High concentration of DNA in condensed chromatin

2003 ◽  
Vol 81 (3) ◽  
pp. 91-99 ◽  
Author(s):  
Joan-Ramon Daban
Keyword(s):  
Chromatin Condensation ◽  
Higher Order ◽  
Order Structure ◽  
Local Concentration ◽  
High Concentration ◽  
Metaphase Chromosomes ◽  
Face To Face ◽  
The Face ◽  
Chromatin Packing ◽  
High Concentrations

The lengths of the DNA molecules of eukaryotic genomes are much greater than the dimensions of the metaphase chromosomes in which they are contained during mitosis. From this observation it has been generally assumed that the linear packing ratio of DNA is an adequate measure of the degree of DNA compaction. This review summarizes the evidence suggesting that the local concentration of DNA is more appropriate than the linear packing ratio for the study of chromatin condensation. The DNA concentrations corresponding to most of the models proposed for the 30–40 nm chromatin fiber are not high enough for the construction of metaphase chromosomes. The interdigitated solenoid model has a higher density because of the stacking of nucleosomes in secondary helices and, after further folding into chromatids, it yields a final concentration of DNA that approaches the experimental value found for condensed chromosomes. Since recent results have shown that metaphase chromosomes contain high concentrations of the chromatin packing ions Mg2+ and Ca2+, it is discussed that dynamic rather than rigid models are required to explain the condensation of the extended fibers observed in the absence of these cations. Finally, considering the different lines of evidence demonstrating the stacking of nucleosomes in different chromatin complexes, it is suggested that the face-to-face interactions between nucleosomes may be the driving force for the formation of higher order structures with a high local concentration of DNA.Key words: chromosomes, metaphase chromosomes, chromatin, chromatin higher order structure, DNA.

scholarly journals Natural chromatin is heterogeneous and self-associates in vitro

2018 ◽  
Vol 29 (13) ◽  
pp. 1652-1663 ◽  
Author(s):  
Shujun Cai ◽  
Yajiao Song ◽  
Chen Chen ◽  
Jian Shi ◽  
Lu Gan
Keyword(s):  
Divalent Cations ◽  
Large Mass ◽  
Higher Order ◽  
Linker Histone ◽  
Order Structure ◽  
Face To Face ◽  
Chromatin Packing ◽  
Electron Cryotomography

The 30-nm fiber is commonly formed by oligonucleosome arrays in vitro but rarely found inside cells. To determine how chromatin higher-order structure is controlled, we used electron cryotomography (cryo-ET) to study the undigested natural chromatin released from two single-celled organisms in which 30-nm fibers have not been observed in vivo: picoplankton and yeast. In the presence of divalent cations, most of the chromatin from both organisms is condensed into a large mass in vitro. Rare irregular 30-nm fibers, some of which include face-to-face nucleosome interactions, do form at the periphery of this mass. In the absence of divalent cations, picoplankton chromatin decondenses into open zigzags. By contrast, yeast chromatin mostly remains condensed, with very few open motifs. Yeast chromatin packing is largely unchanged in the absence of linker histone and mildly decondensed when histones are more acetylated. Natural chromatin is therefore generally nonpermissive of regular motifs, even at the level of oligonucleosomes.

Molecular features of heterochromatin condensation

1993 ◽  
Vol 51 ◽  
pp. 72-73
Author(s):  
B.A. Hamkalo ◽  
K. Lundgren ◽  
M.H. Parseghian ◽  
M.Z. Radic ◽  
M. Saghbini
Keyword(s):  
Protein Interactions ◽  
Chromatin Condensation ◽  
Higher Order ◽  
Centromeric Heterochromatin ◽  
Order Structure ◽  
Sequence Motif ◽  
Dna Curvature ◽  
Mitotic Chromosomes ◽  
Metaphase Chromosomes ◽  
Molecular Features

Eukaryotic chromosomes are nonuniformly condensed in both interphase and metaphase. This difference is most apparent in mitotic chromosomes in which centromeric heterochromatin is distinguishable from euchromatic arms because of a higher degree of condensation. This difference prevails in interphase and has led to the designation of this type of heterochromatin as “constitutive”. Differences in condensation presumably are a consequence of differential stability of higher order chromatin structure. Since higher order structure is likely to be due to distinctive DNA-protein and protein-protein interactions, our goal is to identify components of such interactions as a first step in understanding the molecular basis for differential chromatin condensation.Analysis of the structure of the mouse major centromeric satellite DNA revealed the presence of stable DNA curvature which could be reversed if certain small ligands which recognize a sequence motif common to this highly repeated DNA were bound to the DNA. In addition, growth of cells in the presence of these ligands prevented complete condensation of centromere regions of metaphase chromosomes (Fig.1).

Heat capacities and volumes of NaCl, MgCl2, CaCl2, and NiCl2 up to 6 molal in water

1981 ◽  
Vol 59 (21) ◽  
pp. 3049-3054 ◽  
Author(s):  
Gèrald Perron ◽  
Alain Roux ◽  
Jacques E. Desnoyers
Keyword(s):  
Aqueous Solutions ◽  
Long Range ◽  
Higher Order ◽  
Heat Capacities ◽  
Range Order ◽  
Long Range Order ◽  
High Concentration ◽  
Concentration Region ◽  
Partial Molar Heat Capacities ◽  
High Concentrations

It has been claimed by Enderby and co-workers that changes in long-range order occur in NiCl2 aqueous solutions at high concentrations. To investigate the possibility of a transition, the partial molar heat capacities and volumes of NiCl2, CaCl2, MgCl2, and NaCl were measured and compared in water at 25 °C up to 6 mol kg−1. In the case of NaCl, data were also measured at 5 and 45 °C. A slight change in slope of [Formula: see text] is observed for NiCl2 around 4 mol kg−1 which may suggest a third or higher order transition. However, the change is too small to support unambiguously any particular model for the high concentration region.

scholarly journals FACE-TO-FACE VERSUS THREADED DISCUSSIONS: THE ROLE OF TIME AND HIGHER-ORDER THINKING

2019 ◽  
Vol 7 (3) ◽  
Author(s):  
Katrina A. Meyer
Keyword(s):  
Cognitive Processing ◽  
Higher Order Thinking ◽  
Higher Order ◽  
Online Discussions ◽  
Course Evaluations ◽  
Threaded Discussions ◽  
Face To Face ◽  
Experience Of Time ◽  
The Face

This study compares the experiences of students in face-to-face (in class) discussions with threaded discussions and also evaluates the threaded discussions for evidence of higher-order thinking. Students were enrolled in graduate-level classes that used both modes (face-to-face and online) for course-related discussions; their end-of-course evaluations of both experiences were grouped for analysis and themes constructed based on their comments. Themes included the “expansion of time,” “experience of time,” “quality of the discussion,” “needs of the student,” and “faculty expertise.” While there are advantages to holding discussions in either setting, students most frequently noted that using threaded discussions increased the amount of time they spent on class objectives and that they appreciated the extra time for reflection on course issues. The face-to-face format also had value as a result of its immediacy and energy, and some students found one mode a better “fit” with their preferred learning mode. The analysisof higher-order thinking was based on a content analysis of the threaded discussions only. Each posting was coded as one of the four cognitive-processing categories described by Garrison and colleagues: 18% were triggering questions, 51% were exploration, 22% were integration, and 7% resolution. A fifth category – social – was appropriate for 3% of the responses and only 12% of the postings included a writing error. This framework provides some support for the assertion that higher-order thinking can and does occur in online discussions; strategies for increasing the number of responses in the integration and resolution categories are discussed.

Higher order structure in metaphase chromosomes

Chromosoma ◽  
1978 ◽  
Vol 69 (3) ◽  
pp. 363-372 ◽  
Author(s):  
J. B. Rattner ◽  
B. A. Hamkalo
Keyword(s):  
Higher Order ◽  
Order Structure ◽  
Metaphase Chromosomes

scholarly journals Nucleosome packing in interphase chromatin.

1979 ◽  
Vol 81 (2) ◽  
pp. 453-457 ◽  
Author(s):  
J B Rattner ◽  
B A Hamkalo
Keyword(s):  
Electron Microscope ◽  
Chromatin Condensation ◽  
Higher Order ◽  
Chromatin Fiber ◽  
Interphase Chromatin ◽  
Metaphase Chromosomes ◽  
Microscope Analysis ◽  
Electron Microscope Analysis ◽  
Chromatin Fibers

Higher-order chromatin fibers (200--300 A in diameter) are reproducibly released from nuclei after lysis in the absence of formalin and/or detergent. Electron microscope analysis of these fibers shows that they are composed of a continuous array of closely apposed nucleosomes which display several distinct packing patterns. Analysis of the organization of nucleosomes within these arrays and their distribution along long stretches of chromatin suggest that the basic 100-A chromatin fiber is not packed into discrete superbeads and is not folded into a uniform solenoid within the native 250-A fiber. Furthermore, because similar higher-order fibers have been visualized in metaphase chromosomes, the existence of this fiber class appears to be independent of the degree of in vivo chromatin condensation.

scholarly journals Temporal properties of higher-order interactions in social networks

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Giulia Cencetti ◽  
Federico Battiston ◽  
Bruno Lepri ◽  
Márton Karsai
Keyword(s):  
Social Networks ◽  
Social Interactions ◽  
Social Dynamics ◽  
Temporal Dynamics ◽  
Higher Order ◽  
Order Structure ◽  
Face To Face ◽  
Work Settings ◽  
Temporal Properties ◽  
Social Settings

AbstractHuman social interactions in local settings can be experimentally detected by recording the physical proximity and orientation of people. Such interactions, approximating face-to-face communications, can be effectively represented as time varying social networks with links being unceasingly created and destroyed over time. Traditional analyses of temporal networks have addressed mostly pairwise interactions, where links describe dyadic connections among individuals. However, many network dynamics are hardly ascribable to pairwise settings but often comprise larger groups, which are better described by higher-order interactions. Here we investigate the higher-order organizations of temporal social networks by analyzing five publicly available datasets collected in different social settings. We find that higher-order interactions are ubiquitous and, similarly to their pairwise counterparts, characterized by heterogeneous dynamics, with bursty trains of rapidly recurring higher-order events separated by long periods of inactivity. We investigate the evolution and formation of groups by looking at the transition rates between different higher-order structures. We find that in more spontaneous social settings, group are characterized by slower formation and disaggregation, while in work settings these phenomena are more abrupt, possibly reflecting pre-organized social dynamics. Finally, we observe temporal reinforcement suggesting that the longer a group stays together the higher the probability that the same interaction pattern persist in the future. Our findings suggest the importance of considering the higher-order structure of social interactions when investigating human temporal dynamics.

scholarly journals Percolation on stationary tessellations: models, mean values, and second-order structure

2014 ◽  
Vol 51 (A) ◽  
pp. 311-332 ◽  
Author(s):  
Günter Last ◽  
Eva Ochsenreither
Keyword(s):  
Voronoi Tessellation ◽  
Order Structure ◽  
Observation Window ◽  
Important Special Case ◽  
Planar Case ◽  
Intrinsic Volumes ◽  
Mean Values ◽  
Face To Face ◽  
The Face ◽  
Black Faces

We consider a stationary face-to-face tessellationXofRdand introduce several percolation models by colouring some of the faces black in a consistent way. Our main model is cell percolation, where cells are declared black with probabilitypand white otherwise. We are interested in geometric properties of the unionZof black faces. Under natural integrability assumptions, we first express asymptotic mean values of intrinsic volumes in terms of Palm expectations associated with the faces. In the second part of the paper we focus on cell percolation on normal tessellations and study asymptotic covariances of intrinsic volumes ofZ∩W, where the observation windowWis assumed to be a convex body. Special emphasis is given to the planar case where the formulae become more explicit, though we need to assume the existence of suitable asymptotic covariances of the face processes ofX. We check these assumptions in the important special case of a Poisson-Voronoi tessellation.

scholarly journals Highly disordered histone H1−DNA model complexes and their condensates

2018 ◽  
Vol 115 (47) ◽  
pp. 11964-11969 ◽  
Author(s):  
Abigail L. Turner ◽  
Matthew Watson ◽  
Oscar G. Wilkins ◽  
Laura Cato ◽  
Andrew Travers ◽  
...  
Keyword(s):  
Posttranslational Modifications ◽  
Chromatin Condensation ◽  
Bound State ◽  
Histone H1 ◽  
Higher Order ◽  
Disordered Proteins ◽  
Order Structure ◽  
Dependent Manner ◽  
Model Complexes

Disordered proteins play an essential role in a wide variety of biological processes, and are often posttranslationally modified. One such protein is histone H1; its highly disordered C-terminal tail (CH1) condenses internucleosomal linker DNA in chromatin in a way that is still poorly understood. Moreover, CH1 is phosphorylated in a cell cycle-dependent manner that correlates with changes in the chromatin condensation level. Here we present a model system that recapitulates key aspects of the in vivo process, and also allows a detailed structural and biophysical analysis of the stages before and after condensation. CH1 remains disordered in the DNA-bound state, despite its nanomolar affinity. Phase-separated droplets (coacervates) form, containing higher-order assemblies of CH1/DNA complexes. Phosphorylation at three serine residues, spaced along the length of the tail, has little effect on the local properties of the condensate. However, it dramatically alters higher-order structure in the coacervate and reduces partitioning to the coacervate phase. These observations show that disordered proteins can bind tightly to DNA without a disorder-to-order transition. Importantly, they also provide mechanistic insights into how higher-order structures can be exquisitely sensitive to perturbation by posttranslational modifications, thus broadening the repertoire of mechanisms that might regulate chromatin and other macromolecular assemblies.

scholarly journals Percolation on stationary tessellations: models, mean values, and second-order structure

2014 ◽  
Vol 51 (A) ◽  
pp. 311-332 ◽  
Author(s):  
Günter Last ◽  
Eva Ochsenreither
Keyword(s):  
Voronoi Tessellation ◽  
Order Structure ◽  
Observation Window ◽  
Important Special Case ◽  
Planar Case ◽  
Intrinsic Volumes ◽  
Mean Values ◽  
Face To Face ◽  
The Face ◽  
Black Faces

We consider a stationary face-to-face tessellation X of Rd and introduce several percolation models by colouring some of the faces black in a consistent way. Our main model is cell percolation, where cells are declared black with probability p and white otherwise. We are interested in geometric properties of the union Z of black faces. Under natural integrability assumptions, we first express asymptotic mean values of intrinsic volumes in terms of Palm expectations associated with the faces. In the second part of the paper we focus on cell percolation on normal tessellations and study asymptotic covariances of intrinsic volumes of Z ∩ W, where the observation window W is assumed to be a convex body. Special emphasis is given to the planar case where the formulae become more explicit, though we need to assume the existence of suitable asymptotic covariances of the face processes of X. We check these assumptions in the important special case of a Poisson-Voronoi tessellation.

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