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Shim AR, Frederick J, Pujadas EM, Kuo T, Ye IC, Pritchard JA, Dunton CL, Gonzalez PC, Acosta N, Jain S, Anthony NM, Almassalha LM, Szleifer I, Backman V. Formamide denaturation of double-stranded DNA for fluorescence in situ hybridization (FISH) distorts nanoscale chromatin structure. PLoS One 2024; 19:e0301000. [PMID: 38805476 PMCID: PMC11132451 DOI: 10.1371/journal.pone.0301000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/10/2024] [Indexed: 05/30/2024] Open
Abstract
As imaging techniques rapidly evolve to probe nanoscale genome organization at higher resolution, it is critical to consider how the reagents and procedures involved in sample preparation affect chromatin at the relevant length scales. Here, we investigate the effects of fluorescent labeling of DNA sequences within chromatin using the gold standard technique of three-dimensional fluorescence in situ hybridization (3D FISH). The chemical reagents involved in the 3D FISH protocol, specifically formamide, cause significant alterations to the sub-200 nm (sub-Mbp) chromatin structure. Alternatively, two labeling methods that do not rely on formamide denaturation, resolution after single-strand exonuclease resection (RASER)-FISH and clustered regularly interspaced short palindromic repeats (CRISPR)-Sirius, had minimal impact on the three-dimensional organization of chromatin. We present a polymer physics-based analysis of these protocols with guidelines for their interpretation when assessing chromatin structure using currently available techniques.
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Affiliation(s)
- Anne R. Shim
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Jane Frederick
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Emily M. Pujadas
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Tiffany Kuo
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - I. Chae Ye
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Joshua A. Pritchard
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Cody L. Dunton
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Paola Carrillo Gonzalez
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Nicolas Acosta
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Surbhi Jain
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Nicholas M. Anthony
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Luay M. Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, Illinois, United States of America
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Department of Chemistry, Northwestern University, Evanston, Illinois, United States of America
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
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Woodworth MA, Ng KKH, Halpern AR, Pease NA, Nguyen PHB, Kueh HY, Vaughan JC. Multiplexed single-cell profiling of chromatin states at genomic loci by expansion microscopy. Nucleic Acids Res 2021; 49:e82. [PMID: 34048564 PMCID: PMC8373070 DOI: 10.1093/nar/gkab423] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 04/09/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Proper regulation of genome architecture and activity is essential for the development and function of multicellular organisms. Histone modifications, acting in combination, specify these activity states at individual genomic loci. However, the methods used to study these modifications often require either a large number of cells or are limited to targeting one histone mark at a time. Here, we developed a new method called Single Cell Evaluation of Post-TRanslational Epigenetic Encoding (SCEPTRE) that uses Expansion Microscopy (ExM) to visualize and quantify multiple histone modifications at non-repetitive genomic regions in single cells at a spatial resolution of ∼75 nm. Using SCEPTRE, we distinguished multiple histone modifications at a single housekeeping gene, quantified histone modification levels at multiple developmentally-regulated genes in individual cells, and evaluated the relationship between histone modifications and RNA polymerase II loading at individual loci. We find extensive variability in epigenetic states between individual gene loci hidden from current population-averaged measurements. These findings establish SCEPTRE as a new technique for multiplexed detection of combinatorial chromatin states at single genomic loci in single cells.
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Affiliation(s)
- Marcus A Woodworth
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Kenneth K H Ng
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Aaron R Halpern
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Nicholas A Pease
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Phuc H B Nguyen
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.,Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
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3
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Krufczik M, Sievers A, Hausmann A, Lee JH, Hildenbrand G, Schaufler W, Hausmann M. Combining Low Temperature Fluorescence DNA-Hybridization, Immunostaining, and Super-Resolution Localization Microscopy for Nano-Structure Analysis of ALU Elements and Their Influence on Chromatin Structure. Int J Mol Sci 2017; 18:ijms18051005. [PMID: 28481278 PMCID: PMC5454918 DOI: 10.3390/ijms18051005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/25/2017] [Accepted: 05/02/2017] [Indexed: 01/12/2023] Open
Abstract
Immunostaining and fluorescence in situ hybridization (FISH) are well established methods for specific labelling of chromatin in the cell nucleus. COMBO-FISH (combinatorial oligonucleotide fluorescence in situ hybridization) is a FISH method using computer designed oligonucleotide probes specifically co-localizing at given target sites. In combination with super resolution microscopy which achieves spatial resolution far beyond the Abbe Limit, it allows new insights into the nano-scaled structure and organization of the chromatin of the nucleus. To avoid nano-structural changes of the chromatin, the COMBO-FISH labelling protocol was optimized omitting heat treatment for denaturation of the target. As an example, this protocol was applied to ALU elements—dispersed short stretches of DNA which appear in different kinds in large numbers in primate genomes. These ALU elements seem to be involved in gene regulation, genomic diversity, disease induction, DNA repair, etc. By computer search, we developed a unique COMBO-FISH probe which specifically binds to ALU consensus elements and combined this DNA–DNA labelling procedure with heterochromatin immunostainings in formaldehyde-fixed cell specimens. By localization microscopy, the chromatin network-like arrangements of ALU oligonucleotide repeats and heterochromatin antibody labelling sites were simultaneously visualized and quantified. This novel approach which simultaneously combines COMBO-FISH and immunostaining was applied to chromatin analysis on the nanoscale after low-linear-energy-transfer (LET) radiation exposure at different doses. Dose-correlated curves were obtained from the amount of ALU representing signals, and the chromatin re-arrangements during DNA repair after irradiation were quantitatively studied on the nano-scale. Beyond applications in radiation research, the labelling strategy of immunostaining and COMBO-FISH with localization microscopy will also offer new potentials for analyses of subcellular elements in combination with other specific chromatin targets.
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Affiliation(s)
- Matthias Krufczik
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Aaron Sievers
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Annkathrin Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Jin-Ho Lee
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Georg Hildenbrand
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
- Department of Radiation Oncology, University Medical Center Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 3-5, 68159 Mannheim, Germany.
| | - Wladimir Schaufler
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
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Markaki Y, Smeets D, Fiedler S, Schmid VJ, Schermelleh L, Cremer T, Cremer M. The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture. Bioessays 2012; 34:412-26. [PMID: 22508100 DOI: 10.1002/bies.201100176] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Three-dimensional structured illumination microscopy (3D-SIM) has opened up new possibilities to study nuclear architecture at the ultrastructural level down to the ~100 nm range. We present first results and assess the potential using 3D-SIM in combination with 3D fluorescence in situ hybridization (3D-FISH) for the topographical analysis of defined nuclear targets. Our study also deals with the concern that artifacts produced by FISH may counteract the gain in resolution. We address the topography of DAPI-stained DNA in nuclei before and after 3D-FISH, nuclear pores and the lamina, chromosome territories, chromatin domains, and individual gene loci. We also look at the replication patterns of chromocenters and the topographical relationship of Xist-RNA within the inactive X-territory. These examples demonstrate that an appropriately adapted 3D-FISH/3D-SIM approach preserves key characteristics of the nuclear ultrastructure and that the gain in information obtained by 3D-SIM yields new insights into the functional nuclear organization.
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Affiliation(s)
- Yolanda Markaki
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
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5
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Cummings BS, Schnellmann RG. Measurement of cell death in mammalian cells. ACTA ACUST UNITED AC 2012; Chapter 12:Unit 12.8. [PMID: 22294120 DOI: 10.1002/0471141755.ph1208s25] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This unit presents methods used to assess cell death in mammalian cells. The unit is divided into five sections: (1) a brief overview of cytotoxicity and pathways of cell death, (2) an improved method to measure cell death using lactate dehydrogenase (LDH) release as a marker of membrane integrity, (3) a flow cytometry method that simultaneously measures two types of cell death, oncosis and apoptosis, (4) use of nuclear morphology to assess apoptosis and oncosis, and (5) a brief discussion of the use of cytotoxicity assays to determine the mechanisms of cell death.
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Affiliation(s)
- Brian S Cummings
- Medical University of South Carolina, Charleston, South Carolina, USA
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Tirichine L, Andrey P, Biot E, Maurin Y, Gaudin V. 3D fluorescent in situ hybridization using Arabidopsis leaf cryosections and isolated nuclei. PLANT METHODS 2009; 5:11. [PMID: 19650905 PMCID: PMC2731090 DOI: 10.1186/1746-4811-5-11] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Accepted: 08/03/2009] [Indexed: 05/23/2023]
Abstract
BACKGROUND Fluorescent hybridization techniques are widely used to study the functional organization of different compartments within the mammalian nucleus. However, few examples of such studies are known in the plant kingdom. Indeed, preservation of nuclei 3D structure, which is required for nuclear organization studies, is difficult to fulfill. RESULTS We report a rapid protocol for fluorescent in situ hybridization (FISH) performed on 3D isolated nuclei and thin cryosectioned leaves of Arabidopsis thaliana. The use of direct labeling minimized treatment steps, shortening the overall procedure. Using image analysis, we measured different parameters related to nucleus morphology and overall 3D structure. CONCLUSION Our work describes a 3D-FISH protocol that preserves the 3D structure of Arabidopsis interphase nuclei. Moreover, we report for the first time FISH using cryosections of Arabidopsis leaves. This protocol is a valuable tool to investigate nuclear architecture and chromatin organization.
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Affiliation(s)
- Leïla Tirichine
- Laboratoire de Biologie Cellulaire, INRA UR 501, IJPB, Route de Saint-Cyr, F-78026 Versailles, France
- Institut des Sciences du Végétal, CNRS, avenue de la Terrasse, F-91198 Gif-sur-Yvette, France
| | - Philippe Andrey
- Neurobiologie de l'Olfaction et de la Prise Alimentaire, INRA UMR 1197, Domaine de Vilvert, F-78350 Jouy-en-Josas, France
- Université Paris-Sud 11, UMR 1197, F-91400 Orsay, France
- IFR 144 Neuro-Sud, Paris, France
- Université Pierre et Marie Curie, Paris, France
| | - Eric Biot
- Laboratoire de Biologie Cellulaire, INRA UR 501, IJPB, Route de Saint-Cyr, F-78026 Versailles, France
| | - Yves Maurin
- Neurobiologie de l'Olfaction et de la Prise Alimentaire, INRA UMR 1197, Domaine de Vilvert, F-78350 Jouy-en-Josas, France
- Université Paris-Sud 11, UMR 1197, F-91400 Orsay, France
- IFR 144 Neuro-Sud, Paris, France
| | - Valérie Gaudin
- Laboratoire de Biologie Cellulaire, INRA UR 501, IJPB, Route de Saint-Cyr, F-78026 Versailles, France
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Batram C, Baddeley D, Kreth G, Cremer C. High precision size measurement of centromere 8 and the 8q24/c-myc gene region in metaphase and interphase human fibroblasts indicate differential condensation. J Struct Biol 2008; 164:293-303. [PMID: 18835450 DOI: 10.1016/j.jsb.2008.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 09/05/2008] [Accepted: 09/05/2008] [Indexed: 11/28/2022]
Abstract
The hypothesis that distinct chromatin domains expand and are remodelled differently when they undergo transcription, replication or cell cycle processes is well accepted. The condensation changes by which chromosomes are transformed at the metaphase-interphase transition are especially interesting and therefore extensively studied by light microscopy; however, quantitative information of the size on specific small chromatin domains during the cell cycle is scarce. In this respect, a serious problem is the determination of structural features close to the resolution limit. In this report we use a novel approach to quantify the lateral extent of the 8q24/c-myc gene domain and the centromeric region of chromosome 8 in doubly labelled normal human foreskin fibroblasts using confocal laser scanning microscopy (CLSM). The domains were analysed in both metaphase spreads and interphase nuclei. These high precision measurements revealed a somewhat smaller (few 10s of nm) lateral extension of the centromere region in metaphase compared to interphase. Surprisingly, within the same cells the lateral extension of the 8q24/c-myc region was significantly smaller in interphase than in metaphase. For comparison the centromere size was more condensed in metaphase than in interphase. This implies a different folding behaviour for specific chromatin domains with opposite condensation behaviour.
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Affiliation(s)
- C Batram
- Applied Optics and Information Processing, Kirchhoff Institute of Physics, University of Heidelberg, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany.
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8
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Siegel TN, Hekstra DR, Cross GAM. Analysis of the Trypanosoma brucei cell cycle by quantitative DAPI imaging. Mol Biochem Parasitol 2008; 160:171-4. [PMID: 18501977 DOI: 10.1016/j.molbiopara.2008.04.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2008] [Revised: 03/27/2008] [Accepted: 04/04/2008] [Indexed: 11/25/2022]
Abstract
Trypanosoma brucei has two DNA compartments: the nucleus and the kinetoplast. DNA replication of these two compartments only partially coincides. Woodward and Gull [Woodward R, Gull K. Timing of nuclear and kinetoplast DNA replication and early morphological events in the cell cycle of Trypanosoma brucei. J Cell Sci 1990;95:49-57] comprehensively studied the relative timing of the replication and segregation of nuclear DNA (nDNA) and kinetoplast DNA (kDNA). Others have since assumed the consistency of morphological indicators of cell-cycle stage among strains and conditions. We report the use of quantitative DAPI imaging to determine the cell-cycle stage of individual procyclic cells. Using this approach, we found that kinetoplast elongation occurs mainly during nuclear S phase and not during G2, as previously assumed. We confirmed this finding by sorting cells by DNA content, followed by fluorescence microscopy. In addition, simultaneous quantitative imaging at two wavelengths can be used to determine the abundance of cell-cycle-regulated proteins during the cell cycle. We demonstrate this technique by co-staining for the non-acetylated state of lysine 4 of histone H4 (H4K4), which is enriched during nuclear S phase.
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Affiliation(s)
- T Nicolai Siegel
- Laboratory of Molecular Parasitology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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Kim IH, Nagel J, Otten S, Knerr B, Eils R, Rohr K, Dietzel S. Quantitative comparison of DNA detection by GFP-lac repressor tagging, fluorescence in situ hybridization and immunostaining. BMC Biotechnol 2007; 7:92. [PMID: 18096031 PMCID: PMC2254608 DOI: 10.1186/1472-6750-7-92] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Accepted: 12/20/2007] [Indexed: 11/26/2022] Open
Abstract
Background GFP-fusion proteins and immunostaining are methods broadly applied to investigate the three-dimensional organization of cells and cell nuclei, the latter often studied in addition by fluorescence in situ hybridization (FISH). Direct comparisons of these detection methods are scarce, however. Results We provide a quantitative comparison of all three approaches. We make use of a cell line that contains a transgene array of lac operator repeats which are detected by GFP-lac repressor fusion proteins. Thus we can detect the same structure in individual cells by GFP fluorescence, by antibodies against GFP and by FISH with a probe against the transgene array. Anti-GFP antibody detection was repeated after FISH. Our results show that while all four signals obtained from a transgene array generally showed qualitative and quantitative similarity, they also differed in details. Conclusion Each of the tested methods revealed particular strengths and weaknesses, which should be considered when interpreting respective experimental results. Despite the required denaturation step, FISH signals in structurally preserved cells show a surprising similarity to signals generated before denaturation.
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Affiliation(s)
- Il-Han Kim
- University of Heidelberg, BIOQUANT, IPMB, and German Cancer Research Center (DKFZ), Dept. Bioinformatics and FunctionalGenomics, Biomedical Computer Vision Group, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.
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10
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Schwarz-Finsterle J, Stein S, Grossmann C, Schmitt E, Trakhtenbrot L, Rechavi G, Amariglio N, Cremer C, Hausmann M. Comparison of triple helical COMBO-FISH and standard FISH by means of quantitative microscopic image analysis of abl/bcr positions in cell nuclei. ACTA ACUST UNITED AC 2007; 70:397-406. [PMID: 17069891 DOI: 10.1016/j.jbbm.2006.09.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Revised: 06/28/2006] [Accepted: 09/07/2006] [Indexed: 01/07/2023]
Abstract
In this study, a novel DNA fluorescence labelling technique, called triple helical COMBO-FISH (Combinatorial Oligo Fluorescence In Situ Hybridisation), was compared to the standard FISH (Fluorescence In Situ Hybridisation by means of commercially available probe kits) by quantitative evaluation of the nuclear position of the hybridisation signals of the Abelson murine leukaemia (abl) region and the breakpoint cluster region (bcr) in 3D-conserved cell nuclei of lymphocytes and CML blood cells. Two sets of 31 homopyrimidine oligonucleotides each, corresponding to co-localising sequences in the abl region of chromosome 9 and in the bcr region of chromosome 22 were synthesised. Probe types and sizes (in bases) as well as the binding mechanisms of both FISH techniques were completely different. In accordance to established findings that cell type specific radial positioning of chromosomes and sub-chromosomal elements is evolutionarily conserved, no significant difference was found between the two FISH techniques for the radial localisation of the barycentre of the analysed genomic loci. Thermal denaturation and hypotonic treatment of cell nuclei subjected to standard FISH, however, led to different absolute radii and volumes of the cell nuclei, in comparison to the quantities determined for the triple helical COMBO-FISH technique; the chromatin appears to shrink in laterally enlarged, flat nuclei. Consequently, the absolute distances of the homologous labelled sites shifted to greater values. For precise quantitative microscopic analysis of genomic loci, fluorescence labelling procedures are recommended that well maintain the native chromatin topology. Triple helical COMBO-FISH may offer such an approach.
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MESH Headings
- Base Sequence
- Case-Control Studies
- Cell Nucleus/genetics
- Chromosomes, Artificial, Bacterial/genetics
- Chromosomes, Human, Pair 22/genetics
- Chromosomes, Human, Pair 9/genetics
- DNA Probes/genetics
- Genes, abl
- Humans
- In Situ Hybridization, Fluorescence/methods
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Lymphocytes/ultrastructure
- Proto-Oncogene Proteins c-bcr/genetics
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Affiliation(s)
- Jutta Schwarz-Finsterle
- Kirchhoff-Institute of Physics, University of Heidelberg, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
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11
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Hepperger C, Otten S, von Hase J, Dietzel S. Preservation of large-scale chromatin structure in FISH experiments. Chromosoma 2006; 116:117-33. [PMID: 17119992 PMCID: PMC1824788 DOI: 10.1007/s00412-006-0084-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Revised: 08/11/2006] [Accepted: 09/23/2006] [Indexed: 02/01/2023]
Abstract
The nuclear organization of specific endogenous chromatin regions can be investigated only by fluorescence in situ hybridization (FISH). One of the two fixation procedures is typically applied: (1) buffered formaldehyde or (2) hypotonic shock with methanol acetic acid fixation followed by dropping of nuclei on glass slides and air drying. In this study, we compared the effects of these two procedures and some variations on nuclear morphology and on FISH signals. We analyzed mouse erythroleukemia and mouse embryonic stem cells because their clusters of subcentromeric heterochromatin provide an easy means to assess preservation of chromatin. Qualitative and quantitative analyses revealed that formaldehyde fixation provided good preservation of large-scale chromatin structures, while classical methanol acetic acid fixation after hypotonic treatment severely impaired nuclear shape and led to disruption of chromosome territories, heterochromatin structures, and large transgene arrays. Our data show that such preparations do not faithfully reflect in vivo nuclear architecture.
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Affiliation(s)
- Claudia Hepperger
- Department Biologie II, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Simone Otten
- Department Biologie II, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Johann von Hase
- Kirchhoff Institut für Physik, Universität Heidelberg, Heidelberg, Germany
| | - Steffen Dietzel
- Department Biologie II, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
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12
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Solovei I, Cavallo A, Schermelleh L, Jaunin F, Scasselati C, Cmarko D, Cremer C, Fakan S, Cremer T. Spatial preservation of nuclear chromatin architecture during three-dimensional fluorescence in situ hybridization (3D-FISH). Exp Cell Res 2002; 276:10-23. [PMID: 11978004 DOI: 10.1006/excr.2002.5513] [Citation(s) in RCA: 209] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
3D-FISH has become a major tool for studying the higher order chromatin organization in the cell nucleus. It is not clear, however, to what extent chromatin arrangement in the nucleus after fixation and 3D-FISH still reflects the order in living cells. To study this question, we compared higher order chromatin arrangements in living cells with those found after the 3D-FISH procedure. For in vivo studies we employed replication labeling of DNA with Cy3-conjugated nucleotides and/or chromatin labeling by GFP-tagged histone 2B. At the light microscope level, we compared the intranuclear distribution of H2B-GFP-tagged chromatin and the positions of replication-labeled chromatin domains in the same individual cells in vivo, after fixation with 4% paraformaldehyde, and after 3D-FISH. Light microscope data demonstrate a high degree of preservation of the spatial arrangement of approximately 1-Mb chromatin domains. Subsequent electron microscope investigations of chromatin structure showed strong alterations in the ultrastructure of the nucleus caused mainly by the heat denaturation step. Through this step chromatin acquires the appearance of a net with mesh size of 50-200 nm roughly corresponding to the average displacement of the chromatin domains observed at light microscope level. We conclude that 3D-FISH is a useful tool to study chromosome territory structure and arrangements down to the level of approximately 1-Mb chromatin domain positions. However, important ultrastructural details of the chromatin architecture are destroyed by the heat denaturation step, thus putting a limit to the usefulness of 3D-FISH analyses at nanometer scales.
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Affiliation(s)
- Irina Solovei
- Department of Biology II, Ludwig-Maximilians University of Munich, Germany.
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Hazzouri M, Rousseaux S, Mongelard F, Usson Y, Pelletier R, Faure AK, Vourc'h C, Sèle B. Genome organization in the human sperm nucleus studied by FISH and confocal microscopy. Mol Reprod Dev 2000; 55:307-15. [PMID: 10657050 DOI: 10.1002/(sici)1098-2795(200003)55:3<307::aid-mrd9>3.0.co;2-p] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The sperm nucleus has a unique chromatin structure where the DNA is highly condensed and associated with specific proteins, the protamines. It is a nondividing cell which is also transcriptionally inactive. After fusion with an oocyte, the sperm nucleus undergoes decondensation and, in the same time, starts replication and transcription. It has been suggested that somatic chromosomes during interphase are organized in territories which display a cell type and cell cycle specific distribution. The purpose of this work was to investigate whether chromosomes would also have a specific distribution in the sperm nucleus, which could be related to its inactive state, and have implications on the early stages of fertilization. In the present study, centromeric and telomeric sequences were detected by fluorescent techniques performed on human decondensed spermatozoa. Chromosome painting probes were used to detect the chromosome X and chromosome 13 on interphase sperm nuclei. The fluorescent signals were captured in 3D with a confocal microscope. For each of these chromatin structures, the volume, position, and distribution of the signals were analyzed in samples of 30 nuclei with the help of image analysis software. The centromeres appeared grouped in several foci that were randomly distributed within the sperm nucleus. The telomeres gave an approximately haploid number of small signals, evenly distributed throughout the nucleus. The chromosomes X and 13 occupied 4.7% and 3. 7% of the total nuclear volume, respectively. Interestingly, the X chromosome territory showed a preferential position in the anterior half of the volume of the nucleus, whereas chromosome 13 had a random position. This work shows a particular distribution of chromosome territories in the human sperm nucleus that could be related to mechanisms implicated in its specific functions. The analysis of more chromosomes and chromosomal structures, including the Y chromosome, would help to understand the structure of the human sperm chromatin, and its fundamental and clinical implications.
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Affiliation(s)
- M Hazzouri
- Unité INSERM U309, UJF, Institut Albert Bonniot, Faculté de Médecine de Grenoble, Domaine de la Merci, La Tronche, France
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Capparelli R, Cottone C, D'Apice L, Viscardi M, Iannelli D. Reply to the letter by dr. vinogradov. CYTOMETRY 1999; 37:246. [PMID: 10520207 DOI: 10.1002/(sici)1097-0320(19991101)37:3<246::aid-cyto13>3.0.co;2-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- R Capparelli
- Facolta di Agraria, Universita Degli Studi di Napoli Federico II, Naples, Italy
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