1
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Burgers TCQ, Vlijm R. Fluorescence-based super-resolution-microscopy strategies for chromatin studies. Chromosoma 2023:10.1007/s00412-023-00792-9. [PMID: 37000292 PMCID: PMC10356683 DOI: 10.1007/s00412-023-00792-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/28/2023] [Accepted: 03/16/2023] [Indexed: 04/01/2023]
Abstract
Super-resolution microscopy (SRM) is a prime tool to study chromatin organisation at near biomolecular resolution in the native cellular environment. With fluorescent labels DNA, chromatin-associated proteins and specific epigenetic states can be identified with high molecular specificity. The aim of this review is to introduce the field of diffraction-unlimited SRM to enable an informed selection of the most suitable SRM method for a specific chromatin-related research question. We will explain both diffraction-unlimited approaches (coordinate-targeted and stochastic-localisation-based) and list their characteristic spatio-temporal resolutions, live-cell compatibility, image-processing, and ability for multi-colour imaging. As the increase in resolution, compared to, e.g. confocal microscopy, leads to a central role of the sample quality, important considerations for sample preparation and concrete examples of labelling strategies applicable to chromatin research are discussed. To illustrate how SRM-based methods can significantly improve our understanding of chromatin functioning, and to serve as an inspiring starting point for future work, we conclude with examples of recent applications of SRM in chromatin research.
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Affiliation(s)
- Thomas C Q Burgers
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Rifka Vlijm
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands.
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2
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Levchenko SM, Pliss A, Peng X, Prasad PN, Qu J. Fluorescence lifetime imaging for studying DNA compaction and gene activities. LIGHT, SCIENCE & APPLICATIONS 2021; 10:224. [PMID: 34728612 PMCID: PMC8563720 DOI: 10.1038/s41377-021-00664-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 10/04/2021] [Accepted: 10/18/2021] [Indexed: 05/04/2023]
Abstract
Optical imaging is a most useful and widespread technique for the investigation of the structure and function of the cellular genomes. However, an analysis of immensely convoluted and irregularly compacted DNA polymer is highly challenging even by modern super-resolution microscopy approaches. Here we propose fluorescence lifetime imaging (FLIM) for the advancement of studies of genomic structure including DNA compaction, replication as well as monitoring of gene expression. The proposed FLIM assay employs two independent mechanisms for DNA compaction sensing. One mechanism relies on the inverse quadratic relation between the fluorescence lifetimes of fluorescence probes incorporated into DNA and their local refractive index, variable due to DNA compaction density. Another mechanism is based on the Förster resonance energy transfer (FRET) process between the donor and the acceptor fluorophores, both incorporated into DNA. Both these proposed mechanisms were validated in cultured cells. The obtained data unravel a significant difference in compaction of the gene-rich and gene-poor pools of genomic DNA. We show that the gene-rich DNA is loosely compacted compared to the dense DNA domains devoid of active genes.
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Affiliation(s)
- Svitlana M Levchenko
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Artem Pliss
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260-3000, USA
| | - Xiao Peng
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Paras N Prasad
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260-3000, USA.
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China.
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3
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Botchway SW, Farooq S, Sajid A, Robinson IK, Yusuf M. Contribution of advanced fluorescence nano microscopy towards revealing mitotic chromosome structure. Chromosome Res 2021; 29:19-36. [PMID: 33686484 DOI: 10.1007/s10577-021-09654-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 01/07/2023]
Abstract
The organization of chromatin into higher-order structures and its condensation process represent one of the key challenges in structural biology. This is important for elucidating several disease states. To address this long-standing problem, development of advanced imaging methods has played an essential role in providing understanding into mitotic chromosome structure and compaction. Amongst these are two fast evolving fluorescence imaging technologies, specifically fluorescence lifetime imaging (FLIM) and super-resolution microscopy (SRM). FLIM in particular has been lacking in the application of chromosome research while SRM has been successfully applied although not widely. Both these techniques are capable of providing fluorescence imaging with nanometer information. SRM or "nanoscopy" is capable of generating images of DNA with less than 50 nm resolution while FLIM when coupled with energy transfer may provide less than 20 nm information. Here, we discuss the advantages and limitations of both methods followed by their contribution to mitotic chromosome studies. Furthermore, we highlight the future prospects of how advancements in new technologies can contribute in the field of chromosome science.
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Affiliation(s)
- S W Botchway
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Research Complex at Harwell, Oxford, UK
| | - S Farooq
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan
| | - A Sajid
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan
| | - I K Robinson
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.,Brookhaven National Lab, Upton, NY, 11973, USA
| | - M Yusuf
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan. .,London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.
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4
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Yusuf M, Farooq S, Robinson I, Lalani EN. Cryo-nanoscale chromosome imaging-future prospects. Biophys Rev 2020; 12:1257-1263. [PMID: 33006727 PMCID: PMC7575669 DOI: 10.1007/s12551-020-00757-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/04/2020] [Indexed: 01/30/2023] Open
Abstract
The high-order structure of mitotic chromosomes remains to be fully elucidated. How nucleosomes compact at various structural levels into a condensed mitotic chromosome is unclear. Cryogenic preservation and imaging have been applied for over three decades, keeping biological structures close to the native in vivo state. Despite being extensively utilized, this field is still wide open for mitotic chromosome research. In this review, we focus specifically on cryogenic efforts for determining the mitotic nanoscale chromatin structures. We describe vitrification methods, current status, and applications of advanced cryo-microscopy including future tools required for resolving the native architecture of these fascinating structures that hold the instructions to life.
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Affiliation(s)
- Mohammed Yusuf
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan.
| | - Safana Farooq
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan
| | - Ian Robinson
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
- Brookhaven National Lab, Upton, NY, 11973, USA
| | - El-Nasir Lalani
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan
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5
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Lu J, Mazidi H, Ding T, Zhang O, Lew MD. Single-Molecule 3D Orientation Imaging Reveals Nanoscale Compositional Heterogeneity in Lipid Membranes. Angew Chem Int Ed Engl 2020; 59:17572-17579. [PMID: 32648275 PMCID: PMC7794097 DOI: 10.1002/anie.202006207] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/15/2020] [Indexed: 12/21/2022]
Abstract
In soft matter, thermal energy causes molecules to continuously translate and rotate, even in crowded environments, thereby impacting the spatial organization and function of most molecular assemblies, such as lipid membranes. Directly measuring the orientation and spatial organization of large collections (>3000 molecules μm-2 ) of single molecules with nanoscale resolution remains elusive. In this paper, we utilize SMOLM, single-molecule orientation localization microscopy, to directly measure the orientation spectra (3D orientation plus "wobble") of lipophilic probes transiently bound to lipid membranes, revealing that Nile red's (NR) orientation spectra are extremely sensitive to membrane chemical composition. SMOLM images resolve nanodomains and enzyme-induced compositional heterogeneity within membranes, where NR within liquid-ordered vs. liquid-disordered domains shows a ≈4° difference in polar angle and a ≈0.3π sr difference in wobble angle. As a new type of imaging spectroscopy, SMOLM exposes the organizational and functional dynamics of lipid-lipid, lipid-protein, and lipid-dye interactions with single-molecule, nanoscale resolution.
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Affiliation(s)
- Jin Lu
- Department of Electrical and Systems Engineering, Center for Science and Engineering of Living Systems, Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Hesam Mazidi
- Department of Electrical and Systems Engineering, Center for Science and Engineering of Living Systems, Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Tianben Ding
- Department of Electrical and Systems Engineering, Center for Science and Engineering of Living Systems, Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Oumeng Zhang
- Department of Electrical and Systems Engineering, Center for Science and Engineering of Living Systems, Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Matthew D Lew
- Department of Electrical and Systems Engineering, Center for Science and Engineering of Living Systems, Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
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6
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Lu J, Mazidi H, Ding T, Zhang O, Lew MD. Single‐Molecule 3D Orientation Imaging Reveals Nanoscale Compositional Heterogeneity in Lipid Membranes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jin Lu
- Department of Electrical and Systems Engineering Center for Science and Engineering of Living Systems Institute of Materials Science and Engineering Washington University in St. Louis St. Louis MO 63130 USA
| | - Hesam Mazidi
- Department of Electrical and Systems Engineering Center for Science and Engineering of Living Systems Institute of Materials Science and Engineering Washington University in St. Louis St. Louis MO 63130 USA
| | - Tianben Ding
- Department of Electrical and Systems Engineering Center for Science and Engineering of Living Systems Institute of Materials Science and Engineering Washington University in St. Louis St. Louis MO 63130 USA
| | - Oumeng Zhang
- Department of Electrical and Systems Engineering Center for Science and Engineering of Living Systems Institute of Materials Science and Engineering Washington University in St. Louis St. Louis MO 63130 USA
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering Center for Science and Engineering of Living Systems Institute of Materials Science and Engineering Washington University in St. Louis St. Louis MO 63130 USA
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7
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Birk UJ. Super-Resolution Microscopy of Chromatin. Genes (Basel) 2019; 10:E493. [PMID: 31261775 PMCID: PMC6678334 DOI: 10.3390/genes10070493] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/17/2019] [Accepted: 06/26/2019] [Indexed: 01/05/2023] Open
Abstract
Since the advent of super-resolution microscopy, countless approaches and studies have been published contributing significantly to our understanding of cellular processes. With the aid of chromatin-specific fluorescence labeling techniques, we are gaining increasing insight into gene regulation and chromatin organization. Combined with super-resolution imaging and data analysis, these labeling techniques enable direct assessment not only of chromatin interactions but also of the function of specific chromatin conformational states.
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Affiliation(s)
- Udo J Birk
- University of Applied Sciences HTW Chur, Pulvermühlestrasse 57, 7004 Chur, Switzerland.
- Institut für Physik, Universität Mainz, 55122 Mainz, Germany.
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8
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Szydlowski NA, Go JS, Hu YS. Chromatin imaging and new technologies for imaging the nucleome. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2018; 11:e1442. [PMID: 30456928 DOI: 10.1002/wsbm.1442] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/03/2018] [Accepted: 10/16/2018] [Indexed: 12/15/2022]
Abstract
Synergistic developments in advanced fluorescent imaging and labeling techniques enable direct visualization of the chromatin structure and dynamics at the nanoscale level and in live cells. Super-resolution imaging encompasses a class of constantly evolving techniques that break the diffraction limit of fluorescence microscopy. Structured illumination microscopy provides a twofold resolution improvement and can readily achieve live multicolor imaging using conventional fluorophores. Single-molecule localization microscopy increases the spatial resolution by approximately 10-fold at the expense of slower acquisition speed. Stimulated emission-depletion microscopy generates a roughly fivefold resolution improvement with an imaging speed proportional to the scanning area. In parallel, advanced labeling strategies have been developed to "light up" global and sequence-specific DNA regions. DNA binding dyes have been exploited to achieve high labeling densities in single-molecule localization microscopy and enhance contrast in correlated light and electron microscopy. New-generation Oligopaint utilizes bioinformatics analyses to optimize the design of fluorescence in situ hybridization probes. Through sequential and combinatorial labeling, direct characterization of the DNA domain volume and length as well as the spatial organization of distinct topologically associated domains has been reported. In live cells, locus-specific labeling has been achieved by either inserting artificial loci next to the gene of interest, such as the repressor-operator array systems, or utilizing genome editing tools, including zinc finer proteins, transcription activator-like effectors, and the clustered regularly interspaced short palindromic repeats systems. Combined with single-molecule tracking, these labeling techniques enable direct visualization of intra- and inter-chromatin interactions. This article is categorized under: Laboratory Methods and Technologies > Imaging.
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Affiliation(s)
- Nicole A Szydlowski
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
| | - Jane S Go
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
| | - Ying S Hu
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
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9
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Use of 3D imaging for providing insights into high-order structure of mitotic chromosomes. Chromosoma 2018; 128:7-13. [PMID: 30175387 PMCID: PMC6394650 DOI: 10.1007/s00412-018-0678-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/17/2018] [Accepted: 07/24/2018] [Indexed: 11/16/2022]
Abstract
The high-order structure of metaphase chromosomes remains still under investigation, especially the 30-nm structure that is still controversial. Advanced 3D imaging has provided useful information for our understanding of this detailed structure. It is evident that new technologies together with improved sample preparations and image analyses should be adequately combined. This mini review highlights 3D imaging used for chromosome analysis so far with future imaging directions also highlighted.
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10
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Sarmento MJ, Oneto M, Pelicci S, Pesce L, Scipioni L, Faretta M, Furia L, Dellino GI, Pelicci PG, Bianchini P, Diaspro A, Lanzanò L. Exploiting the tunability of stimulated emission depletion microscopy for super-resolution imaging of nuclear structures. Nat Commun 2018; 9:3415. [PMID: 30143630 PMCID: PMC6109149 DOI: 10.1038/s41467-018-05963-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/27/2018] [Indexed: 11/23/2022] Open
Abstract
Imaging of nuclear structures within intact eukaryotic nuclei is imperative to understand the effect of chromatin folding on genome function. Recent developments of super-resolution fluorescence microscopy techniques combine high specificity, sensitivity, and less-invasive sample preparation procedures with the sub-diffraction spatial resolution required to image chromatin at the nanoscale. Here, we present a method to enhance the spatial resolution of a stimulated-emission depletion (STED) microscope based only on the modulation of the STED intensity during the acquisition of a STED image. This modulation induces spatially encoded variations of the fluorescence emission that can be visualized in the phasor plot and used to improve and quantify the effective spatial resolution of the STED image. We show that the method can be used to remove direct excitation by the STED beam and perform dual color imaging. We apply this method to the visualization of transcription and replication foci within intact nuclei of eukaryotic cells.
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Affiliation(s)
- Maria J Sarmento
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry of the A.S.C.R. v.v.i., Prague, Czech Republic
| | - Michele Oneto
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Simone Pelicci
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy
| | - Luca Pesce
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy
| | - Lorenzo Scipioni
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Laura Furia
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142, Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142, Milan, Italy
| | - Paolo Bianchini
- Nanoscopy, 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.
| | - Luca Lanzanò
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.
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11
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Baroux C, Schubert V. Technical Review: Microscopy and Image Processing Tools to Analyze Plant Chromatin: Practical Considerations. Methods Mol Biol 2018; 1675:537-589. [PMID: 29052212 DOI: 10.1007/978-1-4939-7318-7_31] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
In situ nucleus and chromatin analyses rely on microscopy imaging that benefits from versatile, efficient fluorescent probes and proteins for static or live imaging. Yet the broad choice in imaging instruments offered to the user poses orientation problems. Which imaging instrument should be used for which purpose? What are the main caveats and what are the considerations to best exploit each instrument's ability to obtain informative and high-quality images? How to infer quantitative information on chromatin or nuclear organization from microscopy images? In this review, we present an overview of common, fluorescence-based microscopy systems and discuss recently developed super-resolution microscopy systems, which are able to bridge the resolution gap between common fluorescence microscopy and electron microscopy. We briefly present their basic principles and discuss their possible applications in the field, while providing experience-based recommendations to guide the user toward best-possible imaging. In addition to raw data acquisition methods, we discuss commercial and noncommercial processing tools required for optimal image presentation and signal evaluation in two and three dimensions.
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Affiliation(s)
- Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
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12
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D'Abrantes S, Gratton S, Reynolds P, Kriechbaumer V, McKenna J, Barnard S, Clarke DT, Botchway SW. Super-Resolution Nanoscopy Imaging Applied to DNA Double-Strand Breaks. Radiat Res 2017; 189:19-31. [PMID: 29053406 DOI: 10.1667/rr14594.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Genomic deoxyribonucleic acid (DNA) is continuously being damaged by endogenous processes such as metabolism or by exogenous events such as radiation. The specific phosphorylation of histone H2AX on serine residue 139, described as γ-H2AX, is an excellent indicator or marker of DNA double-strand breaks (DSBs). The yield of γ-H2AX (foci) is shown to have some correlation with the dose of radiation or other DSB-causing agents. However, there is some discrepancy in the DNA DSB foci yield among imaging and other methods such as gel electrophoresis. Super-resolution imaging techniques are now becoming widely used as essential tools in biology and medicine, after a slow uptake of their development almost two decades ago. Here we compare several super-resolution techniques used to image and determine the amount and spatial distribution of γ-H2AX foci formation after X-ray irradiation: stimulated emission depletion (STED), ground-state depletion microscopy followed by individual molecule return (GSDIM), structured illumination microscopy (SIM), as well as an improved confocal, Airyscan and HyVolution 2. We show that by using these super-resolution imaging techniques with as low as 30-nm resolution, each focus may be further resolved, thus increasing the number of foci per radiation dose compared to standard microscopy. Furthermore, the DNA repair proteins 53BP1 (after low-LET irradiations) and Ku70/Ku80 (from laser microbeam irradiation) do not always yield a significantly increased number of foci when imaged by the super-resolution techniques, suggesting that γ-H2AX, 53PB1 and Ku70/80 repair proteins do not fully co-localize on the units of higher order chromatin structure.
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Affiliation(s)
- Sofia D'Abrantes
- a Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton, Laboratory, Research Complex at Harwell, Didcot OX11 0QX, United Kingdom
| | - Sarah Gratton
- a Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton, Laboratory, Research Complex at Harwell, Didcot OX11 0QX, United Kingdom
| | - Pamela Reynolds
- b Gray Institute for Radiation Oncology and Biology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Verena Kriechbaumer
- c Plant Cell Biology, Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom
| | - Joseph McKenna
- c Plant Cell Biology, Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom
| | - Stephen Barnard
- d Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, Didcot OX11 0RQ, United Kingdom
| | - Dave T Clarke
- a Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton, Laboratory, Research Complex at Harwell, Didcot OX11 0QX, United Kingdom
| | - Stanley W Botchway
- a Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton, Laboratory, Research Complex at Harwell, Didcot OX11 0QX, United Kingdom
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13
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Wang C, Taki M, Sato Y, Fukazawa A, Higashiyama T, Yamaguchi S. Super-Photostable Phosphole-Based Dye for Multiple-Acquisition Stimulated Emission Depletion Imaging. J Am Chem Soc 2017; 139:10374-10381. [PMID: 28741935 DOI: 10.1021/jacs.7b04418] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As stimulated emission depletion (STED) microscopy can provide structural details of cells with an optical resolution beyond the diffraction limit, it has become an indispensable tool in cell biology. However, the intense STED laser beam usually causes rapid photobleaching of the employed fluorescent dyes, which significantly limits the utility of STED microscopy from a practical perspective. Herein we report a new design of super-photostable dye, PhoxBright 430 (PB430), comprising a fully ring-fused π-conjugated skeleton with an electron-accepting phosphole P-oxide unit. We previously developed a super-photostable dye C-Naphox by combining the phosphole unit with an electron-donating triphenylamine moiety. In PB430, removal of the amino group alters the transition type from intramolecular charge transfer character to π-π* transition character, which gives rise to intense fluorescence insensitive to molecular environment in terms of fluorescence colors and intensity, and bright fluorescence even in aqueous media. PB430 also furnishes high solubility in water, and is capable of labeling proteins with maintaining high fluorescence quantum yields. This dye exhibits outstanding resistance to photoirradiation even under the STED conditions and allows continuous acquisition of STED images. Indeed, using a PB430-conjugated antibody, we succeed in attaining a 3-D reconstruction of super-resolution STED images as well as photostability-based multicolor STED imaging of fluorescently labeled cytoskeletal structures.
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Affiliation(s)
- Chenguang Wang
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Furo, Chikusa, Nagoya 464-8501, Japan
| | - Masayasu Taki
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Furo, Chikusa, Nagoya 464-8501, Japan
| | - Yoshikatsu Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Furo, Chikusa, Nagoya 464-8501, Japan
| | - Aiko Fukazawa
- Department of Chemistry, Graduate School of Science, Nagoya University , Furo, Chikusa, Nagoya 464-8602, Japan
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Furo, Chikusa, Nagoya 464-8501, Japan.,Division of Biological Science, Graduate School of Science, Nagoya University , Furo, Chikusa, Nagoya 464-8602, Japan
| | - Shigehiro Yamaguchi
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Furo, Chikusa, Nagoya 464-8501, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University , Furo, Chikusa, Nagoya 464-8602, Japan
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14
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Adler RA, Wang C, Fukazawa A, Yamaguchi S. Tuning the Photophysical Properties of Photostable Benzo[b]phosphole P-Oxide-Based Fluorophores. Inorg Chem 2017; 56:8718-8725. [DOI: 10.1021/acs.inorgchem.7b00658] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Raúl A. Adler
- Institute
of Transformative Bio-Molecules (WPI-ITbM) and ‡Department of Chemistry, Graduate
School of Science, and Integrated Research Consortium on Chemical
Sciences (IRCCS), Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
| | - Chenguang Wang
- Institute
of Transformative Bio-Molecules (WPI-ITbM) and ‡Department of Chemistry, Graduate
School of Science, and Integrated Research Consortium on Chemical
Sciences (IRCCS), Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
| | - Aiko Fukazawa
- Institute
of Transformative Bio-Molecules (WPI-ITbM) and ‡Department of Chemistry, Graduate
School of Science, and Integrated Research Consortium on Chemical
Sciences (IRCCS), Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
| | - Shigehiro Yamaguchi
- Institute
of Transformative Bio-Molecules (WPI-ITbM) and ‡Department of Chemistry, Graduate
School of Science, and Integrated Research Consortium on Chemical
Sciences (IRCCS), Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
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15
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Hémonnot CYJ, Ranke C, Saldanha O, Graceffa R, Hagemann J, Köster S. Following DNA Compaction During the Cell Cycle by X-ray Nanodiffraction. ACS NANO 2016; 10:10661-10670. [PMID: 28024349 DOI: 10.1021/acsnano.6b05034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
X-ray imaging of intact biological cells is emerging as a complementary method to visible light or electron microscopy. Owing to the high penetration depth and small wavelength of X-rays, it is possible to resolve subcellular structures at a resolution of a few nanometers. Here, we apply scanning X-ray nanodiffraction in combination with time-lapse bright-field microscopy to nuclei of 3T3 fibroblasts and thus relate the observed structures to specific phases in the cell division cycle. We scan the sample at a step size of 250 nm and analyze the individual diffraction patterns according to a generalized Porod's law. Thus, we obtain information on the aggregation state of the nuclear DNA at a real space resolution on the order of the step size and in parallel structural information on the order of few nanometers. We are able to distinguish nucleoli, heterochromatin, and euchromatin in the nuclei and follow the compaction and decompaction during the cell division cycle.
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Affiliation(s)
- Clément Y J Hémonnot
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Christiane Ranke
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Oliva Saldanha
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Rita Graceffa
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Johannes Hagemann
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Sarah Köster
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
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16
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Probing DNA interactions with proteins using a single-molecule toolbox: inside the cell, in a test tube and in a computer. Biochem Soc Trans 2016; 43:139-45. [PMID: 26020443 DOI: 10.1042/bst20140253] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DNA-interacting proteins have roles in multiple processes, many operating as molecular machines which undergo dynamic meta-stable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and the proteins that bind to it must ideally be interrogated at a single molecule level in their native in vivo environments, in a time-resolved manner, fast enough to sample the molecular transitions across the free-energy landscape. Progress has been made over the past decade in utilizing cutting-edge tools of the physical sciences to address challenging biological questions concerning the function and modes of action of several different proteins which bind to DNA. These physiologically relevant assays are technically challenging but can be complemented by powerful and often more tractable in vitro experiments which confer advantages of the chemical environment with enhanced detection signal-to-noise of molecular signatures and transition events. In the present paper, we discuss a range of techniques we have developed to monitor DNA-protein interactions in vivo, in vitro and in silico. These include bespoke single-molecule fluorescence microscopy techniques to elucidate the architecture and dynamics of the bacterial replisome and the structural maintenance of bacterial chromosomes, as well as new computational tools to extract single-molecule molecular signatures from live cells to monitor stoichiometry, spatial localization and mobility in living cells. We also discuss recent developments from our laboratory made in vitro, complementing these in vivo studies, which combine optical and magnetic tweezers to manipulate and image single molecules of DNA, with and without bound protein, in a new super-resolution fluorescence microscope.
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17
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Sathitruangsak C, Righolt CH, Klewes L, Tammur P, Ilus T, Tamm A, Punab M, Olujohungbe A, Mai S. Quantitative superresolution microscopy reveals differences in nuclear DNA organization of multiple myeloma and monoclonal gammopathy of undetermined significance. J Cell Biochem 2015; 116:704-10. [PMID: 25501803 PMCID: PMC5111765 DOI: 10.1002/jcb.25030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/04/2014] [Indexed: 02/06/2023]
Abstract
The mammalian nucleus has a distinct substructure that cannot be visualized directly by conventional microscopy. In this study, the organization of the DNA within the nucleus of multiple myeloma (MM) cells, their precursor cells (monoclonal gammopathy of undetermined significance; MGUS) and control lymphocytes of the representative patients is visualized and quantified by superresolution microscopy. Three‐dimensional structured illumination microscopy (3D‐SIM) increases the spatial resolution beyond the limits of conventional widefield fluorescence microscopy. 3D‐SIM reveals new insights into the nuclear architecture of cancer as we show for the first time that it resolves organizational differences in intranuclear DNA organization of myeloma cells in MGUS and in MM patients. In addition, we report a significant increase in nuclear submicron DNA structure and structure of the DNA‐free space in myeloma nuclei compared to normal lymphocyte nuclei. Our study provides previously unknown details of the nanoscopic DNA architecture of interphase nuclei of the normal lymphocytes, MGUS and MM cells. This study opens new avenues to understanding the disease progression from MGUS to MM. J. Cell. Biochem. 116: 704–710, 2015. © 2014 The Authors. Journal of Cellular Biochemistry published by Wiley Periodicals, Inc.
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Affiliation(s)
- Chirawadee Sathitruangsak
- Manitoba Institute of Cell Biology, University of Manitoba, CancerCare Manitoba, Winnipeg, Manitoba, Canada; Division of Medical Oncology, Department of Internal Medicine, Prince of Songkla University, Songkhla, Thailand
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18
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Annibale P, Gratton E. Advanced fluorescence microscopy methods for the real-time study of transcription and chromatin dynamics. Transcription 2015; 5:e28425. [PMID: 25764219 PMCID: PMC4214231 DOI: 10.4161/trns.28425] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In this contribution we provide an overview of the recent advances allowed by the use of fluorescence microscopy methods in the study of transcriptional processes and their interplay with the chromatin architecture in living cells. Although the use of fluorophores to label nucleic acids dates back at least to about half a century ago,1 two recent breakthroughs have effectively opened the way to use fluorescence routinely for specific and quantitative probing of chromatin organization and transcriptional activity in living cells: namely, the possibility of labeling first the chromatin loci and then the mRNA synthesized from a gene using fluorescent proteins. In this contribution we focus on methods that can probe rapid dynamic processes by analyzing fast fluorescence fluctuations.
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Affiliation(s)
- Paolo Annibale
- a Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
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19
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Serra F, Di Stefano M, Spill YG, Cuartero Y, Goodstadt M, Baù D, Marti-Renom MA. Restraint-based three-dimensional modeling of genomes and genomic domains. FEBS Lett 2015; 589:2987-95. [PMID: 25980604 DOI: 10.1016/j.febslet.2015.05.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/05/2015] [Accepted: 05/05/2015] [Indexed: 10/23/2022]
Abstract
Chromosomes are large polymer molecules composed of nucleotides. In some species, such as humans, this polymer can sum up to meters long and still be properly folded within the nuclear space of few microns in size. The exact mechanisms of how the meters long DNA is folded into the nucleus, as well as how the regulatory machinery can access it, is to a large extend still a mystery. However, and thanks to newly developed molecular, genomic and computational approaches based on the Chromosome Conformation Capture (3C) technology, we are now obtaining insight on how genomes are spatially organized. Here we review a new family of computational approaches that aim at using 3C-based data to obtain spatial restraints for modeling genomes and genomic domains.
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Affiliation(s)
- François Serra
- Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Marco Di Stefano
- Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Yannick G Spill
- Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Yasmina Cuartero
- Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Michael Goodstadt
- Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Davide Baù
- Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Marc A Marti-Renom
- Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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20
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Beliveau BJ, Boettiger AN, Avendaño MS, Jungmann R, McCole RB, Joyce EF, Kim-Kiselak C, Bantignies F, Fonseka CY, Erceg J, Hannan MA, Hoang HG, Colognori D, Lee JT, Shih WM, Yin P, Zhuang X, Wu CT. Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nat Commun 2015; 6:7147. [PMID: 25962338 PMCID: PMC4430122 DOI: 10.1038/ncomms8147] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 04/09/2015] [Indexed: 01/06/2023] Open
Abstract
Fluorescence in situ hybridization (FISH) is a powerful single-cell technique for studying nuclear structure and organization. Here we report two advances in FISH-based imaging. We first describe the in situ visualization of single-copy regions of the genome using two single-molecule super-resolution methodologies. We then introduce a robust and reliable system that harnesses single-nucleotide polymorphisms (SNPs) to visually distinguish the maternal and paternal homologous chromosomes in mammalian and insect systems. Both of these new technologies are enabled by renewable, bioinformatically designed, oligonucleotide-based Oligopaint probes, which we augment with a strategy that uses secondary oligonucleotides (oligos) to produce and enhance fluorescent signals. These advances should substantially expand the capability to query parent-of-origin-specific chromosome positioning and gene expression on a cell-by-cell basis.
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Affiliation(s)
- Brian J. Beliveau
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alistair N. Boettiger
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02138, USA
| | - Maier S. Avendaño
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ralf Jungmann
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ruth B. McCole
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Eric F. Joyce
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Caroline Kim-Kiselak
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Frédéric Bantignies
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Institut de Génétique Humaine, CNRS UPR 1142, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Chamith Y. Fonseka
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mohammed A. Hannan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hien G. Hoang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David Colognori
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Boston, Massachusetts 02114, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Jeannie T. Lee
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Boston, Massachusetts 02114, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - William M. Shih
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Xiaowei Zhuang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02138, USA
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Chao-ting Wu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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21
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Lakadamyali M, Cosma MP. Advanced microscopy methods for visualizing chromatin structure. FEBS Lett 2015; 589:3023-30. [PMID: 25896023 DOI: 10.1016/j.febslet.2015.04.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 03/30/2015] [Accepted: 04/01/2015] [Indexed: 12/29/2022]
Abstract
In the recent years it has become clear that our genome is not randomly organized and its architecture is tightly linked to its function. While genomic studies have given much insight into genome organization, they mostly rely on averaging over large populations of cells, are not compatible with living cells and have limited resolution. For studying genome organization in single living cells, microscopy is indispensable. In addition, the visualization of biological structures helps to understand their function. Up to now, fluorescence microscopy has allowed us to probe the larger scale organization of chromosome territories in the micron length scales, however, the smaller length scales remained invisible due to the diffraction limited spatial resolution of fluorescence microscopy. Thanks to the advent of super-resolution microscopy methods, we are finally starting to be able to probe the nanoscale organization of chromatin in vivo and these methods have the potential to greatly advance our knowledge about chromatin structure and function relationship.
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Affiliation(s)
- Melike Lakadamyali
- ICFO-Institut de Ciències Fotòniques, Mediterranean Technology Park, 08860 Barcelona, Spain.
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010 Barcelona, Spain.
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22
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Yao J, Wang L, Li C, Zhang C, Wang LV. Photo-imprint super-resolution photoacoustic microscopy. ACTA ACUST UNITED AC 2015. [DOI: 10.1117/12.2077350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Junjie Yao
- Washington Univ. in St. Louis (United States)
| | - Lidai Wang
- Washington Univ. in St. Louis (United States)
| | - Chiye Li
- Washington Univ. in St. Louis (United States)
| | - Chi Zhang
- Washington Univ. in St. Louis (United States)
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23
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Yusuf M, Chen B, Hashimoto T, Estandarte AK, Thompson G, Robinson I. Staining and embedding of human chromosomes for 3-d serial block-face scanning electron microscopy. Biotechniques 2014; 57:302-7. [PMID: 25495730 DOI: 10.2144/000114236] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 10/21/2014] [Indexed: 11/23/2022] Open
Abstract
The high-order structure of human chromosomes is an important biological question that is still under investigation. Studies have been done on imaging human mitotic chromosomes using mostly 2-D microscopy methods. To image micron-sized human chromosomes in 3-D, we developed a procedure for preparing samples for serial block-face scanning electron microscopy (SBFSEM). Polyamine chromosomes are first separated using a simple filtration method and then stained with heavy metal. We show that the DNA-specific platinum blue provides higher contrast than osmium tetroxide. A two-step procedure for embedding chromosomes in resin is then used to concentrate the chromosome samples. After stacking the SBFSEM images, a familiar X-shaped chromosome was observed in 3-D.
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Affiliation(s)
- Mohammed Yusuf
- London Centre for Nanotechnology, University College London, London, UK; Research Complex at Harwell, Rutherford Appleton Laboratory, Oxon, UK
| | - Bo Chen
- London Centre for Nanotechnology, University College London, London, UK; Research Complex at Harwell, Rutherford Appleton Laboratory, Oxon, UK
| | - Teruo Hashimoto
- Corrosion & Protection Centre, School of Materials, The University of Manchester, Manchester, UK
| | - Ana Katrina Estandarte
- London Centre for Nanotechnology, University College London, London, UK; Research Complex at Harwell, Rutherford Appleton Laboratory, Oxon, UK
| | - George Thompson
- Corrosion & Protection Centre, School of Materials, The University of Manchester, Manchester, UK
| | - Ian Robinson
- London Centre for Nanotechnology, University College London, London, UK; Research Complex at Harwell, Rutherford Appleton Laboratory, Oxon, UK
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24
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Khan WA, Rogan PK, Knoll JHM. Localized, non-random differences in chromatin accessibility between homologous metaphase chromosomes. Mol Cytogenet 2014; 7:70. [PMID: 25520753 PMCID: PMC4269072 DOI: 10.1186/s13039-014-0070-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/06/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Condensation differences along the lengths of homologous, mitotic metaphase chromosomes are well known. This study reports molecular cytogenetic data showing quantifiable localized differences in condensation between homologs that are related to differences in accessibility (DA) of associated DNA probe targets. Reproducible DA was observed for ~10% of locus-specific, short (1.5-5 kb) single copy DNA probes used in fluorescence in situ hybridization. RESULTS Fourteen probes (from chromosomes 1, 5, 9, 11, 15, 17, 22) targeting genic and intergenic regions were developed and hybridized to cells from 10 individuals with cytogenetically-distinguishable homologs. Differences in hybridization between homologs were non-random for 8 genomic regions (RGS7, CACNA1B, GABRA5, SNRPN, HERC2, PMP22:IVS3, ADORA2B:IVS1, ACR) and were not unique to known imprinted domains or specific chromosomes. DNA probes within CCNB1, C9orf66, ADORA2B:Promoter-Ex1, PMP22:IVS4-Ex 5, and intergenic region 1p36.3 showed no DA (equivalent accessibility), while OPCML showed unbiased DA. To pinpoint probe locations, we performed 3D-structured illumination microscopy (3D-SIM). This showed that genomic regions with DA had 3.3-fold greater volumetric, integrated probe intensities and broad distributions of probe depths along axial and lateral axes of the 2 homologs, compared to a low copy probe target (NOMO1) with equivalent accessibility. Genomic regions with equivalent accessibility were also enriched for epigenetic marks of open interphase chromatin (DNase I HS, H3K27Ac, H3K4me1) to a greater extent than regions with DA. CONCLUSIONS This study provides evidence that DA is non-random and reproducible; it is locus specific, but not unique to known imprinted regions or specific chromosomes. Non-random DA was also shown to be heritable within a 2 generation family. DNA probe volume and depth measurements of hybridized metaphase chromosomes further show locus-specific chromatin accessibility differences by super-resolution 3D-SIM. Based on these data and the analysis of interphase epigenetic marks of genomic intervals with DA, we conclude that there are localized differences in compaction of homologs during mitotic metaphase and that these differences may arise during or preceding metaphase chromosome compaction. Our results suggest new directions for locus-specific structural analysis of metaphase chromosomes, motivated by the potential relationship of these findings to underlying epigenetic changes established during interphase.
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Affiliation(s)
- Wahab A Khan
- />Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON N6A 5C1 Canada
- />Cytognomix, Inc, London, ON N6G 4X8 Canada
| | - Peter K Rogan
- />Departments of Biochemistry and Computer Science, University of Western Ontario, London, ON N6A 5C1 Canada
- />Cytognomix, Inc, London, ON N6G 4X8 Canada
| | - Joan HM Knoll
- />Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON N6A 5C1 Canada
- />Cytognomix, Inc, London, ON N6G 4X8 Canada
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25
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Pyne A, Thompson R, Leung C, Roy D, Hoogenboom BW. Single-molecule reconstruction of oligonucleotide secondary structure by atomic force microscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:3257-61. [PMID: 24740866 DOI: 10.1002/smll.201400265] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/20/2014] [Indexed: 05/23/2023]
Abstract
Based on soft-touch atomic force microscopy, a method is described to reconstruct the secondary structure of single extended biomolecules, without the need for crystallization. The method is tested by accurately reproducing the dimensions of the B-DNA crystal structure. Importantly, intramolecular variations in groove depth of the DNA double helix are resolved, which would be inaccessible for methods that rely on ensemble-averaging.
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Affiliation(s)
- Alice Pyne
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London, WC1H 0AH, United Kingdom
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26
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Han R, Li Z, Fan Y, Jiang Y. Recent Advances in Super-Resolution Fluorescence Imaging and Its Applications in Biology. J Genet Genomics 2013; 40:583-95. [DOI: 10.1016/j.jgg.2013.11.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 11/11/2013] [Accepted: 11/11/2013] [Indexed: 11/16/2022]
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27
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Monserrate A, Casado S, Flors C. Correlative Atomic Force Microscopy and Localization-Based Super-Resolution Microscopy: Revealing Labelling and Image Reconstruction Artefacts. Chemphyschem 2013; 15:647-50. [DOI: 10.1002/cphc.201300853] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Indexed: 11/10/2022]
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28
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Dumat B, Bordeau G, Faurel-Paul E, Mahuteau-Betzer F, Saettel N, Metge G, Fiorini-Debuisschert C, Charra F, Teulade-Fichou MP. DNA Switches on the Two-Photon Efficiency of an Ultrabright Triphenylamine Fluorescent Probe Specific of AT Regions. J Am Chem Soc 2013; 135:12697-706. [DOI: 10.1021/ja404422z] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Blaise Dumat
- Institut Curie, CNRS UMR-176, Centre Universitaire d’Orsay, Paris-Sud 91405
Orsay Cedex France
| | - Guillaume Bordeau
- Institut Curie, CNRS UMR-176, Centre Universitaire d’Orsay, Paris-Sud 91405
Orsay Cedex France
| | - Elodie Faurel-Paul
- Institut Curie, CNRS UMR-176, Centre Universitaire d’Orsay, Paris-Sud 91405
Orsay Cedex France
| | | | - Nicolas Saettel
- Institut Curie, CNRS UMR-176, Centre Universitaire d’Orsay, Paris-Sud 91405
Orsay Cedex France
| | - Germain Metge
- CEA-
Saclay, DSM-IRAMIS/SPCSI/Laboratoire NanoPhotonique, 91191 Gif-sur-Yvette, France
| | | | - Fabrice Charra
- CEA-
Saclay, DSM-IRAMIS/SPCSI/Laboratoire NanoPhotonique, 91191 Gif-sur-Yvette, France
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29
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FLORS C. Super-resolution fluorescence imaging of directly labelled DNA: from microscopy standards to living cells. J Microsc 2013; 251:1-4. [DOI: 10.1111/jmi.12054] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 04/24/2013] [Indexed: 01/28/2023]
Affiliation(s)
- C. FLORS
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanoscience); Madrid Spain
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30
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Sengupta P, Van Engelenburg S, Lippincott-Schwartz J. Visualizing cell structure and function with point-localization superresolution imaging. Dev Cell 2013; 23:1092-102. [PMID: 23237943 DOI: 10.1016/j.devcel.2012.09.022] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Fundamental to the success of cell and developmental biology is the ability to tease apart molecular organization in cells and tissues by localizing specific proteins with respect to one another in a native cellular context. However, many key cellular structures (from mitochondrial cristae to nuclear pores) lie below the diffraction limit of visible light, precluding analysis of their organization by conventional approaches. Point-localization superresolution microscopy techniques, such as PALM and STORM, are poised to resolve, with unprecedented clarity, the organizational principles of macromolecular complexes within cells, thus leading to deeper insights into cellular function in both health and disease.
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Affiliation(s)
- Prabuddha Sengupta
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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31
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Sengupta P, Jovanovic-Talisman T, Lippincott-Schwartz J. Quantifying spatial organization in point-localization superresolution images using pair correlation analysis. Nat Protoc 2013; 8:345-54. [PMID: 23348362 PMCID: PMC3925398 DOI: 10.1038/nprot.2013.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The distinctive distributions of proteins within subcellular compartments both at steady state and during signaling events have essential roles in cell function. Here we describe a method for delineating the complex arrangement of proteins within subcellular structures visualized using point-localization superresolution (PL-SR) imaging. The approach, called pair correlation photoactivated localization microscopy (PC-PALM), uses a pair-correlation algorithm to precisely identify single molecules in PL-SR imaging data sets, and it is used to decipher quantitative features of protein organization within subcellular compartments, including the existence of protein clusters and the size, density and number of proteins in these clusters. We provide a step-by-step protocol for PC-PALM, illustrating its analysis capability for four plasma membrane proteins tagged with photoactivatable GFP (PAGFP). The experimental steps for PC-PALM can be carried out in 3 d and the analysis can be done in ∼6-8 h. Researchers need to have substantial experience in single-molecule imaging and statistical analysis to conduct the experiments and carry out this analysis.
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Affiliation(s)
- Prabuddha Sengupta
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tijana Jovanovic-Talisman
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jennifer Lippincott-Schwartz
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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Ziemniak M, Szabelski M, Lukaszewicz M, Nowicka A, Darzynkiewicz E, Rhoads RE, Wieczorek Z, Jemielity J. Synthesis and evaluation of fluorescent cap analogues for mRNA labelling. RSC Adv 2013; 3. [PMID: 24273643 DOI: 10.1039/c3ra42769b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We describe the synthesis and properties of five dinucleotide fluorescent cap analogues labelled at the ribose of the 7-methylguanosine moiety with either anthraniloyl (Ant) or N-methylanthraniloyl (Mant), which have been designed for the preparation of fluorescent mRNAs via transcription in vitro. Two of the analogues bear a methylene modification in the triphosphate bridge, providing resistance against either the Dcp2 or DcpS decapping enzymes. All these compounds were prepared by ZnCl2-mediated coupling of a nucleotide P-imidazolide with a fluorescently labelled mononucleotide. To evaluate the utility of these compounds for studying interactions with cap-binding proteins and cap-related cellular processes, both biological and spectroscopic features of those compounds were determined. The results indicate acceptable quantum yields of fluorescence, pH independence, environmental sensitivity, and photostability. The cap analogues are incorporated by RNA polymerase into mRNA transcripts that are efficiently translated in vitro. Transcripts containing fluorescent caps but unmodified in the triphosphate chain are hydrolysed by Dcp2 whereas those containing a α-β methylene modification are resistant. Model studies exploiting sensitivity of Mant to changes of local environment demonstrated utility of the synthesized compounds for studying cap-related proteins.
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Affiliation(s)
- Marcin Ziemniak
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
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33
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Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Proc Natl Acad Sci U S A 2012; 109:21301-6. [PMID: 23236188 DOI: 10.1073/pnas.1213818110] [Citation(s) in RCA: 299] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A host of observations demonstrating the relationship between nuclear architecture and processes such as gene expression have led to a number of new technologies for interrogating chromosome positioning. Whereas some of these technologies reconstruct intermolecular interactions, others have enhanced our ability to visualize chromosomes in situ. Here, we describe an oligonucleotide- and PCR-based strategy for fluorescence in situ hybridization (FISH) and a bioinformatic platform that enables this technology to be extended to any organism whose genome has been sequenced. The oligonucleotide probes are renewable, highly efficient, and able to robustly label chromosomes in cell culture, fixed tissues, and metaphase spreads. Our method gives researchers precise control over the sequences they target and allows for single and multicolor imaging of regions ranging from tens of kilobases to megabases with the same basic protocol. We anticipate this technology will lead to an enhanced ability to visualize interphase and metaphase chromosomes.
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34
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Cerf A, Tian HC, Craighead HG. Ordered arrays of native chromatin molecules for high-resolution imaging and analysis. ACS NANO 2012; 6:7928-34. [PMID: 22816516 PMCID: PMC3703913 DOI: 10.1021/nn3023624] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Individual chromatin molecules contain valuable genetic and epigenetic information. To date, there have not been reliable techniques available for the controlled stretching and manipulation of individual chromatin fragments for high-resolution imaging and analysis of these molecules. We report the controlled stretching of single chromatin fragments extracted from two different cancerous cell types (M091 and HeLa) characterized through fluorescence microscopy and atomic force microscopy (AFM). Our method combines soft lithography with molecular stretching to form ordered arrays of more than 250,000 individual chromatin fragments immobilized into a beads-on-a-string structure on a solid transparent support. Using fluorescence microscopy and AFM, we verified the presence of histone proteins after the stretching and transfer process.
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Affiliation(s)
- Aline Cerf
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Harvey C. Tian
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Harold G. Craighead
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
- To whom correspondence should be addressed. ; Fax: (607) 255-7658
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Abstract
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We describe the engineering of reversible fluorescence
photoswitching
in DNA with high-density substitution, and its applications in advanced
fluorescence microscopy methods. High-density labeling of DNA with
cyanine dyes can be achieved by polymerase chain reaction using a
modified DNA polymerase that has been evolved to efficiently incorporate
Cy3- and Cy5-labeled cytosine base analogues into double-stranded
DNA. The resulting biopolymer, “CyDNA”, displays hundreds
of fluorophores per DNA strand and is strongly colored and highly
fluorescent, although previous observations suggest that fluorescence
quenching at such high density might be a concern, especially for
Cy5. Herein, we first investigate the mechanisms of fluorescence quenching
in CyDNA and we suggest that two different mechanisms, aggregate formation
and resonance energy transfer, are responsible for fluorescence quenching
at high labeling densities. Moreover, we have been able to re-engineer
CyDNA into a reversible fluorescence photoswitchable biopolymer by
using the properties of the Cy3–Cy5 pair. This novel biopolymer
constitutes a new class of photoactive DNA-based nanomaterial and
is of great interest for advanced microscopy applications. We show
that reversible fluorescence photoswitching in CyDNA can be exploited
in optical lock-in detection imaging. It also lays the foundations
for improved and sequence-specific super-resolution fluorescence microscopy
of DNA.
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Affiliation(s)
- Darren A Smith
- EaStChem School of Chemistry, University of Edinburgh , Joseph Black Building, The King's Buildings, West Mains Rd, Edinburgh EH9 3JJ, United Kingdom
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36
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van de Corput MPC, de Boer E, Knoch TA, van Cappellen WA, Quintanilla A, Ferrand L, Grosveld FG. Super-resolution imaging reveals three-dimensional folding dynamics of the β-globin locus upon gene activation. J Cell Sci 2012; 125:4630-9. [PMID: 22767512 DOI: 10.1242/jcs.108522] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The chromatin architecture is constantly changing because of cellular processes such as proliferation, differentiation and changes in the expression profile during gene activation or silencing. Unravelling the changes that occur in the chromatin structure during these processes has been a topic of interest for many years. It is known that gene activation of large gene loci is thought to occur by means of an active looping mechanism. It was also shown for the β-globin locus that the gene promoter interacts with an active chromatin hub by means of an active looping mechanism. This means that the locus changes in three-dimensional (3D) nuclear volume and chromatin shape. As a means of visualizing and measuring these dynamic changes in chromatin structure of the β-globin locus, we used a 3D DNA-FISH method in combination with 3D image acquisition to volume render fluorescent signals into 3D objects. These 3D chromatin structures were geometrically analysed, and results prior to and after gene activation were quantitatively compared. Confocal and super-resolution imaging revealed that the inactive locus occurs in several different conformations. These conformations change in shape and surface structure upon cell differentiation into a more folded and rounded structure that has a substantially smaller size and volume. These physical measurements represent the first non-biochemical evidence that, upon gene activation, an actively transcribing chromatin hub is formed by means of additional chromatin looping.
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Affiliation(s)
- Mariëtte P C van de Corput
- Department of Cell Biology and Genetics and Center for Biomedical Genetics, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands.
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Cusido J, Battal M, Deniz E, Yildiz I, Sortino S, Raymo FM. Fast Fluorescence Switching within Hydrophilic Supramolecular Assemblies. Chemistry 2012; 18:10399-407. [DOI: 10.1002/chem.201201184] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Indexed: 11/07/2022]
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