Begell House Inc.
Critical Reviews™ in Eukaryotic Gene Expression
CRE
1045-4403
9
3-4
1999
NUCLEAR STRUCTURE AND GENE EXPRESSION (Part One of a Two-Part Series)
v-vi
10.1615/CritRevEukarGeneExpr.v9.i3-4.10
Gary S.
Stein
Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405; University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT 05405
Ronald
Berezney
25 Years of Contributions to Characterizing Gene Expression and Replication within the Three-Dimensional Context of Nuclear Architecture
Evolution of Transcriptional Control from Prokaryotic Beginnings to Eukaryotic Complexities
175-182
10.1615/CritRevEukarGeneExpr.v9.i3-4.20
Lili
Huang
Dana Farber Cancer Institute, 44 Binney St., Boston, MA 02115
Rong J.
Guan
Dana Farber Cancer Institute, 44 Binney St., Boston, MA 02115
Arthur B.
Pardee
Dana Farber Cancer Institute, 44 Binney St., Boston, MA 02115
protein complexes
chromatin structure
histone acetylation
DNA methylation
superrepression.
Mechanisms for regulating gene transcription became increasingly complex as organisms evolved. In prokaryotes the relatively simple mechanism of repression is based on a few proteins that bind to specific DNA sequences in a ligand-dependent fashion. In eukaryotes large complexes that include ligand binding proteins regulate transcription. Lower eukaryotes developed an additional level of control based on protein complexes that include modifying enzymes. The DNA/histone complex, in combination with gene-specific transcriptional factors, is the basis of gene regulation in eukaryotes. Higher eukaryotes took regulation a level further by methylating CpGs in promoter sequences of DNA, thereby allowing binding of histone deacetylases and inhibiting transcription. Finally, long-lasting "superrepression" provides another mechanism for coordinate transcriptional regulation of large blocks of genes.
Interrelationships of Transcriptional Machinery with Nuclear Architecture
183-190
10.1615/CritRevEukarGeneExpr.v9.i3-4.30
Gary S.
Stein
Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405; University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT 05405
Andre J.
van Wijnen
Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, Worcester, MA 01655
Janet L.
Stein
Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405; University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT 05405
Jane B.
Lian
Department of Biochemistry, University of Vermont, 89 Beaumont Ave., Given E210B,
Burlington, VT 05405, USA; University of Vermont Cancer Center, Burlington, Vermont, USA
gene expression
intranuclear trafficking
nuclear matrix
chromatin.
There is increasing evidence for functional linkages between nuclear architecture and the regulation of gene expression. The nuclear matrix provides a paradigm for involvement of nuclear morphology in assembly of the biochemical machinery for physiological control of transcription. Mechanisms are being experimentally defined that direct regulatory factors to subnuclear sites that support gene expression. Consequently, we are gaining insight into the rules that govern transcriptional control within the three-dimensional context of nuclear organization.
Synthesis, Processing, and Transport of RNA within the Three-Dimensional Context of the Cell Nucleus
191-201
10.1615/CritRevEukarGeneExpr.v9.i3-4.40
Roeland W.
Dirks
Department of Molecular Cell Biology, Leiden University Medical Center, Wassenaarseweg 72,2333 AL Leiden, The Netherlands
Claudia M.
Hattinger
CCRI, St. Anna Children's Hospital, Kinderspitagasse 6, 1090 Vienna, Austria
Chris
Molenaar
Department of Molecular Cell Biology, Leiden University Medical Center, Wassenaarseweg 72,2333 AL Leiden, The Netherlands
Sabine P.
Snaar
Department of Molecular Cell Biology, Leiden University Medical Center, Wassenaarseweg 72,2333 AL Leiden, The Netherlands
FISH
transcription
RNA processing
RNA transport
living cell microscopy.
Fluorescence in situ hybridization and immunocytochemical techniques have contributed significantly to our current understanding of how transcription, RNA processing, and RNA transport are spatially and temporally organized in the cell nucleus. New technologies enabling the visualization of nuclear components in living cells specifically advanced our knowledge of the dynamic aspects of these nuclear processes. The picture that emerges from the work reviewed here shows that the positioning of genes within the three-dimensional nuclear space is of crucial importance, not only for its expression, but also for the efficient processing of its transcripts. Splicing factors are recruited from speckles to sites of active transcription, which can be present within, at the periphery, or at a relatively large distance from speckles. Furthermore, results are discussed showing that transcripts are exported by means of random diffusion.
Nuclear Structure, Gene Expression and Development
203-212
10.1615/CritRevEukarGeneExpr.v9.i3-4.50
Karen
Brown
MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, London W12 ONN, United Kingdom
nucleus
transcription
chromatin.
This article considers the extent to which features of nuclear structure are involved in the regulation of genome function. The recent renaissance in imaging technology has inspired a new determination to assign specific functions to nuclear domains or structures, many of which have been described as "factories" to express the idea that they coordinate nuclear processes in an efficient way. Visual data have been combined with genetic and biochemical information to support the idea that nuclear organization has functional significance. Particular DNA sequences or chromatin structures may nucleate domains that are permissive or restrictive of transcription, to which active or inactive loci could be recruited. Associations within the nucleus, as well as many nuclear structures, are transient and change dynamically during cell cycle progression and development. Despite this complexity, elucidation of the possible structural basis of epigenetic phenomena, such as the inheritance of a "cellular memory" of gene expression status, is an important goal for cell biology.
Topics for discussion include the regulatory effect of chromatin structure on gene expression, putative "nuclear addresses" for genes and proteins, the functional significance of nuclear bodies, and the role of the nuclear matrix in nuclear compartmentalization.
Intranuclear Trafficking of Messenger RNA
213-219
10.1615/CritRevEukarGeneExpr.v9.i3-4.60
Maria
Carmo-Fonseca
Institute of Histology and Embryology, Faculty of Medicine, University of Lisbon, 1649-028 Lisboa Codex, Portugal
Noelia
Custodio
Institute of Histology and Embryology, Faculty of Medicine, University of Lisbon, 1649-028 Lisboa Codex, Portugal
Angelo
Calado
Institute of Histology and Embryology, Faculty of Medicine, University of Lisbon, 1649-028 Lisboa Codex, Portugal
mRNA transport
mRNA surveillance
transcriptional termination
splicing
cleavage and polyadenylation.
Within the nucleus, protein-encoding genes are transcribed into messenger RNA by RNA polymerase II. Messenger RNAs migrate to the cytoplasm, but before reaching their final destination the primary transcripts must undergo a series of modifications that include 5′-capping, splicing, and 3′-cleavage/polyadenylation. Errors in these processing events can originate aberrant products that, if translated, would produce abnormal proteins. Therefore, it is not surprising that eukaryotes have evolved a surveillance mechanism that recognizes and rapidly degrades aberrant mRNAs. Recent experiments provide exciting insights into how proper mRNAs are distinguished and selected for export. Transcription by RNA polymerase II is directly coupled to pre-mRNA processing, and the mechanism that targets the processing machinery to the polymerase complex suggests a model for co-transcriptional proofreading. Furthermore, there is evidence that at least some mRNAs move randomly throughout the nucleus, presumably by free diffusion. In this light, retention of aberrant mRNAs by the transcription/processing machinery is crucial to prevent their diffusion to the nuclear pores and eventual translocation to the cytoplasm.
Interplay between Chromatin Modifying and Remodeling Complexes in Transcriptional Regulation
221-230
10.1615/CritRevEukarGeneExpr.v9.i3-4.70
Rimma
Belotserkovskaya
Molecular Genetics Program, The Wistar Institute, Philadelphia, PA 19104
Shelley L.
Berger
Molecular Genetics Program, The Wistar Institute, Philadelphia, PA 19104
SWI/SNF
SAGA
chromatin remodeling
histone modification.
The question of a possible functional relationship between different chromatin-altering enzymatic activities is of great interest. Several remarkable parallels have been revealed regarding the action of the remodeling complex SWI/SNF and the histone acetylation complex SAGA during transcriptional activation in S. cerevisiae. Many promoters, but not all, that require one complex require the other as well. Mutations that disrupt both complexes cause much more severe phenotypes than single mutations. Both types of complexes are recruited to specific promoters by interaction with DNA-bound acidic activators, resulting in targeted acetylation and transcriptional activation. Taken together the data argue for independent mechanisms, but similar recruitment and functional interplay between these two types of chromatin-altering activities.
Histone Acetyltransferase Complexes and Their Link to Transcription
231-243
10.1615/CritRevEukarGeneExpr.v9.i3-4.80
LeAnn
Howe
Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802-4500
Christine E.
Brown
Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802-4500
Thomas
Lechner
Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802-4500
Jerry L.
Workman
Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802-4500
histone
transcription
acetyltransferase complexes.
Early studies revealing the relationship between the state of histone acetylation and gene transcription were largely indirect. Increasing information regarding the enzymes that catalyze transcription linked acetylation is beginning to clarify this issue. This review attempts to relate previous data regarding the distribution of histone acetylation within different chromatin regions with recent data regarding the substrate specificity, subunit composition, and recruitment of the known histone acetyltransferase complexes.
Chromatin Structure Revisited
245-255
10.1615/CritRevEukarGeneExpr.v9.i3-4.90
Jordanka
Zlatanova
Biochip Technology Center, Argonne National Laboratory, Argonne, IL 60439-4833
Sanford H.
Leuba
Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20896-5055
Kensal
van Holde
Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331-7305
core particle
chromatosome
linker histone
HMG1
extended chromatin fiber
condensed chromatin fiber.
Independently of the enormous progress in our understanding of the structure of the core particle, there remain a multitude of structural questions still to be answered. The main points discussed here can be summarized as follows: (1) The meaning of the term 'core particle' should be widened to reflect the fact that the actual length of DNA wrapped around the histone octamer in the context of the chromatin fiber may vary between ≈100 and ≈170 bp. (2) In the chromatosome, the linker histone forms a bridge between one terminus of the chromatosomal DNA and a point close to the dyad axis. (3) The particle that contains one molecule of HMG1 may be classified as a bona fide chromatosome. (4) In the extended fiber, the partition of the nucleosomal DNA into core and linker is a dynamic feature, responding to environmental influences; fiber structure-related constraints demand that linker length be beyond a certain minimal value. (5) The compact fiber structure seems to be rather irregular; the precise nature of this structure is still to be determined. Finally, the term 30-nm fiber should be dropped as a designator of the compact or condensed chromatin fiber structure.
Lamins and Lamin-Binding Proteins in Functional Chromatin Organization
257-265
10.1615/CritRevEukarGeneExpr.v9.i3-4.100
Josef
Gotzmann
Institute of Tumor Biology-Cancer Research, University of Vienna, A-1090 Vienna, Austria
Roland
Foisner
Department of Biochemistry and Molecular Cell Biology, University of Vienna, A-1030 Vienna, Austria
lamina-associated polypeptide
lamin B receptor
nuclear assembly
nuclear lamina.
Lamins are the major components of the nuclear lamina, a two-dimensional filamentous network at the periphery of the nucleus in higher eukaryotes, directly underlying the inner nuclear membrane. Several integral proteins of the inner nuclear membrane bind to lamins and may link the nuclear membrane to the core lamina network. The lamins and the lamin-binding proteins lamina-associated polypeptide (LAP)2β and lamin B receptor (LBR) have been described to bind to DNA or to interact with chromatin via histones, BAF-1, and HP1 chromodomain proteins, respectively, and may provide anchorage sites for chromatin fibers at the nuclear periphery. In addition, lamin A structures on intranuclear filaments, or lamin B in replication foci have been described in the nuclear interior, but their specific roles remain unclear. An isoform of the LAP2 protein family, LAP2α, has been found to colocalize with A-type lamins in the nucleoplasm and might be involved in intranuclear structure organization. In the course of cell-cycle-dependent dynamics of the nucleus in higher eukaryotes, lamins as well as lamin-binding proteins seem to possess important functions during various steps of post-mitotic nuclear reassembly, including cross-linking of chromatides, nuclear membrane targeting, nuclear lamina assembly, and the formation of a replication-competent nucleus.
Chromatin Structure and Nuclear Remodeling
267-277
10.1615/CritRevEukarGeneExpr.v9.i3-4.110
Kristen M.
Johansen
Department of Zoology and Genetics, 3156 Molecular Biology Building, Iowa State University, Ames, Iowa 50011
Jorgen
Johansen
Department of Zoology and Genetics, 3156 Molecular Biology Building, Iowa State University, Ames, Iowa 50011
Ye
Jin
Department of Zoology and Genetics, Iowa State University, Ames, Iowa 50011
Diana L.
Walker
Department of Zoology and Genetics, Iowa State University, Ames, Iowa 50011
Dong
Wang
Department of Zoology and Genetics, Iowa State University, Ames, Iowa 50011
Yanming
Wang
Department of Zoology and Genetics, Iowa State University, Ames, Iowa 50011
Drosophila
nuclear kinase
chromatin structure
mitosis
nucleoskeleton.
Nuclear architecture is remodeled during interphase in response to changes in gene activity as well as to changing structural and functional requirements during cell division. Using the monoclonal antibody mAb2A, we have identified two proteins that appear to play important roles in these processes: JIL-1 is a tandem serine-threonine kinase implicated in the regulation of chromatin structure, whereas Skeletor is a novel protein participating in structural nuclear remodeling during the cell cycle. Antibody staining and live imaging of JIL-1 -GFP transgenic flies show that JIL-1 localizes to the gene-rich interband regions of larval polytene chromosomes and is upregulated almost twofold on the hypertranscribed male X chromosome compared with autosomes. We propose that JIL-1 may play a role in transcriptional control potentially by regulating chromatin structure. The other mAb2A antigen, Skeletor, is distributed in a nuclear meshwork pattern that can be observed in stereo pair images to reorganize during the cell cycle to form a spindle-like structure at prometaphase that is distinct from the microtubule spindle apparatus. Taking advantage of the powerful molecular and genetic approaches offered in Drosophila, the study of these two proteins promises to yield new insight into what defines nuclear architecture at the molecular level and how its remodeling is regulated.
Chromosomal DNA Loops May Constitute Basic Units of the Eukaryotic Genome Organization and Evolution
279-283
10.1615/CritRevEukarGeneExpr.v9.i3-4.120
Sergey V.
Razin
Laboratory of Structural and Functional Organization of hromosomes, Institute of Gene Biology of the Russian Academy of Sciences, Vavilov Str. 34/5, 117334 Moscow, Russia
nuclear matrix
DNA loops
topoisomerase II
illegitimate recombination
genome evolution.
In eukaryotic cell nuclei the genome is organized into large loops attached to the nuclear matrix. Rearrangements of the genome frequently occur via an illegitimate recombination between loop anchorage sites resulting in deletion or repositioning of DNA loops. The illegitimate recombination between loop anchorage sites is possibly mediated by topoisomerase II. Treatments stabilizing intermediate covalent complexes of topoisomerase II with DNA seem to increase the possibility of illegitimate recombination between loop anchorage regions. On the basis of these and some other observations we suggest that chromosomal DNA loops constitute basic units of the genome evolution, or, in other words, structural blocks of the eukaryotic genome.
The Nuclear Lamina: Molecular Organization and Interaction with Chromatin
285-293
10.1615/CritRevEukarGeneExpr.v9.i3-4.130
Michal
Goldberg
Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
Amnon
Harel
Department of Biology, University of California at San Diego, La Jolla, California, USA
Yosef
Gruenbaum
Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
nuclear envelope
nuclear lamins
lamina-associated proteins
nuclear assembly
chromatin.
The nuclear lamina is located between the inner nuclear membrane and the peripheral chromatin. It is composed mainly of nuclear lamins and lamina-associated proteins. The nuclear lamina is involved in nuclear organization, cell cycle regulation, and differentiation. As such, impairment in its architecture and/or function leads to genetic diseases and apoptosis. This article describes the molecular organization of the nuclear lamins, their assembly into filaments, their distribution within the nucleus, and the complex network of interactions between them and other proteins of the inner nuclear membrane. Recent findings unraveled evidence for specific interactions between proteins of the nuclear lamina and the chromatin. These include interactions between nuclear lamins and core histones, Lamina Associated Polypeptide 2 (LAP2), and the Barrier to Autointegration Factor (BAF) and interactions between lamin B receptor (LBR) and the chromodomain protein HP1. Taken together, these studies attribute a role for both the nuclear lamins and the lamina-associated proteins, LAP2 and LBR, in nuclear organization and nuclear assembly.
MARs of Antigen Receptor and Co-Receptor Genes
295-310
10.1615/CritRevEukarGeneExpr.v9.i3-4.140
Richard H.
Scheuermann
Departments of Pathology University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75235
William T.
Garrard
Departments of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75235
immunoglobulin and T-cell receptor genes
transcription
gene rearrangement
somatic hypermutation
DNA methylation
SAR
nuclear matrix
histone acetylation
chromatin remodeling.
MARs are cis-acting DNA sequences that function both negatively and positively in conjunction with transcriptional enhancers to regulate antigen receptor and co-receptor genes. Evidence exists that certain tissue-specific nuclear proteins are involved in this regulation, including SATB1, Bright, and Cux/CDP, possibly by modulating intranuclear gene location, histone acetylation, DNA methylation, and/or nucleosome positioning.
Origin and Roles of Nuclear Matrix Proteins. Specific Functions of the MAR-Binding Protein MeCP2/ARBP
311-318
10.1615/CritRevEukarGeneExpr.v9.i3-4.150
Wolf H.
Stratling
Institut fur Medizinische Biochemie und Molekularbiologie, Universitats-Krankenhaus Eppendorf, Martinistr. 52, D-20246 Hamburg, Germany
Fang
Yu
Institut fur Medizinische Biochemie und Molekularbiologie, Universitats-Krankenhaus Eppendorf, Martinistr. 52, D-20246 Hamburg, Germany
sites of transcription and RNA processing
hnRNP proteins
scaffold
transcriptional repression
satellite DNA.
HnRNP proteins are the major protein components of the nuclear matrix, and sites of nascent transcripts and RNA maturation are its main sources. The evidence for and the roles of functional and structural loops in interphase chromatin and metaphase chromosomes is discussed. Recent data suggest a specific role for the matrix attachment region (MAR)- and methyl-CpG-binding protein MeCP2/ARBP. This repressor protein binds to MARs and, through interaction with mSin3 A, recruits a corepressor complex containing histone deacetylases. This in turn is thought to generate a localized silenced chromatin structure. Transfection experiments are presented in support of this model.
Does NuMA Have a Scaffold Function in the Interphase Nucleus?
319-328
10.1615/CritRevEukarGeneExpr.v9.i3-4.160
Jens
Harborth
Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37070 Goettingen, Germany
Mary
Osborn
Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37070 Goettingen, Germany
nuclear matrix
multiarm oligomer
self-assembly.
We review the properties of NuMA, concentrating on a possible role for NuMA as a scaffold protein in the interphase nucleus. NuMA is a component of the nuclear matrix in interphase cells and translocates to the spindle poles in mitosis. NuMA has a secondary structure in which a long central rod domain that forms a double-stranded coiled coil is flanked by globular terminal domains. In vitro assembly experiments with bacterially expressed recombinant protein showed that NuMA seems not to form filaments, but instead builds multiarm oligomers by interaction of the C-terminal globular domains. Transient overexpression of NuMA in HeLa cells induced the formation of a three-dimensional lattice with a quasihexagonal organization that fills the nucleus. Use of mutant constructs showed that the lattice spacing depended on the length of the rod domain. Using a 12-arm oligomer as the structural unit, computer modeling can explain the observed nuclear lattices. The flexibility of the NuMA molecule as well as its dynamic capacity to form lattices is a hint that NuMA may play a structural role in the architecture of the normal interphase nucleus.
Nuclear Matrix and Protein Kinase CK2 Signaling
329-336
10.1615/CritRevEukarGeneExpr.v9.i3-4.170
Khalil
Ahmed
Cellular and Molecular Biochemistry Research Laboratory (151), Department of Laboratory Medicine and Pathology, University of Minnesota and the Department of Veterans Affairs Medical Center, Minneapolis, MN 55417
nuclear matrix
protein kinase CK2
signaling
nucleosome
growth stimuli
transcription.
The dynamic functional nature of the nuclear matrix dictates that it provide a locus for molecules involved in nuclear transduction of signals, such as those participating in cell growth control. Protein kinases are key elements in a variety of signaling mechanisms and certain of these enzymes have been shown to associate with the NM. Among these, the protein ser/thr kinase CK2 has attracted considerable attention because of its involvement in cell growth. NM appears to be a preferential locus for CK2, as evidenced from its rapid modulation in the NM in response to hormonal and growth factor signals. Differential regulation of CK2 is also noted in the transcriptionally active and inactive nucleosomes. A number of potential substrates for CK2 are localized to the NM. Likewise, distinct substrates for CK2 are noted in the transcriptionally active compared with inactive nucleosomes. The dynamics of phosphorylation of these substrates and that of the association of CK2 activity to these fractions suggests that CK2 may play a role in the functional activities of NM and provide a link between the NM and nucleosomes by serving as a factor in promoting the transition of inactive to active nucleosome.
The Role of the Nuclear Matrix in Cancer Chemotherapy
337-343
10.1615/CritRevEukarGeneExpr.v9.i3-4.180
H. J.
Muenchen
Department of Internal Medicine, University of Michigan Comprehensive Cancer Center, Ann Arbor, Ml 48109-0680
Kenneth J.
Pienta
Department of Internal Medicine, University of Michigan Comprehensive Cancer Center, Ann Arbor, Ml 48109-0680
alkylating agents
anticancer agents
antimetabolites
ionizing radiation
topoisomerase I
topoisomerase II.
The nuclear matrix is the site of many nuclear functions including transcription, replication, formation of chromatin loops, and control of DNA supercoiling. It contains various structural and functional components that represent targets for antineoplastic agents. Antimetabolites and topoisomerase II inhibitors interact specifically with matrix-associated enzymes, DNA primase, and DNA topoisomerase II, respectively. Alkylating agents and ionizing radiation interact with nuclear matrix proteins and matrix-associated DNA. Many nuclear functions, including multidrug resistance, and others which lead to cell death, have been shown to be compromised when these anticancer agents interact with the nuclear matrix.
Functional Links between Nuclear Structure, Gene Expression, DNA Replication, and Methylation
345-351
10.1615/CritRevEukarGeneExpr.v9.i3-4.190
Heinrich
Leonhardt
Max Delbruck Center for Molecular Medicine, 13125 Berlin, Germany
Hans-Peter
Rahn
Max Delbruck Center for Molecular Medicine, 13125 Berlin, Germany
M. Cristina
Cardoso
Max Delbruck Center for Molecular Medicine, 13125 Berlin, Germany
functional organization of the nucleus
targeting sequence
DNA methyltransferase
DNA ligase I
PCNA
chromatin structure.
Over the last decades it became clear that mammalian nuclei are highly organized. Nuclear processes like DNA replication and RNA metabolism take place in distinct subnuclear foci, which are enriched for enzymes involved in the corresponding biochemical reactions. This colocalization of functions with their respective factors is often referred to as functional organization of the nucleus. This organization is achieved by assembly of different enzymes and regulatory factors into high-molecular-weight complexes that are tethered to insoluble nuclear structures. Recently, several links between nuclear structure, gene expression, DNA replication, and methylation have been described that illustrate the interrelation of higher-order structures and nuclear functions. New insights into the functional organization of the nucleus and how it could explain the high precision and overall coordination of nuclear processes are discussed.
DNA Replication and Nuclear Organization: Prospects for a Soluble In Vitro System
353-361
10.1615/CritRevEukarGeneExpr.v9.i3-4.200
Daniela S.
Dimitrova
Department of Biochemistry and Molecular Biology, S.U.N.Y. Health Science Center, 750 East Adams Street, Syracuse, NY 13210
David M.
Gilbert
Department of Biochemistry and Molecular Biology, S.U.N.Y. Health Science Center, 750 East Adams Street, Syracuse, NY 13210
nucleus
chromosome domains
replication origins
replication timing
gene expression
development.
The role of nuclear structure in the replication of eukaryotic DNA has been the subject of debate for many decades. The recent demonstration that once-per-cell-cycle replication can take place in vitro without a nucleus, providing sufficiently high concentrations of replication factors are supplied, suggests that one role of the nucleus is to concentrate essential factors. This important finding has paved the way for the establishment of a purified biochemical system for replication of eukaryotic DNA. However, this soluble system, derived from Xenopus egg extracts, initiates replication within any DNA sequence and does not recapitulate the spatial and temporal regulation of DNA replication that is observed in most cells. In both Xenopus and Drosophila embryos, site-specific initiation of replication is not observed until after nuclei become transcriptionally active at the blastula stage of development. Furthermore, programmed changes in both the locations of origins and the time during S-phase at which sequences are replicated accompany key stages of metazoan development. Recent findings indicate that these changes correlate with changes in nuclear organization and that the spatial and temporal program for replication is established early in Gl-phase when nuclei are structurally and functionally reorganized after mitosis.
The Effects of Heat-Shock on Nuclear Matrix-Associated DNA-Replication Complexes
363-371
10.1615/CritRevEukarGeneExpr.v9.i3-4.210
Robert
VanderWaal
Mallinckrodt Institute of Radiology, Radiation Oncology Center, Section of Cancer Biology, Washington University School of Medicine, St. Louis, MO 63108
William D.
Wright
Mallinckrodt Institute of Radiology, Radiation Oncology Center, Section of Cancer Biology, Washington University School of Medicine, St. Louis, MO 63108
Joseph L. Roti
Roti
Mallinckrodt Institute of Radiology, Radiation Oncology Center, Section of Cancer Biology, Washington University School of Medicine, St. Louis, MO 63108
heat shock
nuclear matrix
DNA replication factories.
To better understand the role of the nuclear matrix in heat-induced cell killing, we have investigated the effects of heat shock on DNA replication complexes. Changes in protein extractability are observed following heat shock, including stabilization of which stabilize DNA replication complexes in association with the nuclear matrix. This situation is accompanied by differential delays in the progress and completion of DNA synthesis and the transition from type I to type II DNA replication patterns. Interestingly, prolonged delays in restarting DNA synthesis produced significant protection from heat-induced cell killing. These results show that nuclear matrix-associated DNA replication complexes may be important targets for heat-induced cell killing.
Rules to Remodel By: What Drives Nuclear Envelope Disassembly and Reassembly during Mitosis?
373-381
10.1615/CritRevEukarGeneExpr.v9.i3-4.220
Spyros D.
Georgatos
Dept. of Basic Sciences, University of Crete, School of Medicine, 71 110 Heraklion, Crete, Greece
Panayiotis A.
Theodoropoulos
Dept. of Basic Sciences, University of Crete, School of Medicine, 71 110 Heraklion, Crete, Greece
nuclear envelope
microtubules
cell-free assays
assembly
disassembly.
In higher eukaryotic cells the nuclear envelope is reversibly disassembled during mitosis. Under in vivo conditions this process occurs in a sequential, stepwise fashion and involves a variety of structural intermediates. Here we discuss the topological features of these intermediates and their transient interactions with chromatin and the cytoskeleton. As it becomes apparent, nuclear envelope disassembly and reassembly are regulated at multiple levels by modulating the affinity of protein-protein interactions, limiting the availability of structural subunits in different areas of the mitotic cytoplasm, and redirecting mechanical forces exerted by the microtubules.
SUBJECT INDEX
383-384
10.1615/CritRevEukarGeneExpr.v9.i3-4.230
AUTHOR INDEX
385
10.1615/CritRevEukarGeneExpr.v9.i3-4.240