scholarly journals Dynamic Nature of Cleavage Bodies and Their Spatial Relationship to DDX1 Bodies, Cajal Bodies, and Gems

2006 ◽  
Vol 17 (3) ◽  
pp. 1126-1140 ◽  
Author(s):  
Lei Li ◽  
Ken Roy ◽  
Sachin Katyal ◽  
Xuejun Sun ◽  
Stacey Bléoo ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Actin Polymerization ◽  
Spatial Relationship ◽  
S Phase ◽  
Nuclear Bodies ◽  
Cajal Bodies ◽  
Rna Transcription ◽  
Nuclear Structures ◽  
The Relationship ◽  
Striking Effect

DDX1 bodies, cleavage bodies, Cajal bodies (CBs), and gems are nuclear suborganelles that contain factors involved in RNA transcription and/or processing. Although all four nuclear bodies can exist as distinct entities, they often colocalize or overlap with each other. To better understand the relationship between these four nuclear bodies, we examined their spatial distribution as a function of the cell cycle. Here, we report that whereas DDX1 bodies, CBs and gems are present throughout interphase, CPSF-100-containing cleavage bodies are predominantly found during S and G2 phases, whereas CstF-64-containing cleavage bodies are primarily observed during S phase. All four nuclear bodies associate with each other during S phase, with cleavage bodies colocalizing with DDX1 bodies, and cleavage bodies/DDX1 bodies residing adjacent to gems and CBs. Although inhibitors of RNA transcription had no effect on DDX1 bodies or cleavage bodies, inhibitors of DNA replication resulted in loss of CstF-64-containing cleavage bodies. A striking effect on nuclear structures was observed with latrunculin B, an inhibitor of actin polymerization, resulting in the formation of needlelike nuclear spicules made up of CstF-64, CPSF-100, RNA, and RNA polymerase II. Our results suggest that cleavage body components are highly dynamic in nature.

scholarly journals RNA polymerase II transcription is concentrated outside replication domains throughout S-phase

1994 ◽  
Vol 107 (6) ◽  
pp. 1449-1456 ◽  
Author(s):  
D.G. Wansink ◽  
E.E. Manders ◽  
I. van der Kraan ◽  
J.A. Aten ◽  
R. van Driel ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Spatial Relationship ◽  
S Phase ◽  
Double Labelling ◽  
Confocal Immunofluorescence Microscopy ◽  
Nuclear Domain ◽  
Confocal Immunofluorescence ◽  
Nuclear Domains ◽  
Transcription And Replication

Transcription and replication are, like many other nuclear functions and components, concentrated in nuclear domains. Transcription domains and replication domains may play an important role in the coordination of gene expression and gene duplication in S-phase. We have investigated the spatial relationship between transcription and replication in S-phase nuclei after fluorescent labelling of nascent RNA and nascent DNA, using confocal immunofluorescence microscopy. Permeabilized human bladder carcinoma cells were labelled with 5-bromouridine 5′-triphosphate and digoxigenin-11-deoxyuridine 5′-triphosphate to visualize sites of RNA synthesis and DNA synthesis, respectively. Transcription by RNA polymerase II was localized in several hundreds of domains scattered throughout the nucleoplasm in all stages of S-phase. This distribution resembled that of nascent DNA in early S-phase. In contrast, replication patterns in late S-phase consisted of fewer, larger replication domains. In double-labelling experiments we found that transcription domains did not colocalize with replication domains in late S-phase nuclei. This is in agreement with the notion that late replicating DNA is generally not actively transcribed. Also in early S-phase nuclei, transcription domains and replication domains did not colocalize. We conclude that nuclear domains exist, large enough to be resolved by light microscopy, that are characterized by a high activity of either transcription or replication, but never both at the same time. This probably means that as soon as the DNA in a nuclear domain is being replicated, transcription of that DNA essentially stops until replication in the entire domain is completed.

The roles of nucleolar structure and function in the subcellular location of the HIV-1 Rev protein

1995 ◽  
Vol 108 (8) ◽  
pp. 2811-2823 ◽  
Author(s):  
M. Dundr ◽  
G.H. Leno ◽  
M.L. Hammarskjold ◽  
D. Rekosh ◽  
C. Helga-Maria ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Critical Role ◽  
Regulation Of Expression ◽  
Rna Transcription ◽  
Nucleolar Structure ◽  
Class 1 ◽  
Protein B23 ◽  
Hiv 1 ◽  
Rev Protein

The human immunodeficiency virus 1 (HIV-1) Rev transactivator protein plays a critical role in the regulation of expression of structural proteins by controlling the pathway of mRNA transport. The Rev protein is located predominantly in the nucleoli of HIV-1 infected or Rev-expressing cells. Previous studies demonstrated that the Rev protein forms a specific complex in vitro with protein B23 which is suggested to be a nucleolar receptor and/or carrier for the Rev protein. To study the role of the nucleolus and nucleolar proteins in Rev function, transfected COS-7 or transformed CMT3 cells expressing the Rev protein were examined for subcellular locations of Rev and other proteins using indirect immunofluorescence and immunoelectron microscopy. One day after transfection the Rev protein was found in most cells only in the nucleolar dense fibrillar and granular components where it colocalized with protein B23. These were designated class 1 cells. In a second class of cells Rev and B23 accumulated in the nucleoplasm as well as in nucleoli. Treatment of class 1 cells with actinomycin D (AMD) under conditions that blocked only RNA polymerase I transcription caused Rev to completely redistribute from nucleoli to the cytoplasm. Simultaneously, protein B23 was partially released from nucleoli, mostly into the nucleoplasm, with detectable amounts in the cytoplasm. In cells recovering from AMD treatment in the presence of cycloheximide Rev and B23 showed coincident relocation to nucleoli. Class 2 cells were resistant to AMD-induced Rev redistribution. Selective inhibition of RNA polymerase II transcription by alpha-amanitin or by DRB did not cause Rev to be released into the cytoplasm suggesting that active preribosomal RNA transcription is required for the nucleolar location of Rev. However, treatment with either of the latter two drugs at higher doses and for longer times caused partial disruption of nucleoli accompanied by translocation of the Rev protein to the cytoplasm. These results suggest that the nucleolar location of Rev depends on continuous preribosomal RNA transcription and a substantially intact nucleolar structure.

scholarly journals Units of chromosome replication and packing

1983 ◽  
Vol 64 (1) ◽  
pp. 179-193
Author(s):  
A.M. Mullinger ◽  
R.T. Johnson
Keyword(s):  
Spatial Distribution ◽  
Light Microscope ◽  
Individual Cell ◽  
S Phase ◽  
Scanning Electron Micrographs ◽  
Metaphase Chromosomes ◽  
Impregnation Technique ◽  
Osmium Impregnation ◽  
The Relationship ◽  
Scanning Electron

Fusion between mitotic and S-phase cells induces the formation of prematurely condensed chromosomes (PCC) in the interphase partner. Viewed in the light microscope, S-phase PCC derived from the Indian muntjac appear to be fragmented and heterogeneous. In scanning electron micrographs prepared by an osmium impregnation technique, which avoids the need to sputter-coat the specimen, the S-phase fragments derived from an individual cell are resolved into about 1000 fibre aggregates, together with more dispersed fibres. Aggregates are roughly spherical and vary in diameter between about 0.25 and 1.6 micron. The spatial distribution of the aggregates shows some order: chains of single aggregates and, less commonly, duplicated chains occur. Regions of the PCC where the fibres are more dispersed are considered to be likely candidates for sites of replication at the time of fusion. The relationship between the condensed aggregate structure of the S-phase PCC and replication clusters is discussed, and also the assembly of aggregates to form metaphase chromosomes.

scholarly journals Nuclear distribution of transcription factors in relation to sites of transcription and RNA polymerase II

1997 ◽  
Vol 110 (15) ◽  
pp. 1781-1791 ◽  
Author(s):  
M.A. Grande ◽  
I. van der Kraan ◽  
L. de Jong ◽  
R. van Driel
Keyword(s):  
Transcription Factors ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Glucocorticoid Receptors ◽  
Cultured Cells ◽  
Spatial Relationship ◽  
Immunofluorescence Labelling ◽  
Transcription Sites ◽  
Nuclear Domains

We have investigated the spatial relationship between sites containing newly synthesized RNA and domains containing proteins involved in transcription, such as RNA polymerase II and the transcription factors TFIIH, Oct1, BRG1, E2F-1 and glucocorticoid receptors, using dual immunofluorescence labelling followed by confocal microscopy on cultured cells. As expected, a high degree of colocalisation between the RNA polymerase II and sites containing newly synthesised RNA was observed. Like the newly synthesised RNA and the RNA polymerase II, we found that all the transcription factors that we studied are distributed more or less homogeneously throughout the nucleoplasm, occupying numerous small domains. In addition to these small domains, TFIIH was found concentrated in coiled bodies and Oct1 in a single large domain of about 1.5 microm in 30% of the cells in an asynchronous HeLa cell culture. Remarkably, we found little or no relationship between the spatial distribution of the glucocorticoid receptor, Oct1 and E2F-1 on the one hand and RNA polymerase II and transcription sites on the other hand. In contrast, a significant but incomplete overlap was observed between the spatial distributions of transcription sites and BRG1 and TFIIH. These results indicate that many of the transcription factor-rich nuclear domains are not actively involved in transcription. They may represent incomplete transcription initiation complexes, inhibitory complexes, or storage sites.

The relationship between cell proliferation and the transcription of the nuclear oncogenes c-myc, c-myb and c-ets-1 during feather morphogenesis in the chick embryo

Development ◽  
1991 ◽  
Vol 111 (3) ◽  
pp. 699-713 ◽  
Author(s):  
X. Desbiens ◽  
C. Queva ◽  
T. Jaffredo ◽  
D. Stehelin ◽  
B. Vandenbunder
Keyword(s):  
Cell Proliferation ◽  
Endothelial Cells ◽  
Spatial Distribution ◽  
Chick Embryo ◽  
Expression Patterns ◽  
S Phase ◽  
Skin Morphogenesis ◽  
Dermal Cells ◽  
The Relationship

We have described the expression of three nuclear protooncogenes, c-myc, c-myb and c-ets-1 during feather morphogenesis in the chick embryo. In parallel with the expression patterns obtained by in situ hybridization, we have mapped the spatial distribution of S-phase cells by monitoring the incorporation of 5-bromodeoxyuridine. We do not detect c-myc or c-myb transcripts during the early stages when S-phase cells are scattered in the dermis and in the epidermis. Rather c-ets-1 transcripts are abundant in the dermal cells which divide and accumulate under the uniform epidermis. At the onset of the formation of the feather bud, cells within each rudiment cease DNA replicative activities and c-myc transcripts are detected both in the epidermis and in the underlying dermis. This expression precedes the reentry into the S phase. The transcription of c-myb, which has been previously tightly linked to hemopoietic cells is also detected in the developing skin. This expression is essentially located in proliferating epidermal cells on and after the beginning of feather outgrowth. As feather outgrowth proceeds, the distribution of c-myc and c-myb transcripts is restricted to the highly proliferating epidermis. In contrast c-ets-1 transcripts are never detected in the epidermis. During the later stages of skin morphogenesis, the transcription of c-ets-1 is restricted to the endothelial cells of blood vessels, as previously described. We suggest that the differential expression of these nuclear oncogenes reflects the activation of different mitotic controlling pathways during the development of the skin.

Replication factories and nuclear bodies: the ultrastructural characterization of replication sites during the cell cycle

1994 ◽  
Vol 107 (8) ◽  
pp. 2191-2202 ◽  
Author(s):  
P. Hozak ◽  
D.A. Jackson ◽  
P.R. Cook
Keyword(s):  
Electron Microscopy ◽  
Light And Electron Microscopy ◽  
S Phase ◽  
Nuclear Bodies ◽  
Nuclear Antigen ◽  
Thin Sections ◽  
Permeabilized Cells ◽  
Ultrastructural Characterization ◽  
Replication Sites ◽  
Proliferating Cell

Sites of replication in synchronized HeLa cells were visualized by light and electron microscopy; cells were permeabilized and incubated with biotin-16-dUTP, and incorporation sites were immunolabelled. Electron microscopy of thick resinless sections from which approximately 90% chromatin had been removed showed that most DNA synthesis occurs in specific dense structures (replication factories) attached to a diffuse nucleoskeleton. These factories appear at the end of G1-phase and quickly become active; as S-phase progresses, they increase in size and decrease in number like sites of incorporation seen by light microscopy. Electron microscopy of conventional thin sections proved that these factories are a subset of nuclear bodies; they changed in the same characteristic way and contained DNA polymerase alpha and proliferating cell nuclear antigen. As replication factories can be observed and labelled in non-permeabilized cells, they cannot be aggregation artifacts. Some replication occurs outside factories at discrete sites on the diffuse skeleton; it becomes significant by mid S-phase and later becomes concentrated beneath the lamina.

Analyzing Resilience in Local Labor Market Areas: A Spatial Analysis for the Case of Italy

2019 ◽  
Vol 65 (3) ◽  
pp. 189-208
Author(s):  
Barbara Martini ◽  
Marco Platania
Keyword(s):  
Labor Market ◽  
Spatial Analysis ◽  
Spatial Data ◽  
Spatial Relationship ◽  
Spatial Data Analysis ◽  
Market Area ◽  
Observation Unit ◽  
Local Labor Market ◽  
Market Areas ◽  
The Relationship

Abstract The aim of the paper is to analyse if and in which way specialization, geographical localization and spill-over effects affect resilience. The research is carried out using LLMAs (Local Labor Market Areas) as observational unit and spatial data analysis techniques (Anselin 1999, LeSage & Pace, 2009) in Italy. Resilience literature focalized its attention on regions. Despite this, there is no general agreement regarding the most appropriate observation unit. Our aim is not only to investigate the relationship between specialization and resilience at smaller scale using the LLMAs as observation unit but also to explore the spatial relationship among them. Results highlight a strong spatial correlation among LLMAs. As consequence resilience is not only influenced by specialization but also by geographical localization through spill-over effects. JEL Classifications: R10, R12, C23, C33 Spatial analysis; Resilience; Labor Market Area; Italy

scholarly journals Examining the Relationship between Urban Land Expansion and Economic Linkage Using Coupling Analysis: A Case Study of the Yangtze River Economic Belt, China

2020 ◽  
Vol 12 (3) ◽  
pp. 1227 ◽  
Author(s):  
Bowen Chen ◽  
Changyan Wu ◽  
Xianjin Huang ◽  
Xuefeng Yang
Keyword(s):  
Land Use ◽  
Yangtze River ◽  
Spatial Relationship ◽  
Urban Land ◽  
Sustainable Land Use ◽  
Policy Implications ◽  
The Yangtze River ◽  
Negative Effects ◽  
Urban Land Expansion ◽  
The Relationship

Urban land expansion (ULE) has caused negative effects as a result of urbanization and industrialization in China in the past few decades. Strengthening economic linkage and the cooperation among regions has great implications for effectively controlling disorderly ULE and achieving sustainable and intensive land use. Previous research has rarely investigated the relationship between ULE and economic linkage. Therefore, this study analyzes the spatial patterns of ULE and economic linkage in the Yangtze River Economic Belt (YREB) of China via social network analysis and a gravity model. Moreover, the spatial relationship and coupling level between ULE and economic linkage are investigated by building a bivariate spatial autocorrelation model and a coupling coordination degree model, respectively. The results indicate that the YREB experienced rapid ULE, and the area increased from 4.24 × 104 km2 in 1990 to 7.89 × 104 km2 in 2015. The cities that experience rapid ULE have gradually transferred from the east to the west of the YREB. In addition, the economic linkage in eastern cities is evidently higher than that of western cities. Our bivariate spatial model further proves that there are strong negative spatial correlation characteristics between ULE and economic linkage. This indicates that the higher the economic linkage, the lower the speed of ULE. Moreover, the coupling coordination between ULE and economic linkage show that the overall coupling stage changed from an antagonistic stage to a running-in stage. However, the coupling coordination in the YREB presented significant spatial heterogeneity, and most cities in urban agglomeration had a relationship between ULE and economic linkage that was barely balanced, slightly unbalanced, or seriously unbalanced. By considering the limitations and obstacles of current initiatives, suggestions and policy implications for sustainable land use at large regional scales are suggested.

scholarly journals Regulation of Initiation of S Phase, Replication Checkpoint Signaling, and Maintenance of Mitotic Chromosome Structures during S Phase by Hsk1 Kinase in the Fission Yeast

2001 ◽  
Vol 12 (5) ◽  
pp. 1257-1274 ◽  
Author(s):  
Tadayuki Takeda ◽  
Keiko Ogino ◽  
Kazuo Tatebayashi ◽  
Hideo Ikeda ◽  
Ken-ichi Arai ◽  
...  
Keyword(s):  
Dna Replication ◽  
Synthetic Lethality ◽  
S Phase ◽  
Regulatory Subunit ◽  
Temperature Sensitive ◽  
Origin Firing ◽  
Replication Checkpoint ◽  
Checkpoint Signaling ◽  
Checkpoint Pathway ◽  
Nuclear Structures

Hsk1, Saccharomyces cerevisiae Cdc7-related kinase in Shizosaccharomyces pombe, is required for G1/S transition and its kinase activity is controlled by the regulatory subunit Dfp1/Him1. Analyses of a newly isolated temperature-sensitive mutant, hsk1-89, reveal that Hsk1 plays crucial roles in DNA replication checkpoint signaling and maintenance of proper chromatin structures during mitotic S phase through regulating the functions of Rad3 (ATM)-Cds1 and Rad21 (cohesin), respectively, in addition to expected essential roles for initiation of mitotic DNA replication through phosphorylating Cdc19 (Mcm2). Checkpoint defect inhsk1-89 is indicated by accumulation ofcut cells at 30°C. hsk1-89 displays synthetic lethality in combination with rad3 deletion, indicating that survival of hsk1-89 depends on Rad3-dependent checkpoint pathway. Cds1 kinase activation, which normally occurs in response to early S phase arrest by nucleotide deprivation, is largely impaired in hsk1-89. Furthermore, Cds1-dependent hyperphosphorylation of Dfp1 in response to hydroxyurea arrest is eliminated in hsk1-89, suggesting that sufficient activation of Hsk1-Dfp1 kinase is required for S phase entry and replication checkpoint signaling.hsk1-89 displays apparent defect in mitosis at 37°C leading to accumulation of cells with near 2C DNA content and with aberrant nuclear structures. These phenotypes are similar to those ofrad21-K1 and are significantly enhanced in ahsk1-89 rad21-K1 double mutant. Consistent with essential roles of Rad21 as a component for the cohesin complex, sister chromatid cohesion is partially impaired in hsk1-89, suggesting a possibility that infrequent origin firing of the mutant may affect the cohesin functions during S phase.

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