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 Nonequilibrium Theory of Epigenomic Microphase Separation in the Cell Nucleus

2019 ◽  
Vol 123 (22) ◽  
Author(s):  
Davide Michieletto ◽  
Davide Colì ◽  
Davide Marenduzzo ◽  
Enzo Orlandini
Keyword(s):  
Cell Nucleus ◽  
Microphase Separation ◽  
Nonequilibrium Theory

scholarly journals Transcription organizes euchromatin via microphase separation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Lennart Hilbert ◽  
Yuko Sato ◽  
Ksenia Kuznetsova ◽  
Tommaso Bianucci ◽  
Hiroshi Kimura ◽  
...  
Keyword(s):  
Phase Separation ◽  
Cell Nucleus ◽  
Transcriptional Activity ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Microphase Separation ◽  
Rna Polymerases ◽  
Typical Pattern ◽  
Inactive Chromatin ◽  
Theory And Experiment

AbstractIn eukaryotes, DNA is packed inside the cell nucleus in the form of chromatin, which consists of DNA, proteins such as histones, and RNA. Euchromatin, which is permissive for transcription, is spatially organized into transcriptionally inactive domains interspersed with pockets of transcriptional activity. While transcription and RNA have been implicated in euchromatin organization, it remains unclear how their interplay forms and maintains transcription pockets. Here we combine theory and experiment to analyze the dynamics of euchromatin organization as pluripotent zebrafish cells exit mitosis and begin transcription. We show that accumulation of RNA induces formation of transcription pockets which displace transcriptionally inactive chromatin. We propose that the accumulating RNA recruits RNA-binding proteins that together tend to separate from transcriptionally inactive euchromatin. Full phase separation is prevented because RNA remains tethered to transcribed euchromatin through RNA polymerases. Instead, smaller scale microphases emerge that do not grow further and form the typical pattern of euchromatin organization.

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 The domain-within-domain packing of euchromatin can be described as multiplicative cascades

2020 ◽  
Author(s):  
Amra Noa ◽  
Hui-Shun Kuan ◽  
Vera Aschmann ◽  
Vasily Zaburdaev ◽  
Lennart Hilbert
Keyword(s):  
Cell Nucleus ◽  
Large Scale ◽  
Microphase Separation ◽  
Three Dimensional ◽  
Super Resolution ◽  
Theoretical Models ◽  
Theoretical Physics ◽  
Domain Organization ◽  
Multiplicative Cascades ◽  
Microscopy Images

ABSTRACTThe genome is packed into the cell nucleus in the form of chromatin. Biochemical approaches have revealed that chromatin is packed within domains, which group into larger domains, and so forth. Such domain-within-domain packing, also called hierarchical packing, is equally visible in super-resolution microscopy images of large-scale chromatin organization. While previous work has suggested that chromatin is partitioned into distinct domains via microphase separation, it is unclear how these domains organize into a hierarchical packing. A particular challenge is to find an image analysis approach that fully incorporates such hierarchical packing, so that hypothetical governing mechanisms of euchromatin packing can be compared against the results of such an analysis. Here, we obtain 3D STED super-resolution images from pluripotent zebrafish embryos labeled with improved DNA fluorescence stains, and demonstrate how the hierarchical packing of euchromatin in these images can be described as multiplicative cascades. Multiplicative cascades are an established theoretical concept to describe the placement of ever-smaller structures within bigger structures. Importantly, these cascades can generate artificial image data by applying a single rule again and again, and can be fully specified using only four parameters. Here, we show how the typical patterns of euchromatin organization are reflected in the values of these four parameters. In particular, we can pinpoint the values required to mimic a microphase-separated configuration of euchromatin. We suspect that the concept of multiplicative cascades can also be applied to images of other types of chromatin. In particular, cascade parameters could serve as test quantities to assess whether microphase separation or other theoretical models accurately reproduce the hierarchical packing of chromatin.SIGNIFICANCEDNA is stored inside the cell nucleus in the form of chromatin. Chromatin exhibits a striking three-dimensional organization, where small domains group into larger domains, which again group into larger domains, and so forth. While this hierarchical domain-within-domain organization is obvious from microscopy images, it is still not entirely clear how it is established, or how it should be properly characterized. Here, we demonstrate that multiplicative cascades – a concept from theoretical physics used to characterize for example cloud patterns, galaxy locations, or soil patterns – are also ideally suited to describe the domain-within-domain organization of chromatin. This description is rather simple, using only four numbers, and can thus facilitate testing of competing theories for the domain-within-domain organization of chromatin.

X-Ray Analysis of Frozen Hydrated Sections:The Unconventional Approach

1982 ◽  
Vol 40 ◽  
pp. 754-757
Author(s):  
R. Beeuwkes ◽  
A. Saubermann ◽  
P. Echlin ◽  
S. Churchill
Keyword(s):  
Ratio Method ◽  
Frozen Sections ◽  
Technical Problems ◽  
Sample Handling ◽  
X Ray ◽  
Common Group ◽  
Ideal Method ◽  
Classic Paper ◽  
Physical Principles ◽  
The Ideal

Fifteen years ago, Hall described clearly the advantages of the thin section approach to biological x-ray microanalysis, and described clearly the ratio method for quantitive analysis in such preparations. In this now classic paper, he also made it clear that the ideal method of sample preparation would involve only freezing and sectioning at low temperature. Subsequently, Hall and his coworkers, as well as others, have applied themselves to the task of direct x-ray microanalysis of frozen sections. To achieve this goal, different methodological approachs have been developed as different groups sought solutions to a common group of technical problems. This report describes some of these problems and indicates the specific approaches and procedures developed by our group in order to overcome them. We acknowledge that the techniques evolved by our group are quite different from earlier approaches to cryomicrotomy and sample handling, hence the title of our paper. However, such departures from tradition have been based upon our attempt to apply basic physical principles to the processes involved. We feel we have demonstrated that such a break with tradition has valuable consequences.

The Basic Physical Principles of Ion, Electron, and X-Ray Detectors and Their Application to Microanalysis

1985 ◽  
Vol 43 ◽  
pp. 154-157
Author(s):  
A.J. Tousimis
Keyword(s):  
Ion Beam ◽  
Depth Resolution ◽  
Sample Surface ◽  
High Energy ◽  
X Rays ◽  
X Ray ◽  
Electrons And Ions ◽  
Spatial Depth ◽  
Minimum Surface Area ◽  
Physical Principles

An integral and of prime importance of any microtopography and microanalysis instrument system is its electron, x-ray and ion detector(s). The resolution and sensitivity of the electron microscope (TEM, SEM, STEM) and microanalyzers (SIMS and electron probe x-ray microanalyzers) are closely related to those of the sensing and recording devices incorporated with them.Table I lists characteristic sensitivities, minimum surface area and depth analyzed by various methods. Smaller ion, electron and x-ray beam diameters than those listed, are possible with currently available electromagnetic or electrostatic columns. Therefore, improvements in sensitivity and spatial/depth resolution of microanalysis will follow that of the detectors. In most of these methods, the sample surface is subjected to a stationary, line or raster scanning photon, electron or ion beam. The resultant radiation: photons (low energy) or high energy (x-rays), electrons and ions are detected and analyzed.

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.

Morphological studies of linear (AB)n multiblock copolymers and their blends

1992 ◽  
Vol 50 (1) ◽  
pp. 384-385
Author(s):  
Richard J. Spontak ◽  
Steven D. Smith ◽  
Arman Ashraf
Keyword(s):  
Electron Microscopy ◽  
Microphase Separation ◽  
Multiblock Copolymers ◽  
First Order ◽  
Morphological Studies ◽  
Transmission Electron ◽  
First Order Phase Transition ◽  
Covalently Bonded ◽  
Total Molecular Weight ◽  
First Order Phase

Block copolymers are composed of sequences of dissimilar chemical moieties covalently bonded together. If the block lengths of each component are sufficiently long and the blocks are thermodynamically incompatible, these materials are capable of undergoing microphase separation, a weak first-order phase transition which results in the formation of an ordered microstructural network. Most efforts designed to elucidate the phase and configurational behavior in these copolymers have focused on the simple AB and ABA designs. Few studies have thus far targeted the perfectly-alternating multiblock (AB)n architecture. In this work, two series of neat (AB)n copolymers have been synthesized from styrene and isoprene monomers at a composition of 50 wt% polystyrene (PS). In Set I, the total molecular weight is held constant while the number of AB block pairs (n) is increased from one to four (which results in shorter blocks). Set II consists of materials in which the block lengths are held constant and n is varied again from one to four (which results in longer chains). Transmission electron microscopy (TEM) has been employed here to investigate the morphologies and phase behavior of these materials and their blends.

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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