Polymer physics, scaling and heterogeneity in the spatial organisation of chromosomes in the cell nucleus

Soft Matter ◽  
2013 ◽  
Vol 9 (36) ◽  
pp. 8631 ◽  
Author(s):  
M. Barbieri ◽  
A. Scialdone ◽  
A. Gamba ◽  
A. Pombo ◽  
M. Nicodemi
Keyword(s):  
Cell Nucleus ◽  
Polymer Physics ◽  
Spatial Organisation

scholarly journals Nonequilibrium Theory of Epigenomic Microphase Separation in the Cell Nucleus

2019 ◽  
Author(s):  
Davide Michieletto ◽  
Davide Colì ◽  
Davide Marenduzzo ◽  
Enzo Orlandini
Keyword(s):  
Cell Nucleus ◽  
Qualitative Agreement ◽  
Microphase Separation ◽  
Epigenetic Mark ◽  
Genome Organisation ◽  
Equilibrium Models ◽  
Spatial Organisation ◽  
Equilibrium Processes ◽  
Nonequilibrium Theory ◽  
Physical Principles

Understanding the spatial organisation of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical – or epigenetic – marks that are deposited along the genome are thought to play an important, yet poorly understood, role in determining genome organisation and cell identity. The physical principles underlying the interplay between epigenetic dynamics and genome folding remain elusive. Here we propose and study a theory that assumes a coupling between epigenetic mark and genome densities, and which can be applied at the scale of the whole nucleus. We show that equilibrium models are not compatible with experiments and a qualitative agreement is recovered by accounting for non-equilibrium processes which can stabilise microphase separated epigenomic domains. We finally discuss the potential biophysical origin of these terms.

scholarly journals Models of polymer physics for the architecture of the cell nucleus

2018 ◽  
Vol 11 (4) ◽  
pp. e1444 ◽  
Author(s):  
Andrea Esposito ◽  
Carlo Annunziatella ◽  
Simona Bianco ◽  
Andrea M. Chiariello ◽  
Luca Fiorillo ◽  
...  
Keyword(s):  
Cell Nucleus ◽  
Polymer Physics

A model of the large-scale organization of chromatin

2013 ◽  
Vol 41 (2) ◽  
pp. 508-512 ◽  
Author(s):  
Mariano Barbieri ◽  
Mita Chotalia ◽  
James Fraser ◽  
Liron-Mark Lavitas ◽  
Josée Dostie ◽  
...  
Keyword(s):  
Experimental Data ◽  
Present Article ◽  
Cell Nucleus ◽  
Large Scale ◽  
Spatial Organization ◽  
Molecular Mechanisms ◽  
Three Dimensional ◽  
Polymer Physics ◽  
Self Organization ◽  
Dna Binding Factors

In the cell nucleus, chromosomes have a complex spatial organization, spanning several length scales, which serves vital functional purposes. It is unknown, however, how their three-dimensional architecture is orchestrated. In the present article, we review the application of a model based on classical polymer physics, the strings and binders switch model, to explain the molecular mechanisms of chromatin self-organization. We explore the scenario where chromatin architecture is shaped and regulated by the interactions of chromosomes with diffusing DNA-binding factors via thermodynamics mechanisms and compare it with available experimental data.

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.

Polymer Physics

2009 ◽  
Author(s):  
Fumihiko Tanaka
Keyword(s):  
Polymer Physics

Super-Resolution Microscopy in Studying the Structure and Function of the Cell Nucleus

Acta Naturae ◽  
2017 ◽  
Vol 9 (4) ◽  
pp. 42-51
Author(s):  
S. S. Ryabichko ◽  
◽  
A. N. Ibragimov ◽  
L. A. Lebedeva ◽  
E. N. Kozlov ◽  
...  
Keyword(s):  
Cell Nucleus ◽  
Super Resolution ◽  
Structure And Function ◽  
And Function ◽  
Super Resolution Microscopy

Expression of Ki-67 has Correlation with the Degree and Size of Endometriosis Cysts

2015 ◽  
Vol 1 (1) ◽  
Author(s):  
Ruswana Anwar ◽  
Muhammad Alif ◽  
Adhi Pribadi
Keyword(s):  
Laparoscopic Surgery ◽  
Cell Nucleus ◽  
Significant Relationship ◽  
Strong Relationship ◽  
Cyst Size ◽  
Ki 67 ◽  
Cut Method ◽  
Close Relationship ◽  
Dividing Cells ◽  
Aggressive Tumor

Endometriosis is one of the most common gynecological problem. Cells resulted in chronic inflammation and progressive, proliferative, invasive and even infiltrating an area that resembles the character of the malignancy. Ki-67 is an antigen on the cell nucleus that is found only in actively dividing cells. Expression of Ki-67 are associated with an aggressive tumor and metastasis. This study aims to determine the level of Ki-67 expression correlation with stage and size of the endometriosis cyst. Methods research is observational analytic cross cut method on 56 paraffin blocks of patients who have been diagnosed with endometriosis and had performed a laparotomy or laparoscopic surgery in Dr Hasan Sadikin Hospital. The results showed a significant relationship between the level of expression of Ki-67 with endometriosis cyst size (p <0.001) with a fairly strong relationship (0.55) according to statistics based on criteria Guilford. Moreover the results also showed a significant relationship between the level of expression of Ki-67 with endometriosis stage (p <0.001) with a fairly close relationship (0.564) according to statistics based on criteria Guilford. It can be concluded that the expression of Ki-67 associated with cyst size and stage of endometriosis. Keywords: Ki-67, endometriosis stage, endometriosis cyst

Sign in / Sign up

Export Citation Format

Share Document