scholarly journals Modeling diffusional transport in the interphase cell nucleus

2007 ◽  
Vol 127 (4) ◽  
pp. 045102 ◽  
Author(s):  
Annika Wedemeier ◽  
Holger Merlitz ◽  
Chen-Xu Wu ◽  
Jörg Langowski
Keyword(s):  
Cell Nucleus ◽  
Interphase Cell

scholarly journals Mapping replicational sites in the eucaryotic cell nucleus.

1989 ◽  
Vol 108 (1) ◽  
pp. 1-11 ◽  
Author(s):  
H Nakayasu ◽  
R Berezney
Keyword(s):  
Cell Nucleus ◽  
Nuclear Matrix ◽  
Nuclear Dna ◽  
Fluorescent Microscopy ◽  
Mouse Fibroblast ◽  
Type I ◽  
Interphase Cell ◽  
Permeabilized Cells ◽  
Replication Sites

We have used fluorescent microscopy to map DNA replication sites in the interphase cell nucleus after incorporation of biotinylated dUTP into permeabilized PtK-1 kangaroo kidney or 3T3 mouse fibroblast cells. Discrete replication granules were found distributed throughout the nuclear interior and along the periphery. Three distinct patterns of replication sites in relationship to chromatin domains in the cell nucleus and the period of S phase were detected and termed type I (early to mid S), type II (mid to late S) and type III (late S). Similar patterns were seen with in vivo replicated DNA using antibodies to 5-bromodeoxyuridine. Extraction of the permeabilized cells with DNase I and 0.2 M ammonium sulfate revealed a striking maintenance of these replication granules and their distinct intranuclear arrangements with the remaining nuclear matrix structures despite the removal of greater than 90% of the total nuclear DNA. The in situ prepared nuclear matrix structures also incorporated biotinylated dUTP into replication granules that were indistinguishable from those detected within the intact nucleus.

The ultrastructural study of the interphase cell nucleus of Lacandonia schismatica (Lacandoniaceae: Triuridales) reveals a non-typical extranucleolar particle

1992 ◽  
Vol 75 (2) ◽  
pp. 101-110 ◽  
Author(s):  
Luis Felipe Jiménez-Garcia ◽  
Lourdes Teresa Agredano-Moreno ◽  
Maria Lourdes Segura-Valdez ◽  
Olga Margarita Echeverria ◽  
Esteban Martinez ◽  
...  
Keyword(s):  
Cell Nucleus ◽  
Ultrastructural Study ◽  
Interphase Cell

scholarly journals Computer methods of analysis of chromosome contacts in the cell nucleus based on sequencing technology data

2017 ◽  
Vol 63 (5) ◽  
pp. 418-422 ◽  
Author(s):  
Y.L. Orlov ◽  
O. Thierry ◽  
A.G. Bogomolov ◽  
A.V. Tsukanov ◽  
E.V. Kulakova ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Transcription ◽  
Cell Nucleus ◽  
Binding Sites ◽  
Dimensional Space ◽  
Genome Structure ◽  
Three Dimensional ◽  
Gene Location ◽  
Interphase Cell ◽  
Eukaryotic Genes

The study spatial chromosome structure and chromosome folding in the interphase cell nucleus is an important challenge of world science. Detection of eukaryotic genome regions that physically interact with each other could be done by modern sequencing technologies. A basic method of chromosome folding by total sequencing of contacting DNA fragments is HI-C. Long-range chromosomal interactions play an important role in gene transcription and regulation. The study of chromosome interactions, 3D (three-dimensional) genome structure and its effect on gene transcription allows revealing fundamental biological processes from a viewpoint of structural regulation and are important for cancer research. The technique of chromatin immunoprecipitation and subsequent sequencing (ChIP-seq) make possible to determine binding sites of transcription factors that regulate expression of eukaryotic genes; genome transcription factors binding maps have been. The ChIA-PET technology allows exploring not only target protein binding sites, but also pairs of such sites on proximally located and interacting with each other chromosomes co-located in three-dimensional space of the cell nucleus. Here we discuss the principles of the construction of genomic maps and matrices of chromosome contacts according to ChIA-PET and Hi-C data that capture the chromosome conformation and overview existing software for 3D genome analysis including in house programs of gene location analysis in topological domains.

ULTRASTRUCTURAL LOCALIZATION OF PROTEINS AND NUCLEOPROTEINS IN THE INTERPHASE NUCLEUS

1972 ◽  
Vol 71 (2_Suppla) ◽  
pp. S11-S34 ◽  
Author(s):  
Michel Bouteille
Keyword(s):  
Present State ◽  
Cell Nucleus ◽  
Interphase Nucleus ◽  
Cell Activity ◽  
Ultrastructural Localization ◽  
Nuclear Inclusions ◽  
Interphase Cell

ABSTRACT A review is given on the present state of knowledge of the location of diffuse and »figured« proteins, and ribonucleoproteins in the interphase cell nucleus. Attention is focused on structures of still obscure function, and on various types of nuclear inclusions which do not seem to be constant, but are presumably related to the degree of cell activity, whether physiologic or pathologic.

Organization of transcription and pre-mRNA splicing within the mammalian cell nucleus

1995 ◽  
Vol 53 ◽  
pp. 768-769
Author(s):  
D.L. Spector ◽  
S. Huang ◽  
S. Kaurin
Keyword(s):  
Rna Polymerase Ii ◽  
Cell Nucleus ◽  
Functional Organization ◽  
Mrna Splicing ◽  
Splicing Factors ◽  
Interchromatin Granule Clusters ◽  
Interchromatin Granule ◽  
Nuclear Regions ◽  
Relationship Of ◽  
Perichromatin Fibrils

We have been interested in the organization of RNA polymerase II transcription and pre-mRNA splicing within the cell nucleus. Several models have been proposed for the functional organization of RNA within the eukaryotic nucleus and for the relationship of this organization to the distribution of pre-mRNA splicing factors. One model suggests that RNAs which must be spliced are capable of recruiting splicing factors to the sites of transcription from storage and/or reassembly sites. When one examines the organization of splicing factors in the nucleus in comparison to the sites of chromatin it is clear that splicing factors are not localized in coincidence with heterochromatin (Fig. 1). Instead, they are distributed in a speckled pattern which is composed of both perichromatin fibrils and interchromatin granule clusters. The perichromatin fibrils are distributed on the periphery of heterochromatin and on the periphery of interchromatin granule clusters as well as being diffusely distributed throughout the nucleoplasm. These nuclear regions have been previously shown to represent initial sites of incorporation of 3H-uridine.

Immunolocalization of nuclear antigens in cryofixed cells which have been prepared by molecular distillation drying or freeze-substitution

1990 ◽  
Vol 48 (3) ◽  
pp. 898-899
Author(s):  
David L. Spector ◽  
Robert J. Derby
Keyword(s):  
Cell Nucleus ◽  
Molecular Distillation ◽  
Functional Organization ◽  
Freeze Substitution ◽  
3 Dimensional ◽  
Small Nuclear Ribonucleoprotein ◽  
Nuclear Antigens ◽  
Dimensional Reconstruction ◽  
Nuclear Regions ◽  
Immunoperoxidase Labeling

Studies in our laboratory are involved in evaluating the structural and functional organization of the mammalian cell nucleus. Since several major classes (U1, U2, U4/U6, U5) of small nuclear ribonucleoprotein particles (snRNPs) play a crucial role in the processing of pre-mRNA molecules, we have been interested in the localization of these particles within the cell nucleus. Using pre-embedding immunoperoxidase labeling combined with 3-dimensional reconstruction, we have recently shown that nuclear regions enriched in snRNPs form a reticular network within the nucleoplasm which extends between the nucleolar surface and the nuclear envelope. In the present study we were inte rested in extending these nuclear localizations using cell preparation techniques which avoid slow penetration of fixatives, chemical crosslinking of potential antigens and solvent extraction. CHOC 400 cells were cryofixed using a CF 100 ultra rapid cooling device (LifeCell Corp.). After cryofixation cells were molecular distillation dried, vapor osmicated, in filtra ted in 100% Spurr resin in vacuo and polymerized in molds a t 60°C. Using this procedure we were able to evaluate the distribution of snRNPs in resin embedded cells which had not been chemically fixed, incubated in cryoprotectants or extracted with solvents.

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