluorescently labeled ATTO633-ATP) is restricted more than that of a larger one (10,000 MW Alexa647-dextran), when comparing diffusion in cardiomyocytes to that in solution. We attempt to provide a resolution to this counterintuitive result by applying a quantitative stochastic model of diffusion. Modeling results suggest the presence of periodic intracellular barriers situated ∼1 μm apart having very low permeabilities and a small effect of molecular crowding in volumes between the barriers. Such intracellular structuring could restrict diffusion of molecules of energy metabolism, reactive oxygen species, and apoptotic signals, enacting a significant role in normally functioning cardiomyocytes as well as in pathological conditions of the heart.
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Capoulade J, Wachsmuth M, Hufnagel L, Knop M. Quantitative fluorescence imaging of protein diffusion and interaction in living cells. Nat Biotechnol 2011; 29:835-9. [PMID: 21822256 DOI: 10.1038/nbt.1928] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 06/27/2011] [Indexed: 11/09/2022]
Abstract
Diffusion processes and local dynamic equilibria inside cells lead to nonuniform spatial distributions of molecules, which are essential for processes such as nuclear organization and signaling in cell division, differentiation and migration. To understand these mechanisms, spatially resolved quantitative measurements of protein abundance, mobilities and interactions are needed, but current methods have limited capabilities to study dynamic parameters. Here we describe a microscope based on light-sheet illumination that allows massively parallel fluorescence correlation spectroscopy (FCS) measurements and use it to visualize the diffusion and interactions of proteins in mammalian cells and in isolated fly tissue. Imaging the mobility of heterochromatin protein HP1α (ref. 4) in cell nuclei we could provide high-resolution diffusion maps that reveal euchromatin areas with heterochromatin-like HP1α-chromatin interactions. We expect that FCS imaging will become a useful method for the precise characterization of cellular reaction-diffusion processes.
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Affiliation(s)
- Jérémie Capoulade
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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Erdel F, Müller-Ott K, Baum M, Wachsmuth M, Rippe K. Dissecting chromatin interactions in living cells from protein mobility maps. Chromosome Res 2011; 19:99-115. [PMID: 20848178 DOI: 10.1007/s10577-010-9155-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The genome of eukaryotes is organized into a dynamic nucleoprotein complex referred to as chromatin, which can adopt different functional states. Both the DNA and the protein component of chromatin are subject to various post-translational modifications that define the cell's gene expression program. Their readout and establishment occurs in a spatio-temporally coordinated manner that is controlled by numerous chromatin-interacting proteins. Binding to chromatin in living cells can be measured by a spatially resolved analysis of protein mobility using fluorescence microscopy based approaches. Recent advancements in the acquisition of protein mobility data using fluorescence bleaching and correlation methods provide data sets on diffusion coefficients, binding kinetics, and cellular concentrations on different time and length scales. The combination of different techniques is needed to dissect the complex interplay of diffusive translocations, binding events, and mobility constraints of the chromatin environment. While bleaching techniques have their strength in the characterization of particles that are immobile on the second/minute time scale, a correlation analysis is advantageous to characterize transient binding events with millisecond residence time. The application and synergy effects of the different approaches to obtain protein mobility and interaction maps in the nucleus are illustrated for the analysis of heterochromatin protein 1.
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Affiliation(s)
- Fabian Erdel
- Deutsches Krebsforschungszentrum and BioQuant, Research Group Genome Organization and Function, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
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