Polymer models for the mechanisms of chromatin 3D folding: review and perspective

2020 ◽  
Vol 22 (36) ◽  
pp. 20189-20201
Author(s):  
Rui Zhou ◽  
Yi Qin Gao
Keyword(s):  
Physical Models ◽  
Interphase Chromatin ◽  
Polymer Models ◽  
Chromatin Folding

In this perspective paper, classical physical models for mammalian interphase chromatin folding are reviewed.

scholarly journals Cross-linking of DNA Segments by Histone H1 Explains H1 Associated Phenomena of Chromatin Folding

2019 ◽  
Vol 1 (2) ◽  
pp. 6-10
Author(s):  
Qazi Hamid ◽  
Ojaswee Dahal ◽  
Osama Dasti ◽  
Ziledar Ali
Keyword(s):  
Molecular Mechanism ◽  
Salt Bridge ◽  
Histone H1 ◽  
Cross Linking ◽  
Cooperative Binding ◽  
Interphase Chromatin ◽  
Phosphodiester Bonds ◽  
Arginine Residues ◽  
Chromatin Folding ◽  
Positively Charged

Molecular mechanism for the cooperative and non-cooperative binding of histone H1 to DNA, its rearrangement and exchange between chromatin fibers and its role in the folding of interphase chromatin are proposed in this communication. The mechanism of H1 binding to DNA described here is simple and is based on two established facts; (i) histone H1 can crosslink two DNA segments through salt bridge formation between its positively charged lysine and arginine residues and the negatively charged phosphodiester bonds of the DNA segments, (ii) cations reduce the negative charges on DNA segments and thus decrease the force of repulsion between them.

Direct measurement of chromatin diffusion and constraint in living cells using a gfp-lac repressor fusion protein

1996 ◽  
Vol 54 ◽  
pp. 740-741
Author(s):  
W.F. Marshall ◽  
A.F. Straight ◽  
A. Murray ◽  
J.C. Fung ◽  
J. Marko ◽  
...  
Keyword(s):  
Chromatin Condensation ◽  
Nuclear Architecture ◽  
Experimental Parameter ◽  
Lac Repressor ◽  
Physical Models ◽  
Theoretical Research ◽  
Fundamental Aspect ◽  
Interphase Chromatin ◽  
Homolog Pairing ◽  
Pairing Site

The polymer dynamics of interphase chromatin is at present a poorly understood aspect of nuclear organization, but one with profound consequences on events within the nucleus. The rates of many important processes, such as meiotic homolog pairing, site-specific recombination, and chromatin condensation, all involve the motion of chromatin within the nucleus. How fast can such rearrangements occur? Because interphase chromatin is likely to behave as a tangle of random-walk polymers, there is likely to be a substantial hindrance to diffusion. Therefore, the rate at which a given site on a chromosome can diffuse within the nucleus may limit the rate at which events requiring chromatin motion can occur. Furthermore, the polymer physics of interphase chromatin is an interesting line of theoretical research in its own right, and knowledge of diffusion rates is an important experimental parameter to consider when evaluating physical models. Finally, a fundamental aspect of nuclear architecture is the extent to which chromatin is anchored to a nuclear skeleton. Such matrix attachments would result in constrained diffusion, which can be detected by analysis of chromatin motion.

scholarly journals Condensin II inactivation in interphase does not affect chromatin folding or gene expression

2018 ◽  
Author(s):  
Nezar Abdennur ◽  
Wibke Schwarzer ◽  
Aleksandra Pekowska ◽  
Indra Alon Shaltiel ◽  
Wolfgang Huber ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromosome Organization ◽  
Domain Formation ◽  
Interphase Chromatin ◽  
Control Of Gene Expression ◽  
Chromosomal Architecture ◽  
Chromatin Folding ◽  
Mouse Hepatocytes ◽  
Or Gene ◽  
And Control

SummaryCondensin complexes have been proposed to play a prominent role in interphase chromatin organization and control of gene expression. Here, we report that the deletion of the central condensin II kleisin subunit Ncaph2 in differentiated mouse hepatocytes does not lead to significant changes in chromosome organization or in gene expression. Both observations challenge current views that implicate condensin in interphase chromosomal domain formation and in enhancer-promoter interactions. Instead, we suggest that the previously reported effects of condensin perturbation may result from their structural role during mitosis, which might indirectly impact the re-establishment of interphase chromosomal architecture after cell division.

scholarly journals Polymer physics of nuclear organization and function

2016 ◽  
Author(s):  
A. Amitai ◽  
D. Holcman
Keyword(s):  
Nuclear Organization ◽  
Gene Activation ◽  
Physical Models ◽  
Biophysical Parameters ◽  
Theoretical Approaches ◽  
Search Mechanism ◽  
Polymer Models ◽  
Or Gene ◽  
Microscopy Data ◽  
And Function

AbstractWe review here recent progress to link the nuclear organization to its function, based on elementary physical processes such as diffusion, polymer dynamics of DNA, chromatin and the search mechanism for a small target by double-stranded DNA (dsDNA) break. These physical models and their analysis make it possible to compute critical rates involved in cell reorganization timing, which depends on many parameters. In the framework of polymer models, various empirical observations are interpreted as anomalous diffusion of chromatin at various time scales. The reviewed theoretical approaches offer a framework for extracting features, biophysical parameters, predictions, and so on, based on a large variety of experimental data, such as chromosomal capture data, single particle trajectories, and more. Combining theoretical approaches with live cell microscopy data should unveil some of the still unexplained behavior of the nucleus in carrying out some of its key function involved in survival, DNA repair or gene activation.

scholarly journals Chromatin folding - from biology to polymer models and back

2011 ◽  
Vol 124 (6) ◽  
pp. 839-845 ◽  
Author(s):  
M. Tark-Dame ◽  
R. van Driel ◽  
D. W. Heermann
Keyword(s):  
Polymer Models ◽  
Chromatin Folding

Recent Radiative and Collisional Atomic Data of Astrophysical Interest

1988 ◽  
Vol 102 ◽  
pp. 129-132
Author(s):  
K.L. Baluja ◽  
K. Butler ◽  
J. Le Bourlot ◽  
C.J. Zeippen
Keyword(s):  
Mass Production ◽  
Bound States ◽  
Physical Models ◽  
Impact Excitation ◽  
Electron Impact Excitation ◽  
Atomic Data ◽  
Isoelectronic Sequence ◽  
Astrophysical Interest ◽  
Radiative Transitions ◽  
Forbidden Transitions

SummaryUsing sophisticated computer programs and elaborate physical models, accurate radiative and collisional atomic data of astrophysical interest have been or are being calculated. The cases treated include radiative transitions between bound states in the 2p4and 2s2p5configurations of many ions in the oxygen isoelectronic sequence, the photoionisation of the ground state of neutral iron, the electron impact excitation of the fine-structure forbidden transitions within the 3p3ground configuration of CℓIII, Ar IV and K V, and the mass-production of radiative data for ions in the oxygen and fluorine isoelectronic sequences, as part of the international Opacity Project.

The ionic strength dependence of chromatin folding

1978 ◽  
Vol 36 (2) ◽  
pp. 220-221
Author(s):  
F. Thoma ◽  
TH. Koller
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
Ionic Strength ◽  
Specimen Preparation ◽  
Preparation Technique ◽  
Carbon Supports ◽  
Ionic Strength Dependence ◽  
Chromatin Folding ◽  
Strength Dependence ◽  
Preparation Techniques

Under a variety of electron microscope specimen preparation techniques different forms of chromatin appearance can be distinguished: beads-on-a-string, a 100 Å nucleofilament, a 250 Å fiber and a compact 300 to 500 Å fiber.Using a standardized specimen preparation technique we wanted to find out whether there is any relation between these different forms of chromatin or not. We show that with increasing ionic strength a chromatin fiber consisting of a row of nucleo- somes progressively folds up into a solenoid-like structure with a diameter of about 300 Å.For the preparation of chromatin for electron microscopy the avoidance of stretching artifacts during adsorption to the carbon supports is of utmost importance. The samples are fixed with 0.1% glutaraldehyde at 4°C for at least 12 hrs. The material was usually examined between 24 and 48 hrs after the onset of fixation.

Cryo-TEM of amphiphilic polymer and amphiphile/polymer solutions

1993 ◽  
Vol 51 ◽  
pp. 876-877
Author(s):  
Yeshayahu Talmon
Keyword(s):  
Microstructural Characterization ◽  
Building Blocks ◽  
Quantitative Information ◽  
Physical Models ◽  
Specimen Preparation ◽  
Time Resolved ◽  
Temperature Changes ◽  
Temperature And Humidity ◽  
Microstructured Fluids ◽  
Air Streams

To achieve complete microstructural characterization of self-aggregating systems, one needs direct images in addition to quantitative information from non-imaging, e.g., scattering or Theological measurements, techniques. Cryo-TEM enables us to image fluid microstructures at better than one nanometer resolution, with minimal specimen preparation artifacts. Direct images are used to determine the “building blocks” of the fluid microstructure; these are used to build reliable physical models with which quantitative information from techniques such as small-angle x-ray or neutron scattering can be analyzed.To prepare vitrified specimens of microstructured fluids, we have developed the Controlled Environment Vitrification System (CEVS), that enables us to prepare samples under controlled temperature and humidity conditions, thus minimizing microstructural rearrangement due to volatile evaporation or temperature changes. The CEVS may be used to trigger on-the-grid processes to induce formation of new phases, or to study intermediate, transient structures during change of phase (“time-resolved cryo-TEM”). Recently we have developed a new CEVS, where temperature and humidity are controlled by continuous flow of a mixture of humidified and dry air streams.

THE MECHANISM OF RAISING AND QUANTIFICATION OF SPECIFIC HEAT FLUX AT BOILING OF NANOFLUIDS IN FREE CONVECTION CONDITIONS

2017 ◽  
pp. 25-34
Author(s):  
V.N. Moraru
Keyword(s):  
Heat Transfer ◽  
Heat Flux ◽  
Heat Capacity ◽  
Specific Heat ◽  
Chemical Properties ◽  
Heating Surface ◽  
Physical Models ◽  
Superheated Liquid ◽  
Two Phase ◽  
Boiling Process

The results of our work and a number of foreign studies indicate that the sharp increase in the heat transfer parameters (specific heat flux q and heat transfer coefficient _) at the boiling of nanofluids as compared to the base liquid (water) is due not only and not so much to the increase of the thermal conductivity of the nanofluids, but an intensification of the boiling process caused by a change in the state of the heating surface, its topological and chemical properties (porosity, roughness, wettability). The latter leads to a change in the internal characteristics of the boiling process and the average temperature of the superheated liquid layer. This circumstance makes it possible, on the basis of physical models of the liquids boiling and taking into account the parameters of the surface state (temperature, pressure) and properties of the coolant (the density and heat capacity of the liquid, the specific heat of vaporization and the heat capacity of the vapor), and also the internal characteristics of the boiling of liquids, to calculate the value of specific heat flux q. In this paper, the difference in the mechanisms of heat transfer during the boiling of single-phase (water) and two-phase nanofluids has been studied and a quantitative estimate of the q values for the boiling of the nanofluid is carried out based on the internal characteristics of the boiling process. The satisfactory agreement of the calculated values with the experimental data is a confirmation that the key factor in the growth of the heat transfer intensity at the boiling of nanofluids is indeed a change in the nature and microrelief of the heating surface. Bibl. 20, Fig. 9, Tab. 2.

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