Functional compartmentalization of the cell nucleus plays an important role in the regulation of genome activity by providing accumulation of enzymes and auxiliary factors in the reaction centers, ...such as transcription factories, Cajal bodies, speckles, etc. The mechanisms behind the nucleus functional compartmentalization are still poorly understood. There are reasons to believe that the key role in the nucleus compartmentalization belongs to the process of liquid–liquid phase separation. In this brief review, we analyze results of experimental studies demonstrating that liquid–liquid phase separation not only governs functional compartmentalization of the cell nucleus but also contributes to the formation of the 3D genomic architecture.
Chromatin communities stabilized by protein machinery play essential role in gene regulation and refine global polymeric folding of the chromatin fiber. However, treatment of these communities in the ...framework of the classical network theory (stochastic block model, SBM) does not take into account intrinsic linear connectivity of the chromatin loci. Here we propose the polymer block model, paving the way for community detection in polymer networks. On the basis of this new model we modify the non-backtracking flow operator and suggest the first protocol for annotation of compartmental domains in sparse single cell Hi-C matrices. In particular, we prove that our approach corresponds to the maximum entropy principle. The benchmark analyses demonstrates that the spectrum of the polymer non-backtracking operator resolves the true compartmental structure up to the theoretical detectability threshold, while all commonly used operators fail above it. We test various operators on real data and conclude that the sizes of the non-backtracking single cell domains are most close to the sizes of compartments from the population data. Moreover, the found domains clearly segregate in the gene density and correlate with the population compartmental mask, corroborating biological significance of our annotation of the chromatin compartmental domains in single cells Hi-C matrices.
Cys2His2 (C2H2)-type zinc fingers are widespread DNA binding motifs in eukaryotic transcription factors. Zinc fingers are short protein motifs composed of two or three β-layers and one α-helix. Two ...cysteine and two histidine residues located in certain positions bind zinc to stabilize the structure. Four other amino acid residues localized in specific positions in the
N
-terminal region of the α-helix participate in DNA binding by interacting with hydrogen donors and acceptors exposed in the DNA major groove. The number of zinc fingers in a single protein can vary over a wide range, thus enabling variability of target DNA sequences. Besides DNA binding, zinc fingers can also provide protein-protein and RNA-protein interactions. For the most part, proteins containing the C2H2-type zinc fingers are
trans
regulators of gene expression that play an important role in cellular processes such as development, differentiation, and suppression of malignant cell transformation (oncosuppression).
This issue of
Biochemistry
(
Moscow
) is devoted to the cell nucleus and mechanisms of transcription regulation. Over the years, biochemical processes in the cell nucleus have been studied in ...isolation, outside the context of their spatial organization. Now it is clear that segregation of functional processes within a compartmentalized cell nucleus is very important for the implementation of basic genetic processes. The functional compartmentalization of the cell nucleus is closely related to the spatial organization of the genome, which in turn plays a key role in the operation of epigenetic mechanisms. In this issue of
Biochemistry
(
Moscow
), we present a selection of review articles covering the functional architecture of the eukaryotic cell nucleus, the mechanisms of genome folding, the role of stochastic processes in establishing 3D architecture of the genome, and the impact of genome spatial organization on transcription regulation.
Heat Stress-Induced DNA Damage Kantidze, O L; Velichko, A K; Luzhin, A V ...
Acta naturae,
04/2016, Letnik:
8, Številka:
2
Journal Article
Odprti dostop
Although the heat-stress response has been extensively studied for decades, very little is known about its effects on nucleic acids and nucleic acid-associated processes. This is due to the fact that ...the research has focused on the study of heat shock proteins and factors (HSPs and HSFs), their involvement in the regulation of transcription, protein homeostasis, etc. Recently, there has been some progress in the study of heat stress effects on DNA integrity. In this review, we summarize and discuss well-known and potential mechanisms of formation of various heat stress-induced DNA damage.
It is well known that DNA folding in the eukaryotic cell nucleus is tightly coupled with the operation of epigenetic mechanisms defining the repertoires of the genes expressed in different types of ...cells. To understand these mechanisms, it is important to know how DNA is packaged in chromatin. About 30 years ago a hypothesis was formulated, according to which epigenetic mechanisms operate not at the level of individual genes, but rather groups of genes localized in structurally and functionally isolated genomic segments that were called structural and functional domains. The question of what exactly these domains constitute has been re-examined multiple times as our knowledge of principles of chromatin folding has changed. In this review, we discuss structural and functional genomic domains in light of the current model of interphase chromosome organization based on the results of analysis of spatial proximity between remote genomic elements.
The first papers coining the term “nuclear matrix” were published 40 years ago. Here, we review the data obtained during the nuclear matrix studies and discuss the contribution of this controversial ...concept to our current understanding of nuclear architecture and three-dimensional organization of genome.
Negative hydrogen ion sources are of great demand in modern physics as injectors into accelerators and drivers for neutral beam injectors for fusion devices. It has been shown earlier that the use of ...the gasdynamic ECR discharge provides the opportunity to extract up to 80 mA/cm2 of negative ion current density. We studied experimentally the volumetric negative hydrogen ion production and vacuum ultraviolet emission in a gasdynamic ECR discharge. The high-density plasma was sustained by the pulsed 37 GHz / 100 kW gyrotron radiation in a magnetic configuration consisting of two consecutive simple mirror traps. The future prospects of the volumetric H− source based on the gasdynamic ECR discharge related to the transition from pulsed to continuous operating mode with the use of an improved magnetic confinement system are discussed. Numerical simulation of the negative hydrogen ion beam extraction at the continuous operating mode facility was performed. Optimal configuration of the extraction electrodes and the electron damping magnets was found.
The results of the investigation of the dense ECR discharge hydrogen plasma flux formation in the magnetic field of a single solenoid are presented in this work. The transversal flux profile obtained ...at the optimal system parameters is shown. The possibility of the formation of homogeneous plasma fluxes with density of 750 mA/cm
2
and total current of 5 A is demonstrated. The results of the first experiments of the hydrogen ion beam extraction from the ECR discharge plasma in the single magnetic coil are presented. The record values of the ion current density higher than 1.5 A/cm
2
were obtained. The results of the research presented in this paper show the prospects of the proposed system for applications such as the neutral beam injector development for the plasma heating in the controlled fusion facilities.
The terahertz frequency range currently remains the least studied from the point of view of gas-discharge physics. Recent progress in its mastering is associated, first of all, with the creation of ...powerful sources of terahertz radiation - gyrotrons. Nevertheless, the discharge sustained by the powerful radiation of the terahertz frequency range is of interest not only from the fundamental point of view (because of its lack of knowledge), but also from the applied one. This paper presents results of investigations aimed at studying the point-like THz discharge as a source of vacuum ultraviolet radiation and at research of CW THz plasma torch existing at atmospheric pressure and therefore having promising applications in various fields: plasma medicine, plasma chemistry, material processing etc. It is shown that it is possible to create a point-like plasma in an inhomogeneous gas flow with the density above the cut-off one (4·1015 cm−3 for 0.67 THz). It has been demonstrated that such plasma is an effective source of VUV and EUV radiation. Investigations of the atmospheric plasma torch, sustained by CW sub-terahertz radiation (1 kW @ 0.26 THz), demonstrated the possibility of the creation dense non-equilibrium plasma (2·1015 cm−3) with electron temperature in the range from 1 to 2 eV.
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