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Boldyreva LV, Andreyeva EN, Pindyurin AV. Position Effect Variegation: Role of the Local Chromatin Context in Gene Expression Regulation. Mol Biol 2022. [DOI: 10.1134/s0026893322030049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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2
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Cho IK, Lee S, Chang CL, Li QX. Identification of protein related to dietary vitamin B 3 deficiency in Mediterranean fruit fly larvae. ANALYTICAL SCIENCE ADVANCES 2021; 2:416-426. [PMID: 38715956 PMCID: PMC10989592 DOI: 10.1002/ansa.202100017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 03/20/2021] [Accepted: 04/15/2021] [Indexed: 05/12/2024]
Abstract
Mediterranean fruit fly (medfly), Ceratitis capitata, is among the most destructive agricultural pest. The sterile insect technique (SIT) can effectively control medfly populations. To rear healthy medflies for the purpose of SIT, it is essential to supplement B vitamins in the diet. However, the function of the dietary B vitamins in C. capitata larvae is not known. With the microscopic analysis, several organs in the head were examined and the spiracle formation and sensory organs were normally formed between the niacin-supplied and niacin-absent groups. However, formation of the ocular depression was differently developed between the two groups, although the hypostomal sclerite was formed properly. These results signify that niacin deficiency maybe interrupt development of medfly larvae ocular depression. Proteomic analyses using LC MS/MS detected a total of 1845 proteins in two flies. A total of 607 of the 1845 proteins were overexpressed and one third (598 proteins) were downexpressed in the niacin-deficient larvae, while about one third were similarly expressed. Overexpressed proteins in the niacin-deficient larvae included ryanodine receptor 44 F, intergrin-PS, spalt-major homeotic protein, and chiffon protein. One of important overexpressed proteins was optomotor-blind protein in relation to wing development in the niacin-deficient medfly larvae.
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Affiliation(s)
- Il Kyu Cho
- Department of Molecular Biosciences and BioengineeringUniversity of Hawaii at ManoaHonoluluHawaii
- Eco‐Friendly Agri‐Bio Research CenterJeonnam Bioindustry FoundationGokseongJeonnam57510Republic of Korea
| | - Sung‐Eun Lee
- Department of Molecular Biosciences and BioengineeringUniversity of Hawaii at ManoaHonoluluHawaii
- School of Applied BiosciencesKyungpook National UniversityDaegu41566Republic of Korea
| | | | - Qing X. Li
- Department of Molecular Biosciences and BioengineeringUniversity of Hawaii at ManoaHonoluluHawaii
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Peter M, Aschauer DF, Rose R, Sinning A, Grössl F, Kargl D, Kraitsy K, Burkard TR, Luhmann HJ, Haubensak W, Rumpel S. Rapid nucleus-scale reorganization of chromatin in neurons enables transcriptional adaptation for memory consolidation. PLoS One 2021; 16:e0244038. [PMID: 33951054 PMCID: PMC8099114 DOI: 10.1371/journal.pone.0244038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/05/2021] [Indexed: 12/27/2022] Open
Abstract
The interphase nucleus is functionally organized in active and repressed territories defining the transcriptional status of the cell. However, it remains poorly understood how the nuclear architecture of neurons adapts in response to behaviorally relevant stimuli that trigger fast alterations in gene expression patterns. Imaging of fluorescently tagged nucleosomes revealed that pharmacological manipulation of neuronal activity in vitro and auditory cued fear conditioning in vivo induce nucleus-scale restructuring of chromatin within minutes. Furthermore, the acquisition of auditory fear memory is impaired after infusion of a drug into auditory cortex which blocks chromatin reorganization in vitro. We propose that active chromatin movements at the nucleus scale act together with local gene-specific modifications to enable transcriptional adaptations at fast time scales. Introducing a transgenic mouse line for photolabeling of histones, we extend the realm of systems available for imaging of chromatin dynamics to living animals.
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Affiliation(s)
- Manuel Peter
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Dominik F. Aschauer
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Renata Rose
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Anne Sinning
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Florian Grössl
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Dominic Kargl
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Klaus Kraitsy
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Preclinical Phenotyping, Vienna Biocenter Core Facilities, Vienna, Austria
| | - Thomas R. Burkard
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Heiko J. Luhmann
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Wulf Haubensak
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Simon Rumpel
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
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Solodovnikov AA, Gvozdev VA, Lavrov SA. High Level of Gene Transcription at the Embryonic Stage Leads to the Suppression of Heterochromatic Trans-Inactivation in Drosophila melanogaster Adults. BIOCHEMISTRY (MOSCOW) 2021; 85:472-479. [PMID: 32569554 DOI: 10.1134/s0006297920040070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In some cases, gene transfer from euchromatin to constitutive heterochromatin as a result of chromosomal rearrangement is accompanied by epigenetic inactivation of this gene (cis-inactivation). In the case of trans-inactivation, transgenes in the normal chromosome are repressed by the cis-inactivation-causing rearranged homologous chromosome. Trans-inactivation is a result of the somatic pairing of homologs and the transfer of the normal chromosomal segment to the heterochromatic compartment of the nucleus. Previously, we have shown that the degree of trans-inactivation of the UAS-eGFP reporter gene in adult flies depends on its transcription level that can be regulated by temperature using the GAL4 transcription activator and its temperature-sensitive inhibitor GAL80ts. In this paper, we investigated the epigenetic inheritance of the active/repressed state of the trans-inactivated reporter gene at different expression levels by measuring eGFP fluorescence in the individual cells of Malpighian tubules in adult flies. High expression levels at the embryonic stage protected the eGFP gene from trans-inactivation in adult flies. The activated state was inherited over the entire period of development and differentiation, while the activating effect of GAL4 was turned off.
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Affiliation(s)
- A A Solodovnikov
- Institute of Molecular Genetics of the Russian Academy of Sciences, Moscow, 123182, Russia
| | - V A Gvozdev
- Institute of Molecular Genetics of the Russian Academy of Sciences, Moscow, 123182, Russia
| | - S A Lavrov
- Institute of Molecular Genetics of the Russian Academy of Sciences, Moscow, 123182, Russia.
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5
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Ma Y, Buttitta L. Chromatin organization changes during the establishment and maintenance of the postmitotic state. Epigenetics Chromatin 2017; 10:53. [PMID: 29126440 PMCID: PMC5681785 DOI: 10.1186/s13072-017-0159-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/30/2017] [Indexed: 02/06/2023] Open
Abstract
Background Genome organization changes during development as cells differentiate. Chromatin motion becomes increasingly constrained and heterochromatin clusters as cells become restricted in their developmental potential. These changes coincide with slowing of the cell cycle, which can also influence chromatin organization and dynamics. Terminal differentiation is often coupled with permanent exit from the cell cycle, and existing data suggest a close relationship between a repressive chromatin structure and silencing of the cell cycle in postmitotic cells. Heterochromatin clustering could also contribute to stable gene repression to maintain terminal differentiation or cell cycle exit, but whether clustering is initiated by differentiation, cell cycle changes, or both is unclear. Here we examine the relationship between chromatin organization, terminal differentiation and cell cycle exit. Results We focused our studies on the Drosophila wing, where epithelial cells transition from active proliferation to a postmitotic state in a temporally controlled manner. We find there are two stages of G0 in this tissue, a flexible G0 period where cells can be induced to reenter the cell cycle under specific genetic manipulations and a state we call “robust,” where cells become strongly refractory to cell cycle reentry. Compromising the flexible G0 by driving ectopic expression of cell cycle activators causes a global disruption of the clustering of heterochromatin-associated histone modifications such as H3K27 trimethylation and H3K9 trimethylation, as well as their associated repressors, Polycomb and heterochromatin protein 1 (HP1). However, this disruption is reversible. When cells enter a robust G0 state, even in the presence of ectopic cell cycle activity, clustering of heterochromatin-associated modifications is restored. If cell cycle exit is bypassed, cells in the wing continue to terminally differentiate, but heterochromatin clustering is severely disrupted. Heterochromatin-dependent gene silencing does not appear to be required for cell cycle exit, as compromising the H3K27 methyltransferase Enhancer of zeste, and/or HP1 cannot prevent the robust cell cycle exit, even in the face of normally oncogenic cell cycle activities. Conclusions Heterochromatin clustering during terminal differentiation is a consequence of cell cycle exit, rather than differentiation. Compromising heterochromatin-dependent gene silencing does not disrupt cell cycle exit. Electronic supplementary material The online version of this article (10.1186/s13072-017-0159-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yiqin Ma
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Laura Buttitta
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
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Spichal M, Fabre E. The Emerging Role of the Cytoskeleton in Chromosome Dynamics. Front Genet 2017; 8:60. [PMID: 28580009 PMCID: PMC5437106 DOI: 10.3389/fgene.2017.00060] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 04/28/2017] [Indexed: 01/15/2023] Open
Abstract
Chromosomes underlie a dynamic organization that fulfills functional roles in processes like transcription, DNA repair, nuclear envelope stability, and cell division. Chromosome dynamics depend on chromosome structure and cannot freely diffuse. Furthermore, chromosomes interact closely with their surrounding nuclear environment, which further constrains chromosome dynamics. Recently, several studies enlighten that cytoskeletal proteins regulate dynamic chromosome organization. Cytoskeletal polymers that include actin filaments, microtubules and intermediate filaments can connect to the nuclear envelope via Linker of the Nucleoskeleton and Cytoskeleton (LINC) complexes and transfer forces onto chromosomes inside the nucleus. Monomers of these cytoplasmic polymers and related proteins can also enter the nucleus and play different roles in the interior of the nucleus than they do in the cytoplasm. Nuclear cytoskeletal proteins can act as chromatin remodelers alone or in complexes with other nuclear proteins. They can also act as transcription factors. Many of these mechanisms have been conserved during evolution, indicating that the cytoskeletal regulation of chromosome dynamics is an essential process. In this review, we discuss the different influences of cytoskeletal proteins on chromosome dynamics by focusing on the well-studied model organism budding yeast.
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Affiliation(s)
- Maya Spichal
- Department of Genetics, University of North Carolina, Chapel HillNC, United States
| | - Emmanuelle Fabre
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, CNRS UMR 7212, INSERM U944, Hôpital St. Louis 1Paris, France
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7
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Abstract
Chromosomes underlie a dynamic organization that fulfills functional roles in processes like transcription, DNA repair, nuclear envelope stability, and cell division. Chromosome dynamics depend on chromosome structure and cannot freely diffuse. Furthermore, chromosomes interact closely with their surrounding nuclear environment, which further constrains chromosome dynamics. Recently, several studies enlighten that cytoskeletal proteins regulate dynamic chromosome organization. Cytoskeletal polymers that include actin filaments, microtubules and intermediate filaments can connect to the nuclear envelope via Linker of the Nucleoskeleton and Cytoskeleton (LINC) complexes and transfer forces onto chromosomes inside the nucleus. Monomers of these cytoplasmic polymers and related proteins can also enter the nucleus and play different roles in the interior of the nucleus than they do in the cytoplasm. Nuclear cytoskeletal proteins can act as chromatin remodelers alone or in complexes with other nuclear proteins. They can also act as transcription factors. Many of these mechanisms have been conserved during evolution, indicating that the cytoskeletal regulation of chromosome dynamics is an essential process. In this review, we discuss the different influences of cytoskeletal proteins on chromosome dynamics by focusing on the well-studied model organism budding yeast.
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Affiliation(s)
- Maya Spichal
- Department of Genetics, University of North Carolina, Chapel HillNC, United States
| | - Emmanuelle Fabre
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, CNRS UMR 7212, INSERM U944, Hôpital St. Louis 1Paris, France
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8
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Abstract
Trans-inactivation is the repression of genes on a normal chromosome under the influence of a rearranged homologous chromosome demonstrating the position effect variegation (PEV). This phenomenon was studied in detail on the example of brownDominant allele causing the repression of wild-type brown gene on the opposite chromosome. We have investigated another trans-inactivation-inducing chromosome rearrangement, In(2)A4 inversion. In both cases, brownDominant and In(2)A4, the repression seems to be the result of dragging of the euchromatic region of the normal chromosome into the heterochromatic environment. It was found that cis-inactivation (classical PEV) and trans-inactivation show different patterns of distribution along the chromosome and respond differently to PEV modifying genes. It appears that the causative mechanism of trans-inactivation is de novo heterochromatin assembly on euchromatic sequences dragged into the heterochromatic nuclear compartment. Trans-inactivation turns out to be the result of a combination of heterochromatin-induced position effect and the somatic interphase chromosome pairing that is widespread in Diptera.
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Affiliation(s)
- Aleksei S Shatskikh
- a Department of Molecular Genetics of the Cell , Institute of Molecular Genetics, Russian Academy of Science , Moscow , Russia
| | - Yuriy A Abramov
- a Department of Molecular Genetics of the Cell , Institute of Molecular Genetics, Russian Academy of Science , Moscow , Russia
| | - Sergey A Lavrov
- a Department of Molecular Genetics of the Cell , Institute of Molecular Genetics, Russian Academy of Science , Moscow , Russia
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9
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The Differences Between Cis- and Trans-Gene Inactivation Caused by Heterochromatin in Drosophila. Genetics 2015; 202:93-106. [PMID: 26500261 DOI: 10.1534/genetics.115.181693] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/13/2015] [Indexed: 11/18/2022] Open
Abstract
Position-effect variegation (PEV) is the epigenetic disruption of gene expression near the de novo-formed euchromatin-heterochromatin border. Heterochromatic cis-inactivation may be accompanied by the trans-inactivation of genes on a normal homologous chromosome in trans-heterozygous combination with a PEV-inducing rearrangement. We characterize a new genetic system, inversion In(2)A4, demonstrating cis-acting PEV as well as trans-inactivation of the reporter transgenes on the homologous nonrearranged chromosome. The cis-effect of heterochromatin in the inversion results not only in repression but also in activation of genes, and it varies at different developmental stages. While cis-actions affect only a few juxtaposed genes, trans-inactivation is observed in a 500-kb region and demonstrates а nonuniform pattern of repression with intermingled regions where no transgene repression occurs. There is no repression around the histone gene cluster and in some other euchromatic sites. trans-Inactivation is accompanied by dragging of euchromatic regions into the heterochromatic compartment, but the histone gene cluster, located in the middle of the trans-inactivated region, was shown to be evicted from the heterochromatin. We demonstrate that trans-inactivation is followed by de novo HP1a accumulation in the affected transgene; trans-inactivation is specifically favored by the chromatin remodeler SAYP and prevented by Argonaute AGO2.
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10
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Jerabek H, Heermann DW. How chromatin looping and nuclear envelope attachment affect genome organization in eukaryotic cell nuclei. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:351-81. [PMID: 24380599 DOI: 10.1016/b978-0-12-800046-5.00010-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
To understand how interphase chromatin is organized in eukaryotic cell nuclei, it is essential to understand what kind of interactions influence the nuclear architecture and to what extent. Using a mesoscale model that incorporates chromatin-chromatin interactions as well as binding of chromatin to the nuclear envelope, we can show that chromatin loops and envelope bonds are major players in genome organization because they largely affect the entropy of the chromatin fibres. The model allows us to consistently reproduce multiple characteristic chromatin parameters in agreement with experimental data. We focus on the question of how an inversion of the nuclear architecture, in the course of which the highly active euchromatin changes its preferential position from the nuclear center to the periphery, can be achieved. We find that the transition between the common and inverted organization is driven by the strength of the envelope interaction and the nuclear chromatin density.
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Affiliation(s)
- Hansjoerg Jerabek
- Institute for Theoretical Physics, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg, Germany
| | - Dieter W Heermann
- Institute for Theoretical Physics, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg, Germany; The Jackson Laboratory, Bar Harbor, Maine, USA; Shanghai Center for Bioinformation Technology (SCBIT), Shanghai, PR China.
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11
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Abstract
Although intercellular bridges resulting from incomplete cytokinesis were discovered in somatic Drosophila tissues decades ago, the impact of these structures on intercellular communication and tissue biology is largely unknown. In this work, we demonstrate that the ~250-nanometer-diameter somatic ring canals permit diffusion of cytoplasmic contents between connected cells and across mitotic clone boundaries and enable the equilibration of protein between transcriptionally mosaic follicle cells in the Drosophila ovary. We obtained similar, although more restricted, results in the larval imaginal discs. Our work illustrates the lack of cytoplasmic autonomy in these tissues and suggests a role for somatic ring canals in promoting homogeneous protein expression within the tissue.
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Affiliation(s)
- Peter F McLean
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
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12
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Li HB, Ohno K, Gui H, Pirrotta V. Insulators target active genes to transcription factories and polycomb-repressed genes to polycomb bodies. PLoS Genet 2013; 9:e1003436. [PMID: 23637616 PMCID: PMC3630138 DOI: 10.1371/journal.pgen.1003436] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 02/21/2013] [Indexed: 01/14/2023] Open
Abstract
Polycomb bodies are foci of Polycomb proteins in which different Polycomb target genes are thought to co-localize in the nucleus, looping out from their chromosomal context. We have shown previously that insulators, not Polycomb response elements (PREs), mediate associations among Polycomb Group (PcG) targets to form Polycomb bodies. Here we use live imaging and 3C interactions to show that transgenes containing PREs and endogenous PcG-regulated genes are targeted by insulator proteins to different nuclear structures depending on their state of activity. When two genes are repressed, they co-localize in Polycomb bodies. When both are active, they are targeted to transcription factories in a fashion dependent on Trithorax and enhancer specificity as well as the insulator protein CTCF. In the absence of CTCF, assembly of Polycomb bodies is essentially reduced to those representing genomic clusters of Polycomb target genes. The critical role of Trithorax suggests that stable association with a specialized transcription factory underlies the cellular memory of the active state. We have studied the nuclear localization of genes that are regulated by Polycomb mechanisms. The genomes of higher eukaryotes contain hundreds of genes that are regulated by Polycomb mechanisms. Once repressed by Polycomb complexes, they tend to stay repressed; but, when activated, they bind Trithorax protein and tend to maintain the active state epigenetically. Polycomb repression has been reported to make these genes associate in the nucleus to form “Polycomb bodies.” We find that this association is not caused by Polycomb complexes but by insulator elements accompanying the genes. We show that, when these genes are in the active state, the binding of Trithorax targets them to other nuclear regions where transcription occurs, so-called transcription factories. In these nuclear re-positionings the insulator provides the associative power while the state of activity determines whether a gene goes to a Polycomb body or to a transcription factory. The strong effect of Trithorax suggests the possibility that the stable association with a transcription factory it produces may account for the epigenetic memory of the active state.
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Affiliation(s)
- Hua-Bing Li
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
| | - Katsuhito Ohno
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
| | - Hongxing Gui
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
| | - Vincenzo Pirrotta
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
- * E-mail:
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13
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Cheutin T, Cavalli G. Progressive polycomb assembly on H3K27me3 compartments generates polycomb bodies with developmentally regulated motion. PLoS Genet 2012; 8:e1002465. [PMID: 22275876 PMCID: PMC3262012 DOI: 10.1371/journal.pgen.1002465] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 11/22/2011] [Indexed: 11/24/2022] Open
Abstract
Polycomb group (PcG) proteins are conserved chromatin factors that maintain silencing of key developmental genes outside of their expression domains. Recent genome-wide analyses showed a Polycomb (PC) distribution with binding to discrete PcG response elements (PREs). Within the cell nucleus, PcG proteins localize in structures called PC bodies that contain PcG-silenced genes, and it has been recently shown that PREs form local and long-range spatial networks. Here, we studied the nuclear distribution of two PcG proteins, PC and Polyhomeotic (PH). Thanks to a combination of immunostaining, immuno-FISH, and live imaging of GFP fusion proteins, we could analyze the formation and the mobility of PC bodies during fly embryogenesis as well as compare their behavior to that of the condensed fraction of euchromatin. Immuno-FISH experiments show that PC bodies mainly correspond to 3D structural counterparts of the linear genomic domains identified in genome-wide studies. During early embryogenesis, PC and PH progressively accumulate within PC bodies, which form nuclear structures localized on distinct euchromatin domains containing histone H3 tri-methylated on K27. Time-lapse analysis indicates that two types of motion influence the displacement of PC bodies and chromatin domains containing H2Av-GFP. First, chromatin domains and PC bodies coordinately undergo long-range motions that may correspond to the movement of whole chromosome territories. Second, each PC body and chromatin domain has its own fast and highly constrained motion. In this motion regime, PC bodies move within volumes slightly larger than those of condensed chromatin domains. Moreover, both types of domains move within volumes much smaller than chromosome territories, strongly restricting their possibility of interaction with other nuclear structures. The fast motion of PC bodies and chromatin domains observed during early embryogenesis strongly decreases in late developmental stages, indicating a possible contribution of chromatin dynamics in the maintenance of stable gene silencing. The three-dimensional organization of genes and associated proteins is critical for gene regulation. Polycomb group proteins are important developmental regulators controlling the expression of hundreds of genes. They are not homogeneously distributed in the cell nucleus, instead forming nuclear subcompartments called Polycomb bodies. We investigated the dynamics of Polycomb bodies during Drosophila embryonic development, demonstrating that two Polycomb proteins, Polycomb and Polyhomeotic, gradually assemble onto bodies enriched in histone H3 trimethylated on lysine 27, a hallmark of Polycomb silencing. Polycomb bodies are not the most condensed euchromatic part of the genome. Instead, a large amount of genomic chromatin is organized in a histone- and DNA–dense structure distinct from Polycomb bodies. Polycomb bodies move, meet, and split dynamically during development. Their motion has two regimes: a fast, highly constrained motion and a slower regime where multiple bodies undergo long-range coordinated movements potentially corresponding to chromosome territory movements. These regimes are not restricted to Polycomb but also extend to bulk “condensed euchromatin,” which is characterized by slower motion and a narrower radius of confinement. Both motion regimes progressively slow down during development, suggesting that regulation of chromatin dynamics may play an important role in the maintenance of gene silencing in differentiated cells.
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Affiliation(s)
- Thierry Cheutin
- Institut de Génétique Humaine, CNRS UPR 1142, Montpellier, France
| | - Giacomo Cavalli
- Institut de Génétique Humaine, CNRS UPR 1142, Montpellier, France
- * E-mail:
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14
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Meldi L, Brickner JH. Compartmentalization of the nucleus. Trends Cell Biol 2011; 21:701-8. [PMID: 21900010 PMCID: PMC3970429 DOI: 10.1016/j.tcb.2011.08.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 08/03/2011] [Accepted: 08/04/2011] [Indexed: 12/14/2022]
Abstract
The nucleus is a spatially organized compartment. The most obvious way in which this is achieved is at the level of chromosomes. The positioning of chromosomes with respect to nuclear landmarks and with respect to each other is both non-random and cell-type specific. This suggests that cells possess molecular mechanisms to influence the folding and disposition of chromosomes within the nucleus. The localization of many proteins is also heterogeneous within the nucleus. Therefore, chromosome folding and the localization of proteins leads to a model in which individual genes are positioned in distinct protein environments that can affect their transcriptional state. We focus here on the spatial organization of the nucleus and how it impacts upon gene expression.
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Affiliation(s)
- Lauren Meldi
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
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15
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Insulators, not Polycomb response elements, are required for long-range interactions between Polycomb targets in Drosophila melanogaster. Mol Cell Biol 2010; 31:616-25. [PMID: 21135119 DOI: 10.1128/mcb.00849-10] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genomic binding sites of Polycomb group (PcG) complexes have been found to cluster, forming Polycomb "bodies" or foci in mammalian or fly nuclei. These associations are thought to be driven by interactions between PcG complexes and result in enhanced repression. Here, we show that a Polycomb response element (PRE) with strong PcG binding and repressive activity cannot mediate trans interactions. In the case of the two best-studied interacting PcG targets in Drosophila, the Mcp and the Fab-7 regulatory elements, we find that these associations are not dependent on or caused by the Polycomb response elements they contain. Using functional assays and physical colocalization by in vivo fluorescence imaging or chromosome conformation capture (3C) methods, we show that the interactions between remote copies of Mcp or Fab-7 elements are dependent on the insulator activities present in these elements and not on their PREs. We conclude that insulator binding proteins rather than PcG complexes are likely to be the major determinants of the long-range higher-order organization of PcG targets in the nucleus.
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16
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Abstract
The expression patterns of many protein-coding genes are orchestrated in response to exogenous stimuli, as well as cell-type-specific developmental programs. In recent years, researchers have shown that dynamic chromatin movements and interactions in the nucleus play a crucial role in gene regulation. In this review, we highlight our current understanding of the organization of chromatin in the interphase nucleus and the impact of chromatin dynamics on gene expression. We also discuss the current state of knowledge with regard to the localization of active and inactive genes within the three-dimensional nuclear space. Furthermore, we address recent findings that demonstrate the movements of chromosomal regions and genomic loci in association with changes in transcriptional activity. Finally, we discuss the role of intra- and interchromosomal interactions in the control of coregulated genes.
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Affiliation(s)
- Michael R Hübner
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
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17
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Markovic MP, Kylsten P, Dushay MS. Drosophila lamin mutations cause melanotic mass formation and lamellocyte differentiation. Mol Immunol 2009; 46:3245-50. [PMID: 19716177 DOI: 10.1016/j.molimm.2009.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 08/02/2009] [Accepted: 08/04/2009] [Indexed: 11/25/2022]
Abstract
The fruit fly immune system is a valuable model for invertebrate and innate immunity. Cellular immune reactions in Drosophila are of great interest, especially the molecular genetic mechanisms of hemocyte differentiation and the encapsulation of foreign bodies. Here we report that changes in the lamin gene cause melanotic masses. These darkened clusters of cells result from autoimmune-like encapsulation of self-tissue, as shown by the presence in lam larvae of lamellocytes, effector hemocytes that appear in larvae following wounding or parasitization. Lamins thus affect immunity in Drosophila, and lam mutations can serve as genetic tools to dissect cellular immune signaling and effector pathways.
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Abstract
While heterochromatic gene silencing in cis is often accompanied by nucleosomal compaction, characteristic histone modifications, and recruitment of heterochromatin proteins, little is known concerning genes silenced by heterochromatin in trans. An insertion of heterochromatic satellite DNA in the euchromatic brown (bw) gene of Drosophila melanogaster results in bwDominant (bwD), which can inactivate loci on the homolog by relocation near the centric heterochromatin (trans-inactivation). Nucleosomal compaction was found to accompany trans-inactivation, but stereotypical heterochromatic histone modifications were mostly absent on silenced reporter genes. HP1 was enriched on trans-inactivated reporter constructs and this enrichment was more pronounced on adult chromatin than on larval chromatin. Interestingly, this HP1 enrichment in trans was unaccompanied by an increase in the 2MeH3K9 mark, which is generally thought to be the docking site for HP1 in heterochromatin. However, a substantial increase in the 2MeH3K9 mark was found on or near the bwD satellite insertion in cis, but did not spread further. These observations suggest that the interaction of HP1 with chromatin in cis is fundamentally different from that in trans. Our molecular data agree well with the differential phenotypic effect on bwD trans-inactivation of various genes known to be involved in histone modification and cis gene silencing.
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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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20
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Interplay of developmentally regulated gene expression and heterochromatic silencing in trans in Drosophila. Genetics 2008; 178:749-59. [PMID: 18245337 DOI: 10.1534/genetics.107.083105] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The brown(Dominant) (bw(D)) allele of Drosophila contains a heterochromatic block that causes the locus to interact with centric heterochromatin. This association silences bw(+) in heterozygotes (trans-inactivation) and is dependent on nuclear organizational changes later in development, suggesting that trans-inactivation may not be possible until later in development. To study this, a P element containing an upstream activating sequence (UAS)-GFP reporter was inserted 5 kb from the bw(D) insertion site. Seven different GAL4 driver lines were used and GFP fluorescence was compared in the presence or the absence of bw(D). We measured silencing in different tissues and stages of development and found variable silencing of GFP expression driven by the same driver. When UAS-GFP was not expressed until differentiation in the eye imaginal disc it was more easily trans-inactivated than when it was expressed earlier in undifferentiated cells. In contrast to some studies by other workers on silencing in cis, we did not find consistent correlation of silencing with level of expression or evidence of relaxation of silencing with terminal differentiation. We suggest that such contrasting results may be attributed to a potentially different role played by nuclear organization in cis and trans position-effect variegation.
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21
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Girton JR, Johansen KM. Chromatin structure and the regulation of gene expression: the lessons of PEV in Drosophila. ADVANCES IN GENETICS 2008; 61:1-43. [PMID: 18282501 DOI: 10.1016/s0065-2660(07)00001-6] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Position-effect variegation (PEV) was discovered in 1930 in a study of X-ray-induced chromosomal rearrangements. Rearrangements that place euchromatic genes adjacent to a region of centromeric heterochromatin give a variegated phenotype that results from the inactivation of genes by heterochromatin spreading from the breakpoint. PEV can also result from P element insertions that place euchromatic genes into heterochromatic regions and rearrangements that position euchromatic chromosomal regions into heterochromatic nuclear compartments. More than 75 years of studies of PEV have revealed that PEV is a complex phenomenon that results from fundamental differences in the structure and function of heterochromatin and euchromatin with respect to gene expression. Molecular analysis of PEV began with the discovery that PEV phenotypes are altered by suppressor and enhancer mutations of a large number of modifier genes whose products are structural components of heterochromatin, enzymes that modify heterochromatic proteins, or are nuclear structural components. Analysis of these gene products has led to our current understanding that formation of heterochromatin involves specific modifications of histones leading to the binding of particular sets of heterochromatic proteins, and that this process may be the mechanism for repressing gene expression in PEV. Other modifier genes produce products whose function is part of an active mechanism of generation of euchromatin that resists heterochromatization. Current studies of PEV are focusing on defining the complex patterns of modifier gene activity and the sequence of events that leads to the dynamic interplay between heterochromatin and euchromatin.
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Affiliation(s)
- Jack R Girton
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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22
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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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23
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Rafalska-Metcalf IU, Janicki SM. Show and tell: visualizing gene expression in living cells. J Cell Sci 2007; 120:2301-7. [PMID: 17606985 DOI: 10.1242/jcs.008664] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The development of non-invasive methods of visualizing proteins and nucleic acids in living cells has provided profound insight into how they move and interact with each other in vivo. It is possible to evaluate basic mechanisms of gene expression, and to define their temporal and spatial parameters by using this methodology to label endogenous genes and make reporter constructs that allow specific DNA and RNA regulatory elements to be localized. This Commentary highlights recent reports that have used these techniques to study nuclear organization, transcription factor dynamics and the kinetics of RNA synthesis. These studies show how imaging gene expression in single living cells can reveal new regulatory mechanisms. They also expand our understanding of the role of chromatin and RNA dynamics in modulating cellular responses to developmental and environmental signals.
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24
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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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25
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Thakar R, Gordon G, Csink AK. Dynamics and anchoring of heterochromatic loci during development. J Cell Sci 2006; 119:4165-75. [PMID: 16984972 DOI: 10.1242/jcs.03183] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Positioning a euchromatic gene near heterochromatin can influence its expression. To better understand expression-relevant changes in locus positioning, we monitored in vivo movement of centromeres and a euchromatic locus (with and without a nearby insertion of heterochromatin) in developing Drosophila tissue. In most undifferentiated nuclei, the rate of diffusion and step size of the locus is unaffected by the heterochromatic insertion. Interestingly, although the movement observed here is non directional, the heterochromatic insertion allows the flanking euchromatic region to enter and move within the heterochromatic compartment. This study also finds that a constraint on chromatin movement is imposed which is a factor of distance from the centric heterochromatic compartment. This restraint prevents the heterochromatic locus from moving away from the centric heterochromatin compartment. Therefore, because of the constraint, even distinct and non-random nuclear organizations can be attained from random chromatin movements. We also find a general constraint on chromatin movement is imposed during differentiation, which stabilizes changes in nuclear organization in differentiated nuclei.
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Affiliation(s)
- Rajika Thakar
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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26
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Fritsch C, Ploeger G, Arndt-Jovin DJ. Drosophila under the lens: imaging from chromosomes to whole embryos. Chromosome Res 2006; 14:451-64. [PMID: 16821139 DOI: 10.1007/s10577-006-1068-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Microscopy has been a very powerful tool for Drosophila research since its inception, proving to be essential for the evaluation of mutant phenotypes, the understanding of cellular and tissue physiology, and the illumination of complex biological questions. In this article we review the breadth of this field, making note of some of the seminal papers. We expand on the use of microscopy to study questions related to gene locus and nuclear architecture, presenting new data using fluorescence in-situ hybridization techniques that demonstrate the flexibility of Drosophila chromosomes. Finally, we review the burgeoning use of fluorescence in-vivo imaging methods to yield quantitative information about cellular processes.
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Affiliation(s)
- Cornelia Fritsch
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37070, Göttingen, Germany
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27
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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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