151
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Suissa M, Place C, Goillot E, Freyssingeas E. Internal dynamics of a living cell nucleus investigated by dynamic light scattering. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2008; 26:435-48. [PMID: 19230214 DOI: 10.1140/epje/i2007-10346-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Recent progresses in cellular biology have shown that the nucleus of a living cell is a structured integration of many functional domains with a complex spatial organization. This organization, as well as molecular and biochemical processes, is time regulated. In the past years many investigations have been performed using fluorescent microscopy techniques to study the internal dynamics of the nucleus of a living cell. These investigations, however, have never focussed on the global internal dynamics of the nucleus, which is still unknown. In this article we present an original light scattering experimental device that we built to investigate this dynamics during biological processes. By means of this experimental set-up, we investigated the global dynamics of the nucleus of a living cell treated with a DNA replication inhibitor. This dynamics presents different and independent kinds of relaxation well separated in time that vary as a function of the cell cycle phases.
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Affiliation(s)
- M Suissa
- Université de Lyon, Laboratoire de Physique, Ecole Normale Supérieure de Lyon, CNRS, 46 allée d'Italie, 69364 Lyon, France
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152
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Fedorova E, Zink D. Nuclear architecture and gene regulation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1783:2174-84. [PMID: 18718493 DOI: 10.1016/j.bbamcr.2008.07.018] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Revised: 07/15/2008] [Accepted: 07/20/2008] [Indexed: 12/27/2022]
Abstract
The spatial organization of eukaryotic genomes in the cell nucleus is linked to their transcriptional regulation. In mammals, on which this review will focus, transcription-related chromatin positioning is regulated at the level of chromosomal sub-domains and individual genes. Most of the chromatin remains stably positioned during interphase. However, some loci display dynamic relocalizations upon transcriptional activation, which are dependent on nuclear actin and myosin. Transcription factors in association with chromatin modifying complexes seem to play a central role in regulating chromatin dynamics and positioning. Recent results obtained in this regard also give insight into the question how the different levels of transcriptional regulation are integrated and coordinated with other processes involved in gene expression. Corresponding findings will be discussed.
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Affiliation(s)
- Elena Fedorova
- Russian Academy of Sciences, I.P. Pavlov Institute of Physiology, Department of Sensory Physiology, Nab. Makarova 6, 199034 St. Petersburg, Russia
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153
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Egli D, Birkhoff G, Eggan K. Mediators of reprogramming: transcription factors and transitions through mitosis. Nat Rev Mol Cell Biol 2008; 9:505-16. [PMID: 18568039 DOI: 10.1038/nrm2439] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It is thought that most cell types of the human body share the same genetic information as that contained in the zygote from which they originate. Consistent with this view, animal cloning studies demonstrated that the intact genome of a differentiated cell can be reprogrammed to support the development of an entire organism and allow the production of pluripotent stem cells. Recent progress in reprogramming research now points to an important role for transcription factors in the establishment and the maintenance of cellular phenotypes, and to cell division as a mediator of transitions between different states of gene expression.
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Affiliation(s)
- Dieter Egli
- The Stowers Medical Institute, Harvard Stem Cell Institute and the Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
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154
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Chromatin structure influences the sensitivity of DNA to gamma-radiation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1783:2398-414. [PMID: 18706456 DOI: 10.1016/j.bbamcr.2008.07.010] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 07/11/2008] [Accepted: 07/11/2008] [Indexed: 11/23/2022]
Abstract
For the first time, DNA double-strand breaks (DSBs) were directly visualized in functionally and structurally different chromatin domains of human cells. The results show that genetically inactive condensed chromatin is much less susceptible to DSB induction by gamma-rays than expressed, decondensed domains. Higher sensitivity of open chromatin for DNA damage was accompanied by more efficient DSB repair. These findings follow from comparing DSB induction and repair in two 11 Mbp-long chromatin regions, one with clusters of highly expressed genes and the other, gene-poor, containing mainly genes having only low transcriptional activity. The same conclusions result from experiments with whole chromosome territories, differing in gene density and consequently in chromatin condensation. It follows from our further results that this lower sensitivity of DNA to the damage by ionizing radiation in heterochromatin is not caused by the simple chromatin condensation but very probably by the presence of a higher amount of proteins compared to genetically active and decondensed chromatin. In addition, our results show that some agents potentially used for cell killing in cancer therapy (TSA, hypotonic and hypertonic) influence cell survival of irradiated cells via changes in chromatin structure and efficiency of DSB repair in different ways.
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155
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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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156
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Mateos-Langerak J, Goetze S, Leonhardt H, Cremer T, van Driel R, Lanctôt C. Nuclear architecture: Is it important for genome function and can we prove it? J Cell Biochem 2008; 102:1067-75. [PMID: 17786936 DOI: 10.1002/jcb.21521] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Gene regulation in higher eukaryotes has been shown to involve regulatory sites, such as promoters and enhancers which act at the level of individual genes, and mechanisms which control the functional state of gene clusters. A fundamental question is whether additional levels of genome control exist. Nuclear organization and large-scale chromatin structure may constitute such a level and play an important role in the cell-type specific orchestration of the expression of thousands of genes in eukaryotic cells. Numerous observations indicate a tight correlation between genome activity and nuclear and large-scale chromatin structure. However, causal relationships are rare. Here we explore how these might be uncovered.
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Affiliation(s)
- Julio Mateos-Langerak
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
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157
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Wiland E, Zegało M, Kurpisz M. Interindividual differences and alterations in the topology of chromosomes in human sperm nuclei of fertile donors and carriers of reciprocal translocations. Chromosome Res 2008; 16:291-305. [PMID: 18256895 DOI: 10.1007/s10577-007-1194-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Revised: 07/11/2007] [Accepted: 07/11/2007] [Indexed: 11/26/2022]
Abstract
Recently it has been shown that the nucleus of the human spermatozoon appears to possess a specific architecture. The current prevailing view is that spatial organization of the male genome contains information critical for the spermatozoon's function as well as for early embryonic development. The purpose of this study was to determine whether there are alterations in intranuclear localization of centromeres in spermatozoa of chromosomes associated with particular reciprocal chromosome translocations (RCT). We analyzed the longitudinal and spatial localization of centromeres of selected chromosomes in sperm nuclei of four control males with normal karyotypes as well as in six carriers of reciprocal chromosome translocations: t(1;7), t(7;2), t(7;13), t(7;9), t(9;14), and t(4;13). Our study revealed that chromosomes with translocations may have shifted their intranuclear localization and that these translocations may influence the localization of other chromosomes in sperm nuclei. The chromocenter in sperm nuclei of translocation carriers was widened toward the apical side in comparison with chromocenter sites visible in control males. Our study also revealed interindividual differences in the localization of the Y chromosome centromere in the chromocenter area of sperm from fertile individuals.
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MESH Headings
- Adult
- Cell Nucleus/genetics
- Centromere/metabolism
- Chromosomes, Human/metabolism
- Chromosomes, Human/ultrastructure
- Chromosomes, Human, Pair 1
- Chromosomes, Human, Pair 13
- Chromosomes, Human, Pair 14
- Chromosomes, Human, Pair 2
- Chromosomes, Human, Pair 4
- Chromosomes, Human, Pair 7
- Chromosomes, Human, Pair 9
- Chromosomes, Human, Y/metabolism
- Chromosomes, Human, Y/ultrastructure
- Fertility/genetics
- Genetic Heterogeneity
- Heterozygote
- Humans
- Male
- Models, Biological
- Spermatozoa/ultrastructure
- Tissue Donors
- Translocation, Genetic
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Affiliation(s)
- Ewa Wiland
- Institute of Human Genetics, Polish Academy of Sciences, ul. Strzeszyńska 32, 60-479, Poznań, Poland
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158
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Kumaran RI, Spector DL. A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence. ACTA ACUST UNITED AC 2008; 180:51-65. [PMID: 18195101 PMCID: PMC2213611 DOI: 10.1083/jcb.200706060] [Citation(s) in RCA: 289] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The peripheral nuclear lamina, which is largely but not entirely associated with inactive chromatin, is considered to be an important determinant of nuclear structure and gene expression. We present here an inducible system to target a genetic locus to the nuclear lamina in living mammalian cells. Using three-dimensional time-lapse microscopy, we determined that targeting of the locus requires passage through mitosis. Once targeted, the locus remains anchored to the nuclear periphery in interphase as well as in daughter cells after passage through a subsequent mitosis. Upon transcriptional induction, components of the gene expression machinery are recruited to the targeted locus, and we visualized nascent transcripts at the nuclear periphery. The kinetics of transcriptional induction at the nuclear lamina is similar to that observed at an internal nuclear region. This new cell system provides a powerful approach to study the dynamics of gene function at the nuclear periphery in living cells.
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Affiliation(s)
- R Ileng Kumaran
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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159
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Kikuchi S, Tanaka H, Wako T, Tsujimoto H. Centromere separation and association in the nuclei of an interspecific hybrid between Torenia fournieri and T. baillonii (Scrophulariaceae) during mitosis and meiosis. Genes Genet Syst 2008; 82:369-75. [PMID: 17991992 DOI: 10.1266/ggs.82.369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In the nuclei of some interspecific hybrid and allopolyploid plant species, each genome occupies a separate spatial domain. To analyze this phenomenon, we studied localization of the centromeres in the nuclei of a hybrid between Torenia fournieri and T. baillonii during mitosis and meiosis using three-dimensional fluorescence in situ hybridization (3D-FISH) probed with species-specific centromere repeats. Centromeres of each genome were located separately in undifferentiated cells but not differentiated cells, suggesting that cell division might be the possible force causing centromere separation. However, no remarkable difference of dividing distance was detected between chromatids with different centromeres in anaphase and telophase, indicating that tension of the spindle fiber attached to each chromatid is not the cause of centromere separation in Torenia. In differentiated cells, centromeres in both genomes were not often observed for the expected chromosome number, indicating centromere association. In addition, association of centromeres from the same genome was observed at a higher frequency than between different genomes. This finding suggests that centromeres within one genome are spatially separated from those within the other. This close position may increase possibility of association between centromeres of the same genome. In meiotic prophase, all centromeres irrespective of the genome were associated in a certain portion of the nucleus. Since centromere association in the interspecific hybrid and amphiploid was tighter than that in the diploid parents, it is possible that this phenomenon may be involved in sorting and pairing of homologous chromosomes.
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Affiliation(s)
- Shinji Kikuchi
- The United Graduated School of Agricultural Sciences, Tottori University
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160
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Levsky JM, Shenoy SM, Chubb JR, Hall CB, Capodieci P, Singer RH. The spatial order of transcription in mammalian cells. J Cell Biochem 2008; 102:609-17. [PMID: 17849428 PMCID: PMC4956920 DOI: 10.1002/jcb.21495] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have previously developed technology for multiplexing probes for the detection of transcription of many genes simultaneously within single cells. This has allowed us to determine the spatial localization of multiple genes with respect to each other in the nucleus, and ultimately the expression profile of the cell with respect to surrounding cells in a tissue. Six parameters of transcriptional organization in individual cells from culture and tissue were used to characterize significant differences in intracellular and intercellular expression patterns while preserving cellular morphology and histological context. We found that, unlike yeast, mammalian expression is excluded from the periphery and in addition, a subtle but complex organization underlies the transcriptional activity of these cells, both intra- and intercellularly. The approach has sufficient spatial resolution to be applied to the detection of chromosomal translocations or the identification of cancer cells.
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Affiliation(s)
- Jeffrey M. Levsky
- Department of Anatomy & Structural Biology, Albert Einstein College of Medicine,1300 Morris Park Avenue, Bronx, New York 10461, USA
| | - Shailesh M. Shenoy
- Department of Anatomy & Structural Biology, Albert Einstein College of Medicine,1300 Morris Park Avenue, Bronx, New York 10461, USA
| | - Jonathan R. Chubb
- Department of Anatomy & Structural Biology, Albert Einstein College of Medicine,1300 Morris Park Avenue, Bronx, New York 10461, USA
- Department of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Charles B. Hall
- Department of Epidemiology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
| | - Paola Capodieci
- Aureon Laboratories, 28 Wells Ave, Yonkers, New York 10701, USA
| | - Robert H. Singer
- Department of Anatomy & Structural Biology, Albert Einstein College of Medicine,1300 Morris Park Avenue, Bronx, New York 10461, USA
- Correspondence to: Robert H. Singer,
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161
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Abstract
Recent advances have demonstrated that placing genes in a specific nuclear context plays an important role in the regulation of coordinated gene expression, thus adding an additional level of complexity to the mechanisms of gene regulation. Differentiation processes are characterized by dynamic changes in gene activation and silencing. These alterations are often accompanied by gene relocations in relation to other genomic regions or to nuclear compartments. Unraveling of mechanisms and dynamics of chromatin positioning will thus expand our knowledge about cellular differentiation.
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Affiliation(s)
- Christian Schöfer
- Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090 Vienna, Austria.
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162
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Rauch J, Knoch TA, Solovei I, Teller K, Stein S, Buiting K, Horsthemke B, Langowski J, Cremer T, Hausmann M, Cremer C. Light optical precision measurements of the active and inactive Prader-Willi syndrome imprinted regions in human cell nuclei. Differentiation 2007; 76:66-82. [PMID: 18039333 DOI: 10.1111/j.1432-0436.2007.00237.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Despite the major advancements during the last decade with respect to both knowledge of higher order chromatin organization in the cell nucleus and the elucidation of epigenetic mechanisms of gene control, the true three-dimensional (3D) chromatin structure of endogenous active and inactive gene loci is not known. The present study was initiated as an attempt to close this gap. As a model case, we compared the chromatin architecture between the genetically active and inactive domains of the imprinted Prader-Willi syndrome (PWS) locus in human fibroblast and lymphoblastoid cell nuclei by 3D fluorescence in situ hybridization and quantitative confocal laser scanning microscopy. The volumes and 3D compactions of identified maternal and paternal PWS domains were determined in stacks of light optical serial sections using a novel threshold-independent approach. Our failure to detect volume and compaction differences indicates that possible differences are below the limits of light optical resolution. To overcome this limitation, spectral precision distance microscopy, a method of localization microscopy at the nanometer scale, was used to measure 3D distances between differentially labeled probes located both within the PWS region and in its neighborhood. This approach allows the detection of intranuclear differences between 3D distances down to about 70-90 nm, but again did not reveal clearly detectable differences between active and inactive PWS domains. Despite this failure, a comparison of the experimental 3D distance measurements with computer simulations of chromatin folding strongly supports a non-random higher order chromatin configuration of the PWS locus and argues against 3D configurations based on giant chromatin loops. Our results indicate that the search for differences between endogenous active and inactive PWS domains must be continued at still smaller scales than hitherto possible with conventional light microscopic procedures. The possibilities to achieve this goal are discussed.
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Affiliation(s)
- Joachim Rauch
- Kirchhoff Institute of Physics, University of Heidelberg, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
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163
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Fournier A, Florin A, Lefebvre C, Solly F, Leroux D, Callanan M. Genetics and epigenetics of 1q rearrangements in hematological malignancies. Cytogenet Genome Res 2007; 118:320-7. [DOI: 10.1159/000108316] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 02/09/2007] [Indexed: 12/11/2022] Open
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164
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Kosak ST, Scalzo D, Alworth SV, Li F, Palmer S, Enver T, Lee JSJ, Groudine M. Coordinate gene regulation during hematopoiesis is related to genomic organization. PLoS Biol 2007; 5:e309. [PMID: 18031200 PMCID: PMC2080650 DOI: 10.1371/journal.pbio.0050309] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Accepted: 09/25/2007] [Indexed: 01/31/2023] Open
Abstract
Gene loci are found in nuclear subcompartments that are related to their expression status. For instance, silent genes are often localized to heterochromatin and the nuclear periphery, whereas active genes tend to be found in the nuclear center. Evidence also suggests that chromosomes may be specifically positioned within the nucleus; however, the nature of this organization and how it is achieved are not yet fully understood. To examine whether gene regulation is related to a discernible pattern of genomic organization, we analyzed the linear arrangement of co-regulated genes along chromosomes and determined the organization of chromosomes during the differentiation of a hematopoietic progenitor to erythroid and neutrophil cell types. Our analysis reveals that there is a significant tendency for co-regulated genes to be proximal, which is related to the association of homologous chromosomes and the spatial juxtaposition of lineage-specific gene domains. We suggest that proximity in the form of chromosomal gene distribution and homolog association may be the basis for organizing the genome for coordinate gene regulation during cellular differentiation.
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Affiliation(s)
- Steven T Kosak
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - David Scalzo
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Sam V Alworth
- SVision, Bellevue, Washington, United States of America
| | - Fusheng Li
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Stephanie Palmer
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Tariq Enver
- MRC Molecular Haematology Unit, Oxford University, United Kingdom
| | | | - Mark Groudine
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Radiation Oncology, University of Washington School of Medicine, Seattle, Washington, United States of America
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165
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Soutoglou E, Misteli T. Mobility and immobility of chromatin in transcription and genome stability. Curr Opin Genet Dev 2007; 17:435-42. [PMID: 17905579 PMCID: PMC2118061 DOI: 10.1016/j.gde.2007.08.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Revised: 07/16/2007] [Accepted: 08/17/2007] [Indexed: 01/07/2023]
Abstract
Chromatin is increasingly recognized as a highly dynamic entity. Chromosome sites in lower and higher eukaryotes undergo frequent, rapid, and constrained local motion and occasional slow, long-range movements. Recent observations have revealed some of the functional relevance of chromatin mobility. Paradoxically, both the mobility and immobility of chromatin appear to have functional consequences: Local diffusional motion of chromatin is important in gene regulation, but global chromatin immobility plays a key role in maintenance of genomic stability.
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Affiliation(s)
- Evi Soutoglou
- National Cancer Institute, NIH, Bethesda, MD 20892, United States
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166
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Pajerowski JD, Dahl KN, Zhong FL, Sammak PJ, Discher DE. Physical plasticity of the nucleus in stem cell differentiation. Proc Natl Acad Sci U S A 2007; 104:15619-24. [PMID: 17893336 PMCID: PMC2000408 DOI: 10.1073/pnas.0702576104] [Citation(s) in RCA: 590] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Cell differentiation in embryogenesis involves extensive changes in gene expression structural reorganization within the nucleus, including chromatin condensation and nucleoprotein immobilization. We hypothesized that nuclei in naive stem cells would therefore prove to be physically plastic and also more pliable than nuclei in differentiated cells. Micromanipulation methods indeed show that nuclei in human embryonic stem cells are highly deformable and stiffen 6-fold through terminal differentiation, and that nuclei in human adult stem cells possess an intermediate stiffness and deform irreversibly. Because the nucleo-skeletal component Lamin A/C is not expressed in either type of stem cell, we knocked down Lamin A/C in human epithelial cells and measured a deformability similar to that of adult hematopoietic stem cells. Rheologically, lamin-deficient states prove to be the most fluid-like, especially within the first approximately 10 sec of deformation. Nuclear distortions that persist longer than this are irreversible, and fluorescence-imaged microdeformation with photobleaching confirms that chromatin indeed flows, distends, and reorganizes while the lamina stretches. The rheological character of the nucleus is thus set largely by nucleoplasm/chromatin, whereas the extent of deformation is modulated by the lamina.
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Affiliation(s)
- J. David Pajerowski
- *Molecular and Cell Biophysics Laboratory, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104
| | - Kris Noel Dahl
- Departments of Chemical and Biomedical Engineering, 5000 Forbes Avenue, Carnegie Mellon University, Pittsburgh, PA 15213; and
| | - Franklin L. Zhong
- *Molecular and Cell Biophysics Laboratory, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104
| | - Paul J. Sammak
- Division of Developmental and Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15213
| | - Dennis E. Discher
- *Molecular and Cell Biophysics Laboratory, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104
- To whom correspondence should be addressed. E-mail:
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167
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de Laat W, Grosveld F. Inter-chromosomal gene regulation in the mammalian cell nucleus. Curr Opin Genet Dev 2007; 17:456-64. [PMID: 17884460 DOI: 10.1016/j.gde.2007.07.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Revised: 07/23/2007] [Accepted: 07/30/2007] [Indexed: 12/17/2022]
Abstract
Cellular phenotypes can critically rely on mono-allelic gene expression. Recent studies suggest that in mammalian cells inter-chromosomal DNA interactions may mediate the decision which allele to activate and which to silence. Here, these findings are discussed in the context of knowledge on gene competition, chromatin dynamics, and nuclear organization. We argue that data obtained by 4C technology strongly support the idea that chromatin folds according to self-organizing principles. In this concept, the nuclear positioning of a given locus is probabilistic as it also depends on the properties of neighbouring DNA segments and, by extrapolation, the whole chromosome. The linear distribution of repetitive DNA sequences and of active and inactive DNA regions is important for the folding and relative positioning of chromosomes. This stochastic concept of nuclear organization predicts that tissue-specific interactions between two selected loci present on different chromosomes will be rare.
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Affiliation(s)
- Wouter de Laat
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
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168
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Teller K, Solovei I, Buiting K, Horsthemke B, Cremer T. Maintenance of imprinting and nuclear architecture in cycling cells. Proc Natl Acad Sci U S A 2007; 104:14970-5. [PMID: 17848516 PMCID: PMC1986597 DOI: 10.1073/pnas.0704285104] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Indexed: 12/16/2022] Open
Abstract
Dynamic gene repositioning has emerged as an additional level of epigenetic gene regulation. An early example was the report of a transient, spatial convergence (< or =2 microm) of oppositely imprinted regions ("kissing"), including the Angelman syndrome/Prader-Willi syndrome (AS/PWS) locus and the Beckwith-Wiedemann syndrome locus in human lymphocytes during late S phase. It was argued that kissing is required for maintaining opposite imprints in cycling cells. Employing 3D-FISH with a BAC contig covering the AS/PWS region, light optical, serial sectioning, and quantitative 3D-image analysis, we observed that both loci always retained a compact structure and did not form giant loops. Three-dimensional distances measured among various, homologous AS/PWS segments in 393 human lymphocytes, 132 human fibroblasts, and 129 lymphoblastoid cells from Gorilla gorilla revealed a wide range of distances at any stage of interphase and in G(0). At late S phase, 4% of nuclei showed distances < or =2 microm, 49% showed distances >6 microm, and 18% even showed distances >8 microm. A similar distance variability was found for Homo sapiens (HSA) 15 centromeres in a PWS patient with a deletion of the maternal AS/PWS locus and for the Beckwith-Wiedemann syndrome loci in human lymphocytes. A transient kiss during late S phase between loci widely separated at other stages of the cell cycle seems incompatible with known global constraints of chromatin movements in cycling cells. Further experiments suggest that the previously observed convergence of AS/PWS loci during late S phase was most likely a side effect of the convergence of nucleolus organizer region-bearing acrocentric human chromosomes, including HSA 15.
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Affiliation(s)
- Kathrin Teller
- *Department of Biology II, Ludwig Maximilians University, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Irina Solovei
- *Department of Biology II, Ludwig Maximilians University, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Karin Buiting
- Institut für Humangenetik, Universitaetsklinikum Essen, Hufelandstrasse 55, 45122 Essen, Germany; and
| | - Bernhard Horsthemke
- Institut für Humangenetik, Universitaetsklinikum Essen, Hufelandstrasse 55, 45122 Essen, Germany; and
| | - Thomas Cremer
- *Department of Biology II, Ludwig Maximilians University, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
- Munich Center for Integrated Protein Science, 81377 Munich, Germany
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169
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Sexton T, Umlauf D, Kurukuti S, Fraser P. The role of transcription factories in large-scale structure and dynamics of interphase chromatin. Semin Cell Dev Biol 2007; 18:691-7. [PMID: 17950637 DOI: 10.1016/j.semcdb.2007.08.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2007] [Accepted: 08/22/2007] [Indexed: 02/04/2023]
Abstract
The genome is spatially organized inside nuclei, with chromosomes and genes occupying preferential positions relative to each other and to various nuclear landmarks. What drives this organization is unclear, but recent findings suggest there are extensive intra- and inter-chromosomal communications between various genomic regions that appear to play important roles in genome function. Here we review transcription factories, distinct sub-nuclear foci where nascent transcription occurs. We argue that the spatially restricted, limited number of transcription sites compels transcribed regions of the genome to dynamically self-organize into tissue-specific conformations, thus playing a major role in the three-dimensional interphase organization of the genome.
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Affiliation(s)
- Tom Sexton
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
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170
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Chuang CH, Belmont AS. Moving chromatin within the interphase nucleus-controlled transitions? Semin Cell Dev Biol 2007; 18:698-706. [PMID: 17905613 PMCID: PMC2117624 DOI: 10.1016/j.semcdb.2007.08.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Accepted: 08/22/2007] [Indexed: 12/17/2022]
Abstract
The past decade has seen an increasing appreciation for nuclear compartmentalization as an underlying determinant of interphase chromosome nuclear organization. To date, attention has focused primarily on describing differential localization of particular genes or chromosome regions as a function of differentiation, cell cycle position, and/or transcriptional activity. The question of how exactly interphase chromosome compartmentalization is established and in particular how interphase chromosomes might move during changes in nuclear compartmentalization has received less attention. Here we review what is known concerning chromatin mobility in relationship to physiologically regulated changes in nuclear interphase chromosome organization.
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Affiliation(s)
| | - Andrew S. Belmont
- * Corresponding author Andrew Belmont, Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, B107 CLSL, 601 S. Goodwin Ave., Urbana, IL 61801 USA, tel: +1 217-244-2311, fax: +1 217-244-1648, email address:
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171
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Kalmárová M, Smirnov E, Masata M, Koberna K, Ligasová A, Popov A, Raska I. Positioning of NORs and NOR-bearing chromosomes in relation to nucleoli. J Struct Biol 2007; 160:49-56. [PMID: 17698369 PMCID: PMC2446407 DOI: 10.1016/j.jsb.2007.06.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Revised: 06/19/2007] [Accepted: 06/21/2007] [Indexed: 01/15/2023]
Abstract
It is widely accepted that chromosomes occupy more or less fixed positions in mammalian interphase nucleus. However, relation between large-scale order of chromosome positioning and gene activity remains unclear. We used the model of the human ribosomal genes to address specific aspects of this problem. Ribosomal genes are organized at particular chromosomal sites in clusters termed nucleolus organizer regions (NORs). Only some NORs, called competent are generally accepted to be transcriptionally active during interphase. Importantly in this respect, the regularities in distribution of competent, and non-competent NORs among the specific chromosomes were already established in two human-derived cell lines: transformed HeLa and primary LEP cells. In the present study, using FISH and immunocytochemistry, we found that in HeLa and LEP cells the large-scale positioning of the NOR-bearing chromosomes with regard to nucleoli is linked to the transcription activity of rDNA. Namely, the tendency of rDNA-bearing chromosomes to associate with nucleoli correlates with the number of transcriptionally competent NORs in the respective chromosome homologs. Regarding the position of NORs, we found that not only competent but also most of the non-competent NORs are included in the nucleoli. Some intranucleolar NORs (supposedly non-competent) are situated on elongated chromatin protrusions connecting nucleoli with respective chromosome territories spatially distanced from nucleoli.
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Affiliation(s)
- Markéta Kalmárová
- Institute of Cellular Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Czech Republic.
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172
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Berr A, Schubert I. Interphase chromosome arrangement in Arabidopsis thaliana is similar in differentiated and meristematic tissues and shows a transient mirror symmetry after nuclear division. Genetics 2007; 176:853-63. [PMID: 17409060 PMCID: PMC1894613 DOI: 10.1534/genetics.107.073270] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Accepted: 03/15/2007] [Indexed: 12/21/2022] Open
Abstract
Whole-mount fluorescence in situ hybridization (FISH) was applied to Arabidopsis thaliana seedlings to determine the three-dimensional (3D) interphase chromosome territory (CT) arrangement and heterochromatin location within the positional context of entire tissues or in particular cell types of morphologically well-preserved seedlings. The interphase chromosome arrangement was found to be similar between all inspected meristematic and differentiated root and shoot cells, indicating a lack of a gross reorganization during differentiation. The predominantly random CT arrangement (except for a more frequent association of the homologous chromosomes bearing a nucleolus organizer) and the peripheric location of centromeric heterochromatin were as previously observed for flow-sorted nuclei, but centromeres tend to fuse more often in nonendoreduplicating cells and NORs in differentiated cells. After mitosis, sister nuclei revealed a symmetric arrangement of homologous CTs waning with the progress of the cell cycle or in the course of differentiation. Thus, the interphase chromosome arrangement in A. thaliana nuclei seems to be constrained mainly by morphological features such as nuclear shape, presence or absence of a nucleolus organizer on chromosomes, nucleolar volume, and/or endopolyploidy level.
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Affiliation(s)
| | - Ingo Schubert
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany
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173
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Gotoh E. Visualizing the dynamics of chromosome structure formation coupled with DNA replication. Chromosoma 2007; 116:453-62. [PMID: 17503067 DOI: 10.1007/s00412-007-0109-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Revised: 04/02/2007] [Accepted: 04/18/2007] [Indexed: 11/25/2022]
Abstract
A basic question of cell biology is how DNA folds to chromosome. Numbers of examples have suggested the involvement of DNA replication in chromosome structure formation. To visualize and identify the dynamics of chromosome structure formation and to elucidate the involvement of DNA replication in chromosome construction, Cy3-2'-deoxyuridine-5'-triphosphate direct-labeled active replicating DNA was observed in prematurely condensed chromosomes (PCCs) under a confocal scanning microscope utilized with drug-induced premature chromosome condensation (PCC) technique that facilitates the visualization of interphase chromatin as condensed chromosome form. S-phase PCCs revealed clearly the drastic dynamics of chromosome formation that transits during S-phase from a 'cloudy nebula' to numerous numbers of 'beads on a string' and finally to 'striped arrays of banding structured chromosome' along with the progress of DNA replication. The number, distribution, and shape of replication foci were also measured in individual subphases of S-phase more precisely than reported previously; maximally, approximately 1,400 foci of 0.35 microm average radius size were scored at the beginning of the S-phase, and the number reduced to approximately 100 at the end of the S-phase. Drug-induced PCC clearly provided the new insight that eukaryote DNA replication is tightly coupled with the chromosome condensation/compaction for the construction of the higher-ordered structure of the eukaryote chromosome.
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Affiliation(s)
- Eisuke Gotoh
- Division of Genetic Resources, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
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174
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Abstract
The cell nucleus is a highly structured compartment where nuclear components are thought to localize in non-random positions. Correct positioning of large chromatin domains may have a direct impact on the localization of other nuclear components, and can therefore influence the global functionality of the nuclear compartment. DNA methylation of cytosine residues in CpG dinucleotides is a prominent epigenetic modification of the chromatin fiber. DNA methylation, in conjunction with the biochemical modification pattern of histone tails, is known to lock chromatin in a close and transcriptionally inactive conformation. The relationship between DNA methylation and large-scale organization of nuclear architecture, however, is poorly understood. Here we briefly summarize present concepts of nuclear architecture and current data supporting a link between DNA methylation and the maintenance of large-scale nuclear organization.
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Affiliation(s)
- J Espada
- Cancer Epigenetics Laboratory, Spanish National Cancer Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
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175
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Lanctôt C, Cheutin T, Cremer M, Cavalli G, Cremer T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat Rev Genet 2007; 8:104-15. [PMID: 17230197 DOI: 10.1038/nrg2041] [Citation(s) in RCA: 585] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The regulation of gene expression is mediated by interactions between chromatin and protein complexes. The importance of where and when these interactions take place in the nucleus is currently a subject of intense investigation. Increasing evidence indicates that gene activation or silencing is often associated with repositioning of the locus relative to nuclear compartments and other genomic loci. At the same time, however, structural constraints impose limits on chromatin mobility. Understanding how the dynamic nature of the positioning of genetic material in the nuclear space and the higher-order architecture of the nucleus are integrated is therefore essential to our overall understanding of gene regulation.
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Affiliation(s)
- Christian Lanctôt
- Department Biologie II, Ludwig-Maximilians Universität, Grosshadernerstr. 2, Planegg-Martinsried, Germany.
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176
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Malhas A, Lee CF, Sanders R, Saunders NJ, Vaux DJ. Defects in lamin B1 expression or processing affect interphase chromosome position and gene expression. J Cell Biol 2007; 176:593-603. [PMID: 17312019 PMCID: PMC2064018 DOI: 10.1083/jcb.200607054] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Accepted: 01/24/2007] [Indexed: 11/22/2022] Open
Abstract
Radial organization of nuclei with peripheral gene-poor chromosomes and central gene-rich chromosomes is common and could depend on the nuclear boundary as a scaffold or position marker. To test this, we studied the role of the ubiquitous nuclear envelope (NE) component lamin B1 in NE stability, chromosome territory position, and gene expression. The stability of the lamin B1 lamina is dependent on lamin endoproteolysis (by Rce1) but not carboxymethylation (by Icmt), whereas lamin C lamina stability is not affected by the loss of full-length lamin B1 or its processing. Comparison of wild-type murine fibroblasts with fibroblasts lacking full-length lamin B1, or defective in CAAX processing, identified genes that depend on a stable processed lamin B1 lamina for normal expression. We also demonstrate that the position of mouse chromosome 18 but not 19 is dependent on such a stable nuclear lamina. The results implicate processed lamin B1 in the control of gene expression as well as chromosome position.
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Affiliation(s)
- Ashraf Malhas
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, England, UK
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177
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Lanctôt C, Kaspar C, Cremer T. Positioning of the mouse Hox gene clusters in the nuclei of developing embryos and differentiating embryoid bodies. Exp Cell Res 2007; 313:1449-59. [PMID: 17346703 DOI: 10.1016/j.yexcr.2007.01.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Revised: 01/15/2007] [Accepted: 01/21/2007] [Indexed: 02/06/2023]
Abstract
Expression of Hox genes located on different chromosomes is precisely regulated and synchronized during development. In order to test the hypothesis that the Hox loci might cluster in nuclear space in order to share regulatory components, we performed 3D FISH on cryosections of developing mouse embryos and differentiating embryoid bodies. We did not observe any instances of co-localization of 4 different Hox alleles. Instances of 2 different alleles touching each other were found in 20-47% of nuclei depending on the tissue. The frequency of such "kissing" events was not significantly different in cells expressing a high proportion of the Hox clusters when compared to cells expressing none or only a few Hox genes. We found that the HoxB and HoxC clusters, which are located in gene-rich regions, were involved more frequently in gene kissing in embryonic nuclei. In the case of HoxB, this observation correlated with the positioning of the corresponding chromosome towards the interior of the nucleus. Our results indicate that co-regulation of the different Hox clusters is not associated with co-localization of the loci at a single regulatory compartment and that the chromosomal context may influence the extent to which they contact each other in the nucleus.
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Affiliation(s)
- Christian Lanctôt
- Department Biology II, Ludwig-Maximilians University Munich, Grosshadernerstr. 2, Planegg-Martinsried, 82152, Germany.
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178
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Meaburn KJ, Misteli T, Soutoglou E. Spatial genome organization in the formation of chromosomal translocations. Semin Cancer Biol 2007; 17:80-90. [PMID: 17137790 PMCID: PMC1805052 DOI: 10.1016/j.semcancer.2006.10.008] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Accepted: 10/17/2006] [Indexed: 10/24/2022]
Abstract
Chromosomal translocations and genomic instability are universal hallmarks of tumor cells. While the molecular mechanisms leading to the formation of translocations are rapidly being elucidated, a cell biological understanding of how chromosomes undergo translocations in the context of the cell nucleus in vivo is largely lacking. The recent realization that genomes are non-randomly arranged within the nuclear space has profound consequences for mechanisms of chromosome translocations. We review here the emerging principles of spatial genome organization and discuss the implications of non-random spatial genome organization for the genesis and specificity of cancerous chromosomal translocations.
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Affiliation(s)
- Karen J Meaburn
- National Cancer Institute, NIH, Bethesda, MD 20892, United States.
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179
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Ono A, Kono K, Ikebe D, Muto A, Sun J, Kobayashi M, Ueda K, Melo JV, Igarashi K, Tashiro S. Nuclear positioning of the BACH2 gene in BCR-ABL positive leukemic cells. Genes Chromosomes Cancer 2007; 46:67-74. [PMID: 17044046 DOI: 10.1002/gcc.20390] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACH2 is a B-cell-specific transcription repressor and is also know as a tumor suppressor in B cell malignancy. Expression of BACH2 is induced in BCR-ABL positive lymphoid cell lines including BV173 by imatinib, a molecular targeting agent for the treatment of chronic myeloid leukemia (CML). Here we show that the activity of the BACH2 gene is related to the nuclear positioning of the gene loci. We examined the spatial association of the BACH2 gene with the centromeric heterochromatin, a transcriptionally repressive subnuclear compartment, by comparing cells with low (BV173 and K562) and high (NAMALWA) levels of BACH2 mRNA. The BACH2 gene was located closer to the centromeric heterochromatin in BV173 and K562 cells as compared to NAMALWA cells. In BV173 cells, the BACH2-centromere distance increased after imatinib treatment to levels similar to those in NAMALWA cells. We also found that diethylmaleate, an oxidative stressor, enhanced the antiproliferative effect of imatinib in only BV173 cells. Since BACH2 induces apoptosis by oxidative stress, these observations suggest that down-regulation of the BACH2 gene through the interaction with centromeric heterochromatin would take part in leukomogenesis of BCR-ABL positive lymphoid leukemia.
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Affiliation(s)
- Atsushi Ono
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Graduate school of Biomedical Science, Hiroshima University, Hiroshima, Japan
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180
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Albiez H, Cremer M, Tiberi C, Vecchio L, Schermelleh L, Dittrich S, Küpper K, Joffe B, Thormeyer T, von Hase J, Yang S, Rohr K, Leonhardt H, Solovei I, Cremer C, Fakan S, Cremer T. Chromatin domains and the interchromatin compartment form structurally defined and functionally interacting nuclear networks. Chromosome Res 2006; 14:707-33. [PMID: 17115328 DOI: 10.1007/s10577-006-1086-x] [Citation(s) in RCA: 194] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 08/04/2006] [Accepted: 08/04/2006] [Indexed: 11/28/2022]
Abstract
In spite of strong evidence that the nucleus is a highly organized organelle, a consensus on basic principles of the global nuclear architecture has not so far been achieved. The chromosome territory-interchromatin compartment (CT-IC) model postulates an IC which expands between chromatin domains both in the interior and the periphery of CT. Other models, however, dispute the existence of the IC and claim that numerous chromatin loops expand between and within CTs. The present study was undertaken to resolve these conflicting views. (1) We demonstrate that most chromatin exists in the form of higher-order chromatin domains with a compaction level at least 10 times above the level of extended 30 nm chromatin fibers. A similar compaction level was obtained in a detailed analysis of a particularly gene-dense chromosome region on HSA 11, which often expanded from its CT as a finger-like chromatin protrusion. (2) We further applied an approach which allows the experimental manipulation of both chromatin condensation and the width of IC channels in a fully reversible manner. These experiments, together with electron microscopic observations, demonstrate the existence of the IC as a dynamic, structurally distinct nuclear compartment, which is functionally linked with the chromatin compartment.
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Affiliation(s)
- Heiner Albiez
- Department of Biology II, LMU Biozentrum, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
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181
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Maeshima K, Yahata K, Sasaki Y, Nakatomi R, Tachibana T, Hashikawa T, Imamoto F, Imamoto N. Cell-cycle-dependent dynamics of nuclear pores: pore-free islands and lamins. J Cell Sci 2006; 119:4442-51. [PMID: 17074834 DOI: 10.1242/jcs.03207] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nuclear pores are sophisticated gateways on the nuclear envelope that control macromolecular transport between the cytoplasm and nucleoplasm. So far the structural and functional aspects of nuclear pores have been extensively studied, but their distribution and density, which might reflect nuclear organization and function, remain unknown. Here, we report the cell-cycle-dependent dynamics of nuclear pores. Large distinct subdomains lacking nuclear pores are present on the nuclear surface of HeLaS3 cells in early cell-cycle stages. Such `pore-free islands' gradually become dispersed in G1-S phase. Surprisingly, the islands are enriched with inner nuclear membrane proteins lamin A/C and emerin, but exclude lamin B. Lamin-A/C-enriched pore-free islands were also observed in human normal diploid fibroblasts and several cell lines, showing the generality of this phenomenon. Knockdown and ectopic expression analyses demonstrated that lamin A/C, but not emerin, plays an essential structural and regulatory role in the nuclear pore distribution and the formation of pore-free islands. These data thus provide strong evidence that the dynamics of nuclear pores are regulated by the reorganization of inner nuclear structures.
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Affiliation(s)
- Kazuhiro Maeshima
- Cellular Dynamics Laboratory, Discovery Research Institute, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198 Japan.
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182
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Bártová E, Kozubek S. Nuclear architecture in the light of gene expression and cell differentiation studies. Biol Cell 2006; 98:323-36. [PMID: 16704376 DOI: 10.1042/bc20050099] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
It is evident that primary DNA sequences, that define genomes, are responsible for genome functions. However, the functional properties of chromatin are additionally regulated by heritable modifications known as epigenetic factors and, therefore, genomes should be also considered with respect to their 'epigenomes'. Nucleosome remodelling, DNA methylation and histone modifications are the most prominent epigenetic changes that play fundamental roles in the chromatin-mediated control of gene expression. Another important nuclear feature with functional relevance is the organization of mammalian chromatin into distinct chromosome territories which are surrounded by the interchromatin compartment that is necessary for transport of regulatory molecules to the targeted DNA. The inner structure of the chromosome territories, as well as the arrangement of the chromosomes within the interphase nuclei, has been found to be non-randomly organized. Therefore, a specific nuclear arrangement can be observed in many cellular processes, such as differentiation and tumour cell transformation.
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Affiliation(s)
- Eva Bártová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65, Brno, Czech Republic
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183
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Caporali A, Wark L, Vermolen BJ, Garini Y, Mai S. Telomeric aggregates and end-to-end chromosomal fusions require myc box II. Oncogene 2006; 26:1398-406. [PMID: 16953226 DOI: 10.1038/sj.onc.1209928] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Telomeres of tumor cells form telomeric aggregates (TAs) within the three-dimensional (3D) interphase nucleus. Some of these TAs represent end-to-end chromosomal fusions and may subsequently initiate breakage-bridge-fusion cycles. Wild-type (wt) and myc box II mutant (mt) Myc induce different types of genomic instability when conditionally expressed in mouse proB cells (Ba/F3). Only wt Myc overexpressing Ba/F3 cells are capable of tumor formation in severe combined immunodeficient mice. In this study, we investigated whether telomere dysfunction leading to TA formation is linked to the genetic changes that permit wt c-Myc-dependent transformation of Ba/F3 cells. To this end, we examined the 3D organization of telomeres after the deregulated expression of deletion myc boxII mutant (Delta106) or wt Myc. Delta106-Myc overexpression did not induce TAs, whereas wt-Myc deregulation did. Instead, Delta106-Myc remodelled the 3D telomeric organization such that telomeres aligned in the center of the 3D interphase nucleus forming a telomeric disk owing to a Delta106-induced G1/S cell cycle arrest. In contrast, wt-Myc overexpression led to distorted telomere distribution and TA formation. Analysis of chromosomal alterations using spectral karyotyping confirmed Delta106-Myc and wt-Myc-associated genomic instability. A significant number of chromosomal end-to-end fusions indicative of telomere dysfunction were noted in wt-Myc-expressing cells only. This study suggests that TAs may play a fundamental role in Myc-induced tumorigenesis and provides a novel way to dissect tumor initiation.
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Affiliation(s)
- A Caporali
- Dipartimento di Medicina Sperimentale, Sezione di Biochimica, Biochimica Clinica e Biochimica dell'Esercizio Fisico, Università degli Studi di Parma, Parma, Italy
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184
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Shav-Tal Y, Darzacq X, Singer RH. Gene expression within a dynamic nuclear landscape. EMBO J 2006; 25:3469-79. [PMID: 16900099 PMCID: PMC1538565 DOI: 10.1038/sj.emboj.7601226] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Accepted: 06/07/2006] [Indexed: 01/01/2023] Open
Abstract
Molecular imaging in living cells or organisms now allows us to observe macromolecular assemblies with a time resolution sufficient to address cause-and-effect relationships on specific molecules. These emerging technologies have gained much interest from the scientific community since they have been able to reveal novel concepts in cell biology, thereby changing our vision of the cell. One main paradigm is that cells stochastically vary, thus implying that population analysis may be misleading. In fact, cells should be analyzed within time-resolved single-cell experiments rather than being compared to other cells within a population. Technological imaging developments as well as the stochastic events present in gene expression have been reviewed. Here, we discuss how the structural organization of the nucleus is revealed using noninvasive single-cell approaches, which ultimately lead to the resolution required for the analysis of highly controlled molecular processes taking place within live cells. We also describe the efforts being made towards physiological approaches within the context of living organisms.
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Affiliation(s)
- Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.
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185
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Pickersgill H, Kalverda B, de Wit E, Talhout W, Fornerod M, van Steensel B. Characterization of the Drosophila melanogaster genome at the nuclear lamina. Nat Genet 2006; 38:1005-14. [PMID: 16878134 DOI: 10.1038/ng1852] [Citation(s) in RCA: 423] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Accepted: 06/30/2006] [Indexed: 01/18/2023]
Abstract
The nuclear lamina binds chromatin in vitro and is thought to function in its organization, but genes that interact with it are unknown. Using an in vivo approach, we identified approximately 500 Drosophila melanogaster genes that interact with B-type lamin (Lam). These genes are transcriptionally silent and late replicating, lack active histone marks and are widely spaced. These factors collectively predict lamin binding behavior, indicating that the nuclear lamina integrates variant and invariant chromatin features. Consistently, proximity of genomic regions to the nuclear lamina is partly conserved between cell types, and induction of gene expression or active histone marks reduces Lam binding. Lam target genes cluster in the genome, and these clusters are coordinately expressed during development. This genome-wide analysis gives clear insight into the nature and dynamic behavior of the genome at the nuclear lamina, and implies that intergenic DNA functions in the global organization of chromatin in the nucleus.
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Affiliation(s)
- Helen Pickersgill
- Department of Tumor Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
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186
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Würtele H, Chartrand P. Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology. Chromosome Res 2006; 14:477-95. [PMID: 16823611 DOI: 10.1007/s10577-006-1075-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2006] [Accepted: 05/05/2006] [Indexed: 12/18/2022]
Abstract
Spatial proximity between genomic loci can play important roles in their function and regulation. We have developed an open-ended method based on Chromosome Conformation Capture technology allowing us to perform genome-wide scanning of the loci that form the spatial environment of a given locus at a given time. As a proof of principle we present the use of this methodology to investigate the dynamics of the spatial environment of the HoxB1 gene before and after the induction of its expression in mouse embryonic stem cells. Our results indicate that the HoxB1 locus' immediate spatial environment can be divided roughly into three parts: a first part is represented by a domain of immediate proximity on each side of the HoxB1 locus covering approximately 110 kb, a second part extends to a domain of 800 kb and a third part consists of distal intra-chromosomal and inter-chromosomal interactions. Consistent with FISH studies showing the decondensation and repositioning of HoxB1 outside of its chromosomal territory during its expression, the proportion of inter-chromosomal interactions between HoxB1 and the rest of the genome increases after its induction, while interactions with distal intra-chromosomal loci become less frequent. These results indicate that this technique can be used to determine the dynamics of loci interactions on a genome-wide scale.
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Affiliation(s)
- Hugo Würtele
- Molecular Biology Program, Université de Montreal, CP 6128, succ. Centre-ville, Montréal, Québec, H3C 3J7, Canada
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187
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Taucher-Scholz G, Jakob B. Ion Irradiation as a Tool to Reveal the Spatiotemporal Dynamics of DNA Damage Response Processes. Genome Integr 2006. [DOI: 10.1007/7050_015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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188
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Cremer T, Cremer M, Dietzel S, Müller S, Solovei I, Fakan S. Chromosome territories--a functional nuclear landscape. Curr Opin Cell Biol 2006; 18:307-16. [PMID: 16687245 DOI: 10.1016/j.ceb.2006.04.007] [Citation(s) in RCA: 475] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Accepted: 04/10/2006] [Indexed: 11/17/2022]
Abstract
Understanding nuclear architecture is indispensable for understanding the cell-type-dependent orchestration of active and silent genes and other nuclear functions, such as RNA splicing, DNA replication and repair. Yet, while it is now generally agreed that chromosomes in the cell nucleus are organized as chromosome territories, present models of chromosome territory architecture differ widely with respect to the possible functional implications of dynamic changes of this architecture during the cell cycle and terminal cell differentiation.
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Affiliation(s)
- Thomas Cremer
- Department of Biology II, Ludwig-Maximilians-University, Grosshadernerstrasse 2, D-82152, Martinsried, Germany.
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189
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Shav-Tal Y. The living test-tube: imaging of real-time gene expression. SOFT MATTER 2006; 2:361-370. [PMID: 32680249 DOI: 10.1039/b600234j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cells are dynamic entities. Not only are some cells motile but there is constant motion of organelles, proteins, nucleic acids and other molecules within every living cell. These complex molecular pathways control the life cycle of a cell and all come down to the basic players of the gene expression pathway: DNA, RNA and protein. It is therefore imperative to study biological processes as they naturally occur-in living cells, and to unravel the biophysical rules that govern intracellular dynamics. Towards this end, genetically encoded fluorescent proteins have become one of the major tools available for the study of kinetic processes taking place in real-time. This review will focus on the technical developments available for the study of gene activity in living cells and will summarize the novel biological information extracted from these approaches.
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Affiliation(s)
- Yaron Shav-Tal
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.
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190
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Dirks RW, Tanke HJ. Advances in fluorescent tracking of nucleic acids in living cell. Biotechniques 2006; 40:489-96. [PMID: 16629396 DOI: 10.2144/000112121] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Nucleic acids are typically detected in morphologically preserved fixed cells and tissues using in situ hybridization techniques. This review discusses a variety of established and more challenging fluorescence-based methods for the detection and tracking of DNA or RNA sequences in living cells. Over the past few years, various fluorescent in vivo labeling methods have been developed, and dedicated microscope and image analysis tools have been designed. These advances in technologies indicate that live-cell imaging of nucleic acids is likely to become a standard research tool for understanding genome organization and gene expression regulation in the near future. Recent live-cell imaging studies have already provided important insights into the dynamic behaviors of chromatin and RNAs in the cell.
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Affiliation(s)
- Roeland W Dirks
- Department of Molecular Cell Biology, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL, Leiden, The Netherlands.
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191
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Zink D. The temporal program of DNA replication: new insights into old questions. Chromosoma 2006; 115:273-87. [PMID: 16552593 DOI: 10.1007/s00412-006-0062-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Revised: 02/10/2006] [Accepted: 02/23/2006] [Indexed: 01/26/2023]
Abstract
During the last decades it has been shown that the replication timing program in metazoans is related to chromosome structure, the nuclear positioning and AT/GC content of chromosomal loci, their patterns of histone modifications, and their transcriptional regulation. Here, the current state of knowledge concerning these relationships is reviewed. An integrated view on structure-function relationships in the nucleus is provided and the determination and functional role of the replication timing program is discussed in this context. A corresponding comprehensive model is developed and a key aspect of this model is the suggestion that mammalian chromosomes are organized into stable units equivalent to replicon clusters. It is proposed that the nuclear positions of these units would depend on their histone modifications and determine the replication timing of the whole unit. It is furthermore predicted that replication timing is only indirectly linked to transcriptional regulation and contributes to the maintenance of gene expression patterns. These clear predictions, and the fact that the tools are at hand now to further test them, open an avenue towards solving the long standing problem on how replication timing is determined in metazoan cells.
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Affiliation(s)
- Daniele Zink
- Department Biologie II, Ludwig-Maximilians-Universität München, Biozentrum, Planegg-Martinsried, Germany.
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192
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Mudrak O, Tomilin N, Zalensky A. Chromosome architecture in the decondensing human sperm nucleus. J Cell Sci 2006; 118:4541-50. [PMID: 16179611 PMCID: PMC1409709 DOI: 10.1242/jcs.02581] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Whereas recent studies demonstrated a well-defined nuclear architecture in human sperm nuclei, little is known about the mode of DNA compaction above the elementary structural unit of nucleoprotamine toroids. Here, using fluorescence in-situ hybridization (FISH) with arm-specific DNA probes of chromosomes 1, 2 and 5, we visualized arm domains and established hierarchical levels of sperm chromatin structures. The compact chromosome territories, which in sperm have a preferred intranuclear localization, have an extended conformation represented by a 2000 nm chromatin fiber. This fiber is composed of a 1000 nm chromatin thread bent at 180 degrees near centromere. Two threads of 1000 nm, representing p-arm and q-arm chromatin, run in antiparallel fashion and join at the telomeres. Each 1000 nm thread, in turn, resolves into two rows of chromatin globules 500 nm in diameter interconnected with thinner chromatin strands. We propose a unified comprehensive model of chromosomal and nuclear architecture in human sperm that, as we suggest, is important for successful fertilization and early development.
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Affiliation(s)
- Olga Mudrak
- The Jones Institute for Reproductive Medicine, Eastern Virginia Medical School, Norfolk, VA 23507, USA
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193
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Mai S, Garini Y. The significance of telomeric aggregates in the interphase nuclei of tumor cells. J Cell Biochem 2006; 97:904-15. [PMID: 16408280 DOI: 10.1002/jcb.20760] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Telomeres are TTAGGG repetitive motifs found at the ends of vertebrate chromosomes. In humans, telomeres are protected by shelterin, a complex of six proteins (de Lange [2005] Genes Dev. 19: 2100-2110). Since (Müller [1938] Collecting Net. 13: 181-198; McClintock [1941] Genetics 26: 234-282), their function in maintaining chromosome stability has been intensively studied. This interest, especially in cancer biology, stems from the fact that telomere dysfunction is linked to genomic instability and tumorigenesis (Gisselsson et al. [2001] Proc. Natl. Acad. Sci. USA 98: 12683-12688; Deng et al. [2003] Genes Chromosomes Cancer 37: 92-97; DePinho and Polyak [2004] Nat. Genetics 36: 932-934; Meeker et al. [2004] Clin. Cancer Res. 10: 3317-3326). In the present overview, we will discuss the role of telomeres in genome stability, recent findings on three-dimensional (3D) changes of telomeres in tumor interphase nuclei, and outline future avenues of research.
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MESH Headings
- Animals
- Apoptosis
- Cell Nucleus/chemistry
- Cell Nucleus/genetics
- Chromosome Aberrations
- Chromosomes, Human
- Chromosomes, Human, Pair 10
- Chromosomes, Human, Pair 13
- Chromosomes, Human, Pair 17
- Chromosomes, Human, Pair 5
- Chromosomes, Human, Pair 7
- Evolution, Molecular
- Genome
- Humans
- Interphase/genetics
- Mice
- Neoplasms/genetics
- Neoplasms/metabolism
- Telomere/chemistry
- Telomere/genetics
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Affiliation(s)
- Sabine Mai
- Manitoba Institute of Cell Biology, CancerCare Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0V9.
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194
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Mayer R, Brero A, von Hase J, Schroeder T, Cremer T, Dietzel S. Common themes and cell type specific variations of higher order chromatin arrangements in the mouse. BMC Cell Biol 2005; 6:44. [PMID: 16336643 PMCID: PMC1325247 DOI: 10.1186/1471-2121-6-44] [Citation(s) in RCA: 163] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Accepted: 12/07/2005] [Indexed: 11/10/2022] Open
Abstract
Background Similarities as well as differences in higher order chromatin arrangements of human cell types were previously reported. For an evolutionary comparison, we now studied the arrangements of chromosome territories and centromere regions in six mouse cell types (lymphocytes, embryonic stem cells, macrophages, fibroblasts, myoblasts and myotubes) with fluorescence in situ hybridization and confocal laser scanning microscopy. Both species evolved pronounced differences in karyotypes after their last common ancestors lived about 87 million years ago and thus seem particularly suited to elucidate common and cell type specific themes of higher order chromatin arrangements in mammals. Results All mouse cell types showed non-random correlations of radial chromosome territory positions with gene density as well as with chromosome size. The distribution of chromosome territories and pericentromeric heterochromatin changed during differentiation, leading to distinct cell type specific distribution patterns. We exclude a strict dependence of these differences on nuclear shape. Positional differences in mouse cell nuclei were less pronounced compared to human cell nuclei in agreement with smaller differences in chromosome size and gene density. Notably, the position of chromosome territories relative to each other was very variable. Conclusion Chromosome territory arrangements according to chromosome size and gene density provide common, evolutionary conserved themes in both, human and mouse cell types. Our findings are incompatible with a previously reported model of parental genome separation.
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Affiliation(s)
- Robert Mayer
- Ludwig-Maximilians-Universität München, Department Biologie II, Groβhaderner Str 2, 82152 Planegg-Martinsried, Germany
| | - Alessandro Brero
- Ludwig-Maximilians-Universität München, Department Biologie II, Groβhaderner Str 2, 82152 Planegg-Martinsried, Germany
| | - Johann von Hase
- Kirchhoff Institut für Physik, Universität Heidelberg, Germany
| | - Timm Schroeder
- Institute of Stem Cell Research, GSF – National Research Center for Environment and Health, Neuherberg, Germany
| | - Thomas Cremer
- Ludwig-Maximilians-Universität München, Department Biologie II, Groβhaderner Str 2, 82152 Planegg-Martinsried, Germany
| | - Steffen Dietzel
- Ludwig-Maximilians-Universität München, Department Biologie II, Groβhaderner Str 2, 82152 Planegg-Martinsried, Germany
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195
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Fang Y, Spector DL. Centromere positioning and dynamics in living Arabidopsis plants. Mol Biol Cell 2005; 16:5710-8. [PMID: 16195344 PMCID: PMC1289415 DOI: 10.1091/mbc.e05-08-0706] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Revised: 09/13/2005] [Accepted: 09/15/2005] [Indexed: 11/11/2022] Open
Abstract
The organization and dynamics of the genome have been shown to influence gene expression in many organisms. Data from mammalian tissue culture cells have provided conflicting conclusions with regard to the extent to which chromatin organization is inherited from mother to daughter nuclei. To gain insight into chromatin organization and dynamics, we developed transgenic Arabidopsis lines in which centromeres were tagged with a green fluorescent protein fusion of the centromere-specific histone H3. Using four-dimensional (4-D) live cell imaging, we show that Arabidopsis centromeres are constrained at the nuclear periphery during interphase and that the organization of endoreduplicated sister centromeres is cell type dependent with predominant clustering in root epidermal cells and dispersion in leaf epidermal cells. 4-D tracking of the entire set of centromeres through mitosis, in growing root meristematic cells, demonstrated that global centromere position is not precisely transmitted from the mother cell to daughter cells. These results provide important insight into our understanding of chromatin organization among different cells of a living organism.
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Affiliation(s)
- Yuda Fang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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196
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Foster HA, Bridger JM. The genome and the nucleus: a marriage made by evolution. Genome organisation and nuclear architecture. Chromosoma 2005; 114:212-29. [PMID: 16133352 DOI: 10.1007/s00412-005-0016-6] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2005] [Revised: 06/29/2005] [Accepted: 07/04/2005] [Indexed: 01/15/2023]
Abstract
Genomes are housed within cell nuclei as individual chromosome territories. Nuclei contain several architectural structures that interact and influence the genome. In this review, we discuss how the genome may be organised within its nuclear environment with the position of chromosomes inside nuclei being either influenced by gene density or by chromosomes size. We compare interphase genome organisation in diverse species and reveal similarities and differences between evolutionary divergent organisms. Genome organisation is also discussed with relevance to regulation of gene expression, development and differentiation and asks whether large movements of whole chromosomes are really observed during differentiation. Literature and data describing alterations to genome organisation in disease are also discussed. Further, the nuclear structures that are involved in genome function are described, with reference to what happens to the genome when these structures contain protein from mutant genes as in the laminopathies.
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Affiliation(s)
- Helen A Foster
- Laboratory of Nuclear and Genomic Health, Cell and Chromosome Biology Group, Division of Biosciences, School of Health Sciences and Social Care, Brunel University, Uxbridge UB8 3PH, UK
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197
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Zinner R, Albiez H, Walter J, Peters AHFM, Cremer T, Cremer M. Histone lysine methylation patterns in human cell types are arranged in distinct three-dimensional nuclear zones. Histochem Cell Biol 2005; 125:3-19. [PMID: 16215742 DOI: 10.1007/s00418-005-0049-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2005] [Indexed: 01/09/2023]
Abstract
The impact of histone lysine methylation as an essential epigenetic mechanism for gene regulation has been demonstrated by numerous studies where it was functionally and structurally linked to euchromatin and heterochromatin. Most of these data have been obtained by biochemical and two-dimensional (2D)-microscopic techniques providing little information about the global nuclear arrangement of histone modifications. We investigated the 3D architecture and spatial interrelationships of different histone lysine methylation sites (tri-H3K4, mono-H4K20, mono-H3K9, tri-H3K27, tri-H4K20 and tri-H3K9) in various human cell types. Immunofluorescence and confocal microscopy were used together with a quantitative evaluation of 3D images, to reveal spatial relations of specific methylation sites with either centromeres, nascent RNA or with each other. A close association with centromeres was found only for histone methylation sites previously linked to constitutively repressed chromatin. Differences observed in these sites in relation to the cell cycle emphasize the potential relevance of the dynamic properties of heterochromatin for nuclear functions. Nascent RNA was found associated, though to a different degree, with all histone methylation sites, supporting the increasing evidence that transcription occurs across a wide range of the human genome. Finally we demonstrated by simultaneous visualization of different histone lysine methylation sites that methylation patterns are organized in distinct nuclear zones with little apparent intermingling.
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Affiliation(s)
- Roman Zinner
- Anthropology and Human Genetics, Department of Biology II, Ludwig-Maximilians-University, Grosshadernerstrasse 2, D-82152, Martinsried, Germany
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198
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Saiwaki T, Kotera I, Sasaki M, Takagi M, Yoneda Y. In vivo dynamics and kinetics of pKi-67: transition from a mobile to an immobile form at the onset of anaphase. Exp Cell Res 2005; 308:123-34. [PMID: 15896774 DOI: 10.1016/j.yexcr.2005.04.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Revised: 04/02/2005] [Accepted: 04/04/2005] [Indexed: 11/24/2022]
Abstract
A cell proliferation marker protein, pKi-67, distributes to the chromosome periphery during mitosis and nucleolar heterochromatin in the interphase. We report here on the structural domains of pKi-67 that are required for its correct distribution. While both the LR domain and the conserved domain were involved in localization to the nucleolar heterochromatin, both the LR domain and the Ki-67 repeat domain were required for its distribution to the mitotic chromosome periphery. Using in vivo time-lapse microscopy, GFP-pKi-67 was dynamically tracked from the mitotic chromosome periphery to reforming nucleoli via prenucleolar bodies (PNBs). The signals in PNBs then moved towards and fused into the reforming nucleoli with a thin string-like fluorescence during early G1 phase. An analysis of the in vivo kinetics of pKi-67 using photobleaching indicated that the association of pKi-67 with chromatin was progressively altered from "loose" to "tight" after the onset of anaphase. These findings indicate that pKi-67 dynamically alters the nature of the interaction with chromatin structure during the cell cycle, which is closely related to the reformation process of the interphase nucleolar chromatin.
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Affiliation(s)
- Takuya Saiwaki
- Department of Cell Biology and Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan
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199
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Jakob B, Rudolph JH, Gueven N, Lavin MF, Taucher-Scholz G. Live cell imaging of heavy-ion-induced radiation responses by beamline microscopy. Radiat Res 2005; 163:681-90. [PMID: 15913400 DOI: 10.1667/rr3374] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
To study the dynamics of protein recruitment to DNA lesions, ion beams can be used to generate extremely localized DNA damage within restricted regions of the nuclei. This inhomogeneous spatial distribution of lesions can be visualized indirectly and rapidly in the form of radiation-induced foci using immunocytochemical detection or GFP-tagged DNA repair proteins. To analyze faster protein translocations and a possible contribution of radiation-induced chromatin movement in DNA damage recognition in live cells, we developed a remote-controlled system to obtain high-resolution fluorescence images of living cells during ion irradiation with a frame rate of the order of seconds. Using scratch replication labeling, only minor chromatin movement at sites of ion traversal was observed within the first few minutes of impact. Furthermore, time-lapse images of the GFP-coupled DNA repair protein aprataxin revealed accumulations within seconds at sites of ion hits, indicating a very fast recruitment to damaged sites. Repositioning of the irradiated cells after fixation allowed the comparison of live cell observation with immunocytochemical staining and retrospective etching of ion tracks. These results demonstrate that heavy-ion radiation-induced changes in subnuclear structures can be used to determine the kinetics of early protein recruitment in living cells and that the changes are not dependent on large-scale chromatin movement at short times postirradiation.
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Affiliation(s)
- B Jakob
- Gesellschaft für Schwerionenforschung, Biophysik, D-64291 Darmstadt, Germany.
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200
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Louis SF, Vermolen BJ, Garini Y, Young IT, Guffei A, Lichtensztejn Z, Kuttler F, Chuang TCY, Moshir S, Mougey V, Chuang AYC, Kerr PD, Fest T, Boukamp P, Mai S. c-Myc induces chromosomal rearrangements through telomere and chromosome remodeling in the interphase nucleus. Proc Natl Acad Sci U S A 2005; 102:9613-8. [PMID: 15983382 PMCID: PMC1172233 DOI: 10.1073/pnas.0407512102] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2004] [Accepted: 05/09/2005] [Indexed: 12/16/2022] Open
Abstract
In previous work, we showed that telomeres of normal cells are organized within the 3D space of the interphase nucleus in a nonoverlapping and cell cycle-dependent manner. This order is distorted in tumor cell nuclei where telomeres are found in close association forming aggregates of various numbers and sizes. Here we show that c-Myc overexpression induces telomeric aggregations in the interphase nucleus. Directly proportional to the duration of c-Myc deregulation, we observe three or five cycles of telomeric aggregate formation in interphase nuclei. These cycles reflect the onset and propagation of breakage-bridge-fusion cycles that are initiated by end-to-end telomeric fusions of chromosomes. Subsequent to initial chromosomal breakages, new fusions follow and the breakage-bridge-fusion cycles continue. During this time, nonreciprocal translocations are generated. c-Myc-dependent remodeling of the organization of telomeres thus precedes the onset of genomic instability and subsequently leads to chromosomal rearrangements. Our findings reveal that c-Myc possesses the ability to structurally modify chromosomes through telomeric fusions, thereby reorganizing the genetic information.
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Affiliation(s)
- Sherif F Louis
- Manitoba Institute of Cell Biology, University of Manitoba, 675 McDermot Avenue, Winnipeg, MB, Canada R3E 0V9
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