1
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Ljungman M. Transcription and genome integrity. DNA Repair (Amst) 2022; 118:103373. [PMID: 35914488 DOI: 10.1016/j.dnarep.2022.103373] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/16/2022] [Accepted: 07/17/2022] [Indexed: 11/03/2022]
Abstract
Transcription can cause genome instability by promoting R-loop formation but also act as a mutation-suppressing machinery by sensing of DNA lesions leading to the activation of DNA damage signaling and transcription-coupled repair. Recovery of RNA synthesis following the resolution of repair of transcription-blocking lesions is critical to avoid apoptosis and several new factors involved in this process have recently been identified. Some DNA repair proteins are recruited to initiating RNA polymerases and this may expediate the recruitment of other factors that participate in the repair of transcription-blocking DNA lesions. Recent studies have shown that transcription of protein-coding genes does not always give rise to spliced transcripts, opening the possibility that cells may use the transcription machinery in a splicing-uncoupled manner for other purposes including surveillance of the transcribed genome.
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Affiliation(s)
- Mats Ljungman
- Departments of Radiation Oncology and Environmental Health Sciences, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA.
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2
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Pathak RU, Bihani A, Sureka R, Varma P, Mishra RK. In situ nuclear matrix preparation in Drosophila melanogaster embryos/tissues and its use in studying the components of nuclear architecture. Nucleus 2022; 13:116-128. [PMID: 35239464 PMCID: PMC8896195 DOI: 10.1080/19491034.2022.2043608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The study of nuclear matrix (NuMat) over the last 40 years has been limited to either isolated nuclei from tissues or cells grown in culture. Here, we provide a protocol for NuMat preparation in intact Drosophila melanogaster embryos and its use in dissecting the components of nuclear architecture. The protocol does not require isolation of nuclei and therefore maintains the three-dimensional milieu of an intact embryo, which is biologically more relevant compared to cells in culture. One of the advantages of this protocol is that only a small number of embryos are required. The protocol has been extended to larval tissues like salivary glands with little modification. Taken together, it becomes possible to carry out such studies in parallel to genetic experiments using mutant/transgenic flies. This protocol, therefore, opens the powerful field of fly genetics to cell biology in the study of nuclear architecture. Summary: Nuclear Matrix is a biochemically defined entity and a basic component of the nuclear architecture. Here we present a protocol to isolate and visualize Nuclear Matrix in situ in the Drosophila melanogaster and its potential applications.
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Affiliation(s)
- Rashmi U Pathak
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Ashish Bihani
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | - Parul Varma
- Present Address: Department of Neuroscience, Development and Regenerative Biology, The University of Texas at San Antonio, Texas, USA
| | - Rakesh K Mishra
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India.,Tata Institute for Genetics and Society, Bangalore, India
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3
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Boltsis I, Grosveld F, Giraud G, Kolovos P. Chromatin Conformation in Development and Disease. Front Cell Dev Biol 2021; 9:723859. [PMID: 34422840 PMCID: PMC8371409 DOI: 10.3389/fcell.2021.723859] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/16/2021] [Indexed: 01/23/2023] Open
Abstract
Chromatin domains and loops are important elements of chromatin structure and dynamics, but much remains to be learned about their exact biological role and nature. Topological associated domains and functional loops are key to gene expression and hold the answer to many questions regarding developmental decisions and diseases. Here, we discuss new findings, which have linked chromatin conformation with development, differentiation and diseases and hypothesized on various models while integrating all recent findings on how chromatin architecture affects gene expression during development, evolution and disease.
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Affiliation(s)
- Ilias Boltsis
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Guillaume Giraud
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
- Cancer Research Center of Lyon – INSERM U1052, Lyon, France
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
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4
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Panigrahi A, O'Malley BW. Mechanisms of enhancer action: the known and the unknown. Genome Biol 2021; 22:108. [PMID: 33858480 PMCID: PMC8051032 DOI: 10.1186/s13059-021-02322-1] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
Differential gene expression mechanisms ensure cellular differentiation and plasticity to shape ontogenetic and phylogenetic diversity of cell types. A key regulator of differential gene expression programs are the enhancers, the gene-distal cis-regulatory sequences that govern spatiotemporal and quantitative expression dynamics of target genes. Enhancers are widely believed to physically contact the target promoters to effect transcriptional activation. However, our understanding of the full complement of regulatory proteins and the definitive mechanics of enhancer action is incomplete. Here, we review recent findings to present some emerging concepts on enhancer action and also outline a set of outstanding questions.
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Affiliation(s)
- Anil Panigrahi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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5
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Nozawa RS, Gilbert N. RNA: Nuclear Glue for Folding the Genome. Trends Cell Biol 2019; 29:201-211. [DOI: 10.1016/j.tcb.2018.12.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 12/10/2018] [Accepted: 12/14/2018] [Indexed: 12/20/2022]
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6
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Higher-Order Chromatin Regulation of Inflammatory Gene Expression. Mediators Inflamm 2017; 2017:7848591. [PMID: 28490839 PMCID: PMC5401750 DOI: 10.1155/2017/7848591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/21/2017] [Indexed: 12/14/2022] Open
Abstract
Whether it is caused by viruses and bacteria infection, or low-grade chronic inflammation of atherosclerosis and cellular senescence, the transcription factor (TF) NF-κB plays a central role in the inducible expression of inflammatory genes. Accumulated evidence has indicated that the chromatin environment is the main determinant of TF binding in gene expression regulation, including the stimulus-responsive NF-κB. Dynamic changes in intra- and interchromosomes are the key regulatory mechanisms promoting the binding of TFs. When an inflammatory process is triggered, NF-κB binds to enhancers or superenhancers, triggering the transcription of enhancer RNA (eRNA), driving the chromatin of the NF-κB-binding gene locus to construct transcriptional factories, and forming intra- or interchromosomal contacts. These processes reveal a mechanism in which intrachromosomal contacts appear to be cis-control enhancer-promoter communications, whereas interchromosomal regulatory elements construct trans-form relationships with genes on other chromosomes. This article will review emerging evidence on the genome organization hierarchy underlying the inflammatory response.
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7
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Razin SV, Borunova VV, Iarovaia OV, Vassetzky YS. Nuclear matrix and structural and functional compartmentalization of the eucaryotic cell nucleus. BIOCHEMISTRY (MOSCOW) 2015; 79:608-18. [PMID: 25108324 DOI: 10.1134/s0006297914070037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Becoming popular at the end of the 20th century, the concept of the nuclear matrix implies the existence of a nuclear skeleton that organizes functional elements in the cell nucleus. This review presents a critical analysis of the results obtained in the study of nuclear matrix in the light of current views on the organization of the cell nucleus. Numerous studies of nuclear matrix have failed to provide evidence of the existence of such a structure. Moreover, the existence of a filamentous structure that supports the nuclear compartmentalization appears to be unnecessary, since this function is performed by the folded genome itself.
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Affiliation(s)
- S V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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8
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Razin SV, Iarovaia OV, Vassetzky YS. A requiem to the nuclear matrix: from a controversial concept to 3D organization of the nucleus. Chromosoma 2014; 123:217-24. [PMID: 24664318 DOI: 10.1007/s00412-014-0459-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 03/10/2014] [Accepted: 03/14/2014] [Indexed: 12/13/2022]
Abstract
The first papers coining the term "nuclear matrix" were published 40 years ago. Here, we review the data obtained during the nuclear matrix studies and discuss the contribution of this controversial concept to our current understanding of nuclear architecture and three-dimensional organization of genome.
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Affiliation(s)
- S V Razin
- Institute of Gene Biology of the Russian Academy of Sciences, 119334, Moscow, Russia
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9
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Papantonis A, Cook PR. Transcription factories: genome organization and gene regulation. Chem Rev 2013; 113:8683-705. [PMID: 23597155 DOI: 10.1021/cr300513p] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Argyris Papantonis
- Sir William Dunn School of Pathology, University of Oxford , South Parks Road, Oxford OX1 3RE, United Kingdom
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10
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Abstract
There is considerable evidence that transcription does not occur homogeneously or diffusely throughout the nucleus, but rather at a number of specialized, discrete sites termed transcription factories. The factories are composed of ~4–30 RNA polymerase molecules, and are associated with many other molecules involved in transcriptional activation and mRNA processing. Some data suggest that the polymerase molecules within a factory remain stationary relative to the transcribed DNA, which is thought to be reeled through the factory site. There is also some evidence that transcription factories could help organize chromatin and nuclear structure, contributing to both the formation of chromatin loops and the clustering of active and co-regulated genes.
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Affiliation(s)
- Dietmar Rieder
- Division of Bioinformatics, Biocenter, Innsbruck Medical University Innsbruck, Austria
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11
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Henderson SC, Locke M. The development of branched silk gland nuclei. Tissue Cell 2012; 23:867-80. [PMID: 18621190 DOI: 10.1016/0040-8166(91)90036-s] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/1991] [Indexed: 11/16/2022]
Abstract
Nuclei in the giant polyploid silk gland cells of Calpodes ethlius grow by endomitosis and can develop hundreds of branches during larval life. The shape of the these nuclei is characteristic for each region of the gland. We have found shape to be correlated with arrangement of the nuclear matrix. Scanning electron microscopy showed nuclear matrices with shapes similar to those of feulgen stained nuclei. Profiles of isolated matrices seen by transmission electron microscopy had filaments aligned parallel to the long axis of nuclear branches. DNA stained by Hoechst had a similar parallel alignment within the branches. Nuclear shape may be maintained by a small number of components, since electrophoretic analysis showed only a few abundant polypeptides in the matrix fraction. Silk gland nuclei have some of the same nuclear matrix antigens found in smaller, more regularly shaped, eukaryote nuclei.
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Affiliation(s)
- S C Henderson
- Department of Zoology, University of Western Ontario, London, Ontario, Canada, N6A 5B7
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12
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Papantonis A, Cook PR. Fixing the model for transcription: the DNA moves, not the polymerase. Transcription 2012; 2:41-4. [PMID: 21326910 DOI: 10.4161/trns.2.1.14275] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 11/23/2010] [Accepted: 11/23/2010] [Indexed: 11/19/2022] Open
Abstract
The traditional model for transcription sees active polymerases tracking along their templates. An alternative (controversial) model has active enzymes immobilized in "factories." Recent evidence supports the idea that the DNA moves, not the polymerase, and points to alternative explanations of how regulatory motifs like enhancers and silencers work.
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13
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Razin SV, Gavrilov AA, Pichugin A, Lipinski M, Iarovaia OV, Vassetzky YS. Transcription factories in the context of the nuclear and genome organization. Nucleic Acids Res 2011; 39:9085-92. [PMID: 21880598 PMCID: PMC3241665 DOI: 10.1093/nar/gkr683] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In the eukaryotic nucleus, genes are transcribed in transcription factories. In the present review, we re-evaluate the models of transcription factories in the light of recent and older data. Based on this analysis, we propose that transcription factories result from the aggregation of RNA polymerase II-containing pre-initiation complexes assembled next to each other in the nuclear space. Such an aggregation can be triggered by the phosphorylation of the C-terminal domain of RNA polymerase II molecules and their interaction with various transcription factors. Individual transcription factories would thus incorporate tissue-specific, co-regulated as well as housekeeping genes based only on their initial proximity to each other in the nuclear space. Targeting genes to be transcribed to protein-dense factories that contain all factors necessary for transcription initiation and elongation through chromatin templates clearly favors a more economical utilization and better recycling of the transcription machinery.
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Affiliation(s)
- S V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
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14
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Razin SV, Gavrilov AA, Yarovaya OV. Transcription factories and spatial organization of eukaryotic genomes. BIOCHEMISTRY (MOSCOW) 2011; 75:1307-15. [PMID: 21314597 DOI: 10.1134/s0006297910110015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The phenomenon of association of transcribed genes into so-called transcription factories and also the role of these associations in spatial organization of the eukaryotic genome are actively discussed in the modern literature. Some authors think that the association of transcribed genes into transcription factories constitutes a major factor supporting the function-dependent three-dimensional organization of the interphase genome. In spite of the obvious interest in the problem of spatial organization of transcription in the eukaryotic cell nucleus, the number of experimental studies of transcriptional factories remains rather limited and the results of these studies are often contradictory. In the current review we have tried to critically re-evaluate the published experimental results that constitute the basis for current models and also the models themselves. We have especially analyzed the existing contradictions and attempted to explain them whenever possible. We also discuss new models that can explain the biological significance of clustering of transcribed genes and show possible mechanisms of the origin of transcription factories in the course of evolution.
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Affiliation(s)
- S V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia.
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15
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Abstract
Chromatin is by its very nature a repressive environment which restricts the recruitment of transcription factors and acts as a barrier to polymerases. Therefore the complex process of gene activation must operate at two levels. In the first instance, localized chromatin decondensation and nucleosome displacement is required to make DNA accessible. Second, sequence-specific transcription factors need to recruit chromatin modifiers and remodellers to create a chromatin environment that permits the passage of polymerases. In this review I will discuss the chromatin structural changes that occur at active gene loci and at regulatory elements that exist as DNase I hypersensitive sites.
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Affiliation(s)
- Peter N Cockerill
- Experimental Haematology, Leeds Institute of Molecular Medicine, University of Leeds, UK.
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16
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Keaton MA, Taylor CM, Layer RM, Dutta A. Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes. PLoS One 2011; 6:e17912. [PMID: 21423757 PMCID: PMC3056778 DOI: 10.1371/journal.pone.0017912] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2011] [Accepted: 02/14/2011] [Indexed: 01/30/2023] Open
Abstract
The human genome must be packaged and organized in a functional manner for the regulation of DNA replication and transcription. The nuclear scaffold/matrix, consisting of structural and functional nuclear proteins, remains after extraction of nuclei and anchors loops of DNA. In the search for cis-elements functioning as chromatin domain boundaries, we identified 453 nuclear scaffold attachment sites purified by lithium-3,5-iodosalicylate extraction of HeLa nuclei across 30 Mb of the human genome studied by the ENCODE pilot project. The scaffold attachment sites mapped predominately near expressed genes and localized near transcription start sites and the ends of genes but not to boundary elements. In addition, these regions were enriched for RNA polymerase II and transcription factor binding sites and were located in early replicating regions of the genome. We believe these sites correspond to genome-interactions mediated by transcription factors and transcriptional machinery immobilized on a nuclear substructure.
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Affiliation(s)
- Mignon A. Keaton
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Christopher M. Taylor
- Department of Computer Science, University of New Orleans, New Orleans, Louisiana, United States of America
| | - Ryan M. Layer
- Department of Computer Science, University of Virginia, Charlottesville, Virginia, United States of America
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
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17
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Abstract
Investigations into the organization of transcription have their origins in cell biology. Early studies characterized nascent transcription in relation to discernable nuclear structures and components. Advances in light microscopy, immunofluorescence, and in situ hybridization helped to begin the difficult task of naming the countless individual players and components of transcription and placing them in context. With the completion of mammalian genome sequences, the seemingly boundless task of understanding transcription of the genome became finite and began a new period of rapid advance. Here we focus on the organization of transcription in mammals drawing upon information from lower organisms where necessary. The emerging picture is one of a highly organized nucleus with specific conformations of the genome adapted for tissue-specific programs of transcription and gene expression.
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Affiliation(s)
- Lyubomira Chakalova
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
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18
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Papantonis A, Larkin JD, Wada Y, Ohta Y, Ihara S, Kodama T, Cook PR. Active RNA polymerases: mobile or immobile molecular machines? PLoS Biol 2010; 8:e1000419. [PMID: 20644712 PMCID: PMC2903595 DOI: 10.1371/journal.pbio.1000419] [Citation(s) in RCA: 77] [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: 12/03/2009] [Accepted: 06/02/2010] [Indexed: 12/22/2022] Open
Abstract
It is widely assumed that active RNA polymerases track along their templates to produce a transcript. We test this using chromosome conformation capture and human genes switched on rapidly and synchronously by tumour necrosis factor alpha (TNFalpha); one is 221 kbp SAMD4A, which a polymerase takes more than 1 h to transcribe. Ten minutes after stimulation, the SAMD4A promoter comes together with other TNFalpha-responsive promoters. Subsequently, these contacts are lost as new downstream ones appear; contacts are invariably between sequences being transcribed. Super-resolution microscopy confirms that nascent transcripts (detected by RNA fluorescence in situ hybridization) co-localize at relevant times. Results are consistent with an alternative view of transcription: polymerases fixed in factories reel in their respective templates, so different parts of the templates transiently lie together.
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Affiliation(s)
- Argyris Papantonis
- Sir William Dunn School of Pathology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Joshua D. Larkin
- Sir William Dunn School of Pathology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Youichiro Wada
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Ohta
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Sigeo Ihara
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiko Kodama
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Peter R. Cook
- Sir William Dunn School of Pathology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
- * E-mail:
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19
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Cook PR. A model for all genomes: the role of transcription factories. J Mol Biol 2010; 395:1-10. [PMID: 19852969 DOI: 10.1016/j.jmb.2009.10.031] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2009] [Revised: 09/30/2009] [Accepted: 10/14/2009] [Indexed: 12/26/2022]
Abstract
A model for all genomes involving one major architectural motif is presented: DNA or chromatin loops are tethered to "factories" through the transcription machinery-a polymerase (active or inactive) or its transcription factors (activators or repressors). These loops appear and disappear as polymerases initiate and terminate (and as factors bind and dissociate), so the structure is ever-changing and self-organizing. This model is parsimonious, detailed (and so easily tested), and incorporates elements found in various other models.
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Affiliation(s)
- Peter R Cook
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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20
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Abstract
There is increasing evidence that different transcription units are transcribed together in discrete nuclear structures known as transcription factories. Various new techniques enable us to detect and characterize these structures. We review the latest findings and discuss how they support a model for transcription and chromosome organization.
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21
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Stein GS, Lian JB, van Wijnen AJ, Stein JL, Javed A, Montecino M, Choi JY, Vradii D, Zaidi SK, Pratap J, Young D. Organization of transcriptional regulatory machinery in nuclear microenvironments: implications for biological control and cancer. ADVANCES IN ENZYME REGULATION 2007; 47:242-50. [PMID: 17363043 PMCID: PMC2683591 DOI: 10.1016/j.advenzreg.2006.12.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Gary S Stein
- Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, 55 Lake Ave. North, Worcester, MA 01655, USA.
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22
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Faro-Trindade I, Cook PR. Transcription factories: structures conserved during differentiation and evolution. Biochem Soc Trans 2007; 34:1133-7. [PMID: 17073768 DOI: 10.1042/bst0341133] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Many cellular functions take place in discrete compartments, but our textbooks make little reference to any compartments involved in transcription. We review the evidence that active RNA polymerases and associated factors cluster into 'factories' that carry out many (perhaps all) of the functions required to generate mature transcripts. Clustering ensures high local concentrations and efficient interaction. Then, a gene must associate with the appropriate factory before it can be transcribed. Recent results show that the density and diameter of nucleoplasmic factories remain roughly constant as cells differentiate, despite large changes in the numbers of active polymerases and nucleoplasmic volumes.
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Affiliation(s)
- I Faro-Trindade
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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23
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Engelhardt OG, Fodor E. Functional association between viral and cellular transcription during influenza virus infection. Rev Med Virol 2006; 16:329-45. [PMID: 16933365 DOI: 10.1002/rmv.512] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Influenza viruses replicate and transcribe their segmented negative-sense single-stranded RNA genome in the nucleus of the infected host cell. All RNA synthesising activities associated with influenza virus are performed by the virally encoded RNA-dependent RNA polymerase (RdRp) that consists of three subunits, PA, PB1 and PB2. However, viral transcription is critically dependent on on-going cellular transcription, in particular, on activities associated with the cellular DNA-dependent RNA polymerase II (Pol II). Thus, the viral RdRp uses short 5' capped RNA fragments, derived from cellular Pol II transcripts, as primers for viral mRNA synthesis. These capped RNA primers are generated by cleavage of host Pol II transcripts by an endonuclease activity associated with the viral RdRp. Moreover, some viral transcripts require splicing and since influenza virus does not encode splicing machinery, it is dependent on host splicing, an activity also related to Pol II transcription. Despite these functional links between viral and host Pol II transcription, there has been no evidence that a physical association existed between the two transcriptional machineries. However, recently it was reported that there is a physical interaction between the trimeric viral RdRp and cellular Pol II. The viral RdRp was found to interact with the C-terminal domain (CTD) of initiating Pol II, at a stage in the transcription cycle when capping takes place. It was therefore proposed that this interaction may be required for the viral RNA (vRNA) polymerase to gain access to capped RNA substrates for endonucleolytic cleavage. The virus not only relies on cellular factors to support its own RNA synthesis, but also subverts cellular pathways in order to generate an environment optimised for viral multiplication. In this respect, the interaction of the viral NS1 protein with factors involved in cellular pre-mRNA processing is of particular relevance. The virus also alters the distribution of Pol II on cellular genes, leading to a reduction in elongating Pol II thereby contributing to the phenomenon known as host shut-off.
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24
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Corry GN, Underhill DA. Subnuclear compartmentalization of sequence-specific transcription factors and regulation of eukaryotic gene expression. Biochem Cell Biol 2005; 83:535-47. [PMID: 16094457 DOI: 10.1139/o05-062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
To date, the majority of the research regarding eukaryotic transcription factors has focused on characterizing their function primarily through in vitro methods. These studies have revealed that transcription factors are essentially modular structures, containing separate regions that participate in such activities as DNA binding, protein-protein interaction, and transcriptional activation or repression. To fully comprehend the behavior of a given transcription factor, however, these domains must be analyzed in the context of the entire protein, and in certain cases the context of a multiprotein complex. Furthermore, it must be appreciated that transcription factors function in the nucleus, where they must contend with a variety of factors, including the nuclear architecture, chromatin domains, chromosome territories, and cell-cycle-associated processes. Recent examinations of transcription factors in the nucleus have clarified the behavior of these proteins in vivo and have increased our understanding of how gene expression is regulated in eukaryotes. Here, we review the current knowledge regarding sequence-specific transcription factor compartmentalization within the nucleus and discuss its impact on the regulation of such processes as activation or repression of gene expression and interaction with coregulatory factors.
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Affiliation(s)
- Gareth N Corry
- Department of Medical Genetics, University of Alberta, Edmonton, Canada
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Ioudinkova ES, Petrov AV, Vassetzky YS, Razin SV. Spatial Organization of the Chicken α-Globin Gene Domain in Cells of Different Origins. Mol Biol 2005. [DOI: 10.1007/s11008-005-0105-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Burke B, Tooze J, Warren G. A monoclonal antibody which recognises each of the nuclear lamin polypeptides in mammalian cells. EMBO J 2002; 2:361-7. [PMID: 11894950 PMCID: PMC555141 DOI: 10.1002/j.1460-2075.1983.tb01431.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
A monoclonal IgM has been characterised which recognises the nuclear lamins in all mammalian cells tested. In immunoblotting experiments using both one- and two-dimensional gels it recognises lamins A, B and C. The common antigenic determinant lies on a proteolytic fragment of 46,000 daltons which can be generated from each lamin polypeptide by treatment with chymotrypsin. In immunofluorescence experiments on whole cells and thin frozen sections, the antibody labelled only the nuclear envelope and not the nuclear interior. During mitosis, labelling was found dispersed throughout the cell cytoplasm. By immunoelectron microscopy using the antibody and protein A-gold, only the nucleoplasmic side of the nuclear envelope (the nuclear lamina) was labelled, but there was no labelling of the nuclear pores.
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Affiliation(s)
- B Burke
- European Molecular Biology Laboratory, Heidelberg, FRG
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Akileswaran L, Taraska JW, Sayer JA, Gettemy JM, Coghlan VM. A-kinase-anchoring protein AKAP95 is targeted to the nuclear matrix and associates with p68 RNA helicase. J Biol Chem 2001; 276:17448-54. [PMID: 11279182 DOI: 10.1074/jbc.m101171200] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cell nucleus is structurally and functionally organized by the nuclear matrix. We have examined whether the nuclear cAMP-dependent protein kinase-anchoring protein AKAP95 contains specific signals for targeting to the subnuclear compartment and for interaction with other proteins. AKAP95 was expressed in mammalian cells and found to localize exclusively to the nuclear matrix. Mutational analysis was used to identify determinants for nuclear localization and nuclear matrix targeting of AKAP95. These sites were found to be distinct from previously identified DNA and protein kinase A binding domains. The nuclear matrix-targeting site is unique but conserved among members of the AKAP95 family. Direct binding of AKAP95 to isolated nuclear matrix was demonstrated in situ and found to be dependent on the nuclear matrix-targeting site. Moreover, Far Western blot analysis identified at least three AKAP95-binding proteins in nuclear matrix isolated from rat brain. Yeast two-hybrid cloning identified one binding partner as p68 RNA helicase. The helicase and AKAP95 co-localized in the nuclear matrix of mammalian cells, associated in vitro, and were precipitated as a complex from solubilized cell extracts. The results define novel protein-protein interactions among nuclear matrix proteins and suggest a potential role of AKAP95 as a scaffold for coordinating assembly of hormonally responsive transcription complexes.
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Affiliation(s)
- L Akileswaran
- Neurological Sciences Institute, Oregon Health Sciences University, Beaverton, Oregon 97006, USA
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Hara K, Shiota M, Kido H, Ohtsu Y, Kashiwagi T, Iwahashi J, Hamada N, Mizoue K, Tsumura N, Kato H, Toyoda T. Influenza virus RNA polymerase PA subunit is a novel serine protease with Ser624 at the active site. Genes Cells 2001; 6:87-97. [PMID: 11260254 DOI: 10.1046/j.1365-2443.2001.00399.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Influenza virus RNA polymerase is a multifunctional enzyme that catalyses both transcription and replication of the RNA genome. The function of the influenza virus RNA polymerase PA subunit in viral replication is poorly understood, although the enzyme is known to be required for cRNA --> vRNA synthesis. The protease related activity of PA has been discussed ever since protease-inducing activity was demonstrated in transfection experiments. RESULTS PA protein was highly purified from insect cells infected with the recombinant baculovirus carrying PA cDNA, and a novel chymotrypsin-type serine protease activity was identified with the synthetic peptide, Suc-LLVY-MCA, in the PA protein. [3H]DFP was crosslinked with PA and a mutational analysis revealed that serine624 was as an active site for the protease activity. CONCLUSIONS These results constitute the demonstration of protease activity in PA subunit of the influenza virus RNA polymerase complexes.
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Affiliation(s)
- K Hara
- Departments of Virology, Kurume University School of Medicine, Kurume 830-0011, Japan
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Abstract
Models for replication and transcription often display polymerases that track like locomotives along their DNA templates. However, recent evidence supports an alternative model in which DNA and RNA polymerases are immobilized by attachment to larger structures, where they reel in their templates and extrude newly made nucleic acids. These polymerases do not act independently; they are concentrated in discrete "factories," where they work together on many different templates. Evidence for models involving tracking and immobile polymerases is reviewed.
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Affiliation(s)
- P R Cook
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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Lian JB, Stein GS, Stein JL, van Wijnen AJ. Regulated expression of the bone-specific osteocalcin gene by vitamins and hormones. VITAMINS AND HORMONES 1999; 55:443-509. [PMID: 9949687 DOI: 10.1016/s0083-6729(08)60941-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- J B Lian
- Department of Cell Biology, University of Massachusetts Medical Center, Worcester 01655, USA
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32
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Jackson DA, Iborra FJ, Manders EM, Cook PR. Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei. Mol Biol Cell 1998; 9:1523-36. [PMID: 9614191 PMCID: PMC25378 DOI: 10.1091/mbc.9.6.1523] [Citation(s) in RCA: 212] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Using HeLa cells, we have developed methods to determine 1) the number of RNA polymerases that are active at any moment, 2) the number of transcription sites, and 3) the number of polymerases associated with one transcription unit. To count engaged polymerases, cells were encapsulated in agarose, permeabilized, treated with ribonuclease, and the now-truncated transcripts extended in [32P]uridine triphosphate; then, the number of growing transcripts was calculated from the total number of nucleotides incorporated and the average increment in length of the transcripts. Approximately 15, 000 transcripts were elongated by polymerase I, and approximately 75,000 were elongated by polymerases II and III. Transcription sites were detected after the cells were grown in bromouridine for <2.5 min, after which the resulting bromo-RNA was labeled with gold particles; electron microscopy showed that most extranucleolar transcripts were concentrated in approximately 2400 sites with diameters of approximately 80 nm. The number of polymerases associated with a transcription unit was counted after templates were spread over a large area; most extranucleolar units were associated with one elongating complex. These results suggest that many templates are attached in a "cloud" of loops around a site; each site, or transcription "factory," would contain approximately 30 active polymerases and associated transcripts.
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Affiliation(s)
- D A Jackson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
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Djuric Z, KuKuruga MA, Everett-Bauer CK, Nakeff AN. Flow cytometric analysis of DNA damage in nucleoids from cultured human breast epithelial cells treated with hydrogen peroxide. Free Radic Biol Med 1998; 24:326-31. [PMID: 9433908 DOI: 10.1016/s0891-5849(97)00266-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Flow cytometric analysis of nucleoids is useful to investigate nuclear matrix-DNA associations in cells. We have now applied this technique to examine whether differences in nucleoid structure can be detected between tumor and normal-like human breast epithelial cells. We have previously shown that MCF-7 tumor and MCF-10A normal-like human breast cells exhibit different levels of endogenous oxidative DNA damage as well as differences in response to hydrogen peroxide. We therefore examined whether flow cytometric analysis of nucleoids can be used to detect both endogenous DNA damage and DNA damage induced by hydrogen peroxide in these cells. Nucleoids were prepared by lysis of MCF-7 and MCF-10A cells with a high-salt buffer. The size of the DNA loops around the nuclear matrix core was detected by measuring the forward light-scatter signal in the presence of ethidium bromide. The relaxation and supercoiling of DNA in the presence of low and high concentrations of ethidium bromide, respectively, was similar in MCF-7 tumor and MCF-10A normal-like cells. After treatment of cells with 100 microM and higher of hydrogen peroxide, there was a statistically significant increase in the forward light scatter from nucleoids prepared in the presence of high concentrations of ethidium bromide, and this increase was similar in both cell lines. The changes in the forward light scatter signal with increasing hydrogen peroxide concentration did not mimic the patterns of increases in single strand breaks or formation of 5-hydroxymethyl-2 '-deoxyuridine that we reported previously. This indicates that the flow cytometric technique probably detects other types of changes induced by hydrogen peroxide.
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Affiliation(s)
- Z Djuric
- Barbara Ann Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA
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35
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Stein GS, Lian JB, van Wijnen AJ, Stein JL. The osteocalcin gene: a model for multiple parameters of skeletal-specific transcriptional control. Mol Biol Rep 1997; 24:185-96. [PMID: 9291092 DOI: 10.1023/a:1006803615430] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Influences of promoter regulatory elements that are responsive to basal and tissue-restricted transactivation factors, steroid hormones, growth factors and other physiologic mediators has provided the basis for understanding regulatory mechanisms contributing to developmental expression of osteocalcin, tissue specificity and biological activity (reviewed in [1-3]). These regulatory elements and cognate transcription factors support postproliferative transcriptional activation and steroid hormone (e.g. vitamin D) enhancement at the onset of extracellular matrix mineralization during osteoblast differentiation. Three parameters of nuclear structure contribute to osteocalcin gene transcriptional control. The linear representation of promoter elements provides competency for physiological responsiveness within the contexts of developmental as well as phenotype-dependent regulation. Chromatin structure and nucleosome organization reduce distances between independent regulatory elements providing a basis for integrating components of transcriptional control. The nuclear matrix supports gene expression by imposing physical constraints on chromatin related to three dimensional genomic organization. In addition, the nuclear matrix facilitates gene localization as well as the concentration and targeting of transcription factors. Several lines of evidence are presented which are consistent with involvement of multiple levels of nuclear architecture in tissue-specific gene expression during differentiation. Growth factor and steroid hormone responsive modifications in chromatin structure, nucleosome organization and the nuclear matrix are considered which influence transcription of the bone tissue-specific osteocalcin gene during progressive expression of the osteoblast phenotype.
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Affiliation(s)
- G S Stein
- Department of Cell Biology, University of Massachusetts Medical Center, Worcester 01655, USA
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36
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Menz K, Radomski N, Jost E. INMP, a novel intranuclear matrix protein related to the family of intermediate filament-like proteins: molecular cloning and sequence analysis. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1309:14-20. [PMID: 8950169 DOI: 10.1016/s0167-4781(96)00132-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
An important step in understanding nuclear structure and its function in replication and gene regulation is the cloning and characterisation of nuclear matrix proteins. A full-length cDNA-clone, encoding a novel nuclear matrix protein, was isolated from a (lambda gt11 cDNA library derived from murine macrophages. The antibody used for the screen was raised against a single polypeptide isolated from two-dimensional gel electrophoresis of nuclear matrix preparations. The cDNA encodes a protein of 446 amino acids named INMP for intranuclear matrix protein. INMP displays several salient features, a coiled-coil domain, a leucine zipper, a number of phosphorylation sites and a putative nuclear localisation signal. Sequence homology comparisons indicate that INMP is a unique protein which is evolutionary related to the gene family of intermediate filament-like proteins, especially the nuclear lamins.
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Affiliation(s)
- K Menz
- Genetisches Institut, Justus-Liebig-Universität Giessen, Germany
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37
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Hempel K, Strätling WH. The chicken lysozyme gene 5′ MAR and the Drosophila histone SAR are electroelutable from encapsulated and digested nuclei. J Cell Sci 1996; 109 ( Pt 6):1459-69. [PMID: 8799833 DOI: 10.1242/jcs.109.6.1459] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cultured chicken cells were encapsulated in agarose microbeads, lysed in a near-physiological buffer and resulting encapsulated nuclei were digested with a restriction enzyme and electroeluted. After removal of approximately 97% of the chromatin, the nuclear lamina, residual nucleoli and an internal nuclear network remained. The majority of nascent RNA was also recovered in digested and electroeluted nuclei. Surprisingly, however, the chicken lysozyme gene 5′ MAR was quantitatively electroeluted from digested nuclei of expressing and non-expressing cells, as well as the promoter region and the coding sequence. When encapsulated nuclei were digested partially, the proportion of elutable 5′ MAR chromatin was comparable to that of elutable bulk chromatin. Furthermore, after digestion of encapsulated nuclei from Drosophila Kc cells, the histone SAR was electroeluted to the same extent as bulk chromatin. We conclude that the lysozyme gene 5′ MAR and the histone SAR are not permanently attached to a nuclear matrix or scaffold.
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Affiliation(s)
- K Hempel
- Institut für Physiologische Chemie, Universitäts-Krankenhaus Eppendorf, Hamburg, FR Germany
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38
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Iborra FJ, Pombo A, Jackson DA, Cook PR. Active RNA polymerases are localized within discrete transcription “factories' in human nuclei. J Cell Sci 1996; 109 ( Pt 6):1427-36. [PMID: 8799830 DOI: 10.1242/jcs.109.6.1427] [Citation(s) in RCA: 302] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nascent transcripts in permeabilized HeLa cells were elongated by approximately 30–2,000 nucleotides in Br-UTP or biotin-14-CTP, before incorporation sites were immunolabelled either pre- or post-embedding, and visualized by light or electron microscopy. Analogues were concentrated in approximately 2,100 (range 2,000-2,700) discrete sites attached to a nucleoskeleton and surrounded by chromatin. A typical site contained a cluster (diameter 71 nm) of at least 4, and probably about 20, engaged polymerases, plus associated transcripts that partially overlapped a zone of RNA polymerase II, ribonucleoproteins, and proteins rich in thiols and acidic groups. As each site probably contains many transcription units, these results suggest that active polymerases are confined to these sites, which we call transcription ‘factories’. Results are consistent with transcription occurring as templates slide past attached polymerases, as nascent RNA is extruded into the factories.
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Affiliation(s)
- F J Iborra
- CRC Nuclear Structure and Function Research Group, Sir William Dunn School of Pathology, University of Oxford, UK
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39
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Clemson CM, McNeil JA, Willard HF, Lawrence JB. XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure. J Cell Biol 1996; 132:259-75. [PMID: 8636206 PMCID: PMC2120729 DOI: 10.1083/jcb.132.3.259] [Citation(s) in RCA: 594] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The XIST gene is implicated in X chromosome inactivation, yet the RNA contains no apparent open reading frame. An accumulation of XIST RNA is observed near its site of transcription, the inactive X chromosome (Xi). A series of molecular cytogenetic studies comparing properties of XIST RNA to other protein coding RNAs, support a critical distinction for XIST RNA; XIST does not concentrate at Xi simply because it is transcribed and processed there. Most notably, morphometric and 3-D analysis reveals that XIST RNA and Xi are coincident in 2- and 3-D space; hence, the XIST RNA essentially paints Xi. Several results indicate that the XIST RNA accumulation has two components, a minor one associated with transcription and processing, and a spliced major component, which stably associates with Xi. Upon transcriptional inhibition the major spliced component remains in the nucleus and often encircles the extra-prominent heterochromatic Barr body. The continually transcribed XIST gene and its polyadenylated RNA consistently localize to a nuclear region devoid of splicing factor/poly A RNA rich domains. XIST RNA remains with the nuclear matrix fraction after removal of chromosomal DNA. XIST RNA is released from its association with Xi during mitosis, but shows a unique highly particulate distribution. Collective results indicate that XIST RNA may be an architectural element of the interphase chromosome territory, possibly a component of nonchromatin nuclear structure that specifically associates with Xi. XIST RNA is a novel nuclear RNA which potentially provides a specific precedent for RNA involvement in nuclear structure and cis-limited gene regulation via higher-order chromatin packaging.
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Affiliation(s)
- C M Clemson
- Department of Cell Biology, University of Massachusetts Medical Center, Worcester 01655, USA
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40
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Stein GS, van Wijnen AJ, Stein J, Lian JB, Montecino M. Contributions of nuclear architecture to transcriptional control. INTERNATIONAL REVIEW OF CYTOLOGY 1996; 162A:251-78. [PMID: 8575882 DOI: 10.1016/s0074-7696(08)61233-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Three parameters of nuclear structure contribute to transcriptional control. The linear representation of promoter elements provides competency for physiological responsiveness within the contexts of development as well as cycle- and phenotype-dependent regulation. Chromatin structure and nucleosome organization reduce distances between independent regulatory elements providing a basis for integrating components of transcriptional control. The nuclear matrix supports gene expression by imposing physical constraints on chromatin related to three-dimensional genomic organization. In addition, the nuclear matrix facilitates gene localization as well as the concentration and targeting of transcription factors. Several lines of evidence are presented that are consistent with involvement of multiple levels of nuclear architecture in cell growth and tissue-specific gene expression during differentiation. Growth factor and steroid hormone responsive modifications in chromatin structure, nucleosome organization, and the nuclear matrix that influence transcription of the cell cycle-regulated histone gene and the bone tissue-specific osteocalcin gene during progressive expression of the osteoblast phenotype are considered.
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Affiliation(s)
- G S Stein
- Department of Cell Biology, University of Massachusetts Medical Center, Worcester 01655, USA
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41
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Affiliation(s)
- T S Replogle
- University of Michigan Comprehensive Cancer Center, Ann Arbor 48109-0680, USA
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42
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Boulikas T. Chromatin domains and prediction of MAR sequences. INTERNATIONAL REVIEW OF CYTOLOGY 1996; 162A:279-388. [PMID: 8575883 DOI: 10.1016/s0074-7696(08)61234-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Polynuceosomes are constrained into loops or domains and are insulated from the effects of chromatin structure and torsional strain from flanking domains by the cross-complexation of matrix-attached regions (MARs) and matrix proteins. MARs or SARs have an average size of 500 bp, are spaced about every 30 kb, and are control elements maintaining independent realms of gene activity. A fraction of MARs may cohabit with core origin replication (ORIs) and another fraction might cohabit with transcriptional enhancers. DNA replication, transcription, repair, splicing, and recombination seem to take place on the nuclear matrix. Classical AT-rich MARs have been proposed to anchor the core enhancers and core origins complexed with low abundancy transcription factors to the nuclear matrix via the cooperative binding to MARs of abundant classical matrix proteins (topoisomerase II, histone H1, lamins, SP120, ARBP, SATB1); this creates a unique nuclear microenvironment rich in regulatory proteins able to sustain transcription, replication, repair, and recombination. Theoretical searches and experimental data strongly support a model of activation of MARs and ORIs by transcription factors. A set of 21 characteristics are deduced or proposed for MAR/ORI sequences including their enrichment in inverted repeats, AT tracts, DNA unwinding elements, replication initiator protein sites, homooligonucleotide repeats (i.e., AAA, TTT, CCC), curved DNA, DNase I-hypersensitive sites, nucleosome-free stretches, polypurine stretches, and motifs with a potential for left-handed and triplex structures. We are establishing Banks of ORI and MAR sequences and have undertaken a large project of sequencing a large number of MARs in an effort to determine classes of DNA sequences in these regulatory elements and to understand their role at the origins of replication and transcriptional enhancers.
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Affiliation(s)
- T Boulikas
- Institute of Molecular Medical Sciences, Palo Alto, California 94306, USA
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43
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Iarovaia O, Hancock R, Lagarkova M, Miassod R, Razin SV. Mapping of genomic DNA loop organization in a 500-kilobase region of the Drosophila X chromosome by the topoisomerase II-mediated DNA loop excision protocol. Mol Cell Biol 1996; 16:302-8. [PMID: 8524309 PMCID: PMC231004 DOI: 10.1128/mcb.16.1.302] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The recently developed procedure of chromosomal DNA loop excision by topoisomerase II-mediated DNA cleavage at matrix attachment sites (S. V. Razin, R. Hancock, O. Iarovaia, O. Westergaard, I. Gromova, and G. P. Georgiev, Cold Spring Harbor Symp. Quant. Biol. 58:25-35, 1993; I. I. Gromova, B. Thompsen, and S. V. Razin, Proc. Natl. Acad. Sci. USA 92:102-106, 1995) has been employed for mapping the DNA loop anchorage sites in a 500-kb region of the Drosophila melanogaster X chromosome. Eleven anchorage sites delimiting 10 DNA loops ranging in size from 20 to 90 kb were found within this region. Ten of these 11 anchorage sites colocalize with previously mapped scaffold attachment regions. However, a number of other scaffold attachment regions are found to be located in loop DNA.
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Affiliation(s)
- O Iarovaia
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
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44
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Razin SV, Gromova II, Iarovaia OV. Specificity and functional significance of DNA interaction with the nuclear matrix: new approaches to clarify the old questions. INTERNATIONAL REVIEW OF CYTOLOGY 1996; 162B:405-48. [PMID: 8557493 DOI: 10.1016/s0074-7696(08)62623-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In this chapter the specificity of chromosomal DNA partitioning into topological loops is discussed. Different experimental approaches used for the analysis of the above problem are critically reviewed. This discussion is followed by presentation of a novel approach for mapping the DNA loop anchorage sites that we have developed. This approach, based on the excision of the whole DNA loops by topoisomerase II-mediated DNA cleavage at matrix attachment sites, seems to constitute a unique tool for the analysis of topological organization of chromosomal DNA in living cells. We also discuss experimental results indicating that the DNA-loop anchorage sites form "weak points" in chromosomes that are preferentially sensitive to cleavage with both endogenous and exogenous nucleases. In connection with this discussion, rationales for the supposition that DNA loops constitute basic units of eukaryotic genome organization and evolution are considered. The chapter concludes by suggesting a new model of spatial organization of eukaryotic genome within the cell nucleus that resolves apparent contradictions between different data on the specificity of DNA interaction with the nuclear matrix.
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Affiliation(s)
- S V Razin
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia
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45
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van Steensel B, Brink M, van der Meulen K, van Binnendijk EP, Wansink DG, de Jong L, de Kloet ER, van Driel R. Localization of the glucocorticoid receptor in discrete clusters in the cell nucleus. J Cell Sci 1995; 108 ( Pt 9):3003-11. [PMID: 8537440 DOI: 10.1242/jcs.108.9.3003] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cell nucleus is highly organized. Many nuclear functions are localized in discrete domains, suggesting that compartmentalization is an important aspect of the regulation and coordination of nuclear functions. We investigated the subnuclear distribution of the glucocorticoid receptor, a hormone-dependent transcription factor. By immunofluorescent labeling and confocal microscopy we found that after stimulation with the agonist dexamethasone the glucocorticoid receptor is concentrated in 1,000-2,000 clusters in the nucleoplasm. This distribution was observed in several cell types and with three different antibodies against the glucocorticoid receptor. A similar subnuclear distribution of glucocorticoid receptors was found after treatment of cells with the antagonist RU486, suggesting that the association of the glucocorticoid receptor in clusters does not require transformation of the receptor to a state that is able to activate transcription. By dual labeling we found that most dexamethasone-induced receptor clusters do not colocalize with sites of pre-mRNA synthesis. We also show that RNA polymerase II is localized in a large number of clusters in the nucleus. Glucocorticoid receptor clusters did not significantly colocalize with these RNA polymerase II clusters or with domains containing the splicing factor SC-35. Taken together, these results suggest that most clustered glucocorticoid receptor molecules are not directly involved in activation of transcription.
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Affiliation(s)
- B van Steensel
- E.C. Slater Institute, University of Amsterdam, The Netherlands
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46
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Abstract
Previous studies have demonstrated the presence of the insulin receptor in the cell nucleus. Recently, it was shown that the insulin receptor also exhibits nuclear tyrosine kinase activity. In the present investigation, I have searched for structural correlates to a nuclear localization of the insulin receptor as well as to other potential nuclear actions of this molecule. Interestingly, this analysis yielded that the insulin receptor (alpha-subunit) contains a bipartite nuclear localization signal (consistent with the preceding experimental data), several zinc finger-like motifs and an RGG box. These findings have intriguing implications with regard to a presumable role of the insulin receptor (alpha-subunit) as a gene regulatory molecule.
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47
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van Steensel B, Jenster G, Damm K, Brinkmann AO, van Driel R. Domains of the human androgen receptor and glucocorticoid receptor involved in binding to the nuclear matrix. J Cell Biochem 1995; 57:465-78. [PMID: 7768981 DOI: 10.1002/jcb.240570312] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Steroid receptors have been reported to bind to the nuclear matrix. The nuclear matrix is operationally defined as the residual nuclear structure that remains after extraction of most of the chromatin and all soluble and loosely bound components. To obtain insight in the molecular mechanism of the interaction of steroid receptors with the nuclear matrix, we studied the binding of several deletion mutants of the human androgen receptor (hAR) and the human glucocorticoid receptor (hGR) to the nuclear matrix. Receptor binding was tested for two different nuclear matrix preparations: complete matrices, in which most matrix proteins are retained during the isolation procedure, and depleted matrices, which consist of only a subset of these proteins. The results show that the C-terminal domain of the hAR binds tightly to both depleted and complete matrices. In addition, at least one other domain of the hAR binds to complete matrices but not to depleted matrices. In contrast to the hAR, the hGR binds only to complete matrices. For this interaction both the DNA-binding domain and the C-terminal domain of the hGR are required, whereas the N-terminal domain is not. We conclude that specific protein domains of the hAR and the hGR are involved in binding to the nuclear matrix. In addition, our results indicate that the hAR and the hGR are attached to the nuclear matrix through different molecular interactions.
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Affiliation(s)
- B van Steensel
- E.C. Slater Institute, University of Amsterdam, The Netherlands
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48
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The Sequestration of mRNA in the Cytoskeleton and Other Subcellular Structures. Cytoskeleton (Hoboken) 1995. [DOI: 10.1016/s1569-2558(08)60259-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Novel action of retinoic acid. Stabilization of newly synthesized alkaline phosphatase transcripts. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)31808-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Abstract
Current models for RNA synthesis involve an RNA polymerase that tracks along a static template. However, research on chromatin loops suggests that the template slides past a stationary polymerase; individual polymerases tie the chromatin fibre into loops and clusters of polymerases determine the basic structure of the interphase and metaphase chromosome. RNA polymerase is then both a player and a manager of the chromosome loop.
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Affiliation(s)
- P R Cook
- CRC Nuclear Structure and Function Research Group, Sir William Dunn School of Pathology, University of Oxford, UK
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