nucleoid - vertaling naar arabisch
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nucleoid - vertaling naar arabisch

REGION OF A VIRUS, BACTERIAL CELL, MITOCHONDRION OR CHLOROPLAST TO WHICH THE NUCLEIC ACID IS CONFINED
Nucleoid region; Genophore; Nucleoids; Architecture of the Escherichia coli nucleoid; Architecture of the E. coli nucleoid; Escherichia coli nucleoid; Nucleoid architecture
  • '''Formation of the ''Escherichia coli'' nucleoid''' '''A.''' An illustration of an open conformation of the circular genome of ''Escherichia coli''. Arrows represent bi-directional DNA replication. The genetic position of the origin of bi-directional DNA replication (''oriC'') and the site of chromosome decatenation (''dif'') in the replication termination region (''ter'') are marked. Colors represent specific segments of DNA as discussed in C. '''B.''' An illustration of a random coil form adopted by the pure circular DNA of ''Escherichia coli'' at thermal equilibrium without supercoils and additional stabilizing factors.<ref name=":34" /><ref name=":35" /> '''C.''' A cartoon of the chromosome of a newly born ''Escherichia coli'' cell. The genomic DNA is not only condensed by 1000-fold compared to its pure random coil form but is also spatially organized. ''oriC'' and ''dif'' are localized in the mid-cell, and specific regions of the DNA indicated by colors in A organize into spatially distinct domains. Six spatial domains have been identified in ''E. coli''. Four domains (Ori, Ter, Left, and Right) are structured and two (NS-right and NS-left) are non-structured. The condensed and organized form of the DNA together with its associated proteins and RNAs is called nucleoid.
  • '''Nucleoid at ≥1 kb scale. DNA organization by nucleoid-associated proteins.''' DNA is depicted as a grey straight or curved line and the nucleoid-associated proteins are depicted as blue spheres.
  • '''Genome-wide occupancy of nucleoid-associated proteins of ''E. coli''.''' A circular layout of the ''E. coli'' genome depicting genome-wide occupancy of NAPs Fis, H-NS, HU, and IHF in growth and stationary phases in ''E. coli''. Histogram plots of the genome occupancy of NAPs as determined by chromatin-immunoprecipitation coupled with DNA sequencing (ChIP-seq) are shown outside the circular genome. The bin size of the histograms is 300 bp. Figure prepared in circos/0.69-6 using the ChIP-Seq data from.<ref name=":48" /><ref name=":12" />
  • '''DNA supercoiling''' '''A.''' A linear double-stranded DNA becomes a topologically constrained molecule if the two ends are covalently joined, forming a circle. Rules of DNA topology are explained using such a molecule (ccc-DNA) in which a numerical parameter called the linking number (Lk) defines the topology. Lk is a mathematical sum of two geometric parameters, twist (Tw) and writhe (Wr). A twist is the crossing of two strands, and writhe is coiling of the DNA double helix on its axis that requires bending. Lk is always an integer and remains invariant no matter how much the two strands are deformed. It can only be changed by introducing a break in one or both DNA strands by DNA metabolic enzymes called topoisomerases. '''B.''' A torsional strain created by a change in Lk of a relaxed, topologically constrained DNA manifests in the form of DNA supercoiling. A decrease in Lk (Lk<Lk<sub>0</sub>) induces negative supercoiling whereas an increase in Lk (Lk>Lk<sub>0</sub>) induces positive supercoiling. Only negative supercoiling is depicted here. For example, if a cut is introduced into a ccc-DNA and four turns are removed before rejoining the two strands, the DNA becomes negatively supercoiled with a decrease in the number of twists or writhe or both. Writhe can adopt two types of geometric structures called plectoneme and toroid. Plectonemes are characterized by the interwinding of the DNA double helix and an apical loop, whereas spiraling of DNA double helix around an axis forms toroids.
  • '''Basic units of genomic organization in bacteria and eukaryotes''' Genomic DNA, depicted as a grey line, is negatively supercoiled in both bacteria and eukaryotes. However, the negatively supercoiled DNA is organized in the plectonemic form in bacteria, whereas it is organized in the toroidal form in eukaryotes. Nucleoid associated proteins (NAPs), shown as colored spheres, restrain half of the plectonemic supercoils, whereas almost all of the toroidal supercoils are induced as well as restrained by nucleosomes (colored orange), formed by wrapping of DNA around histones.
  • '''Twin supercoiling domain model for transcription-induced supercoiling''' '''A.''' An example of topologically constrained DNA. A grey bar represents a topological constraint, e.g. a protein or a membrane anchor. '''B.''' Accommodation of RNA polymerase for transcription initiation results in the opening of the DNA double helix. '''C.''' An elongating RNA polymerase complex cannot rotate around the helical axis of DNA. Therefore, removal of helical turns by RNA polymerase causes overwinding of the topologically constrained DNA ahead and underwinding of the DNA behind, generating positively and negatively supercoiled DNA, respectively. Supercoiling can manifest as either change in the numbers of twists as shown in C or plectonemic writhe as shown in D.
  • '''The chromosomal DNA within the nucleoid is segregated into independent supercoiled topological domains''' '''A.''' An illustration of a single topological domain of a supercoiled DNA. A single double-stranded cut anywhere would be sufficient to relax the supercoiling tension of the entire domain. '''B.''' An illustration of multiple topological domains in a supercoiled DNA molecule. A presence of supercoiling-diffusion barriers segregates a supercoiled DNA molecule into multiple topological domains. Hypothetical supercoiling diffusion barriers are represented as green spheres. As a result, a single double-stranded cut will only relax one topological domain and not the others. Plectonemic supercoils of DNA within the ''E. coli'' nucleoid are organized into several topological domains, but only four domains with a different number of supercoils are shown for simplicity.
  • '''Nucleoid is spatially organized into chromosomal interactions domains (CIDs) and macrodomains''' '''A.''' Chromosome conformation capture (3C) methods probe 3D genome organization by quantifying physical interactions between genomic loci that are nearby in 3D-space but may be far away in the linear genome. A genome is cross-linked with formaldehyde to preserve physical contacts between genomic loci. Subsequently, the genome is digested with a restriction enzyme. In the next step, a DNA ligation is carried out under diluted DNA concentrations to favor intra-molecular ligation (between cross-linked fragments that are brought into physical proximity by 3D genome organization). A frequency of ligation events between distant DNA sites reflects a physical interaction. In the 3C method, ligation junctions are detected by the semi-quantitative PCR amplification in which amplification efficiency is a rough estimate of pairwise physical contact between genomic regions of interests and its frequency. The 3C method probes a physical interaction between two specific regions identified a priori, whereas its Hi-C version detects physical interactions between all possible pairs of genomic regions simultaneously. In the Hi-C method, digested ends are filled in with a biotinylated adaptor before ligation. Ligated fragments are sheared and then enriched by a biotin-pull down. Ligation junctions are then detected and quantified by the paired-end next-generation sequencing methods. '''B.''' Hi-C data are typically represented in the form of a two-dimensional matrix in which the x-axis and y-axis represent the genomic coordinates. The genome is usually divided into bins of a fixed size, e.g., 5-kb. The size of bins essentially defines the contact resolution. Each entry in the matrix, m<sub>ij</sub>, represents the number of chimeric sequencing reads mapped to genomic loci in bins i and j. A quantification of the reads (represented as a heatmap) denotes the relative frequency of contacts between genomic loci of bins i and j. A prominent feature of the heatmap is a diagonal line that appears due to more frequent physical interaction between loci that are very close to each other in the linear genome. The intensity further from the diagonal line represents the relative frequency of physical interaction between loci that are far away from each other in the linear genome. Triangles of high-intensity along the diagonal line represent highly self-interacting chromosomal interaction domains (CIDs) that are separated by a boundary region that consists of a smaller number of interactions. '''C.''' In many bacterial species including ''E. coli'', it appears that supercoiled topological domains organize as CIDs. Plectonemic supercoiling promotes a high level of interaction among genomic loci within a CID, and a plectoneme-free region (PFR), created due to high transcription activity, acts as a CID boundary. Nucleoid-associated proteins, depicted as closed circles, stabilize the supercoiling-mediated interactions. The actively transcribing RNA polymerase (depicted as a green sphere) in the PFR blocks dissipation of supercoiling between the two domains thus acts as a supercoiling diffusion barrier. The size of the CIDs ranges between 30 and 400 kb. Several triangles (CIDs) merge to form a bigger triangle that represents a macrodomain. In other words, CIDs of a macrodomain physically interact with each other more frequently than with CIDs of a neighboring macrodomain or with genomic loci outside of that macrodomain. A macrodomain may comprise several CIDs. For simplicity, a macrodomain comprising only two CIDs is shown.
  • '''Genome-wide occupancy of MatP and MukB of ''E. coli''''' A circular layout of the ''E. coli'' genome depicting genome-wide occupancy of MatP and MukB in ''E. coli''. The innermost circle depicts the ''E. coli'' genome. The regions of the genome which organize as spatial domains(macrodomains) in the nucleoid are indicated as colored bands. Histogram plots of genome occupancy for MatP and MukB as determined by chromatin-immunoprecipitation coupled with DNA sequencing (ChIP-seq) are shown in outside circles. The bin size of the histograms is 300 bp. The figure was prepared in circos/0.69-6 using the processed ChIP-Seq data from.<ref name=":32" />
  • doi-access = free }}</ref> The translocation of the complex away from its loading site then extrudes DNA loops. The loops are extruded in a rock-climbing manner by the coordinated opening and closing of the MukBEF ring through the MukB head disengagement that occurs due to coordinated ATP hydrolysis in the two dimers.<ref name=":31" /> Dark and light blue circles represent ATP binding and hydrolysis events respectively. MukE is not shown in the complex for simplicity.
  • '''Nucleoid as a helical ellipsoid with longitudinal high-density DNA regions''' '''A.''' A cartoon of ''E. coli'' cell with a curved nucleoid (dark grey). A curved centroids path, denoted by red and green dots, emphasizes the curved shape of the nucleoid<ref name=":19" /> '''B.''' Cross-sectioning of the ''E. coli'' nucleoid visualized by HU-mCherry. Fluorescence intensity is taken as a proxy for DNA density and is represented by blue to red in increasing order.<ref name=":20" />

nucleoid         
‎ نَوَوانِيّ‎
nucleoid         
نَوَوانِيّ
genophore         
حَامِلُ الجِيْن (صبغي في النواة)

Wikipedia

Nucleoid

The nucleoid (meaning nucleus-like) is an irregularly shaped region within the prokaryotic cell that contains all or most of the genetic material. The chromosome of a typical prokaryote is circular, and its length is very large compared to the cell dimensions, so it needs to be compacted in order to fit. In contrast to the nucleus of a eukaryotic cell, it is not surrounded by a nuclear membrane. Instead, the nucleoid forms by condensation and functional arrangement with the help of chromosomal architectural proteins and RNA molecules as well as DNA supercoiling. The length of a genome widely varies (generally at least a few million base pairs) and a cell may contain multiple copies of it.

There is not yet a high-resolution structure known of a bacterial nucleoid, however key features have been researched in Escherichia coli as a model organism. In E. coli, the chromosomal DNA is on average negatively supercoiled and folded into plectonemic loops, which are confined to different physical regions, and rarely diffuse into each other. These loops spatially organize into megabase-sized regions called macrodomains, within which DNA sites frequently interact, but between which interactions are rare. The condensed and spatially organized DNA forms a helical ellipsoid that is radially confined in the cell. The 3D structure of the DNA in the nucleoid appears to vary depending on conditions and is linked to gene expression so that the nucleoid architecture and gene transcription are tightly interdependent, influencing each other reciprocally.

https://en.wikipedia.org/wiki/Nucleoid
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