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Hybridization of DNA from the H3 isochore fraction to human metaphase spreads. FISH with DNA from the H3 isochore fraction as a probe (FITC-detected) was performed on metaphase spreads from male human lymphocytes. Chromosomes were DAPI-banded and arranged into standard karyograms. The inverted DAPI image (a) displays G- and C-bands more darkly stained compared with R-bands. Most of the R-bands hybridized specifically to the DNA probe as the inverted image of the hybridization signals shows (b, FITC fluorescence appears dark) that displays a typical R banding pattern. Note the different signal intensities of distinct R-bands (e.g., on the distal p-arm of chromosome 1 and the q-arm of chromosome 13).
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![S phase replication labeling patterns are preserved. Cells ([a and b]...](profile/Daniele-Zink/publication/12809604/figure/fig1/AS:11431281177772244@1690597441793/S-phase-replication-labeling-patterns-are-preserved-Cells-a-and-b-Hv-human-diploid_Q320.jpg)
We investigated the nuclear higher order compartmentalization of chromatin according to its replication timing (Ferreira et al. 1997) and the relations of this compartmentalization to chromosome structure and the spatial organization of transcription. Our aim was to provide a comprehensive and integrated view on the relations between chromosome str...
Citations
... Chromosomal bands, along with the genes they contain, are not randomly positioned within cell nuclei; rather, they are distributed based on gene density and gene expression patterns [42,43]. In the peripheral region of the nucleus, DNA is highly compacted, and genes in this compartment are typically inactive. ...
Chromosomal translocations can result in phenotypic effects of varying severity, depending on the position of the breakpoints and the rearrangement of genes within the interphase nucleus of the translocated chromosome regions. Balanced translocations are often asymptomatic phenotypically and are typically detected due to a decrease in fertility resulting from issues during meiosis. Robertsonian translocations are among the most common chromosomal abnormalities, often asymptomatic, and can persist in the population as a normal polymorphism. We serendipitously discovered a Robertsonian translocation between chromosome 21 and chromosome 22, which is inherited across three generations without any phenotypic effect, notably only in females. In situ hybridization with alpha-satellite DNAs revealed the presence of both centromeric sequences in the translocated chromosome. The reciprocal translocation resulted in a partial deletion of the short arm of both chromosomes 21, and 22, with the ribosomal RNA genes remaining present in the middle part of the new metacentric chromosome. The rearrangement did not cause alterations to the long arm. The spread of an asymptomatic heterozygous chromosomal polymorphism in a population can lead to mating between heterozygous individuals, potentially resulting in offspring with a homozygous chromosomal configuration for the anomaly they carry. This new karyotype may not produce phenotypic effects in the individual who presents it. The frequency of karyotypes with chromosomal rearrangements in asymptomatic heterozygous form in human populations is likely underestimated, and molecular karyotype by array Comparative Genomic Hybridization (array-CGH) analysis does not allow for the identification of this type of chromosomal anomaly, making classical cytogenetic analysis the preferred method for obtaining clear results on a karyotype carrying a balanced rearrangement.
... The nucleolus is surrounded by a shell of chromatin called perinucleolar chromatin. This chromatin is primarily composed of highly condensed heterochromatic DNA that replicates late in the cell cycle [9,10]. The perinucleolar chromatin encompasses individual telomeres, centromeres, and internal chromosome loci [6]. ...
The nucleolus is a significant nuclear organelle that is primarily known for its role in ribosome biogenesis. However, emerging evidence suggests that the nucleolus may have additional functions. Particularly, it is involved in the organization of the three-dimensional structure of the genome. The nucleolus acts as a platform for the clustering of repressed chromatin, although this process is not yet fully understood, especially in the context of Drosophila. One way to study the regions of the genome that cluster near the nucleolus in Drosophila demands the identification of a reliable nucleolus-localizing signal (NoLS) motif(s) that can highly specifically recruit the protein of interest to the nucleolus. Here, we tested a series of various NoLS motifs from proteins of different species, as well as some of their combinations, for the ability to drive the nucleolar localization of the chimeric H2B-GFP protein. Several short motifs were found to effectively localize the H2B-GFP protein to the nucleolus in over 40% of transfected Drosophila S2 cells. Furthermore, it was demonstrated that NoLS motifs derived from Drosophila proteins exhibited greater efficiency compared to that of those from other species.
... Several studies showed that H1 phosphorylation is a feature of decondensed chromatin rather than highly condensed heterochromatin [6,34]. This claim also supports our observation that phosphorylated histones H1 appear in transcriptionally active nucleoli and in the nuclear interior that is considered to contain more relaxed and transcriptionally active chromatin [35]. We found that the nuclear periphery, abundant in silencing epigenetic marker H3K9me3, is characterized by a low density of phosphorylated histone H1 (Figure 2(Ba-Bc), arrow in the direction of the nuclear periphery). ...
Background:
Variants of linker histone H1 are tissue-specific and are responsible for chromatin compaction accompanying cell differentiation, mitotic chromosome condensation, and apoptosis. Heterochromatinization, as the main feature of these processes, is also associated with pronounced trimethylation of histones H3 at the lysine 9 position (H3K9me3).
Methods:
By confocal microscopy, we analyzed cell cycle-dependent levels and distribution of phosphorylated histone H1 (H1ph) and H3K9me3. By mass spectrometry, we studied post-translational modifications of linker histones.
Results:
Phosphorylated histone H1, similarly to H3K9me3, has a comparable level in the G1, S, and G2 phases of the cell cycle. A high density of phosphorylated H1 was inside nucleoli of mouse embryonic stem cells (ESCs). H1ph was also abundant in prophase and prometaphase, while H1ph was absent in anaphase and telophase. H3K9me3 surrounded chromosomal DNA in telophase. This histone modification was barely detectable in the early phases of mitosis. Mass spectrometry revealed several ESC-specific phosphorylation sites of H1. HDAC1 depletion did not change H1 acetylation but potentiated phosphorylation of H1.2/H1.3 and H1.4 at serine 38 positions.
Conclusions:
Differences in the level and distribution of H1ph and H3K9me3 were revealed during mitotic phases. ESC-specific phosphorylation sites were identified in a linker histone.
... The periphery of cell nucleus is occupied by heterochromatin, which is closely associated with the lamina and the inner nuclear membrane; and the nucleoli are surrounded by dense CC [11][12][13][14][15][16][17][18][19] (Fig.1). ...
The study of human thermoregulation is one of the most developed areas of modern physiology and medicine. This is due to the important role of temperature in normal and pathological conditions. Directly or indirectly almost all systems and organs are involved in maintaining of relatively constant temperature in the body, since their normal functioning is closely related to the temperature of the internal environment (temperature homeostasis). Currently, the existence of two systems of thermoregulation is recognized: a physiological organ-based system with a center in the hypothalamus and a molecular system, which manifests itself in the form of the production of proteins (heat shock- and cold shock proteins) and by activation of RNA thermometers in response to heat or cold shock. Based on studies of the variability of chromosomal heterochromatin regions in the genome of human populations permanently living in various climatic and geographical conditions of Eurasia and Africa, as well as individuals well adapted to the extreme conditions of the high altitudes of the Pamirs and Tien-Shan (mountaineers) and the Far North (oil drillers of the Yamal Peninsula, Eastern Siberia), we came to the conclusion that, apparently, there is a third system of thermoregulation at the cellular level (cell thermoregulation). By cell thermoregulation, we mean the removal of excess heat from the nucleus of an interphase cell in order to avoid the harmful effects of high temperature on the complex molecular processes occurring in the nucleoplasm. We believe that some intracellular formations (a dense layer of condensed chromatin around the nucleus, nucleoli, chromocenters and other membraneless bodies) serve as a structural basis for the removal of heat from the cell nucleus, because the material basis of all these temporary structures in the interphase nucleus is the chromosomal heterochromatin regions. In this review, we discuss a set of data, which indicate that cell thermoregulation, may be a missing link between organism and molecular level in maintaining temperature homeostasis in the human body.
... In other words, the GC-richest bands corresponding to the gene-richest bands are replicated at the beginning of the S phase of the cell cycle ( Figure 2) [74]. Thus, the genomic compartment located towards the inner part of the nucleus presents an open chromatin structure, containing most of the active genes endowed with a high GC level, and is mainly replicated at the onset of the S phase [74][75][76][77]. The opposite properties were observed in the genomic compartment located at the nuclear periphery. ...
... The opposite properties were observed in the genomic compartment located at the nuclear periphery. towards the inner part of the nucleus presents an open chromatin structure, containing most of the active genes endowed with a high GC level, and is mainly replicated at the onset of the S phase [74][75][76][77]. The opposite properties were observed in the genomic compartment located at the nuclear periphery. ...
The last decade has seen significant progress in understanding how the genome is organized spatially within interphase nuclei. Recent analyses have confirmed earlier molecular cytogenetic studies on chromosome positioning within interphase nuclei and provided new information about the topologically associated domains (TADs). Examining the nuances of how genomes are organized within interphase nuclei will provide information fundamental to understanding gene regulation and expression in health and disease. Indeed, the radial spatial positioning of individual gene loci within nuclei has been associated with up- and down-regulation of specific genes, and disruption of normal genome organization within nuclei will result in compromised cellular health. In cancer cells, where reorganization of the nuclear architecture may occur in the presence of chromosomal rearrangements such as translocations, inversions, or deletions, gene repositioning can change their expression. To date, very few studies have focused on radial gene positioning and the correlation to gene expression in cancers. Further investigations would improve our understanding of the biological mechanisms at the basis of cancer and, in particular, in leukemia initiation and progression, especially in those cases where the molecular consequences of chromosomal rearrangements are still unclear. In this review, we summarize the main milestones in the field of genome organization in the nucleus and the alterations to this organization that can lead to cancer diseases.
... The crossover rate was significantly lower in the center of chromosomes relative to their telomeric peripheries. The preferential position of mid-late replicating chromatin is at the nuclear periphery and the central position of early replicating chromatin, also previously observed in mammalian cell nuclei [206,207]. The reduction of recombination rates in macrochromosome centers of the zebra finch (Taeniopygia guttata, Vieillot, 1817) [208] is more extreme than in other birds [111,209], while the white wagtail macrochromosomes exhibited a clear U-shaped distribution of recombination frequencies, adding another example of comparatively reduced recombination in the centers of nuclear architecture [210]. ...
... In contrast to early replicating gene-dense chromatin, gene-poor mid-to-late replicating chromatin may carry binding sites for the reconstituting nuclear lamina during telophase [213]. This could push early replicating gene-dense chromatin into a more interior position, also observed in mammalian cell nuclei [207,214]. Furthermore, late-replicating chromatin has been observed around the nucleoli. Microchromosomes are predominantly early replicating with a small proportion of late-replicating segments [116,119,215]. ...
With more than 70,000 living species, vertebrates have a huge impact on the field of biology and research, including karyotype evolution. One prominent aspect of many vertebrate karyo-types is the enigmatic occurrence of tiny and often cytogenetically indistinguishable microchromo-somes, which possess distinctive features compared to macrochromosomes. Why certain vertebrate species carry these microchromosomes in some lineages while others do not, and how they evolve remain open questions. New studies have shown that microchromosomes exhibit certain unique characteristics of genome structure and organization, such as high gene densities, low heterochro-matin levels, and high rates of recombination. Our review focuses on recent concepts to expand current knowledge on the dynamic nature of karyotype evolution in vertebrates, raising important questions regarding the evolutionary origins and ramifications of microchromosomes. We introduce the basic karyotypic features to clarify the size, shape, and morphology of macro-and micro-chromosomes and report their distribution across different lineages. Finally, we characterize the mechanisms of different evolutionary forces underlying the origin and evolution of microchromo-somes.
... This structure made it possible to elevate problems of 3D-organization of the interphase nucleus in mammalian cells to a fundamentally new level. Numerous studies have shown nonrandom localization of C-, G-, and R-segments, telomeric and centromeric regions of chromosomes in the interphase nucleus [24][25][26][27]. These studies extensively used three-dimensional fluorescent in situ hybridization (3D-FISH) followed by 3D microscopy. ...
The gene composition, function and evolution of B-chromosomes (Bs) have been actively discussed in recent years. However, the additional genomic elements are still enigmatic. One of Bs mysteries is their spatial organization in the interphase nucleus. It is known that heterochromatic compartments are not randomly localized in a nucleus. The purpose of this work was to study the organization and three-dimensional spatial arrangement of Bs in the interphase nucleus. Using microdissection of Bs and autosome centromeric heterochromatic regions of the yellow-necked mouse (Apodemus flavicollis) we obtained DNA probes for further two-dimensional (2D)- and three-dimensional (3D)- fluorescence in situ hybridization (FISH) studies. Simultaneous in situ hybridization of obtained here B-specific DNA probes and autosomal C-positive pericentromeric region-specific probes further corroborated the previously stated hypothesis about the pseudoautosomal origin of the additional chromosomes of this species. Analysis of the spatial organization of the Bs demonstrated the peripheral location of B-specific chromatin within the interphase nucleus and feasible contact with the nuclear envelope (similarly to pericentromeric regions of autosomes and sex chromosomes). It is assumed that such interaction is essential for the regulation of nuclear architecture. It also points out that Bs may follow the same mechanism as sex chromosomes to avoid a meiotic checkpoint.
... The reversible acetylation of amino terminus of H4 lysines 5, 8, 12, and 16 allows less compact chromatin and accessible nucleosomes (Loidl, 1988;Loidl, 1994;Garcia-Ramirez et al., 1995), open chromatin with accessibility to transcription machinery via RNA polymerases II or III Vettese-Dadey et al., 1996). Acetylation of mammalian H4 is found in euchromatin that bypasses early replication and transcription (Sadoni et al., 1999). Heterochromatin has lower acetylation comparable to euchromatin (open chromatin) in endosperm nuclei of Gagea lutea (Buzek et al., 1998). ...
... The recombination events can occur between adjacent (within one 43 kb unit) or remote (across the units) repeats. In particular, the shell of chromatin surrounding nucleoli (perinucleolar chromatin) contains many repetitive sequences, such as LINE/L1 and SINE/Alu, which are regarded as candidates for interaction with rDNA [87][88][89][90]. It was supposed that a recombination between the perinucleolar chromosomal regions and the closely situated IGS loci producing ncRNAs may affect the organization of the nucleolar DNA [14]. ...
In human cells, ribosomal DNA (rDNA) is arranged in ten clusters of multiple tandem repeats. Each repeat is usually described as consisting of two parts: the 13 kb long ribosomal part, containing three genes coding for 18S, 5.8S and 28S RNAs of the ribosomal particles, and the 30 kb long intergenic spacer (IGS). However, this standard scheme is, amazingly, often altered as a result of the peculiar instability of the locus, so that the sequence of each repeat and the number of the repeats in each cluster are highly variable. In the present review, we discuss the causes and types of human rDNA instability, the methods of its detection, its distribution within the locus, the ways in which it is prevented or reversed, and its biological significance. The data of the literature suggest that the variability of the rDNA is not only a potential cause of pathology, but also an important, though still poorly understood, aspect of the normal cell physiology.
... Apart from the lamin meshwork, the nuclear periphery harbours a multitude of proteins that are either anchored in the INM or that interact with lamins and chromatin directly and indirectly. Chromatin at the nuclear periphery is enriched in repressive histone marks such as H3K9me2/3 and H4k20me2, and is depleted of histone acetylation (Kind et al. 2013;Sadoni et al. 1999). Accordingly, artificial tethering of reporter genes to lamina often leads to their repression, indicating that the lamina compartment has active mechanisms to reinforce the repressed state (Zullo et al. 2012;Finlan et al. 2008;Reddy et al. 2008;Leemans et al. 2019). ...
The mammalian genome is complex and presents a dynamic structural organization that reflects function. Organization of the genome inside the mammalian nucleus impacts all nuclear processes including but not limited to transcription, replication and repair, and in many biological contexts such as early development, differentiation and physiological adaptations. However, there is limited understating of how 3D organization of the mammalian genome regulates different nuclear processes. Recent advances in microscopy and a myriad of genomics methods—propelled by next-generation sequencing—have advanced our knowledge of genome organization to a great extent. In this review, we discuss nuclear compartments in general and recent advances in the understanding of how mammalian genome is organized in these compartments with an emphasis on dynamics at the nuclear periphery.
