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Maji A, Ahmed JA, Roy S, Chakrabarti B, Mitra MK. A Lamin-Associated Chromatin Model for Chromosome Organization. Biophys J 2020; 118:3041-3050. [PMID: 32492372 DOI: 10.1016/j.bpj.2020.05.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/09/2020] [Accepted: 05/12/2020] [Indexed: 12/22/2022] Open
Abstract
We propose a simple model for chromatin organization based on the interaction of the chromatin fibers with lamin proteins along the nuclear membrane. Lamin proteins are known to be a major factor that influences chromatin organization and hence gene expression in the cells. We provide a quantitative understanding of lamin-associated chromatin organization in a crowded macromolecular environment by systematically varying the heteropolymer segment distribution and the strength of the lamin-chromatin attractive interaction. Our minimal polymer model reproduces the formation of lamin-associated-domains and provides an in silico tool for quantifying domain length distributions for different distributions of heteropolymer segments. We show that a Gaussian distribution of heteropolymer segments, coupled with strong lamin-chromatin interactions, can qualitatively reproduce observed length distributions of lamin-associated-domains. Further, lamin-mediated interaction can enhance the formation of chromosome territories as well as the organization of chromatin into tightly packed heterochromatin and the loosely packed gene-rich euchromatin regions.
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Affiliation(s)
- Ajoy Maji
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, India
| | - Jahir A Ahmed
- AKI's Poona College of Arts, Science and Commerce, Camp, Pune, India
| | - Subhankar Roy
- Saha Institute of Nuclear Physics, HBNI, Kolkata, India
| | | | - Mithun K Mitra
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, India.
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2
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Gornik SG, Hu I, Lassadi I, Waller RF. The Biochemistry and Evolution of the Dinoflagellate Nucleus. Microorganisms 2019; 7:microorganisms7080245. [PMID: 31398798 PMCID: PMC6723414 DOI: 10.3390/microorganisms7080245] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022] Open
Abstract
Dinoflagellates are known to possess a highly aberrant nucleus-the so-called dinokaryon-that exhibits a multitude of exceptional biological features. These include: (1) Permanently condensed chromosomes; (2) DNA in a cholesteric liquid crystalline state, (3) extremely large DNA content (up to 200 pg); and, perhaps most strikingly, (4) a deficit of histones-the canonical building blocks of all eukaryotic chromatin. Dinoflagellates belong to the Alveolata clade (dinoflagellates, apicomplexans, and ciliates) and, therefore, the biological oddities observed in dinoflagellate nuclei are derived character states. Understanding the sequence of changes that led to the dinokaryon has been difficult in the past with poor resolution of dinoflagellate phylogeny. Moreover, lack of knowledge of their molecular composition has constrained our understanding of the molecular properties of these derived nuclei. However, recent advances in the resolution of the phylogeny of dinoflagellates, particularly of the early branching taxa; the realization that divergent histone genes are present; and the discovery of dinoflagellate-specific nuclear proteins that were acquired early in dinoflagellate evolution have all thrown new light nature and evolution of the dinokaryon.
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Affiliation(s)
- Sebastian G Gornik
- Centre for Organismal Studies (COS), Universität Heidelberg, 69120 Heidelberg, Germany.
| | - Ian Hu
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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3
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How does chromatin package DNA within nucleus and regulate gene expression? Int J Biol Macromol 2017; 101:862-881. [PMID: 28366861 DOI: 10.1016/j.ijbiomac.2017.03.165] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/28/2017] [Accepted: 03/28/2017] [Indexed: 01/26/2023]
Abstract
The human body is made up of 60 trillion cells, each cell containing 2 millions of genomic DNA in its nucleus. How is this genomic deoxyribonucleic acid [DNA] organised into nuclei? Around 1880, W. Flemming discovered a nuclear substance that was clearly visible on staining under primitive light microscopes and named it 'chromatin'; this is now thought to be the basic unit of genomic DNA organization. Since long before DNA was known to carry genetic information, chromatin has fascinated biologists. DNA has a negatively charged phosphate backbone that produces electrostatic repulsion between adjacent DNA regions, making it difficult for DNA to fold upon itself. In this article, we will try to shed light on how does chromatin package DNA within nucleus and regulate gene expression?
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4
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Hoang TV, Kizilyaprak C, Spehner D, Humbel BM, Schultz P. Automatic segmentation of high pressure frozen and freeze-substituted mouse retina nuclei from FIB-SEM tomograms. J Struct Biol 2017; 197:123-134. [DOI: 10.1016/j.jsb.2016.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 10/03/2016] [Accepted: 10/06/2016] [Indexed: 10/20/2022]
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5
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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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6
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Zhou Z, Irudayaraj J. A native chromatin extraction method based on salicylic acid coated magnetic nanoparticles and characterization of chromatin. Analyst 2015; 140:938-44. [PMID: 25475154 DOI: 10.1039/c4an01897d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Native chromatin contains valuable genetic, epigenetic and structural information. Though DNA and nucleosome structures are well defined, less is known about the higher-order chromatin structure. Traditional chromatin extraction methods involve fixation, fragmentation and centrifugation, which might distort the higher-order structural information of native chromatin. We present a simple approach to isolate native chromatin from cultured mammalian cells using salicylic acid coated magnetic nanoparticles (SAMNPs). Chromatin is magnetically separated from cell lysates without any filtration or high-speed centrifugation. The purified chromatin is suitable for the examination of histone modifications and other chromatin associated proteins as confirmed by western blotting analysis. The structure of chromatin was determined by confocal fluorescence microscopy, transmission electron microscopy (TEM) and atomic force microscopy (AFM). High-resolution AFM and TEM images clearly show a classical bead-on-a-string structure. The higher-order chromatin structure is also determined via electron microscopy. Our method provides a simple, inexpensive and an environmentally friendly means to extract native chromatin not possible before, suitable for both biochemical and structural analysis.
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Affiliation(s)
- Zhongwu Zhou
- Bindley Bioscience Center and Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA.
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7
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Müller O, Kepper N, Schöpflin R, Ettig R, Rippe K, Wedemann G. Changing chromatin fiber conformation by nucleosome repositioning. Biophys J 2015; 107:2141-50. [PMID: 25418099 DOI: 10.1016/j.bpj.2014.09.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 09/11/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022] Open
Abstract
Chromatin conformation is dynamic and heterogeneous with respect to nucleosome positions, which can be changed by chromatin remodeling complexes in the cell. These molecular machines hydrolyze ATP to translocate or evict nucleosomes, and establish loci with regularly and more irregularly spaced nucleosomes as well as nucleosome-depleted regions. The impact of nucleosome repositioning on the three-dimensional chromatin structure is only poorly understood. Here, we address this issue by using a coarse-grained computer model of arrays of 101 nucleosomes considering several chromatin fiber models with and without linker histones, respectively. We investigated the folding of the chain in dependence of the position of the central nucleosome by changing the length of the adjacent linker DNA in basepair steps. We found in our simulations that these translocations had a strong effect on the shape and properties of chromatin fibers: i), Fiber curvature and flexibility at the center were largely increased and long-range contacts between distant nucleosomes on the chain were promoted. ii), The highest destabilization of the fiber conformation occurred for a nucleosome shifted by two basepairs from regular spacing, whereas effects of linker DNA changes of ?10 bp in phase with the helical twist of DNA were minimal. iii), A fiber conformation can stabilize a regular spacing of nucleosomes inasmuch as favorable stacking interactions between nucleosomes are facilitated. This can oppose nucleosome translocations and increase the energetic costs for chromatin remodeling. Our computational modeling framework makes it possible to describe the conformational heterogeneity of chromatin in terms of nucleosome positions, and thus advances theoretical models toward a better understanding of how genome compaction and access are regulated within the cell.
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Affiliation(s)
- Oliver Müller
- Institute for Applied Computer Science, University of Applied Sciences Stralsund, Stralsund, Germany
| | - Nick Kepper
- Deutsches Krebsforschungszentrum and BioQuant, Heidelberg, Germany
| | - Robert Schöpflin
- Institute for Applied Computer Science, University of Applied Sciences Stralsund, Stralsund, Germany
| | - Ramona Ettig
- Deutsches Krebsforschungszentrum and BioQuant, Heidelberg, Germany
| | - Karsten Rippe
- Deutsches Krebsforschungszentrum and BioQuant, Heidelberg, Germany
| | - Gero Wedemann
- Institute for Applied Computer Science, University of Applied Sciences Stralsund, Stralsund, Germany.
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8
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Quantitatively imaging chromosomes by correlated cryo-fluorescence and soft x-ray tomographies. Biophys J 2015; 107:1988-1996. [PMID: 25418180 DOI: 10.1016/j.bpj.2014.09.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/28/2014] [Accepted: 09/09/2014] [Indexed: 11/24/2022] Open
Abstract
Soft x-ray tomography (SXT) is increasingly being recognized as a valuable method for visualizing and quantifying the ultrastructure of cryopreserved cells. Here, we describe the combination of SXT with cryogenic confocal fluorescence tomography (CFT). This correlative approach allows the incorporation of molecular localization data, with isotropic precision, into high-resolution three-dimensional (3-D) SXT reconstructions of the cell. CFT data are acquired first using a cryogenically adapted confocal light microscope in which the specimen is coupled to a high numerical aperture objective lens by an immersion fluid. The specimen is then cryo-transferred to a soft x-ray microscope (SXM) for SXT data acquisition. Fiducial markers visible in both types of data act as common landmarks, enabling accurate coalignment of the two complementary tomographic reconstructions. We used this method to identify the inactive X chromosome (Xi) in female v-abl transformed thymic lymphoma cells by localizing enhanced green fluorescent protein-labeled macroH2A with CFT. The molecular localization data were used to guide segmentation of Xi in the SXT reconstructions, allowing characterization of the Xi topological arrangement in near-native state cells. Xi was seen to adopt a number of different topologies with no particular arrangement being dominant.
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Mitchell-Jordan S, Chen H, Franklin S, Stefani E, Bentolila LA, Vondriska TM. Features of endogenous cardiomyocyte chromatin revealed by super-resolution STED microscopy. J Mol Cell Cardiol 2012; 53:552-8. [PMID: 22846883 DOI: 10.1016/j.yjmcc.2012.07.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 07/06/2012] [Accepted: 07/19/2012] [Indexed: 11/30/2022]
Abstract
Despite the extensive knowledge of the functional unit of chromatin-the nucleosome-for which structural information exists at the atomic level, little is known about the endogenous structure of eukaryotic genomes. Chromosomal capture techniques and genome-wide chromatin immunoprecipitation and next generation sequencing have provided complementary insight into global features of chromatin structure, but these methods do not directly measure structural features of the genome in situ. This lack of insight is particularly troublesome in terminally differentiated cells which must reorganize their genomes for large scale gene expression changes in the absence of cell division. For example, cardiomyocytes, which are fully committed and reside in interphase, are capable of massive gene expression changes in response to physiological stimuli, but the global changes in chromatin structure that enable such transcriptional changes are unknown. The present study addressed this problem utilizing super-resolution stimulated emission depletion (STED) microscopy to directly measure chromatin features in mammalian cells. We demonstrate that immunolabeling of histone H3 coupled with STED imaging reveals chromatin domains on a scale of 40-70 nm, several folds better than the resolution of conventional confocal microscopy. An analytical workflow is established to detect changes in chromatin structure following acute stimuli and used to investigate rearrangements in cardiomyocyte genomes following agonists that induce cellular hypertrophy. This approach is readily adaptable to investigation of other nuclear features using a similar antibody-based labeling technique and enables direct measurements of chromatin domain changes in response to physiological stimuli.
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Affiliation(s)
- Scherise Mitchell-Jordan
- Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, USA
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Dynamic Fuzziness During Linker Histone Action. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 725:15-26. [DOI: 10.1007/978-1-4614-0659-4_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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11
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Daban JR. Electron microscopy and atomic force microscopy studies of chromatin and metaphase chromosome structure. Micron 2011; 42:733-50. [PMID: 21703860 DOI: 10.1016/j.micron.2011.05.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 05/01/2011] [Indexed: 11/26/2022]
Abstract
The folding of the chromatin filament and, in particular, the organization of genomic DNA within metaphase chromosomes has attracted the interest of many laboratories during the last five decades. This review discusses our current understanding of chromatin higher-order structure based on results obtained with transmission electron microscopy (TEM), cryo-electron microscopy (cryo-EM), and different atomic force microscopy (AFM) techniques. Chromatin isolated from different cell types in buffers without cations form extended filaments with nucleosomes visible as separated units. In presence of low concentrations of Mg(2+), chromatin filaments are folded into fibers having a diameter of ∼ 30 nm. Highly compact fibers were obtained with isolated chromatin fragments in solutions containing 1-2mM Mg(2+). The high density of these fibers suggested that the successive turns of the chromatin filament are interdigitated. Similar results were obtained with reconstituted nucleosome arrays under the same ionic conditions. This led to the proposal of compact interdigitated solenoid models having a helical pitch of 4-5 nm. These findings, together with the observation of columns of stacked nucleosomes in different liquid crystal phases formed by aggregation of nucleosome core particles at high concentration, and different experimental evidences obtained using other approaches, indicate that face-to-face interactions between nucleosomes are very important for the formation of dense chromatin structures. Chromatin fibers were observed in metaphase chromosome preparations in deionized water and in buffers containing EDTA, but chromosomes in presence of the Mg(2+) concentrations found in metaphase (5-22 mM) are very compact, without visible fibers. Moreover, a recent cryo-electron microscopy analysis of vitreous sections of mitotic cells indicated that chromatin has a disordered organization, which does not support the existence of 30-nm fibers in condensed chromosomes. TEM images of partially denatured chromosomes obtained using different procedures that maintain the ionic conditions of metaphase showed that bulk chromatin in chromosomes is organized forming multilayered plate-like structures. The structure and mechanical properties of these plates were studied using cryo-EM, electron tomography, AFM imaging in aqueous media, and AFM-based nanotribology and force spectroscopy. The results obtained indicated that the chromatin filament forms a flexible two-dimensional network, in which DNA is the main component responsible for the mechanical strength observed in friction force measurements. The discovery of this unexpected structure based on a planar geometry has opened completely new possibilities for the understanding of chromatin folding in metaphase chromosomes. It was proposed that chromatids are formed by many stacked thin chromatin plates oriented perpendicular to the chromatid axis. Different experimental evidences indicated that nucleosomes in the plates are irregularly oriented, and that the successive layers are interdigitated (the apparent layer thickness is 5-6 nm), allowing face-to-face interactions between nucleosomes of adjacent layers. The high density of this structure is in agreement with the high concentration of DNA observed in metaphase chromosomes of different species, and the irregular orientation of nucleosomes within the plates make these results compatible with those obtained with mitotic cell cryo-sections. The multilaminar chromatin structure proposed for chromosomes allows an easy explanation of chromosome banding and of the band splitting observed in stretched chromosomes.
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Affiliation(s)
- Joan-Ramon Daban
- Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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12
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Szerlong HJ, Hansen JC. Nucleosome distribution and linker DNA: connecting nuclear function to dynamic chromatin structure. Biochem Cell Biol 2011; 89:24-34. [PMID: 21326360 DOI: 10.1139/o10-139] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Genetic information in eukaryotes is managed by strategic hierarchical organization of chromatin structure. Primary chromatin structure describes an unfolded nucleosomal array, often referred to as "beads on a string". Chromatin is compacted by the nonlinear rearrangement of nucleosomes to form stable secondary chromatin structures. Chromatin conformational transitions between primary and secondary structures are mediated by both nucleosome-stacking interactions and the intervening linker DNA. Chromatin model system studies find that the topography of secondary structures is sensitive to the spacing of nucleosomes within an array. Understanding the relationship between nucleosome spacing and higher order chromatin structure will likely yield important insights into the dynamic nature of secondary chromatin structure as it occurs in vivo. Genome-wide nucleosome mapping studies find the distance between nucleosomes varies, and regions of uniformly spaced nucleosomes are often interrupted by regions of nonuniform spacing. This type of organization is found at a subset of actively transcribed genes in which a nucleosome-depleted region near the transcription start site is directly adjacent to uniformly spaced nucleosomes in the coding region. Here, we evaluate secondary chromatin structure and discuss the structural and functional implications of variable nucleosome distributions in different organisms and at gene regulatory junctions.
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Affiliation(s)
- Heather J Szerlong
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA.
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Fu H, Freedman BS, Lim CT, Heald R, Yan J. Atomic force microscope imaging of chromatin assembled in Xenopus laevis egg extract. Chromosoma 2011; 120:245-54. [PMID: 21369955 DOI: 10.1007/s00412-010-0307-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 12/14/2010] [Accepted: 12/16/2010] [Indexed: 01/11/2023]
Abstract
Gaps persist in our understanding of chromatin lower- and higher-order structures. Xenopus egg extracts provide a way to study essential chromatin components which are difficult to manipulate in living cells, but nanoscale imaging of chromatin assembled in extracts poses a challenge. We describe a method for preparing chromatin assembled in extracts for atomic force microscopy (AFM) utilizing restriction enzyme digestion followed by transferring to a mica surface. Using this method, we find that buffer dilution of the chromatin assembly extract or incubation of chromatin in solutions of low ionic strength results in loosely compacted chromatin fibers that are prone to unraveling into naked DNA. We also describe a method for direct AFM imaging of chromatin which does not utilize restriction enzymes and reveals higher-order fibers of varying widths. Due to the capability of controlling chromatin assembly conditions, we believe these methods have broad potential for studying physiologically relevant chromatin structures.
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Affiliation(s)
- Hongxia Fu
- Mechanobiology Institute, National University of Singapore
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14
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Matsuda A, Shao L, Boulanger J, Kervrann C, Carlton PM, Kner P, Agard D, Sedat JW. Condensed mitotic chromosome structure at nanometer resolution using PALM and EGFP- histones. PLoS One 2010; 5:e12768. [PMID: 20856676 PMCID: PMC2939896 DOI: 10.1371/journal.pone.0012768] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 08/19/2010] [Indexed: 11/18/2022] Open
Abstract
Photoactivated localization microscopy (PALM) and related fluorescent biological imaging methods are capable of providing very high spatial resolutions (up to 20 nm). Two major demands limit its widespread use on biological samples: requirements for photoactivatable/photoconvertible fluorescent molecules, which are sometimes difficult to incorporate, and high background signals from autofluorescence or fluorophores in adjacent focal planes in three-dimensional imaging which reduces PALM resolution significantly. We present here a high-resolution PALM method utilizing conventional EGFP as the photoconvertible fluorophore, improved algorithms to deal with high levels of biological background noise, and apply this to imaging higher order chromatin structure. We found that the emission wavelength of EGFP is efficiently converted from green to red when exposed to blue light in the presence of reduced riboflavin. The photon yield of red-converted EGFP using riboflavin is comparable to other bright photoconvertible fluorescent proteins that allow <20 nm resolution. We further found that image pre-processing using a combination of denoising and deconvolution of the raw PALM images substantially improved the spatial resolution of the reconstruction from noisy images. Performing PALM on Drosophila mitotic chromosomes labeled with H2AvD-EGFP, a histone H2A variant, revealed filamentous components of ∼70 nm. This is the first observation of fine chromatin filaments specific for one histone variant at a resolution approximating that of conventional electron microscope images (10-30 nm). As demonstrated by modeling and experiments on a challenging specimen, the techniques described here facilitate super-resolution fluorescent imaging with common biological samples.
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Affiliation(s)
- Atsushi Matsuda
- Department of Biochemistry and Biophysics, The Keck Center for Advanced Microscopy, University of California San Francisco, San Francisco, California, United States of America
| | - Lin Shao
- Department of Biochemistry and Biophysics, The Keck Center for Advanced Microscopy, University of California San Francisco, San Francisco, California, United States of America
| | | | - Charles Kervrann
- INRIA Rennes Bretagne Atlantique, Campus Universitaire de Beaulieu, Rennes, France
| | - Peter M. Carlton
- Department of Biochemistry and Biophysics, The Keck Center for Advanced Microscopy, University of California San Francisco, San Francisco, California, United States of America
| | - Peter Kner
- Department of Biochemistry and Biophysics, The Keck Center for Advanced Microscopy, University of California San Francisco, San Francisco, California, United States of America
| | - David Agard
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, The Keck Center for Advanced Microscopy, University of California San Francisco, San Francisco, California, United States of America
| | - John W. Sedat
- Department of Biochemistry and Biophysics, The Keck Center for Advanced Microscopy, University of California San Francisco, San Francisco, California, United States of America
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Asbury TM, Mitman M, Tang J, Zheng WJ. Genome3D: a viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome. BMC Bioinformatics 2010; 11:444. [PMID: 20813045 PMCID: PMC2941692 DOI: 10.1186/1471-2105-11-444] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 09/02/2010] [Indexed: 12/18/2022] Open
Abstract
Background New technologies are enabling the measurement of many types of genomic and epigenomic information at scales ranging from the atomic to nuclear. Much of this new data is increasingly structural in nature, and is often difficult to coordinate with other data sets. There is a legitimate need for integrating and visualizing these disparate data sets to reveal structural relationships not apparent when looking at these data in isolation. Results We have applied object-oriented technology to develop a downloadable visualization tool, Genome3D, for integrating and displaying epigenomic data within a prescribed three-dimensional physical model of the human genome. In order to integrate and visualize large volume of data, novel statistical and mathematical approaches have been developed to reduce the size of the data. To our knowledge, this is the first such tool developed that can visualize human genome in three-dimension. We describe here the major features of Genome3D and discuss our multi-scale data framework using a representative basic physical model. We then demonstrate many of the issues and benefits of multi-resolution data integration. Conclusions Genome3D is a software visualization tool that explores a wide range of structural genomic and epigenetic data. Data from various sources of differing scales can be integrated within a hierarchical framework that is easily adapted to new developments concerning the structure of the physical genome. In addition, our tool has a simple annotation mechanism to incorporate non-structural information. Genome3D is unique is its ability to manipulate large amounts of multi-resolution data from diverse sources to uncover complex and new structural relationships within the genome.
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Affiliation(s)
- Thomas M Asbury
- Department of Biochemistry & Molecular Biology, Medical University of South Carolina, 135 Cannon Street, Suite 303E, Charleston, SC 29425, USA
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Szerlong HJ, Prenni JE, Nyborg JK, Hansen JC. Activator-dependent p300 acetylation of chromatin in vitro: enhancement of transcription by disruption of repressive nucleosome-nucleosome interactions. J Biol Chem 2010; 285:31954-64. [PMID: 20720004 DOI: 10.1074/jbc.m110.148718] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Condensation of chromatin into higher order structures is mediated by intra- and interfiber nucleosome-nucleosome interactions. Our goals in this study were to determine the impact specific activator-dependent histone acetylation had on chromatin condensation and to ascertain whether acetylation-induced changes in chromatin condensation were related to changes in RNA polymerase II (RNAPII) activity. To accomplish this, an in vitro model system was constructed in which the purified transcriptional activators, Tax and phosphorylated CREB (cAMP-response element-binding protein), recruited the p300 histone acetyltransferase to nucleosomal templates containing the human T-cell leukemia virus type-1 promoter sequences. We find that activator-dependent p300 histone acetylation disrupted both inter- and intrafiber nucleosome-nucleosome interactions and simultaneously led to enhanced RNAPII transcription from the decondensed model chromatin. p300 histone acetyltransferase activity had two distinct components: non-targeted, ubiquitous activity in the absence of activators and activator-dependent activity targeted primarily to promoter-proximal nucleosomes. Mass spectrometry identified several unique p300 acetylation sites on nucleosomal histone H3 (H3K9, H3K27, H3K36, and H3K37). Collectively, our data have important implications for understanding both the mechanism of RNAPII transcriptional regulation by chromatin and the molecular determinants of higher order chromatin structure.
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Affiliation(s)
- Heather J Szerlong
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
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Finan K, Cook PR, Marenduzzo D. Non-specific (entropic) forces as major determinants of the structure of mammalian chromosomes. Chromosome Res 2010; 19:53-61. [DOI: 10.1007/s10577-010-9150-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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18
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Kizilyaprak C, Spehner D, Devys D, Schultz P. In vivo chromatin organization of mouse rod photoreceptors correlates with histone modifications. PLoS One 2010; 5:e11039. [PMID: 20543957 PMCID: PMC2882955 DOI: 10.1371/journal.pone.0011039] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 05/15/2010] [Indexed: 12/31/2022] Open
Abstract
Background The folding of genetic information into chromatin plays important regulatory roles in many nuclear processes and particularly in gene transcription. Post translational histone modifications are associated with specific chromatin condensation states and with distinct transcriptional activities. The peculiar chromatin organization of rod photoreceptor nuclei, with a large central domain of condensed chromatin surrounded by a thin border of extended chromatin was used as a model to correlate in vivo chromatin structure, histone modifications and transcriptional activity. Methodology We investigated the functional relationships between chromatin compaction, distribution of histone modifications and location of RNA polymerase II in intact murine rod photoreceptors using cryo-preparation methods, electron tomography and immunogold labeling. Our results show that the characteristic central heterochromatin of rod nuclei is organized into concentric domains characterized by a progressive loosening of the chromatin architecture from inside towards outside and by specific combinations of silencing histone marks. The peripheral heterochromatin is formed by closely packed 30nm fibers as revealed by a characteristic optical diffraction signal. Unexpectedly, the still highly condensed most external heterochromatin domain contains acetylated histones, which are usually associated with active transcription and decondensed chromatin. Histone acetylation is thus not sufficient in vivo for complete chromatin decondensation. The euchromatin domain contains several degrees of chromatin compaction and the histone tails are hyperacetylated, enriched in H3K4 monomethylation and hypo trimethylated on H3K9, H3K27 and H4K20. The transcriptionally active RNA polymerases II molecules are confined in the euchromatin domain and are preferentially located at the vicinity of the interface with heterochromatin. Conclusions Our results show that transcription is located in the most decondensed and highly acetylated chromatin regions, but since acetylation is found associated with compact chromatin it is not sufficient to decondense chromatin in vivo. We also show that a combination of histone marks defines distinct concentric heterochromatin domains.
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Affiliation(s)
- Caroline Kizilyaprak
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Illkirch, France
- Inserm, U964, Illkirch, France
- CNRS, UMR7104, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Danièle Spehner
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Illkirch, France
- Inserm, U964, Illkirch, France
- CNRS, UMR7104, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Didier Devys
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Illkirch, France
- Inserm, U964, Illkirch, France
- CNRS, UMR7104, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Patrick Schultz
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Illkirch, France
- Inserm, U964, Illkirch, France
- CNRS, UMR7104, Illkirch, France
- Université de Strasbourg, Strasbourg, France
- * E-mail:
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19
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Castro-Hartmann P, Milla M, Daban JR. Irregular Orientation of Nucleosomes in the Well-Defined Chromatin Plates of Metaphase Chromosomes. Biochemistry 2010; 49:4043-50. [DOI: 10.1021/bi100125f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Pablo Castro-Hartmann
- Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Maria Milla
- Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Joan-Ramon Daban
- Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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20
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Baddeley D, Weiland Y, Batram C, Birk U, Cremer C. Model based precision structural measurements on barely resolved objects. J Microsc 2010; 237:70-8. [PMID: 20055920 DOI: 10.1111/j.1365-2818.2009.03304.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A model based method for the accurate quantification of the 3D structure of fluorescently labelled cellular objects similar in size to the optical resolution limit is presented. This method is applied to both simulated confocal images of chromatin structures and to real confocal data obtained on a Fluorescence in situ Hybridization (FISH) labelled gene domain. The model assumes that the object is composed of a small number of discrete points which are convolved with the microscope point spread function to give the image. Fitting this model to image data results in a method to assess object structure which is accurate, shows a low bias, and does not require user intervention or the potentially subjective setting of a threshold.
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Affiliation(s)
- D Baddeley
- Kirchhoff Institut für Physik, Universität Heidelberg, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany.
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21
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Olins DE, Olins AL. Nuclear envelope-limited chromatin sheets (ELCS) and heterochromatin higher order structure. Chromosoma 2009; 118:537-48. [PMID: 19521714 DOI: 10.1007/s00412-009-0219-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Revised: 05/07/2009] [Accepted: 05/19/2009] [Indexed: 12/28/2022]
Abstract
The interphase nucleus and nuclear envelope can acquire a myriad of shapes in normal or pathological cell states. There exist a wide variety of indentations and invaginations, of protrusions and evaginations. It has been difficult to classify and name all of these nuclear shapes and, consequently, a barrier to understanding the biochemical and biophysical causes. This review focuses upon one type of nuclear envelope shape change, named "nuclear envelope-limited chromatin sheets" (ELCS), which appears to involve exaggerated nuclear envelope growth, carrying with it one or more layers of approximately 30 nm diameter heterochromatin. A hypothesis on the formation of ELCS is proposed, relating higher order heterochromatin structure in an interphase nucleus, nuclear envelope growth, and nuclear envelope-heterochromatin interactions.
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Affiliation(s)
- Donald E Olins
- Department of Biology, Bowdoin College, Brunswick, ME 04011, USA.
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22
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Studitsky VM. Mechanisms of distant enhancer action on DNA and in chromatin. Mol Biol 2009. [DOI: 10.1134/s0026893309020022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Role of chromatin states in transcriptional memory. Biochim Biophys Acta Gen Subj 2009; 1790:445-55. [PMID: 19236904 DOI: 10.1016/j.bbagen.2009.02.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Revised: 02/10/2009] [Accepted: 02/11/2009] [Indexed: 12/16/2022]
Abstract
Establishment of cellular memory and its faithful propagation is critical for successful development of multicellular organisms. As pluripotent cells differentiate, choices in cell fate are inherited and maintained by their progeny throughout the lifetime of the organism. A major factor in this process is the epigenetic inheritance of specific transcriptional states or transcriptional memory. In this review, we discuss chromatin transitions and mechanisms by which they are inherited by subsequent generations. We also discuss illuminating cases of cellular memory in budding yeast and evaluate whether transcriptional memory in yeast is nuclear or cytoplasmically inherited.
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24
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Dense chromatin plates in metaphase chromosomes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 38:503-22. [DOI: 10.1007/s00249-008-0401-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 12/11/2008] [Accepted: 12/19/2008] [Indexed: 10/21/2022]
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25
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Kalverda B, Röling MD, Fornerod M. Chromatin organization in relation to the nuclear periphery. FEBS Lett 2008; 582:2017-22. [PMID: 18435921 DOI: 10.1016/j.febslet.2008.04.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Accepted: 04/11/2008] [Indexed: 11/15/2022]
Abstract
In the limited space of the nucleus, chromatin is organized in a dynamic and non-random manner. Three ways of chromatin organization are compaction, formation of loops and localization within the nucleus. To study chromatin localization it is most convenient to use the nuclear envelope as a fixed viewpoint. Peripheral chromatin has both been described as silent chromatin, interacting with the nuclear lamina, and active chromatin, interacting with nuclear pore proteins. Current data indicate that the nuclear envelope is a reader as well as a writer of chromatin state, and that its influence is not limited to the nuclear periphery.
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Affiliation(s)
- Bernike Kalverda
- Department of Tumor Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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26
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Rego A, Sinclair PB, Tao W, Kireev I, Belmont AS. The facultative heterochromatin of the inactive X chromosome has a distinctive condensed ultrastructure. J Cell Sci 2008; 121:1119-27. [DOI: 10.1242/jcs.026104] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mammalian inactive X chromosome (Xi) is a model for facultative heterochromatin. Increased DNA compaction for the Xi, and for facultative heterochromatin in general, has long been assumed based on recognition of a distinct Barr body using nucleic-acid staining. This conclusion has been challenged by a report revealing equal volumes occupied by the inactive and active X chromosomes. Here, we use light and electron microscopy to demonstrate in mouse and human fibroblasts a unique Xi ultrastructure, distinct from euchromatin and constitutive heterochromatin, containing tightly packed, heterochromatic fibers/domains with diameters in some cases approaching that of prophase chromatids. Significant space between these packed structures is observed even within condensed regions of the Xi. Serial-section analysis also reveals extensive contacts of the Xi with the nuclear envelope and/or nucleolus, with nuclear envelope association being observed in all cells. Implications of our results for models of Xi gene silencing and chromosome territory organization are discussed.
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Affiliation(s)
- Alena Rego
- Department of Cell and Developmental Biology, University of Illinois, 601 South Goodwin Avenue, Urbana, IL 61801, USA
| | - Paul B. Sinclair
- Department of Cell and Developmental Biology, University of Illinois, 601 South Goodwin Avenue, Urbana, IL 61801, USA
| | - Wei Tao
- Department of Cell and Developmental Biology, University of Illinois, 601 South Goodwin Avenue, Urbana, IL 61801, USA
| | - Igor Kireev
- Department of Cell and Developmental Biology, University of Illinois, 601 South Goodwin Avenue, Urbana, IL 61801, USA
| | - Andrew S. Belmont
- Department of Cell and Developmental Biology, University of Illinois, 601 South Goodwin Avenue, Urbana, IL 61801, USA
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27
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Skibbens RV. Mechanisms of sister chromatid pairing. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 269:283-339. [PMID: 18779060 DOI: 10.1016/s1937-6448(08)01005-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The continuance of life through cell division requires high fidelity DNA replication and chromosome segregation. During DNA replication, each parental chromosome is duplicated exactly and one time only. At the same time, the resulting chromosomes (called sister chromatids) become tightly paired along their length. This S-phase pairing, or cohesion, identifies chromatids as sisters over time. During mitosis in most eukaryotes, sister chromatids bi-orient to the mitotic spindle. After each chromosome pair is properly oriented, the cohesion established during S phase is inactivated in a tightly regulated fashion, allowing sister chromatids to segregate away from each other. Recent findings of cohesin structure and enzymology provide new insights into cohesion, while many critical facets of cohesion (how cohesins tether together sister chromatids and how those tethers are established) remain actively debated.
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Affiliation(s)
- Robert V Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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28
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Bohn M, Heermann DW, van Driel R. Random loop model for long polymers. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 76:051805. [PMID: 18233679 DOI: 10.1103/physreve.76.051805] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Revised: 10/04/2007] [Indexed: 05/25/2023]
Abstract
Remarkably little is known about the higher-order folding motifs of the chromatin fiber inside the cell nucleus. Folding depends among others on local gene density and transcriptional activity and plays an important role in gene regulation. Strikingly, at fiber lengths above 5 to 10 Mb the measured mean square distance <R2> between any two points on the chromatin fiber is independent of polymer length. We propose a polymer model that can explain this leveling-off by means of random looping. We derive an analytical expression for the mean square displacement between two arbitrary beads. Here the average is taken over the thermal ensemble with a fixed but random loop configuration, while quenched averaging over the ensemble of different loop configurations--which turns out to be equivalent to averaging over an ensemble of random matrices--is performed numerically. A detailed investigation of this model shows that loops on all scales are necessary to fit experimental data.
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Affiliation(s)
- Manfred Bohn
- Institute of Theoretical Physics, University of Heidelberg, Philosophenweg 19, D-69120 Heidelberg, Germany.
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29
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Zhou J, Fan JY, Rangasamy D, Tremethick DJ. The nucleosome surface regulates chromatin compaction and couples it with transcriptional repression. Nat Struct Mol Biol 2007; 14:1070-6. [PMID: 17965724 DOI: 10.1038/nsmb1323] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2007] [Accepted: 09/24/2007] [Indexed: 11/09/2022]
Abstract
Although it is believed that the interconversion between permissive and refractory chromatin structures is important in regulating gene transcription, this process is poorly understood. Central to addressing this issue is to elucidate how a nucleosomal array folds into higher-order chromatin structures. Such findings can then provide new insights into how the folding process is regulated to yield different functional states. Using well-defined in vitro chromatin-assembly and transcription systems, we show that a small acidic region on the surface of the nucleosome is crucial both for the folding of a nucleosomal template into the 30-nm chromatin fiber and for the efficient repression of transcription, thereby providing a mechanistic link between these two essential processes. This structure-function relationship has been exploited by complex eukaryotic cells through the replacement of H2A with the specific variant H2A.Bbd, which naturally lacks an acidic patch.
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Affiliation(s)
- Jiansheng Zhou
- The John Curtin School of Medical Research, The Australian National University, PO Box 334, Canberra, Australian Capital Territory 2601, Australia
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30
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Goetze S, Mateos-Langerak J, van Driel R. Three-dimensional genome organization in interphase and its relation to genome function. Semin Cell Dev Biol 2007; 18:707-14. [PMID: 17905616 DOI: 10.1016/j.semcdb.2007.08.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Accepted: 08/22/2007] [Indexed: 01/10/2023]
Abstract
Higher order chromatin structure, i.e. the three-dimensional (3D) organization of the genome in the interphase nucleus, is an important component in the orchestration of gene expression in the mammalian genome. In this review we describe principles of higher order chromatin structure discussing three organizational parameters, i.e. chromatin folding, chromatin compaction and the nuclear position of the chromatin fibre. We argue that principles of 3D genome organization are probabilistic traits, reflected in a considerable cell-to-cell variation in 3D genome structure. It will be essential to understand how such higher order organizational aspects contribute to genome function to unveil global genome regulation.
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Affiliation(s)
- Sandra Goetze
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands.
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31
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van Holde K, Zlatanova J. Chromatin fiber structure: Where is the problem now? Semin Cell Dev Biol 2007; 18:651-8. [PMID: 17905614 DOI: 10.1016/j.semcdb.2007.08.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 08/22/2007] [Indexed: 11/17/2022]
Abstract
The structure of the "30 nm chromatin fiber", as observed in vitro, has been a matter of controversy for 30 years. Recent studies with new and more powerful techniques give some promise for resolution. However, this will not necessarily inform us as to the in vivo structure, which may be both heteromorphic and dynamic. In this chapter, we briefly review the older conjectures and some more recent studies of special interest. We attempt to point out the remaining contradictions and hopeful lines of future research.
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Affiliation(s)
- Ken van Holde
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.
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32
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Mazumder A, Shivashankar GV. Gold-nanoparticle-assisted laser perturbation of chromatin assembly reveals unusual aspects of nuclear architecture within living cells. Biophys J 2007; 93:2209-16. [PMID: 17496030 PMCID: PMC1959558 DOI: 10.1529/biophysj.106.102202] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Chromatin organization within the nucleus is a vital regulator of genome function, yet its mechanical coupling to the nuclear architecture has remained elusive. To directly investigate this coupling, we locally modulated chromatin structure in living cells using nanoparticle-based laser perturbation. Unusual differences in the response of the cell nucleus were observed depending on the nuclear region that was perturbed--the heterochromatin, the euchromatin, and the nuclear envelope. This response varied under different conditions of cellular perturbations such as ATP depletion, apoptosis, and inhibition of histone deacetylases. Our studies implicate heterochromatin organization in imparting mechanical stability to the cell nucleus and suggest that nuclear size and shape are the result of interplay between nuclear and cytoplasmic anchors.
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Affiliation(s)
- Aprotim Mazumder
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India
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33
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Abstract
Despite progress in understanding chromatin function, the structure of the 30 nm chromatin fiber has remained elusive. However, with the recent crystal structure of a short tetranucleosomal array, the 30 nm fiber is beginning to come into view.
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Affiliation(s)
- David J Tremethick
- The John Curtin School of Medical Research, The Australian National University, P.O. Box 334, Canberra, The Australian Capital Territory, Australia, 2601.
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34
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Zhang R, Liu ST, Chen W, Bonner M, Pehrson J, Yen TJ, Adams PD. HP1 proteins are essential for a dynamic nuclear response that rescues the function of perturbed heterochromatin in primary human cells. Mol Cell Biol 2006; 27:949-62. [PMID: 17101789 PMCID: PMC1800672 DOI: 10.1128/mcb.01639-06] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cellular information is encoded genetically in the DNA nucleotide sequence and epigenetically by the "histone code," DNA methylation, and higher-order packaging of DNA into chromatin. Cells possess intricate mechanisms to sense and repair damage to DNA and the genetic code. However, nothing is known of the mechanisms, if any, that repair and/or compensate for damage to epigenetically encoded information, predicted to result from perturbation of DNA and histone modifications or other changes in chromatin structure. Here we show that primary human cells respond to a variety of small molecules that perturb DNA and histone modifications by recruiting HP1 proteins to sites of altered pericentromeric heterochromatin. This response is essential to maintain the HP1-binding kinetochore protein hMis12 at kinetochores and to suppress catastrophic mitotic defects. Recruitment of HP1 proteins to pericentromeres depends on histone H3.3 variant deposition, mediated by the HIRA histone chaperone. These data indicate that defects in pericentromeric epigenetic heterochromatin modifications initiate a dynamic HP1-dependent response that rescues pericentromeric heterochromatin function and is essential for viable progression through mitosis.
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Affiliation(s)
- Rugang Zhang
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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35
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Vadakkan KI, Li B, De Boni U. Cell-type specific proximity of centromeric domains of one homologue each of chromosomes 2 and 11 in nuclei of cerebellar Purkinje neurons. Chromosoma 2006; 115:395-402. [PMID: 16741706 DOI: 10.1007/s00412-006-0069-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2006] [Revised: 04/15/2006] [Accepted: 04/18/2006] [Indexed: 10/24/2022]
Abstract
In Purkinje neurons of the mouse cerebellum, the centromeres of several chromosomes are placed in close proximity to form a distinct pattern of clusters and exhibit reproducible spatial redistributions during development. In granule neurons, an adjacent cell type in the cerebellum, the pattern, size, and number of centromeric aggregations are different from those of Purkinje neurons. The present work was undertaken to test the hypothesis that the same chromosomes form part of one aggregate in a cell-type-specific manner. Fluorescence in situ hybridization (FISH) with chromosome-specific paracentromeric probes was used to identify centromeric regions of individual chromosomes in cerebellar Purkinje and granule neurons of the adult mouse. When pairs of centromeric probes were used in two-color FISH, one homologue each of chromosomes 2 and 11 were routinely found close to each other in Purkinje neurons but not in granule neurons. This finding of specific proximity was limited to the pair 2 and 11, out of the ten chromosome pairs that were randomly selected and studied. Our results indicate that, in adult Purkinje neurons, a cell-type-specific spatial proximity is present between centromeric domains of one homologue each of chromosomes 2 and 11.
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Affiliation(s)
- Kunjumon I Vadakkan
- Department of Physiology, Faculty of Medicine, University of Toronto, M5S 1A8 Toronto, ON, Canada
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36
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Woodcock CL. Chromatin architecture. Curr Opin Struct Biol 2006; 16:213-20. [PMID: 16540311 DOI: 10.1016/j.sbi.2006.02.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2005] [Revised: 02/24/2006] [Accepted: 02/28/2006] [Indexed: 01/21/2023]
Abstract
A complete understanding of the structure-function relationships of chromatin requires extending primarily one dimensional information, obtained from molecular genetic techniques and based on the underlying linear DNA sequence, to the three dimensional conformation. Recent progress in this endeavor has included the examination of fully defined nucleosomes and nucleosomal arrays assembled in vitro using X-ray diffraction, NMR spectroscopy, electron microscopy and atomic force microscopy. These studies have provided valuable insights into the structural roles of histone variants, the impact of histone mutations and the compaction of nucleosomal arrays. In addition, the diverse structural consequences of the binding of specific chromatin 'architectural' proteins are becoming apparent. These approaches provide an essential basis for understanding the conformation of the 'epigenome'.
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Affiliation(s)
- Christopher L Woodcock
- Department of Biology and Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003, USA.
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