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Cremer C, Schock F, Failla AV, Birk U. Modulated illumination microscopy: Application perspectives in nuclear nanostructure analysis. J Microsc 2024. [PMID: 38618985 DOI: 10.1111/jmi.13297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 02/26/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024]
Abstract
The structure of the cell nucleus of higher organisms has become a major topic of advanced light microscopy. So far, a variety of methods have been applied, including confocal laser scanning fluorescence microscopy, 4Pi, STED and localisation microscopy approaches, as well as different types of patterned illumination microscopy, modulated either laterally (in the object plane) or axially (along the optical axis). Based on our experience, we discuss here some application perspectives of Modulated Illumination Microscopy (MIM) and its combination with single-molecule localisation microscopy (SMLM). For example, spatially modulated illumination microscopy/SMI (illumination modulation along the optical axis) has been used to determine the axial extension (size) of small, optically isolated fluorescent objects between ≤ 200 nm and ≥ 40 nm diameter with a precision down to the few nm range; it also allows the axial positioning of such structures down to the 1 nm scale; combined with laterally structured illumination/SIM, a 3D localisation precision of ≤1 nm is expected using fluorescence yields typical for SMLM applications. Together with the nanosizing capability of SMI, this can be used to analyse macromolecular nuclear complexes with a resolution approaching that of cryoelectron microscopy.
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Affiliation(s)
- Christoph Cremer
- Kirchhoff Institute for Physics (KIP), Heidelberg, Germany
- Interdisciplinary Centre for Scientific Computing (IWR), University of Heidelberg, Heidelberg, Germany
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Florian Schock
- Kirchhoff Institute for Physics (KIP), Heidelberg, Germany
| | - Antonio Virgilio Failla
- UKE Microscopy Imaging Facility, University Medical Centre Hamburg Eppendorf, Hamburg, Germany
| | - Udo Birk
- Institute for Photonics and Robotics (IPR), Department of Applied Future Technologies, University of Applied Sciences of the Grisons (FH Graubünden), Chur, Switzerland
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2
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Inguscio CR, Lacavalla MA, Cisterna B, Zancanaro C, Malatesta M. Physical Training Chronically Stimulates the Motor Neuron Cell Nucleus in the Ts65Dn Mouse, a Model of Down Syndrome. Cells 2023; 12:1488. [PMID: 37296609 PMCID: PMC10252427 DOI: 10.3390/cells12111488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/20/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Down syndrome (DS) is a genetically-based disease based on the trisomy of chromosome 21 (Hsa21). DS is characterized by intellectual disability in association with several pathological traits among which early aging and altered motor coordination are prominent. Physical training or passive exercise were found to be useful in counteracting motor impairment in DS subjects. In this study we used the Ts65Dn mouse, a widely accepted animal model of DS, to investigate the ultrastructural architecture of the medullary motor neuron cell nucleus taken as marker of the cell functional state. Using transmission electron microscopy, ultrastructural morphometry, and immunocytochemistry we carried out a detailed investigation of possible trisomy-related alteration(s) of nuclear constituents, which are known to vary their amount and distribution as a function of nuclear activity, as well as the effect of adapted physical training upon them. Results demonstrated that trisomy per se affects nuclear constituents to a limited extent; however, adapted physical training is able to chronically stimulate pre-mRNA transcription and processing activity in motor neuron nuclei of trisomic mice, although to a lesser extent than in their euploid mates. These findings are a step towards understanding the mechanisms underlying the positive effect of physical activity in DS.
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Affiliation(s)
| | | | | | - Carlo Zancanaro
- Department of Neurosciences, Biomedicine and Movement Sciences, Anatomy and Histology Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy; (C.R.I.); (M.A.L.); (B.C.); (M.M.)
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3
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Cremer C, Birk U. Spatially modulated illumination microscopy: application perspectives in nuclear nanostructure analysis. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A: MATHEMATICAL, PHYSICAL AND ENGINEERING SCIENCES 2022; 380:20210152. [PMID: 0 DOI: 10.1098/rsta.2021.0152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/02/2021] [Indexed: 05/19/2023]
Abstract
Thousands of genes and the complex biochemical networks for their transcription are packed in the micrometer sized cell nucleus. To control biochemical processes, spatial organization plays a key role. Hence the structure of the cell nucleus of higher organisms has emerged as a main topic of advanced light microscopy. So far, a variety of methods have been applied for this, including confocal laser scanning fluorescence microscopy, 4Pi-, STED- and localization microscopy approaches, as well as (laterally) structured illumination microscopy (SIM). Here, we summarize the state of the art and discuss application perspectives for nuclear nanostructure analysis of spatially modulated illumination (SMI). SMI is a widefield-based approach to using axially structured illumination patterns to determine the axial extension (size) of small, optically isolated fluorescent objects between less than or equal to 200 nm and greater than or equal to 40 nm diameter with a precision down to the few nm range; in addition, it allows the axial positioning of such structures down to the 1 nm scale. Combined with SIM, a three-dimensional localization precision of less than or equal to 1 nm is expected to become feasible using fluorescence yields typical for single molecule localization microscopy applications. Together with its nanosizing capability, this may eventually be used to analyse macromolecular complexes and other nanostructures with a topological resolution, further narrowing the gap to Cryoelectron microscopy.
This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 2)’.
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Affiliation(s)
- Christoph Cremer
- Max-Planck Institute for Polymer Research, and Institute of Molecular Biology (IMB), D-55128 Mainz, Germany
- Kirchhoff Institute for Physics (KIP), Interdisciplinary Center for Scientific Computing (IWR), and Institute of Pharmacy and Molecular Biotechnology (IPMB), University Heidelberg, D-69120 Heidelberg, Germany
| | - Udo Birk
- Institute for Photonics and ICT (IPI), University of Applied Sciences (FH Graubünden), CH-7000 Chur, Switzerland
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Lorber D, Volk T. Evaluation of chromatin mesoscale organization. APL Bioeng 2022; 6:010902. [PMID: 35071965 PMCID: PMC8758204 DOI: 10.1063/5.0069286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/29/2021] [Indexed: 11/21/2022] Open
Abstract
Chromatin organization in the nucleus represents an important aspect of transcription regulation. Most of the studies so far focused on the chromatin structure in cultured cells or in fixed tissue preparations. Here, we discuss the various approaches for deciphering chromatin 3D organization with an emphasis on the advantages of live imaging approaches.
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Affiliation(s)
- Dana Lorber
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Talila Volk
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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Maslova A, Krasikova A. FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains. Front Cell Dev Biol 2021; 9:753097. [PMID: 34805161 PMCID: PMC8597843 DOI: 10.3389/fcell.2021.753097] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
The intimate relationships between genome structure and function direct efforts toward deciphering three-dimensional chromatin organization within the interphase nuclei at different genomic length scales. For decades, major insights into chromatin structure at the level of large-scale euchromatin and heterochromatin compartments, chromosome territories, and subchromosomal regions resulted from the evolution of light microscopy and fluorescence in situ hybridization. Studies of nanoscale nucleosomal chromatin organization benefited from a variety of electron microscopy techniques. Recent breakthroughs in the investigation of mesoscale chromatin structures have emerged from chromatin conformation capture methods (C-methods). Chromatin has been found to form hierarchical domains with high frequency of local interactions from loop domains to topologically associating domains and compartments. During the last decade, advances in super-resolution light microscopy made these levels of chromatin folding amenable for microscopic examination. Here we are reviewing recent developments in FISH-based approaches for detection, quantitative measurements, and validation of contact chromatin domains deduced from C-based data. We specifically focus on the design and application of Oligopaint probes, which marked the latest progress in the imaging of chromatin domains. Vivid examples of chromatin domain FISH-visualization by means of conventional, super-resolution light and electron microscopy in different model organisms are provided.
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Affiliation(s)
| | - Alla Krasikova
- Laboratory of Nuclear Structure and Dynamics, Cytology and Histology Department, Saint Petersburg State University, Saint Petersburg, Russia
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Xie L, Liu Z. Single-cell imaging of genome organization and dynamics. Mol Syst Biol 2021; 17:e9653. [PMID: 34232558 PMCID: PMC8262488 DOI: 10.15252/msb.20209653] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/13/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
Probing the architecture, mechanism, and dynamics of genome folding is fundamental to our understanding of genome function in homeostasis and disease. Most chromosome conformation capture studies dissect the genome architecture with population- and time-averaged snapshots and thus have limited capabilities to reveal 3D nuclear organization and dynamics at the single-cell level. Here, we discuss emerging imaging techniques ranging from light microscopy to electron microscopy that enable investigation of genome folding and dynamics at high spatial and temporal resolution. Results from these studies complement genomic data, unveiling principles underlying the spatial arrangement of the genome and its potential functional links to diverse biological activities in the nucleus.
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Affiliation(s)
- Liangqi Xie
- Janelia Research CampusHoward Hughes Medical InstituteAshburnVAUSA
| | - Zhe Liu
- Janelia Research CampusHoward Hughes Medical InstituteAshburnVAUSA
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Hoboth P, Šebesta O, Hozák P. How Single-Molecule Localization Microscopy Expanded Our Mechanistic Understanding of RNA Polymerase II Transcription. Int J Mol Sci 2021; 22:6694. [PMID: 34206594 PMCID: PMC8269275 DOI: 10.3390/ijms22136694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 11/16/2022] Open
Abstract
Classical models of gene expression were built using genetics and biochemistry. Although these approaches are powerful, they have very limited consideration of the spatial and temporal organization of gene expression. Although the spatial organization and dynamics of RNA polymerase II (RNAPII) transcription machinery have fundamental functional consequences for gene expression, its detailed studies have been abrogated by the limits of classical light microscopy for a long time. The advent of super-resolution microscopy (SRM) techniques allowed for the visualization of the RNAPII transcription machinery with nanometer resolution and millisecond precision. In this review, we summarize the recent methodological advances in SRM, focus on its application for studies of the nanoscale organization in space and time of RNAPII transcription, and discuss its consequences for the mechanistic understanding of gene expression.
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Affiliation(s)
- Peter Hoboth
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic;
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic;
| | - Ondřej Šebesta
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic;
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic;
- Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
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8
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Cremer M, Brandstetter K, Maiser A, Rao SSP, Schmid VJ, Guirao-Ortiz M, Mitra N, Mamberti S, Klein KN, Gilbert DM, Leonhardt H, Cardoso MC, Aiden EL, Harz H, Cremer T. Cohesin depleted cells rebuild functional nuclear compartments after endomitosis. Nat Commun 2020; 11:6146. [PMID: 33262376 PMCID: PMC7708632 DOI: 10.1038/s41467-020-19876-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 10/28/2020] [Indexed: 01/05/2023] Open
Abstract
Cohesin plays an essential role in chromatin loop extrusion, but its impact on a compartmentalized nuclear architecture, linked to nuclear functions, is less well understood. Using live-cell and super-resolved 3D microscopy, here we find that cohesin depletion in a human colon cancer derived cell line results in endomitosis and a single multilobulated nucleus with chromosome territories pervaded by interchromatin channels. Chromosome territories contain chromatin domain clusters with a zonal organization of repressed chromatin domains in the interior and transcriptionally competent domains located at the periphery. These clusters form microscopically defined, active and inactive compartments, which likely correspond to A/B compartments, which are detected with ensemble Hi-C. Splicing speckles are observed nearby within the lining channel system. We further observe that the multilobulated nuclei, despite continuous absence of cohesin, pass through S-phase with typical spatio-temporal patterns of replication domains. Evidence for structural changes of these domains compared to controls suggests that cohesin is required for their full integrity.
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Affiliation(s)
- Marion Cremer
- Anthropology and Human Genomics, Department Biology II, Ludwig-Maximilians-Universität München, München, Germany.
| | - Katharina Brandstetter
- Human Biology & BioImaging, Center for Molecular Biosystems, Department Biology II, Ludwig-Maximilians-Universität München, München, Germany
| | - Andreas Maiser
- Human Biology & BioImaging, Center for Molecular Biosystems, Department Biology II, Ludwig-Maximilians-Universität München, München, Germany
| | - Suhas S P Rao
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Structural Biology, Stanford University School of Medicine, California, USA
| | - Volker J Schmid
- Bayesian Imaging and Spatial Statistics Group, Department of Statistics, Ludwig-Maximilians-Universität München, München, Germany
| | - Miguel Guirao-Ortiz
- Human Biology & BioImaging, Center for Molecular Biosystems, Department Biology II, Ludwig-Maximilians-Universität München, München, Germany
| | - Namita Mitra
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Stefania Mamberti
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Kyle N Klein
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Heinrich Leonhardt
- Human Biology & BioImaging, Center for Molecular Biosystems, Department Biology II, Ludwig-Maximilians-Universität München, München, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX, USA
| | - Hartmann Harz
- Human Biology & BioImaging, Center for Molecular Biosystems, Department Biology II, Ludwig-Maximilians-Universität München, München, Germany.
| | - Thomas Cremer
- Anthropology and Human Genomics, Department Biology II, Ludwig-Maximilians-Universität München, München, Germany.
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Meluzzi D, Arya G. Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data. Methods 2020; 181-182:24-34. [PMID: 31470090 PMCID: PMC7044057 DOI: 10.1016/j.ymeth.2019.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/24/2019] [Accepted: 08/23/2019] [Indexed: 02/08/2023] Open
Abstract
Chromosome conformation capture (3C) and its variants are powerful experimental techniques for probing intra- and inter-chromosomal interactions within cell nuclei at high resolution and in a high-throughput, quantitative manner. The contact maps derived from such experiments provide an avenue for inferring the 3D spatial organization of the genome. This review provides an overview of the various computational methods developed in the past decade for addressing the very important but challenging problem of deducing the detailed 3D structure or structure population of chromosomal domains, chromosomes, and even entire genomes from 3C contact maps.
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Affiliation(s)
- Dario Meluzzi
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, United States.
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Cremer T, Cremer M, Hübner B, Silahtaroglu A, Hendzel M, Lanctôt C, Strickfaden H, Cremer C. The Interchromatin Compartment Participates in the Structural and Functional Organization of the Cell Nucleus. Bioessays 2020; 42:e1900132. [PMID: 31994771 DOI: 10.1002/bies.201900132] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/24/2019] [Indexed: 12/11/2022]
Abstract
This article focuses on the role of the interchromatin compartment (IC) in shaping nuclear landscapes. The IC is connected with nuclear pore complexes (NPCs) and harbors splicing speckles and nuclear bodies. It is postulated that the IC provides routes for imported transcription factors to target sites, for export routes of mRNA as ribonucleoproteins toward NPCs, as well as for the intranuclear passage of regulatory RNAs from sites of transcription to remote functional sites (IC hypothesis). IC channels are lined by less-compacted euchromatin, called the perichromatin region (PR). The PR and IC together form the active nuclear compartment (ANC). The ANC is co-aligned with the inactive nuclear compartment (INC), comprising more compacted heterochromatin. It is postulated that the INC is accessible for individual transcription factors, but inaccessible for larger macromolecular aggregates (limited accessibility hypothesis). This functional nuclear organization depends on still unexplored movements of genes and regulatory sequences between the two compartments.
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Affiliation(s)
- Thomas Cremer
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Marion Cremer
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Barbara Hübner
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University (LMU), Biocenter, Grosshadernerstr. 2, 82152, Martinsried, Germany
| | - Asli Silahtaroglu
- Department of Cellular and Molecular Medicine Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, Byg.18.03, 2200, Copenhagen N, Denmark
| | - Michael Hendzel
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada
| | - Christian Lanctôt
- Integration Santé, 1250 Avenue de la Station local 2-304, Shawinigan, Québec, G9N 8K9, Canada
| | - Hilmar Strickfaden
- Department of Oncology, Cross Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada
| | - Christoph Cremer
- Institute of Molecular Biology (IMB) Ackermannweg 4, 55128 Mainz, Germany, and Institute of Pharmacy & Molecular Biotechnology (IPMB), University Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
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Heurteau A, Perrois C, Depierre D, Fosseprez O, Humbert J, Schaak S, Cuvier O. Insulator-based loops mediate the spreading of H3K27me3 over distant micro-domains repressing euchromatin genes. Genome Biol 2020; 21:193. [PMID: 32746892 PMCID: PMC7397589 DOI: 10.1186/s13059-020-02106-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 07/14/2020] [Indexed: 12/16/2022] Open
Abstract
Abstract
Background
Chromosomes are subdivided spatially to delimit long-range interactions into topologically associating domains (TADs). TADs are often flanked by chromatin insulators and transcription units that may participate in such demarcation. Remarkably, single-cell Drosophila TAD units correspond to dynamic heterochromatin nano-compartments that can self-assemble. The influence of insulators on such dynamic compartmentalization remains unclear. Moreover, to what extent heterochromatin domains are fully compartmentalized away from active genes remains unclear from Drosophila to human.
Results
Here, we identify H3K27me3 micro-domains genome-wide in Drosophila, which are attributed to the three-dimensional spreading of heterochromatin marks into euchromatin. Whereas depletion of insulator proteins increases H3K27me3 spreading locally, across heterochromatin borders, it concomitantly decreases H3K27me3 levels at distant micro-domains discrete sites. Quantifying long-range interactions suggests that random interactions between heterochromatin TADs and neighbor euchromatin cannot predict the presence of micro-domains, arguing against the hypothesis that they reflect defects in self-folding or in insulating repressive TADs. Rather, micro-domains are predicted by specific long-range interactions with the TAD borders bound by insulator proteins and co-factors required for looping. Accordingly, H3K27me3 spreading to distant sites is impaired by insulator mutants that compromise recruitment of looping co-factors. Both depletions and insulator mutants significantly reduce H3K27me3 micro-domains, deregulating the flanking genes.
Conclusions
Our data highlight a new regulatory mode of H3K27me3 by insulator-based long-range interactions controlling distant euchromatic genes.
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Affiliation(s)
- Alexandre Heurteau
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology (CBI), Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université Fédérale Paul Sabatier de Toulouse (UPS), F-31000, Toulouse, France
| | - Charlène Perrois
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology (CBI), Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université Fédérale Paul Sabatier de Toulouse (UPS), F-31000, Toulouse, France
| | - David Depierre
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology (CBI), Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université Fédérale Paul Sabatier de Toulouse (UPS), F-31000, Toulouse, France
| | - Olivier Fosseprez
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology (CBI), Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université Fédérale Paul Sabatier de Toulouse (UPS), F-31000, Toulouse, France
| | - Jonathan Humbert
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology (CBI), Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université Fédérale Paul Sabatier de Toulouse (UPS), F-31000, Toulouse, France
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre Hospitalier Universitaire de Québec City, Quebec, QC, G1R 3S3, Canada
| | - Stéphane Schaak
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology (CBI), Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université Fédérale Paul Sabatier de Toulouse (UPS), F-31000, Toulouse, France
| | - Olivier Cuvier
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology (CBI), Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université Fédérale Paul Sabatier de Toulouse (UPS), F-31000, Toulouse, France.
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Schubert V, Neumann P, Marques A, Heckmann S, Macas J, Pedrosa-Harand A, Schubert I, Jang TS, Houben A. Super-Resolution Microscopy Reveals Diversity of Plant Centromere Architecture. Int J Mol Sci 2020; 21:E3488. [PMID: 32429054 PMCID: PMC7278974 DOI: 10.3390/ijms21103488] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/11/2020] [Accepted: 05/11/2020] [Indexed: 12/20/2022] Open
Abstract
Centromeres are essential for proper chromosome segregation to the daughter cells during mitosis and meiosis. Chromosomes of most eukaryotes studied so far have regional centromeres that form primary constrictions on metaphase chromosomes. These monocentric chromosomes vary from point centromeres to so-called "meta-polycentromeres", with multiple centromere domains in an extended primary constriction, as identified in Pisum and Lathyrus species. However, in various animal and plant lineages centromeres are distributed along almost the entire chromosome length. Therefore, they are called holocentromeres. In holocentric plants, centromere-specific proteins, at which spindle fibers usually attach, are arranged contiguously (line-like), in clusters along the chromosomes or in bands. Here, we summarize findings of ultrastructural investigations using immunolabeling with centromere-specific antibodies and super-resolution microscopy to demonstrate the structural diversity of plant centromeres. A classification of the different centromere types has been suggested based on the distribution of spindle attachment sites. Based on these findings we discuss the possible evolution and advantages of holocentricity, and potential strategies to segregate holocentric chromosomes correctly.
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Affiliation(s)
- Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany; (S.H.); (I.S.); (A.H.)
| | - Pavel Neumann
- Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; (P.N.); (J.M.); (T.-S.J.)
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany; (S.H.); (I.S.); (A.H.)
| | - Jiri Macas
- Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; (P.N.); (J.M.); (T.-S.J.)
| | - Andrea Pedrosa-Harand
- Department of Botany, Federal University of Pernambuco (UFPE), Recife 50670-901, Pernambuco, Brazil;
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany; (S.H.); (I.S.); (A.H.)
| | - Tae-Soo Jang
- Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic; (P.N.); (J.M.); (T.-S.J.)
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany; (S.H.); (I.S.); (A.H.)
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Szalaj P, Plewczynski D. Three-dimensional organization and dynamics of the genome. Cell Biol Toxicol 2018; 34:381-404. [PMID: 29568981 PMCID: PMC6133016 DOI: 10.1007/s10565-018-9428-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/11/2018] [Indexed: 12/30/2022]
Abstract
Genome is a complex hierarchical structure, and its spatial organization plays an important role in its function. Chromatin loops and topological domains form the basic structural units of this multiscale organization and are essential to orchestrate complex regulatory networks and transcription mechanisms. They also form higher-order structures such as chromosomal compartments and chromosome territories. Each level of this intrinsic architecture is governed by principles and mechanisms that we only start to understand. In this review, we summarize the current view of the genome architecture on the scales ranging from chromatin loops to the whole genome. We describe cell-to-cell variability, links between genome reorganization and various genomic processes, such as chromosome X inactivation and cell differentiation, and the interplay between different experimental techniques.
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Affiliation(s)
- Przemyslaw Szalaj
- Centre for Innovative Research, Medical University of Bialystok, Białystok, Poland.
- I-BioStat, Hasselt University, Hasselt, Belgium.
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.
| | - Dariusz Plewczynski
- Centre for Innovative Research, Medical University of Bialystok, Białystok, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
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Cremer T, Cremer M, Cremer C. The 4D Nucleome: Genome Compartmentalization in an Evolutionary Context. BIOCHEMISTRY (MOSCOW) 2018; 83:313-325. [PMID: 29626919 DOI: 10.1134/s000629791804003x] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
4D nucleome research aims to understand the impact of nuclear organization in space and time on nuclear functions, such as gene expression patterns, chromatin replication, and the maintenance of genome integrity. In this review we describe evidence that the origin of 4D genome compartmentalization can be traced back to the prokaryotic world. In cell nuclei of animals and plants chromosomes occupy distinct territories, built up from ~1 Mb chromatin domains, which in turn are composed of smaller chromatin subdomains and also form larger chromatin domain clusters. Microscopic evidence for this higher order chromatin landscape was strengthened by chromosome conformation capture studies, in particular Hi-C. This approach demonstrated ~1 Mb sized, topologically associating domains in mammalian cell nuclei separated by boundaries. Mutations, which destroy boundaries, can result in developmental disorders and cancer. Nucleosomes appeared first as tetramers in the Archaea kingdom and later evolved to octamers built up each from two H2A, two H2B, two H3, and two H4 proteins. Notably, nucleosomes were lost during the evolution of the Dinoflagellata phylum. Dinoflagellate chromosomes remain condensed during the entire cell cycle, but their chromosome architecture differs radically from the architecture of other eukaryotes. In summary, the conservation of fundamental features of higher order chromatin arrangements throughout the evolution of metazoan animals suggests the existence of conserved, but still unknown mechanism(s) controlling this architecture. Notwithstanding this conservation, a comparison of metazoans and protists also demonstrates species-specific structural and functional features of nuclear organization.
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Affiliation(s)
- T Cremer
- Biocenter, Department of Biology II, Ludwig Maximilian University (LMU), Munich, Germany.
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Cremer C, Szczurek A, Schock F, Gourram A, Birk U. Super-resolution microscopy approaches to nuclear nanostructure imaging. Methods 2017; 123:11-32. [PMID: 28390838 DOI: 10.1016/j.ymeth.2017.03.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/23/2017] [Indexed: 12/14/2022] Open
Abstract
The human genome has been decoded, but we are still far from understanding the regulation of all gene activities. A largely unexplained role in these regulatory mechanisms is played by the spatial organization of the genome in the cell nucleus which has far-reaching functional consequences for gene regulation. Until recently, it appeared to be impossible to study this problem on the nanoscale by light microscopy. However, novel developments in optical imaging technology have radically surpassed the limited resolution of conventional far-field fluorescence microscopy (ca. 200nm). After a brief review of available super-resolution microscopy (SRM) methods, we focus on a specific SRM approach to study nuclear genome structure at the single cell/single molecule level, Spectral Precision Distance/Position Determination Microscopy (SPDM). SPDM, a variant of localization microscopy, makes use of conventional fluorescent proteins or single standard organic fluorophores in combination with standard (or only slightly modified) specimen preparation conditions; in its actual realization mode, the same laser frequency can be used for both photoswitching and fluorescence read out. Presently, the SPDM method allows us to image nuclear genome organization in individual cells down to few tens of nanometer (nm) of structural resolution, and to perform quantitative analyses of individual small chromatin domains; of the nanoscale distribution of histones, chromatin remodeling proteins, and transcription, splicing and repair related factors. As a biomedical research application, using dual-color SPDM, it became possible to monitor in mouse cardiomyocyte cells quantitatively the effects of ischemia conditions on the chromatin nanostructure (DNA). These novel "molecular optics" approaches open an avenue to study the nuclear landscape directly in individual cells down to the single molecule level and thus to test models of functional genome architecture at unprecedented resolution.
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Affiliation(s)
- Christoph Cremer
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany; Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany. http://www.optics.imb-mainz.de
| | - Aleksander Szczurek
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Florian Schock
- Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany
| | - Amine Gourram
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Udo Birk
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany; Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany
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Schmid VJ, Cremer M, Cremer T. Quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy. Methods 2017; 123:33-46. [PMID: 28323041 DOI: 10.1016/j.ymeth.2017.03.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/16/2017] [Accepted: 03/10/2017] [Indexed: 01/20/2023] Open
Abstract
Recent advancements of super-resolved fluorescence microscopy have revolutionized microscopic studies of cells, including the exceedingly complex structural organization of cell nuclei in space and time. In this paper we describe and discuss tools for (semi-) automated, quantitative 3D analyses of the spatial nuclear organization. These tools allow the quantitative assessment of highly resolved different chromatin compaction levels in individual cell nuclei, which reflect functionally different regions or sub-compartments of the 3D nuclear landscape, and measurements of absolute distances between sites of different chromatin compaction. In addition, these tools allow 3D mapping of specific DNA/RNA sequences and nuclear proteins relative to the 3D chromatin compaction maps and comparisons of multiple cell nuclei. The tools are available in the free and open source R packages nucim and bioimagetools. We discuss the use of masks for the segmentation of nuclei and the use of DNA stains, such as DAPI, as a proxy for local differences in chromatin compaction. We further discuss the limitations of 3D maps of the nuclear landscape as well as problems of the biological interpretation of such data.
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Affiliation(s)
- Volker J Schmid
- BioImaging Group, Department of Statistics, Ludwig Maximilians-Universität München, Ludwigstrasse 33, 80539 Munich, Germany.
| | - Marion Cremer
- Biocenter, Department Biology II, Ludwig Maximilians-Universität München, Großhadernerstrasse 2, 82152 Martinsried, Germany.
| | - Thomas Cremer
- Biocenter, Department Biology II, Ludwig Maximilians-Universität München, Großhadernerstrasse 2, 82152 Martinsried, Germany.
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Sathitruangsak C, Righolt CH, Klewes L, Tung Chang D, Kotb R, Mai S. Distinct and shared three-dimensional chromosome organization patterns in lymphocytes, monoclonal gammopathy of undetermined significance and multiple myeloma. Int J Cancer 2017; 140:400-410. [PMID: 27711972 PMCID: PMC5132008 DOI: 10.1002/ijc.30461] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 07/11/2016] [Accepted: 09/29/2016] [Indexed: 12/24/2022]
Abstract
The consistent appearance of specific chromosomal translocations in multiple myeloma has suggested that the positioning of chromosomes in the interphase nucleus might play a role in the occurrence of particular chromosomal rearrangements associated with malignant transformation. Using fluorescence in situ hybridization, we have determined the positions of selected chromosome pairs (18 and 19, 9 and 22, 4 and 14, 14 and 16, 11 and 14) in interphase nuclei of myeloma cells compared to normal lymphocytes of treatment-naïve patients. All chromosome pairs were arranged in a nonrandom pattern. Chromosomes commonly involved in myeloma-associated translocations (4 and 14, 14 and 16, 11 and 14) were found in close spatial proximity, and this is correlated with the occurrence of overlapping chromosome territories. The spatial distribution of chromosomes may increase the possibility of chromosomal translocations in multiple myeloma.
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Affiliation(s)
- Chirawadee Sathitruangsak
- Department of Cell BiologyUniversity of Manitoba, Research Institute of Hematology and Oncology, CancerCare ManitobaWinnipegManitobaCanada
- Division of Medical OncologyDepartment of Internal MedicinePrince of Songkla UniversitySongkhlaThailand
| | - Christiaan H. Righolt
- Department of Cell BiologyUniversity of Manitoba, Research Institute of Hematology and Oncology, CancerCare ManitobaWinnipegManitobaCanada
| | - Ludger Klewes
- Department of Cell BiologyUniversity of Manitoba, Research Institute of Hematology and Oncology, CancerCare ManitobaWinnipegManitobaCanada
- Department of Cell BiologyCancerCare Manitoba, Genomic Centre for Cancer Research and Diagnosis (GCCRD)WinnipegManitobaCanada
| | - Doris Tung Chang
- Department of Cell BiologyUniversity of Manitoba, Research Institute of Hematology and Oncology, CancerCare ManitobaWinnipegManitobaCanada
| | - Rami Kotb
- Department of HaematologyCancerCare ManitobaWinnipegManitobaCanada
| | - Sabine Mai
- Department of Cell BiologyUniversity of Manitoba, Research Institute of Hematology and Oncology, CancerCare ManitobaWinnipegManitobaCanada
- Department of Cell BiologyCancerCare Manitoba, Genomic Centre for Cancer Research and Diagnosis (GCCRD)WinnipegManitobaCanada
- Department of Physiology and PathophysiologyUniversity of ManitobaWinnipegManitobaCanada
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Schubert V. Super-resolution Microscopy - Applications in Plant Cell Research. FRONTIERS IN PLANT SCIENCE 2017; 8:531. [PMID: 28450874 PMCID: PMC5390026 DOI: 10.3389/fpls.2017.00531] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/24/2017] [Indexed: 05/10/2023]
Abstract
Most of the present knowledge about cell organization and function is based on molecular and genetic methods as well as cytological investigations. While electron microscopy allows identifying cell substructures until a resolution of ∼1 nm, the resolution of fluorescence microscopy is restricted to ∼200 nm due to the diffraction limit of light. However, the advantage of this technique is the possibility to identify and co-localize specifically labeled structures and molecules. The recently developed super-resolution microscopy techniques, such as Structured Illumination Microscopy, Photoactivated Localization Microscopy, Stochastic Optical Reconstruction Microscopy, and Stimulated Emission Depletion microscopy allow analyzing structures and molecules beyond the diffraction limit of light. Recently, there is an increasing application of these techniques in cell biology. This review evaluates and summarizes especially the data achieved until now in analyzing the organization and function of plant cells, chromosomes and interphase nuclei using super-resolution techniques.
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Wachsmuth M, Knoch TA, Rippe K. Dynamic properties of independent chromatin domains measured by correlation spectroscopy in living cells. Epigenetics Chromatin 2016; 9:57. [PMID: 28035241 PMCID: PMC5192577 DOI: 10.1186/s13072-016-0093-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 09/12/2016] [Indexed: 01/08/2023] Open
Abstract
Background Genome organization into subchromosomal topologically associating domains (TADs) is linked to cell-type-specific gene expression programs. However, dynamic properties of such domains remain elusive, and it is unclear how domain plasticity modulates genomic accessibility for soluble factors. Results Here, we combine and compare a high-resolution topology analysis of interacting chromatin loci with fluorescence correlation spectroscopy measurements of domain dynamics in single living cells. We identify topologically and dynamically independent chromatin domains of ~1 Mb in size that are best described by a loop-cluster polymer model. Hydrodynamic relaxation times and gyration radii of domains are larger for open (161 ± 15 ms, 297 ± 9 nm) than for dense chromatin (88 ± 7 ms, 243 ± 6 nm) and increase globally upon chromatin hyperacetylation or ATP depletion. Conclusions Based on the domain structure and dynamics measurements, we propose a loop-cluster model for chromatin domains. It suggests that the regulation of chromatin accessibility for soluble factors displays a significantly stronger dependence on factor concentration than search processes within a static network. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0093-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Malte Wachsmuth
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Tobias A Knoch
- Biophysical Genomics Group, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Karsten Rippe
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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Szczurek A, Xing J, Birk UJ, Cremer C. Single Molecule Localization Microscopy of Mammalian Cell Nuclei on the Nanoscale. Front Genet 2016; 7:114. [PMID: 27446198 PMCID: PMC4919319 DOI: 10.3389/fgene.2016.00114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 06/02/2016] [Indexed: 11/13/2022] Open
Abstract
Nuclear texture analysis is a well-established method of cellular pathology. It is hampered, however, by the limits of conventional light microscopy (ca. 200 nm). These limits have been overcome by a variety of super-resolution approaches. An especially promising approach to chromatin texture analysis is single molecule localization microscopy (SMLM) as it provides the highest resolution using fluorescent based methods. At the present state of the art, using fixed whole cell samples and standard DNA dyes, a structural resolution of chromatin in the 50–100 nm range is obtained using SMLM. We highlight how the combination of localization microscopy with standard fluorophores opens the avenue to a plethora of studies including the spatial distribution of DNA and associated proteins in eukaryotic cell nuclei with the potential to elucidate the functional organization of chromatin. These views are based on our experience as well as on recently published research in this field.
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Affiliation(s)
| | - Jun Xing
- Superresolution Microscopy, Institute of Molecular Biology Mainz, Germany
| | - Udo J Birk
- Superresolution Microscopy, Institute of Molecular BiologyMainz, Germany; Department of Physics, University of MainzMainz, Germany; Department of Physics, University of MainzMainz, Germany
| | - Christoph Cremer
- Superresolution Microscopy, Institute of Molecular BiologyMainz, Germany; Department of Physics, University of MainzMainz, Germany; Kirchhoff Institute of Physics, University of HeidelbergHeidelberg, Germany; Institute of Pharmacy and Molecular Biotechnology, University of HeidelbergHeidelberg, Germany
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Żurek-Biesiada D, Szczurek AT, Prakash K, Mohana GK, Lee HK, Roignant JY, Birk UJ, Dobrucki JW, Cremer C. Localization microscopy of DNA in situ using Vybrant ® DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution. Exp Cell Res 2016; 343:97-106. [DOI: 10.1016/j.yexcr.2015.08.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/27/2015] [Accepted: 08/30/2015] [Indexed: 12/17/2022]
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Dans PD, Walther J, Gómez H, Orozco M. Multiscale simulation of DNA. Curr Opin Struct Biol 2016; 37:29-45. [DOI: 10.1016/j.sbi.2015.11.011] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 01/05/2023]
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Franek M, Suchánková J, Sehnalová P, Krejčí J, Legartová S, Kozubek S, Večeřa J, Sorokin DV, Bártová E. Advanced Image Acquisition and Analytical Techniques for Studies of Living Cells and Tissue Sections. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2016; 22:326-341. [PMID: 26903193 DOI: 10.1017/s1431927616000052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Studies on fixed samples or genome-wide analyses of nuclear processes are useful for generating snapshots of a cell population at a particular time point. However, these experimental approaches do not provide information at the single-cell level. Genome-wide studies cannot assess variability between individual cells that are cultured in vitro or originate from different pathological stages. Immunohistochemistry and immunofluorescence are fundamental experimental approaches in clinical laboratories and are also widely used in basic research. However, the fixation procedure may generate artifacts and prevents monitoring of the dynamics of nuclear processes. Therefore, live-cell imaging is critical for studying the kinetics of basic nuclear events, such as DNA replication, transcription, splicing, and DNA repair. This review is focused on the advanced microscopy analyses of the cells, with a particular focus on live cells. We note some methodological innovations and new options for microscope systems that can also be used to study tissue sections. Cornerstone methods for the biophysical research of living cells, such as fluorescence recovery after photobleaching and fluorescence resonance energy transfer, are also discussed, as are studies on the effects of radiation at the individual cellular level.
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Affiliation(s)
- Michal Franek
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Jana Suchánková
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Petra Sehnalová
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Jana Krejčí
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Soňa Legartová
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Stanislav Kozubek
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | | | | | - Eva Bártová
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
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Esteves A, Knoll-Gellida A, Canclini L, Silvarrey MC, André M, Babin PJ. Fatty acid binding proteins have the potential to channel dietary fatty acids into enterocyte nuclei. J Lipid Res 2015; 57:219-32. [PMID: 26658423 DOI: 10.1194/jlr.m062232] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Indexed: 12/13/2022] Open
Abstract
Intracellular lipid binding proteins, including fatty acid binding proteins (FABPs) 1 and 2, are highly expressed in tissues involved in the active lipid metabolism. A zebrafish model was used to demonstrate differential expression levels of fabp1b.1, fabp1b.2, and fabp2 transcripts in liver, anterior intestine, and brain. Transcription levels of fabp1b.1 and fabp2 in the anterior intestine were upregulated after feeding and modulated according to diet formulation. Immunofluorescence and electron microscopy immunodetection with gold particles localized these FABPs in the microvilli, cytosol, and nuclei of most enterocytes in the anterior intestinal mucosa. Nuclear localization was mostly in the interchromatin space outside the condensed chromatin clusters. Native PAGE binding assay of BODIPY-FL-labeled FAs demonstrated binding of BODIPY-FLC(12) but not BODIPY-FLC(5) to recombinant Fabp1b.1 and Fabp2. The binding of BODIPY-FLC(12) to Fabp1b.1 was fully displaced by oleic acid. In vivo experiments demonstrated, for the first time, that intestinal absorption of dietary BODIPY-FLC(12) was followed by colocalization of the labeled FA with Fabp1b and Fabp2 in the nuclei. These data suggest that dietary FAs complexed with FABPs are able to reach the enterocyte nucleus with the potential to modulate nuclear activity.
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Affiliation(s)
- Adriana Esteves
- Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Anja Knoll-Gellida
- University Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), F-33615 Pessac, France INSERM, U1211, F-33076, Bordeaux, France
| | - Lucia Canclini
- Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | | | - Michèle André
- University Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), F-33615 Pessac, France INSERM, U1211, F-33076, Bordeaux, France
| | - Patrick J Babin
- University Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), F-33615 Pessac, France INSERM, U1211, F-33076, Bordeaux, France
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Hübner B, Lomiento M, Mammoli F, Illner D, Markaki Y, Ferrari S, Cremer M, Cremer T. Remodeling of nuclear landscapes during human myelopoietic cell differentiation maintains co-aligned active and inactive nuclear compartments. Epigenetics Chromatin 2015; 8:47. [PMID: 26579212 PMCID: PMC4647504 DOI: 10.1186/s13072-015-0038-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 10/26/2015] [Indexed: 01/08/2023] Open
Abstract
Background Previous studies of higher order chromatin organization in nuclei of mammalian species revealed both structural consistency and species-specific differences between cell lines and during early embryonic development. Here, we extended our studies to nuclear landscapes in the human myelopoietic lineage representing a somatic cell differentiation system. Our longterm goal is a search for structural features of nuclei, which are restricted to certain cell types/species, as compared to features, which are evolutionary highly conserved, arguing for their basic functional roles in nuclear organization. Results Common human hematopoietic progenitors, myeloid precursor cells, differentiated monocytes and granulocytes analyzed by super-resolution fluorescence microscopy and electron microscopy revealed profound differences with respect to global chromatin arrangements, the nuclear space occupied by the interchromatin compartment and the distribution of nuclear pores. In contrast, we noted a consistent organization in all cell types with regard to two co-aligned networks, an active (ANC) and an inactive (INC) nuclear compartment delineated by functionally relevant hallmarks. The ANC is enriched in active RNA polymerase II, splicing speckles and histone signatures for transcriptionally competent chromatin (H3K4me3), whereas the INC carries marks for repressed chromatin (H3K9me3). Conclusions Our findings substantiate the conservation of the recently published ANC-INC network model of mammalian nuclear organization during human myelopoiesis irrespective of profound changes of the global nuclear architecture observed during this differentiation process. According to this model, two spatially co-aligned and functionally interacting active and inactive nuclear compartments (ANC and INC) pervade the nuclear space. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0038-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Barbara Hübner
- Department Biology II, Biocenter, Ludwig Maximilians University (LMU), Grosshadernerstr. 2, 82152 Martinsried, Germany ; School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore, Singapore
| | - Mariana Lomiento
- Department of Life Sciences, University of Modena (Unimore), Modena, Italy
| | - Fabiana Mammoli
- Department of Life Sciences, University of Modena (Unimore), Modena, Italy
| | - Doris Illner
- Department Biology II, Biocenter, Ludwig Maximilians University (LMU), Grosshadernerstr. 2, 82152 Martinsried, Germany ; Bundeswehr Institute of Radiobiology, Munich, Germany
| | - Yolanda Markaki
- Department Biology II, Biocenter, Ludwig Maximilians University (LMU), Grosshadernerstr. 2, 82152 Martinsried, Germany
| | - Sergio Ferrari
- Department of Life Sciences, University of Modena (Unimore), Modena, Italy
| | - Marion Cremer
- Department Biology II, Biocenter, Ludwig Maximilians University (LMU), Grosshadernerstr. 2, 82152 Martinsried, Germany
| | - Thomas Cremer
- Department Biology II, Biocenter, Ludwig Maximilians University (LMU), Grosshadernerstr. 2, 82152 Martinsried, Germany
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27
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Kirmes I, Szczurek A, Prakash K, Charapitsa I, Heiser C, Musheev M, Schock F, Fornalczyk K, Ma D, Birk U, Cremer C, Reid G. A transient ischemic environment induces reversible compaction of chromatin. Genome Biol 2015; 16:246. [PMID: 26541514 PMCID: PMC4635527 DOI: 10.1186/s13059-015-0802-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/09/2015] [Indexed: 11/10/2022] Open
Abstract
Background Cells detect and adapt to hypoxic and nutritional stress through immediate transcriptional, translational and metabolic responses. The environmental effects of ischemia on chromatin nanostructure were investigated using single molecule localization microscopy of DNA binding dyes and of acetylated histones, by the sensitivity of chromatin to digestion with DNAseI, and by fluorescence recovery after photobleaching (FRAP) of core and linker histones. Results Short-term oxygen and nutrient deprivation of the cardiomyocyte cell line HL-1 induces a previously undescribed chromatin architecture, consisting of large, chromatin-sparse voids interspersed between DNA-dense hollow helicoid structures 40–700 nm in dimension. The chromatin compaction is reversible, and upon restitution of normoxia and nutrients, chromatin transiently adopts a more open structure than in untreated cells. The compacted state of chromatin reduces transcription, while the open chromatin structure induced upon recovery provokes a transitory increase in transcription. Digestion of chromatin with DNAseI confirms that oxygen and nutrient deprivation induces compaction of chromatin. Chromatin compaction is associated with depletion of ATP and redistribution of the polyamine pool into the nucleus. FRAP demonstrates that core histones are not displaced from compacted chromatin; however, the mobility of linker histone H1 is considerably reduced, to an extent that far exceeds the difference in histone H1 mobility between heterochromatin and euchromatin. Conclusions These studies exemplify the dynamic capacity of chromatin architecture to physically respond to environmental conditions, directly link cellular energy status to chromatin compaction and provide insight into the effect ischemia has on the nuclear architecture of cells. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0802-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ina Kirmes
- Institute for Molecular Biology, 55128, Mainz, Germany
| | | | - Kirti Prakash
- Institute for Molecular Biology, 55128, Mainz, Germany.,Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120, Heidelberg, Germany
| | | | | | | | | | - Karolina Fornalczyk
- Institute for Molecular Biology, 55128, Mainz, Germany.,Department of Molecular Biophysics, University of Łódź, Łódź, Poland
| | - Dongyu Ma
- Institute for Molecular Biology, 55128, Mainz, Germany.,Centre for Biomedicine and Medical Technology Mannheim (CBTM), University of Heidelberg, 68167, Mannheim, Germany
| | - Udo Birk
- Institute for Molecular Biology, 55128, Mainz, Germany
| | - Christoph Cremer
- Institute for Molecular Biology, 55128, Mainz, Germany. .,Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120, Heidelberg, Germany.
| | - George Reid
- Institute for Molecular Biology, 55128, Mainz, Germany.
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28
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Mizuguchi T, Barrowman J, Grewal SIS. Chromosome domain architecture and dynamic organization of the fission yeast genome. FEBS Lett 2015; 589:2975-86. [PMID: 26096785 PMCID: PMC4598268 DOI: 10.1016/j.febslet.2015.06.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 12/20/2022]
Abstract
Advanced techniques including the chromosome conformation capture (3C) methodology and its derivatives are complementing microscopy approaches to study genome organization, and are revealing new details of three-dimensional (3D) genome architecture at increasing resolution. The fission yeast Schizosaccharomyces pombe (S. pombe) comprises a small genome featuring organizational elements of more complex eukaryotic systems, including conserved heterochromatin assembly machinery. Here we review key insights into genome organization revealed in this model system through a variety of techniques. We discuss the predominant role of Rabl-like configuration for interphase chromosome organization and the dynamic changes that occur during mitosis and meiosis. High resolution Hi-C studies have also revealed the presence of locally crumpled chromatin regions called "globules" along chromosome arms, and implicated a critical role for pericentromeric heterochromatin in imposing fundamental constraints on the genome to maintain chromosome territoriality and stability. These findings have shed new light on the connections between genome organization and function. It is likely that insights gained from the S. pombe system will also broadly apply to higher eukaryotes.
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Affiliation(s)
- Takeshi Mizuguchi
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jemima Barrowman
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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29
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Popken J, Brero A, Koehler D, Schmid VJ, Strauss A, Wuensch A, Guengoer T, Graf A, Krebs S, Blum H, Zakhartchenko V, Wolf E, Cremer T. Reprogramming of fibroblast nuclei in cloned bovine embryos involves major structural remodeling with both striking similarities and differences to nuclear phenotypes of in vitro fertilized embryos. Nucleus 2015; 5:555-89. [PMID: 25482066 PMCID: PMC4615760 DOI: 10.4161/19491034.2014.979712] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Nuclear landscapes were studied during preimplantation development of bovine embryos, generated either by in vitro fertilization (IVF), or generated as cloned embryos by somatic cell nuclear transfer (SCNT) of bovine fetal fibroblasts, using 3-dimensional confocal laser scanning microscopy (3D-CLSM) and structured illumination microscopy (3D-SIM). Nuclear landscapes of IVF and SCNT embryonic nuclei were compared with each other and with fibroblast nuclei. We demonstrate that reprogramming of fibroblast nuclei in cloned embryos requires changes of their landscapes similar to nuclei of IVF embryos. On the way toward the 8-cell stage, where major genome activation occurs, a major lacuna, enriched with splicing factors, was formed in the nuclear interior and chromosome territories (CTs) were shifted toward the nuclear periphery. During further development the major lacuna disappeared and CTs were redistributed throughout the nuclear interior forming a contiguous higher order chromatin network. At all stages of development CTs of IVF and SCNT embryonic nuclei were built up from chromatin domain clusters (CDCs) pervaded by interchromatin compartment (IC) channels. Quantitative analyses revealed a highly significant enrichment of RNA polymerase II and H3K4me3, a marker for transcriptionally competent chromatin, at the periphery of CDCs. In contrast, H3K9me3, a marker for silent chromatin, was enriched in the more compacted interior of CDCs. Despite these striking similarities, we also detected major differences between nuclear landscapes of IVF and cloned embryos. Possible implications of these differences for the developmental potential of cloned animals remain to be investigated. We present a model, which integrates generally applicable structural and functional features of the nuclear landscape.
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Key Words
- 3D-CLSM, 3-dimensional confocal laser scanning microscopy
- 3D-SIM, 3-dimensional structured illumination microscopy
- B23, nucleophosmin B23
- BTA, Bos taurus
- CDC, chromatin domain cluster
- CT, chromosome territory
- EM, electron microscopy
- ENC, embryonic nuclei with conventional nuclear architecture
- ENP, embryonic nuclei with peripheral CT distribution
- H3K4me3
- H3K4me3, histone H3 with tri-methylated lysine 4
- H3K9me3
- H3K9me3, histone H3 with tri-methylated lysine 9
- H3S10p, histone H3 with phosphorylated serine 10
- IC, interchromatin compartment
- IVF, in vitro fertilization
- MCB, major chromatin body
- PR, perichromatin region
- RNA polymerase II
- RNA polymerase II-S2p, RNA polymerase II with phosphorylated serine 2 of its CTD domain
- RNA polymerase II-S5p, RNA polymerase II with phosphorylated serine 5 of its CTD domain
- SC-35, splicing factor SC-35
- SCNT, somatic cell nuclear transfer.
- bovine preimplantation development
- chromatin domain
- chromosome territory
- embryonic genome activation
- in vitro fertilization (IVF)
- interchromatin compartment
- major EGA, major embryonic genome activation
- somatic cell nuclear transfer (SCNT)
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Affiliation(s)
- Jens Popken
- a Division of Anthropology and Human Genetics ; Biocenter; LMU Munich ; Munich , Germany
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30
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Rutledge MT, Russo M, Belton JM, Dekker J, Broach JR. The yeast genome undergoes significant topological reorganization in quiescence. Nucleic Acids Res 2015. [PMID: 26202961 PMCID: PMC4787801 DOI: 10.1093/nar/gkv723] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
We have examined the three-dimensional organization of the yeast genome during quiescence by a chromosome capture technique as a means of understanding how genome organization changes during development. For exponentially growing cells we observe high levels of inter-centromeric interaction but otherwise a predominance of intrachromosomal interactions over interchromosomal interactions, consistent with aggregation of centromeres at the spindle pole body and compartmentalization of individual chromosomes within the nucleoplasm. Three major changes occur in the organization of the quiescent cell genome. First, intrachromosomal associations increase at longer distances in quiescence as compared to growing cells. This suggests that chromosomes undergo condensation in quiescence, which we confirmed by microscopy by measurement of the intrachromosomal distances between two sites on one chromosome. This compaction in quiescence requires the condensin complex. Second, inter-centromeric interactions decrease, consistent with prior data indicating that centromeres disperse along an array of microtubules during quiescence. Third, inter-telomeric interactions significantly increase in quiescence, an observation also confirmed by direct measurement. Thus, survival during quiescence is associated with substantial topological reorganization of the genome.
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Affiliation(s)
- Mark T Rutledge
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Mariano Russo
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Jon-Matthew Belton
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Job Dekker
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - James R Broach
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
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31
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Ozer G, Luque A, Schlick T. The chromatin fiber: multiscale problems and approaches. Curr Opin Struct Biol 2015; 31:124-39. [PMID: 26057099 DOI: 10.1016/j.sbi.2015.04.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/08/2015] [Accepted: 04/09/2015] [Indexed: 12/20/2022]
Abstract
The structure of chromatin, affected by many factors from DNA linker lengths to posttranslational modifications, is crucial to the regulation of eukaryotic cells. Combined experimental and computational methods have led to new insights into its structural and dynamical features, from interactions due to the flexible core histone tails or linker histones to the physical mechanism driving the formation of chromosomal domains. Here we present a perspective of recent advances in chromatin modeling techniques at the atomic, mesoscopic, and chromosomal scales with a view toward developing multiscale computational strategies to integrate such findings. Innovative modeling methods that connect molecular to chromosomal scales are crucial for interpreting experiments and eventually deciphering the complex dynamic organization and function of chromatin in the cell.
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Affiliation(s)
- Gungor Ozer
- Department of Chemistry, 100 Washington Square East, New York University, New York, NY 10003, USA
| | - Antoni Luque
- Department of Chemistry, 100 Washington Square East, New York University, New York, NY 10003, USA; Current address: Department of Mathematics & Statistics and Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-7720, USA
| | - Tamar Schlick
- Department of Chemistry, 100 Washington Square East, New York University, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China.
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32
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Zhang Y, Máté G, Müller P, Hillebrandt S, Krufczik M, Bach M, Kaufmann R, Hausmann M, Heermann DW. Radiation induced chromatin conformation changes analysed by fluorescent localization microscopy, statistical physics, and graph theory. PLoS One 2015; 10:e0128555. [PMID: 26042422 PMCID: PMC4456097 DOI: 10.1371/journal.pone.0128555] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 04/28/2015] [Indexed: 12/13/2022] Open
Abstract
It has been well established that the architecture of chromatin in cell nuclei is not random but functionally correlated. Chromatin damage caused by ionizing radiation raises complex repair machineries. This is accompanied by local chromatin rearrangements and structural changes which may for instance improve the accessibility of damaged sites for repair protein complexes. Using stably transfected HeLa cells expressing either green fluorescent protein (GFP) labelled histone H2B or yellow fluorescent protein (YFP) labelled histone H2A, we investigated the positioning of individual histone proteins in cell nuclei by means of high resolution localization microscopy (Spectral Position Determination Microscopy = SPDM). The cells were exposed to ionizing radiation of different doses and aliquots were fixed after different repair times for SPDM imaging. In addition to the repair dependent histone protein pattern, the positioning of antibodies specific for heterochromatin and euchromatin was separately recorded by SPDM. The present paper aims to provide a quantitative description of structural changes of chromatin after irradiation and during repair. It introduces a novel approach to analyse SPDM images by means of statistical physics and graph theory. The method is based on the calculation of the radial distribution functions as well as edge length distributions for graphs defined by a triangulation of the marker positions. The obtained results show that through the cell nucleus the different chromatin re-arrangements as detected by the fluorescent nucleosomal pattern average themselves. In contrast heterochromatic regions alone indicate a relaxation after radiation exposure and re-condensation during repair whereas euchromatin seemed to be unaffected or behave contrarily. SPDM in combination with the analysis techniques applied allows the systematic elucidation of chromatin re-arrangements after irradiation and during repair, if selected sub-regions of nuclei are investigated.
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Affiliation(s)
- Yang Zhang
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120, Heidelberg, Germany
| | - Gabriell Máté
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120, Heidelberg, Germany
| | - Patrick Müller
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120, Heidelberg, Germany
| | - Sabina Hillebrandt
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120, Heidelberg, Germany
| | - Matthias Krufczik
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120, Heidelberg, Germany
| | - Margund Bach
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120, Heidelberg, Germany
| | - Rainer Kaufmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120, Heidelberg, Germany
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120, Heidelberg, Germany
| | - Dieter W. Heermann
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120, Heidelberg, Germany
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33
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Cremer T, Cremer M, Hübner B, Strickfaden H, Smeets D, Popken J, Sterr M, Markaki Y, Rippe K, Cremer C. The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments. FEBS Lett 2015; 589:2931-43. [PMID: 26028501 DOI: 10.1016/j.febslet.2015.05.037] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 02/04/2023]
Abstract
Recent methodological advancements in microscopy and DNA sequencing-based methods provide unprecedented new insights into the spatio-temporal relationships between chromatin and nuclear machineries. We discuss a model of the underlying functional nuclear organization derived mostly from electron and super-resolved fluorescence microscopy studies. It is based on two spatially co-aligned, active and inactive nuclear compartments (ANC and INC). The INC comprises the compact, transcriptionally inactive core of chromatin domain clusters (CDCs). The ANC is formed by the transcriptionally active periphery of CDCs, called the perichromatin region (PR), and the interchromatin compartment (IC). The IC is connected to nuclear pores and serves nuclear import and export functions. The ANC is the major site of RNA synthesis. It is highly enriched in epigenetic marks for transcriptionally competent chromatin and RNA Polymerase II. Marks for silent chromatin are enriched in the INC. Multi-scale cross-correlation spectroscopy suggests that nuclear architecture resembles a random obstacle network for diffusing proteins. An increased dwell time of proteins and protein complexes within the ANC may help to limit genome scanning by factors or factor complexes to DNA exposed within the ANC.
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Affiliation(s)
- Thomas Cremer
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany.
| | - Marion Cremer
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Barbara Hübner
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Hilmar Strickfaden
- University of Alberta, Cross Cancer Institute Dept. of Oncology, Edmonton, AB, Canada
| | - Daniel Smeets
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Jens Popken
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Michael Sterr
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Yolanda Markaki
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) & BioQuant Center, Research Group Genome Organization & Function, Heidelberg, Germany.
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), Mainz and Institute of Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Germany.
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34
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Ollion J, Loll F, Cochennec J, Boudier T, Escudé C. Proliferation-dependent positioning of individual centromeres in the interphase nucleus of human lymphoblastoid cell lines. Mol Biol Cell 2015; 26:2550-60. [PMID: 25947134 PMCID: PMC4571307 DOI: 10.1091/mbc.e14-05-1002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 04/27/2015] [Indexed: 01/01/2023] Open
Abstract
Centromeres are not randomly distributed in interphase nuclei. High-throughput imaging provides an accurate characterization of how their organization varies as a function of the proliferation state in human lymphoblastoid cells. The results suggest the existence of mechanisms that drive the nuclear positioning of centromeres. The cell nucleus is a highly organized structure and plays an important role in gene regulation. Understanding the mechanisms that sustain this organization is therefore essential for understanding genome function. Centromeric regions (CRs) of chromosomes have been known for years to adopt specific nuclear positioning patterns, but the significance of this observation is not yet completely understood. Here, using a combination of fluorescence in situ hybridization and immunochemistry on fixed human cells and high-throughput imaging, we directly and quantitatively investigated the nuclear positioning of specific human CRs. We observe differential attraction of individual CRs toward both the nuclear border and the nucleoli, the former being enhanced in nonproliferating cells and the latter being enhanced in proliferating cells. Similar positioning patterns are observed in two different lymphoblastoid cell lines. Moreover, the positioning of CRs differs from that of noncentromeric regions, and CRs display specific orientations within chromosome territories. These results suggest the existence of not-yet-characterized mechanisms that drive the nuclear positioning of CRs and therefore pave the way toward a better understanding of how CRs affect nuclear organization.
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Affiliation(s)
- Jean Ollion
- Institut National de la Santé et de la Recherche Médicale U1154, Centre National de la Recherche Scientifique UMR7196, Muséum National d'Histoire Naturelle, 75231 Paris, France
| | - François Loll
- Institut National de la Santé et de la Recherche Médicale U1154, Centre National de la Recherche Scientifique UMR7196, Muséum National d'Histoire Naturelle, 75231 Paris, France
| | - Julien Cochennec
- Institut National de la Santé et de la Recherche Médicale U1154, Centre National de la Recherche Scientifique UMR7196, Muséum National d'Histoire Naturelle, 75231 Paris, France
| | - Thomas Boudier
- Université Pierre et Marie Curie, Sorbonne Universités, 75005 Paris, France
| | - Christophe Escudé
- Institut National de la Santé et de la Recherche Médicale U1154, Centre National de la Recherche Scientifique UMR7196, Muséum National d'Histoire Naturelle, 75231 Paris, France
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35
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Popken J, Graf A, Krebs S, Blum H, Schmid VJ, Strauss A, Guengoer T, Zakhartchenko V, Wolf E, Cremer T. Remodeling of the Nuclear Envelope and Lamina during Bovine Preimplantation Development and Its Functional Implications. PLoS One 2015; 10:e0124619. [PMID: 25932910 PMCID: PMC4416817 DOI: 10.1371/journal.pone.0124619] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 03/17/2015] [Indexed: 11/19/2022] Open
Abstract
The present study demonstrates a major remodeling of the nuclear envelope and its underlying lamina during bovine preimplantation development. Up to the onset of major embryonic genome activation (MGA) at the 8-cell stage nuclei showed a non-uniform distribution of nuclear pore complexes (NPCs). NPCs were exclusively present at sites where DNA contacted the nuclear lamina. Extended regions of the lamina, which were not contacted by DNA, lacked NPCs. In post-MGA nuclei the whole lamina was contacted rather uniformly by DNA. Accordingly, NPCs became uniformly distributed throughout the entire nuclear envelope. These findings shed new light on the conditions which control the integration of NPCs into the nuclear envelope. The switch from maternal to embryonic production of mRNAs was accompanied by multiple invaginations covered with NPCs, which may serve the increased demands of mRNA export and protein import. Other invaginations, as well as interior nuclear segments and vesicles without contact to the nuclear envelope, were exclusively positive for lamin B. Since the abundance of these invaginations and vesicles increased in concert with a massive nuclear volume reduction, we suggest that they reflect a mechanism for fitting the nuclear envelope and its lamina to a shrinking nuclear size during bovine preimplantation development. In addition, a deposit of extranuclear clusters of NUP153 (a marker for NPCs) without associated lamin B was frequently observed from the zygote stage up to MGA. Corresponding RNA-Seq data revealed deposits of spliced, maternally provided NUP153 mRNA and little unspliced, newly synthesized RNA prior to MGA, which increased strongly at the initiation of embryonic expression of NUP153 at MGA.
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Affiliation(s)
- Jens Popken
- Division of Anthropology and Human Genetics, Biocenter, LMU Munich, Planegg-Martinsried, Germany
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, Munich, Germany
- * E-mail: (JP); (EW); (TC)
| | - Alexander Graf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | | | - Axel Strauss
- Division of Genetics, Biocenter, LMU Munich, Planegg-Martinsried, Germany
| | - Tuna Guengoer
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, Munich, Germany
| | - Valeri Zakhartchenko
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, Munich, Germany
| | - Eckhard Wolf
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, Munich, Germany
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
- * E-mail: (JP); (EW); (TC)
| | - Thomas Cremer
- Division of Anthropology and Human Genetics, Biocenter, LMU Munich, Planegg-Martinsried, Germany
- * E-mail: (JP); (EW); (TC)
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36
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Arnhold F, Gührs KH, von Mikecz A. Amyloid domains in the cell nucleus controlled by nucleoskeletal protein lamin B1 reveal a new pathway of mercury neurotoxicity. PeerJ 2015; 3:e754. [PMID: 25699204 PMCID: PMC4327309 DOI: 10.7717/peerj.754] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 01/19/2015] [Indexed: 01/17/2023] Open
Abstract
Mercury (Hg) is a bioaccumulating trace metal that globally circulates the atmosphere and waters in its elemental, inorganic and organic chemical forms. While Hg represents a notorious neurotoxicant, the underlying cellular pathways are insufficiently understood. We identify amyloid protein aggregation in the cell nucleus as a novel pathway of Hg-bio-interactions. By mass spectrometry of purified protein aggregates, a subset of spliceosomal components and nucleoskeletal protein lamin B1 were detected as constituent parts of an Hg-induced nuclear aggregome network. The aggregome network was located by confocal imaging of amyloid-specific antibodies and dyes to amyloid cores within splicing-speckles that additionally recruit components of the ubiquitin-proteasome system. Hg significantly enhances global proteasomal activity in the nucleus, suggesting that formation of amyloid speckles plays a role in maintenance of protein homeostasis. RNAi knock down showed that lamin B1 for its part regulates amyloid speckle formation and thus likewise participates in nuclear protein homeostasis. As the Hg-induced cascade of interactions between the nucleoskeleton and protein homeostasis reduces neuronal signalling, amyloid fibrillation in the cell nucleus is introduced as a feature of Hg-neurotoxicity that opens new avenues of future research. Similar to protein aggregation events in the cytoplasm that are controlled by the cytoskeleton, amyloid fibrillation of nuclear proteins may be driven by the nucleoskeleton.
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Affiliation(s)
- Florian Arnhold
- IUF-Leibniz Research Institute for Environmental Medicine at Heinrich-Heine-University Duesseldorf , Duesseldorf , Germany
| | - Karl-Heinz Gührs
- CF Proteomics, FLI-Leibniz-Institute for Age Research, Fritz-Lipman-Institute e.V. , Jena , Germany
| | - Anna von Mikecz
- IUF-Leibniz Research Institute for Environmental Medicine at Heinrich-Heine-University Duesseldorf , Duesseldorf , Germany
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37
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Chromatin-Driven Behavior of Topologically Associating Domains. J Mol Biol 2015; 427:608-25. [DOI: 10.1016/j.jmb.2014.09.013] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 12/19/2022]
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38
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Radivoyevitch T, Li H, Sachs RK. Etiology and treatment of hematological neoplasms: stochastic mathematical models. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 844:317-46. [PMID: 25480649 DOI: 10.1007/978-1-4939-2095-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Leukemias are driven by stemlike cancer cells (SLCC), whose initiation, growth, response to treatment, and posttreatment behavior are often "stochastic", i.e., differ substantially even among very similar patients for reasons not observable with present techniques. We review the probabilistic mathematical methods used to analyze stochastics and give two specific examples. The first example concerns a treatment protocol, e.g., for acute myeloid leukemia (AML), where intermittent cytotoxic drug dosing (e.g., once each weekday) is used with intent to cure. We argue mathematically that, if independent SLCC are growing stochastically during prolonged treatment, then, other things being equal, front-loading doses are more effective for tumor eradication than back loading. We also argue that the interacting SLCC dynamics during treatment is often best modeled by considering SLCC in microenvironmental niches, with SLCC-SLCC interactions occurring only among SLCC within the same niche, and we present a stochastic dynamics formalism, involving "Poissonization," applicable in such situations. Interactions at a distance due to partial control of total cell numbers are also considered. The second half of this chapter concerns chromosomal aberrations, lesions known to cause some leukemias. A specific example is the induction of a Philadelphia chromosome by ionizing radiation, subsequent development of chronic myeloid leukemia (CML), CML treatment, and treatment outcome. This time evolution involves a coordinated sequence of > 10 steps, each stochastic in its own way, at the subatomic, molecular, macromolecular, cellular, tissue, and population scales, with corresponding time scales ranging from picoseconds to decades. We discuss models of these steps and progress in integrating models across scales.
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Affiliation(s)
- Tomas Radivoyevitch
- Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA,
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39
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Szczurek AT, Prakash K, Lee HK, Żurek-Biesiada DJ, Best G, Hagmann M, Dobrucki JW, Cremer C, Birk U. Single molecule localization microscopy of the distribution of chromatin using Hoechst and DAPI fluorescent probes. Nucleus 2014; 5:331-40. [PMID: 25482122 PMCID: PMC4152347 DOI: 10.4161/nucl.29564] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/06/2014] [Accepted: 06/12/2014] [Indexed: 12/12/2022] Open
Abstract
Several approaches have been described to fluorescently label and image DNA and chromatin in situ on the single-molecule level. These superresolution microscopy techniques are based on detecting optically isolated, fluorescently tagged anti-histone antibodies, fluorescently labeled DNA precursor analogs, or fluorescent dyes bound to DNA. Presently they suffer from various drawbacks such as low labeling efficiency or interference with DNA structure. In this report, we demonstrate that DNA minor groove binding dyes, such as Hoechst 33258, Hoechst 33342, and DAPI, can be effectively employed in single molecule localization microscopy (SMLM) with high optical and structural resolution. Upon illumination with low intensity 405 nm light, a small subpopulation of these molecules stochastically undergoes photoconversion from the original blue-emitting form to a green-emitting form. Using a 491 nm laser excitation, fluorescence of these green-emitting, optically isolated molecules was registered until "bleached". This procedure facilitated substantially the optical isolation and localization of large numbers of individual dye molecules bound to DNA in situ, in nuclei of fixed mammalian cells, or in mitotic chromosomes, and enabled the reconstruction of high-quality DNA density maps. We anticipate that this approach will provide new insights into DNA replication, DNA repair, gene transcription, and other nuclear processes.
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Affiliation(s)
| | - Kirti Prakash
- Institute of Molecular Biology; Mainz, Germany
- Institute for Pharmacy and Molecular Biotechnology; University of Heidelberg; Heidelberg, Germany
| | - Hyun-Keun Lee
- Institute of Molecular Biology; Mainz, Germany
- Department of Physics; University of Mainz; Mainz, Germany
| | | | - Gerrit Best
- Kirchhoff Institute for Physics; University of Heidelberg; Heidelberg, Germany
- University Hospital Heidelberg; University of Heidelberg; Heidelberg, Germany
| | - Martin Hagmann
- Kirchhoff Institute for Physics; University of Heidelberg; Heidelberg, Germany
- University Hospital Heidelberg; University of Heidelberg; Heidelberg, Germany
| | - Jurek W Dobrucki
- Faculty of Biochemistry, Biophysics, and Biotechnology; Jagiellonian University; Kraków, Poland
| | - Christoph Cremer
- Institute of Molecular Biology; Mainz, Germany
- Institute for Pharmacy and Molecular Biotechnology; University of Heidelberg; Heidelberg, Germany
- Department of Physics; University of Mainz; Mainz, Germany
- Kirchhoff Institute for Physics; University of Heidelberg; Heidelberg, Germany
| | - Udo Birk
- Institute of Molecular Biology; Mainz, Germany
- Department of Physics; University of Mainz; Mainz, Germany
- Kirchhoff Institute for Physics; University of Heidelberg; Heidelberg, Germany
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40
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Smeets D, Markaki Y, Schmid VJ, Kraus F, Tattermusch A, Cerase A, Sterr M, Fiedler S, Demmerle J, Popken J, Leonhardt H, Brockdorff N, Cremer T, Schermelleh L, Cremer M. Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci. Epigenetics Chromatin 2014; 7:8. [PMID: 25057298 PMCID: PMC4108088 DOI: 10.1186/1756-8935-7-8] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 04/11/2014] [Indexed: 12/31/2022] Open
Abstract
Background A Xist RNA decorated Barr body is the structural hallmark of the compacted inactive X territory in female mammals. Using super-resolution three-dimensional structured illumination microscopy (3D-SIM) and quantitative image analysis, we compared its ultrastructure with active chromosome territories (CTs) in human and mouse somatic cells, and explored the spatio-temporal process of Barr body formation at onset of inactivation in early differentiating mouse embryonic stem cells (ESCs). Results We demonstrate that all CTs are composed of structurally linked chromatin domain clusters (CDCs). In active CTs the periphery of CDCs harbors low-density chromatin enriched with transcriptionally competent markers, called the perichromatin region (PR). The PR borders on a contiguous channel system, the interchromatin compartment (IC), which starts at nuclear pores and pervades CTs. We propose that the PR and macromolecular complexes in IC channels together form the transcriptionally permissive active nuclear compartment (ANC). The Barr body differs from active CTs by a partially collapsed ANC with CDCs coming significantly closer together, although a rudimentary IC channel system connected to nuclear pores is maintained. Distinct Xist RNA foci, closely adjacent to the nuclear matrix scaffold attachment factor-A (SAF-A) localize throughout Xi along the rudimentary ANC. In early differentiating ESCs initial Xist RNA spreading precedes Barr body formation, which occurs concurrent with the subsequent exclusion of RNA polymerase II (RNAP II). Induction of a transgenic autosomal Xist RNA in a male ESC triggers the formation of an ‘autosomal Barr body’ with less compacted chromatin and incomplete RNAP II exclusion. Conclusions 3D-SIM provides experimental evidence for profound differences between the functional architecture of transcriptionally active CTs and the Barr body. Basic structural features of CT organization such as CDCs and IC channels are however still recognized, arguing against a uniform compaction of the Barr body at the nucleosome level. The localization of distinct Xist RNA foci at boundaries of the rudimentary ANC may be considered as snap-shots of a dynamic interaction with silenced genes. Enrichment of SAF-A within Xi territories and its close spatial association with Xist RNA suggests their cooperative function for structural organization of Xi.
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Affiliation(s)
- Daniel Smeets
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany ; Department of Biochemistry, University of Oxford, Oxford, UK
| | - Yolanda Markaki
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Volker J Schmid
- Institute of Statistics, Ludwig Maximilians University (LMU), Munich, Germany
| | - Felix Kraus
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany ; Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Andrea Cerase
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Michael Sterr
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Susanne Fiedler
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Justin Demmerle
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Jens Popken
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Heinrich Leonhardt
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Neil Brockdorff
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Thomas Cremer
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Lothar Schermelleh
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany ; Department of Biochemistry, University of Oxford, Oxford, UK
| | - Marion Cremer
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
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41
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Schierding W, Cutfield WS, O'Sullivan JM. The missing story behind Genome Wide Association Studies: single nucleotide polymorphisms in gene deserts have a story to tell. Front Genet 2014; 5:39. [PMID: 24600475 PMCID: PMC3927098 DOI: 10.3389/fgene.2014.00039] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 01/31/2014] [Indexed: 11/13/2022] Open
Abstract
Genome wide association studies are central to the evolution of personalized medicine. However, the propensity for single nucleotide polymorphisms (SNPs) to fall outside of genes means that understanding how these polymorphisms alter cellular function requires an expanded view of human genetics. Integrating the study of genome structure (chromosome conformation capture) into its function opens up new avenues of exploration. Changes in the epigenome associated with SNPs in gene deserts will allow us to define complex diseases in a much clearer manner, and usher in a new era of disease pathway exploration.
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Affiliation(s)
| | - Wayne S. Cutfield
- Liggins Institute, University of AucklandAuckland, New Zealand
- Gravida – National Centre for Growth and DevelopmentAuckland, New Zealand
| | - Justin M. O'Sullivan
- Liggins Institute, University of AucklandAuckland, New Zealand
- Gravida – National Centre for Growth and DevelopmentAuckland, New Zealand
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42
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Cremer T, Cremer C, Lichter P. Recollections of a scientific journey published in human genetics: from chromosome territories to interphase cytogenetics and comparative genome hybridization. Hum Genet 2014; 133:403-16. [PMID: 24504674 DOI: 10.1007/s00439-014-1425-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 01/19/2014] [Indexed: 10/25/2022]
Abstract
In line with the intentions of an issue celebrating the 50th anniversary of Human Genetics, we focus on a series of frequently cited studies published in this journal during the 1980s and 1990s. These studies have contributed to the rise of molecular cytogenetics. They yielded evidence that chromosomes occupy distinct territories in the mammalian cell nucleus, first obtained with laser-UV-microbeam experiments and thereafter with chromosome painting, and contributed to the development of interphase cytogenetics and comparative genome hybridization. We provide a personal account of experimental concepts, which were developed by us and others, and describe some of the unforeseeable turns and obstacles, which we had to overcome on the way towards an experimental realization. We conclude with a perspective on current developments and goals of molecular cytogenetics.
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Affiliation(s)
- Thomas Cremer
- LMU Biozentrum, Grosshadernerstr. 2, Martinsried, Germany,
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43
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Newhart A, Janicki SM. Seeing is believing: visualizing transcriptional dynamics in single cells. J Cell Physiol 2014; 229:259-65. [PMID: 23929405 DOI: 10.1002/jcp.24445] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 08/02/2013] [Indexed: 12/29/2022]
Abstract
For a gene to be expressed, the functions of multiple molecular machines must be coordinated at the site of transcription. To understand the role of nuclear organization in transcription, it is necessary to visualize the dynamic interactions of regulatory factors with chromatin and RNA. It is currently possible to localize individual transcription sites in single living mammalian cells by engineering reporter gene constructs to include sequence elements which permit the visualization of nucleic acids in vivo. Upon stable integration, these transgenes form chromatinized arrays, which can be imaged during activation to obtain high-resolution quantitative information about transcriptional dynamics. Modeling can suggest new hypotheses about gene regulation, which can be tested both in the single-cell imaging system and at endogenous genes. This gene-specific imaging strategy has the potential to reveal regulatory mechanisms, which would be difficult to imagine outside of single living cells.
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Affiliation(s)
- Alyshia Newhart
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania
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44
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Wilczynski GM. Significance of higher-order chromatin architecture for neuronal function and dysfunction. Neuropharmacology 2014; 80:28-33. [PMID: 24456745 DOI: 10.1016/j.neuropharm.2014.01.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/08/2014] [Accepted: 01/09/2014] [Indexed: 02/08/2023]
Abstract
Recent studies in neurons indicate that the large-scale chromatin architectural framework, including chromosome territories or lamina-associated chromatin, undergoes dynamic changes that represent an emergent level of regulation of neuronal gene-expression. This phenomenon has been implicated in neuronal differentiation, long-term potentiation, seizures, and disorders of neural plasticity such as Rett syndrome and epilepsy.
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Affiliation(s)
- Grzegorz M Wilczynski
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland.
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45
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Use of halogenated precursors to define a transcription time window after treatment with hypometabolizing molecules. Histochem Cell Biol 2014; 141:243-9. [DOI: 10.1007/s00418-014-1180-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2014] [Indexed: 10/25/2022]
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46
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Computational Models of Large-Scale Genome Architecture. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:275-349. [DOI: 10.1016/b978-0-12-800046-5.00009-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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47
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Waldeck W, Mueller G, Glatting KH, Hotz-Wagenblatt A, Diessl N, Chotewutmonti S, Langowski J, Semmler W, Wiessler M, Braun K. Spatial localization of genes determined by intranuclear DNA fragmentation with the fusion proteins lamin KRED and histone KRED und visible light. Int J Med Sci 2013; 10:1136-48. [PMID: 23869190 PMCID: PMC3714390 DOI: 10.7150/ijms.6121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 06/06/2013] [Indexed: 12/02/2022] Open
Abstract
The highly organized DNA architecture inside of the nuclei of cells is accepted in the scientific world. In the human genome about 3 billion nucleotides are organized as chromatin in the cell nucleus. In general, they are involved in gene regulation and transcription by histone modification. Small chromosomes are localized in a central nuclear position whereas the large chromosomes are peripherally positioned. In our experiments we inserted fusion proteins consisting of a component of the nuclear lamina (lamin B1) and also histone H2A, both combined with the light inducible fluorescence protein KillerRed (KRED). After activation, KRED generates reactive oxygen species (ROS) producing toxic effects and may cause cell death. We analyzed the spatial damage distribution in the chromatin after illumination of the cells with visible light. The extent of DNA damage was strongly dependent on its localization inside of nuclei. The ROS activity allowed to gain information about the location of genes and their functions via sequencing and data base analysis of the double strand breaks of the isolated DNA. A connection between the damaged gene sequences and some diseases was found.
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Affiliation(s)
- Waldemar Waldeck
- 1. German Cancer Research Center, Dept. of Biophysics of Macromolecules, INF 580, D-69120 Heidelberg, Germany
| | - Gabriele Mueller
- 1. German Cancer Research Center, Dept. of Biophysics of Macromolecules, INF 580, D-69120 Heidelberg, Germany
| | - Karl-Heinz Glatting
- 3. German Cancer Research Center, Genomics Proteomics Core Facility HUSAR Bioinformatics Lab, INF 580, D-69120 Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- 3. German Cancer Research Center, Genomics Proteomics Core Facility HUSAR Bioinformatics Lab, INF 580, D-69120 Heidelberg, Germany
| | - Nicolle Diessl
- 4. German Cancer Research Center, Genomics and Proteomics Core Facility High Throughput Sequencing, INF 580, D-69120 Heidelberg, Germany
| | - Sasithorn Chotewutmonti
- 4. German Cancer Research Center, Genomics and Proteomics Core Facility High Throughput Sequencing, INF 580, D-69120 Heidelberg, Germany
| | - Jörg Langowski
- 1. German Cancer Research Center, Dept. of Biophysics of Macromolecules, INF 580, D-69120 Heidelberg, Germany
| | - Wolfhard Semmler
- 2. German Cancer Research Center, Dept. of Medical Physics in Radiology, INF 280, D-69120 Heidelberg, Germany
| | - Manfred Wiessler
- 2. German Cancer Research Center, Dept. of Medical Physics in Radiology, INF 280, D-69120 Heidelberg, Germany
| | - Klaus Braun
- 2. German Cancer Research Center, Dept. of Medical Physics in Radiology, INF 280, D-69120 Heidelberg, Germany
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48
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Abstract
Budding yeast, like other eukaryotes, carries its genetic information on chromosomes that are sequestered from other cellular constituents by a double membrane, which forms the nucleus. An elaborate molecular machinery forms large pores that span the double membrane and regulate the traffic of macromolecules into and out of the nucleus. In multicellular eukaryotes, an intermediate filament meshwork formed of lamin proteins bridges from pore to pore and helps the nucleus reform after mitosis. Yeast, however, lacks lamins, and the nuclear envelope is not disrupted during yeast mitosis. The mitotic spindle nucleates from the nucleoplasmic face of the spindle pole body, which is embedded in the nuclear envelope. Surprisingly, the kinetochores remain attached to short microtubules throughout interphase, influencing the position of centromeres in the interphase nucleus, and telomeres are found clustered in foci at the nuclear periphery. In addition to this chromosomal organization, the yeast nucleus is functionally compartmentalized to allow efficient gene expression, repression, RNA processing, genomic replication, and repair. The formation of functional subcompartments is achieved in the nucleus without intranuclear membranes and depends instead on sequence elements, protein-protein interactions, specific anchorage sites at the nuclear envelope or at pores, and long-range contacts between specific chromosomal loci, such as telomeres. Here we review the spatial organization of the budding yeast nucleus, the proteins involved in forming nuclear subcompartments, and evidence suggesting that the spatial organization of the nucleus is important for nuclear function.
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49
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Hübner B, Cremer T, Neumann J. Correlative microscopy of individual cells: sequential application of microscopic systems with increasing resolution to study the nuclear landscape. Methods Mol Biol 2013; 1042:299-336. [PMID: 23980016 DOI: 10.1007/978-1-62703-526-2_21] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The term correlative microscopy denotes the sequential visualization of one and the same cell using various microscopic techniques. Correlative microscopy provides a unique platform to combine the particular strength of each microscopic approach and compensate for its specific limitations. As an example, we report results of a correlative microscopic study exploring features of the nuclear landscape in HeLa cells. We present a detailed protocol to first investigate distinct structural features of a living cell in space and time (4D) using spinning disk laser scanning microscopy (SDLSM). Then, after fixation and staining of selected structures (e.g., by means of immunodetection), details of these structures are explored at increasingly higher resolution using three-dimensional (3D) confocal laser scanning microscopy (CLSM); super-resolution fluorescence microscopy, such as three-dimensional structured illumination microscopy (3D-SIM); and transmission electron microscopy (TEM). We discuss problems involved in the comparison of images of a given cell nucleus recorded with different microscopic approaches, which requires not only a compensation for different resolutions but also for various distortions.
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Affiliation(s)
- Barbara Hübner
- Department Biology II, Anthropology and Human Genetics, Biocenter, Ludwig-Maximilians-University (LMU), Martinsried, Germany
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50
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Alvarenga EM, Mondin M, Rodrigues VL, Andrade LM, Vidal BDC, Mello MLS. Contribution of AT-, GC-, and methylated cytidine-rich DNA to chromatin composition in Malpighian tubule cell nuclei of Panstrongylus megistus (Hemiptera, Reduviidae). Acta Histochem 2012; 114:665-72. [PMID: 22197484 DOI: 10.1016/j.acthis.2011.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 11/25/2011] [Accepted: 11/28/2011] [Indexed: 12/31/2022]
Abstract
The Malpighian tubule cell nuclei of male Panstrongylus megistus, a vector of Chagas disease, contain one chromocenter, which is composed solely of the Y chromosome. Considering that different chromosomes contribute to the composition of chromocenters in different triatomini species, the aim of this study was to determine the contribution of AT-, GC-, and methylated cytidine-rich DNA in the chromocenter as well as in euchromatin of Malpighian tubule cell nuclei of P. megistus in comparison with published data for Triatoma infestans. Staining with 4',6-diamidino-2-phenylindole/actinomycin D and chromomycin A(3)/distamycin, immunodetection of 5-methylcytidine and AgNOR test were used. The results revealed AT-rich/GC-poor DNA in the male chromocenter, but equally distributed AT and GC DNA sequences in male and female euchromatin, like in T. infestans. Accumulation of argyrophilic proteins encircling the chromocenter did not always correlate with that of GC-rich DNA. Methylated DNA identified by immunodetection was found sparsely distributed in the euchromatin of both sexes and at some points around the chromocenter edge, but it could not be considered responsible for chromatin condensation in the chromocenter, like in T. infestans. However, unlike in T. infestans, no correlation between the chromocenter AT-rich DNA and nucleolus organizing region (NOR) DNA was found in P. megistus.
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