Interphase Nuclei Of Cells Research Articles

Effect of Azithromycin on Genotoxicity in Allium Test

The effect of azithromycin at a concentration of 50-1000.0 mg/l on the pathology of mitosis in the Allium test in the first metaphase after treatment and after the completion of the recovery period is being investigated. Research methods: Allium test, cytogenetic analysis, statistical analysis. The Allium test was conducted on a batch of the Stuttgarter variety which is genetically unstable as the result of micronucleus test. The results of the analysis showed that the tested concentrations of azithromycin (50.0-1000.0 mg/l) in the first mitosis did not cause a significant increase in the values of mitosis pathology (PM) compared with the negative control. However, there was a significant increase (8 times) in the number of cells with PM in the “aftereffect, after 48 hours” variant for a concentration of 300.0 mg/l of azithromycin: from 4.1% to 32.3%. It should be noted that under the action of all tested concentrations of azithromycin, the same tendency is observed as in the control variant in terms of the preservation of the PM spectrum and the dominance, firstly, of the pathology “overrun/lag of chromosomes”, and secondly, the pathology of “asynchronous spindle fission”. The percentage of mentioned PMs ranges from 52 to 74, and from 7 to 22, respectively. Other types of PMs, according to their occurrence in experimental variants, are arranged in the following sequence: c-mitosis, chromosome scattering, chromosome outliers, polyploidy, chromosome stickiness, chromosomal and chromatid bridges, pycnosis of interphase nuclei. Under the action of azithromycin, starting from a concentration of 100.0 mg/l to 1000.0 mg/l, polyploid cells were observed in dividing cells, which contained a tetraploid set of chromosomes. In experimental variants in single cells, a significant increase in the size of the nuclei of interphase cells and the presence of nuclear buds were noted, which is considered as markers of polyploidization and gene amplification. The recovery period (after 48 hours after the action of the antibiotic) for azithromycin does not reduce the number of cells with PM but changes their composition and spectrum.

Abstract P4-08-20: Inhibition of TACC3 blocks the growth of highly aggressive breast cancers with centrosome amplification

Abstract Centrosome amplification (CA) is a hallmark of cancer that is strongly associated with highly aggressive disease and worse clinical outcome. Enhanced mitotic progression via clustering of extra centrosomes is a major coping mechanism utilized by cancer cells with CA that would otherwise undergo mitotic cell death due to formation of multipolar spindles. However, the underlying molecular mechanisms have largely been unexplored. Furthermore, mitosis-targeting inhibitors have mostly been unsuccessful in clinical settings with poor efficacy and severe side effects. Therefore, there is a dire need to uncover novel molecular mechanisms of CA-driven tumor growth and identify therapeutic targets playing key roles not only in mitosis, but also in interphase of cancer cells with CA to achieve durable anti-tumor effect with minimal toxicity. Here, we identified Transforming Acidic Coiled-Coil Containing Protein 3 (TACC3) as a novel CA-directed dependency, driving highly aggressive cell growth by forming distinct functional interactomes during cell cycle progression. We demonstrated, for the first time, that TACC3 interacts with the Kinesin Family Member C1 (KIFC1) via its TACC domain in mitotic cells with CA to promote centrosome clustering (CC) and facilitate mitotic progression. On the other hand, TACC3 interacts with the members of the nucleosome remodeling and deacetylase (NuRD) complex (HDAC2 and MBD2) in the nucleus of interphase cells with CA, thereby suppressing the transcription of key tumor suppressors to facilitate G1/S progression and cell survival. Inhibiting TACC3 in mitotic cells blocks the formation of TACC3/KIFC1 complex, leading to formation of multipolar spindles and activation of spindle assembly checkpoint (SAC)/CDK1/p-Bcl2 axis that ultimately results in mitotic cell death; whereas TACC3 inhibition in interphase cells blocks TACC3/HDAC2/MBD2 complex, leading to enhanced transcription of cyclin-dependent kinase inhibitors (e.g., p21 and p16) and apoptosis regulators (e.g., APAF1), ultimately causing p53-independent G1 arrest and strong apoptosis. Notably, inducing CA by chemical (cytochalasin D) or genomic (PLK4 overexpression or p53 loss) modulations renders cancer cells highly sensitive to TACC3 inhibition, showing the dependency of cells with CA to TACC3. Targeting TACC3 by small molecule inhibitors or CrispR-CAS9-mediated knock-out significantly reduces colony formation ability, inhibits the growth of organoids of patient-derived xenografts (PDXs) with CA, and strongly inhibits tumor growth in breast cancer cell line xenografts and PDXs with CA. Notably, we demonstrated that high CA tumors express much higher levels of TACC3, and high TACC3 expression, in association with its downstream effectors, KIFC1, HDAC2 and MBD2, leads to drastically worse clinical outcome in cancer patients with CA. Altogether, our results show, for the first time, that TACC3 is a multifunctional driver of the growth of the highly aggressive breast tumors with CA and that targeting TACC3 is a promising approach to tackle this aggressive disease. Citation Format: Ozge Saatci, Ozge Akbulut, Metin Cetin, Vitali Sikirzhytski, Ozgur Sahin. Inhibition of TACC3 blocks the growth of highly aggressive breast cancers with centrosome amplification [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-08-20.

Chromosome territory reorganization through artificial chromosome fusion is compatible with cell fate determination and mouse development

Chromosomes occupy discrete spaces in the interphase cell nucleus, called chromosome territory. The structural and functional relevance of chromosome territory remains elusive. We fused chromosome 15 and 17 in mouse haploid embryonic stem cells (haESCs), resulting in distinct changes of territories in the cognate chromosomes, but with little effect on gene expression, pluripotency and gamete functions of haESCs. The karyotype-engineered haESCs were successfully implemented in generating heterozygous (2n = 39) and homozygous (2n = 38) mouse models. Mice containing the fusion chromosome are fertile, and their representative tissues and organs display no phenotypic abnormalities, suggesting unscathed development. These results indicate that the mammalian chromosome architectures are highly resilient, and reorganization of chromosome territories can be readily tolerated during cell differentiation and mouse development.

ЦИТОГЕНЕТИЧЕСКИЕ МАРКЕРЫ ДЛЯ ОТБОРА МАТЕРИНСКИХ ДЕРЕВЬЕВ СОСНЫ ОБЫКНОВЕННОЙ И ЕЛИ БЕЛОЙ, ПРОДУЦИРУЮЩИХ СЕМЕННОЕ ПОТОМСТВО С ОПРЕДЕЛЕННЫМ УРОВНЕМ ГЕНЕТИЧЕСКОЙ СТАБИЛЬНОСТИ

Currently, the depletion of the gene pool of forest woody plants is observed due to the fact that in the course of selective felling, specimens valuable for economic characteristics were destroyed and seeds from the remaining specimens were used, which did not have the best qualities. It was noted that a high level of genetic heterogeneity allows the population to adapt to changing environmental conditions, ensures the stability of the population and is a resource for breeding. The selection of valuable genotypes in the creation of forest seed plantations, which is carried out according to the phenotype, is based on the heterogeneity of populations. Meanwhile, studies show that phenotypically normal trees do not always produce good offspring. The cytogenetic method allows assessing the offspring. With its help, it is possible to distinguish among the seed offspring the mother trees of the group with different levels of stability of the genetic material. The aim of the work was to identify markers among cytogenetic parameters for the selection of trees producing seed offspring with different stability of the genetic material. The objects of the study were seedlings of seeds of phenotypically normal Scots pine trees growing in the Khopersky State Nature Reserve (51°10’56.9″N 41°44’17.2″E), and white spruce growing in the Botanical Garden. prof. B.M. Kozo-Polyansky Voronezh State University (51°42’41.57 «N 39°12’17.57″E). The trees had no visible pest damage. The method of preparation and analysis of preparations of seed sprouts is described in the work of Butorina A.K. (2000). In the course of the study, 20 cytogenetic parameters were determined: the mitotic index (counted with and without taking into account cells at the prophase of mitosis), the level of mitotic pathologies (counted with and without taking into account cells at the prophase of mitotic), the proportions of cells at the stages of prophase, metaphase, anaphase , the proportions of cells with 1–10 nucleoli in the nucleus of interphase cells, the proportion of cells with micronuclei, the proportion of cells with residual nucleoli in interphase and mitosis. Statistical processing of the study results was carried out using the STADIA 7.0 and MedCalc 17.5.3 software. The diagnostic value of the indicator is characterized by the area under the ROC-curve: 0.9–1.0 – excellent; 0.8–0.9 – very good; 0.7–0.8 – good, 0.6–0.7 – average, 0.6 and less – unsatisfactory. Among the cytogenetic indicators, there are those that are suitable for separating the mutable group from the weakly mutable and intermediate, as well as the weakly mutable from the intermediate. In pine, these include the proportion of cells at the prophase stage and the average number of nucleoli in the nucleus, in spruce – the mitotic index without taking into account cells at the prophase stage, the level of mitotic pathologies with and without taking into account cells at the prophase stage and the proportion of cells at the metaphase stage. There are indicators that make it possible to distinguish the mutable group from the weakly mutable and from the intermediate, but are not suitable for separating the weakly mutable group from the intermediate. These include the mitotic index, calculated taking into account cells at the prophase stage in pine, and the proportion of cells at the metaphase and ana-telophase stages in spruce. According to some indicators, it is possible to distinguish the intermediate group from the mutable and the weakly mutable, but it is impossible to distinguish the mutable group from the weakly mutable. In pine, such indicators are the proportion of cells in the metaphase, and in spruce, the proportion of cells with residual nucleoli in the interphase and meta-telophase. Indicators have been identified that make it possible to distinguish only mutable group from weakly mutable (in pine, the proportion of cells at the ana-telophase stage), and weakly mutable group from intermediate (in pine, the mitotic index taking into account cells at the prophase stage, the level of mitotic pathologies with and without taking into account cells at prophase stage, in spruce – mitotic index, taking into account cells at the prophase stage, the proportion of cells with micronuclei).

Changes in Epigenetic Patterns Related to DNA Replication in Vicia faba Root Meristem Cells under Cadmium-Induced Stress Conditions.

Experiments on Vicia faba root meristem cells exposed to 150 µM cadmium chloride (CdCl2) were undertaken to analyse epigenetic changes, mainly with respect to DNA replication stress. Histone modifications examined by means of immunofluorescence labeling included: (1) acetylation of histone H3 on lysine 56 (H3K56Ac), involved in transcription, S phase, and response to DNA damage during DNA biosynthesis; (2) dimethylation of histone H3 on lysine 79 (H3K79Me2), correlated with the replication initiation; (3) phosphorylation of histone H3 on threonine 45 (H3T45Ph), engaged in DNA synthesis and apoptosis. Moreover, immunostaining using specific antibodies against 5-MetC-modified DNA was used to determine the level of DNA methylation. A significant decrease in the level of H3K79Me2, noted in all phases of the CdCl2-treated interphase cell nuclei, was found to correspond with: (1) an increase in the mean number of intranuclear foci of H3K56Ac histones (observed mainly in S-phase), (2) a plethora of nuclear and nucleolar labeling patterns (combined with a general decrease in H3T45Ph), and (3) a decrease in DNA methylation. All these changes correlate well with a general viewpoint that DNA modifications and post-translational histone modifications play an important role in gene expression and plant development under cadmium-induced stress conditions.

FISH By Imaging Flow Cytometry in CLL for Diagnosis and MRD Assessment

▪Chronic lymphocytic leukaemia is a genetically heterogeneous disease with treatment and prognosis varying based on chromosomal abnormalities. These are detectable in up to 80% of cases when tested on the nuclei of interphase cells by fluorescence in situ hybridisation (FISH). Despite the clinical importance of FISH in management, as only up to 200 nuclei are generally assessed, it is not suitable for minimal residual disease (MRD) assessment. Since clinical decisions are based on detection thresholds of 10 -4, MRD assays are restricted to flow cytometry and molecular based assessment. Here we have explored the utility of a cutting-edge automated imaging flow cytometry method that incorporates cell immunophenotype and FISH (“immuno-flowFISH”) to detect chromosomal abnormalities in CLL.Aims: Our aim was to determine the capability of immuno-flowFISH using imaging flow cytometry to detect del(17p) and +12 in CLL, and, the lowest limit of detection. We hypothesized that this integrated automated immuno-flowFISH method would be suitable for MRD assessment of CLL.Methods: Blood from 75 patients with CLL, at diagnosis or on therapy, was analysed. For MRD studies, cells from the CI cell line were spiked into normal blood at concentrations of 0.001 - 10%. After red cell lysis, samples were incubated with CD3, CD5 and CD19 fluorophore-conjugated antibodies (fluorophores: BV480, BV605, AF647). Following fixation and membrane permeabilization, DNA was denatured at 78 oC for 5 mins. FISH probes to 17p12 and centromeres of chromosomes 12 and 17 were added and hybridized for 24 hours at 42 oC. Nuclei were then stained with SYTOX AADvanced and up to 600,000 cells acquired on the Amnis ® ImageStream ®XMk II imaging flow cytometer. Digital images (x60 objective) and quantitative data derived from computational algorithms (IDEAS software) were used to assess FISH signals overlying cell nuclei. IDEAS was then used to assess the number and percent CD19/CD5-positive CLL cells with FISH abnormalities.Results: Between 10,000 and 600,000 cells (mean 60,000) were acquired. CLL (CD19/CD5-positive) and T- (CD3/CD5-positive) cells could be clearly identified by their immunophenotype and assessed individually for probe signals. FISH signals were identifiable on the digital images as specific “spots” overlying the SYTOX AADvanced nuclear stain. The IDEAS software could enumerate the number of FISH spots per cell and this was confirmed by quantitative mean channel fluorescence intensity for each probe. A chromosome 12 or 17 abnormality was detected in 23 of the 75 CLL cases. Of these, 10 cases had only one 17p signal (but 2 for the centromere of chromosome 17), indicative of del(17p). Del(17p) was detected in 2-35% of CD19/CD5-positive cells (i.e. 0.4-23% or 270-35,441 of all cells), the lowest seen in a patient on cytoreductive therapy. In 13/75 cases, there were 3 FISH signals for CEP12, consistent with trisomy 12 (+12) in 0.1-46% of all cells analysed; the lowest number of 0.1% was when 26 out of 26,000 cells analysed were CD19/CD5-positive and had +12. We also performed multi-FISH, incorporating CEP12, CEP17 and 17p probes together with the CD3, CD5 and CD19 antibodies. This required 7-fluorophores (antibodies, probes and nucleus) and confirmed the ability to detect del(17p) and chromosome 12 copy number simultaneously in a single analysis. Spiking of CI CLL cells into normal blood demonstrated that +12 could be detected to a lowest limit of 10 -5. In all analyses, CLL cells had normal diploid spots for the control CEP17 probe, and the CD3/CD5-positive T cells had dual signals for CEP12, CEP17 and 17p12 probes on numerical analysis and on digital imagery.Conclusion: This study of confirms that high-throughput automated imaging flow cytometry, integrating FISH and immunophenotyping, can detect chromosomal defects in CLL. The lowest limit of detection for a FISH-detectable abnormality was 10 -5. This high sensitivity and specificity exceeds current clinical practice (10 -4), and was achieved through the analysis of many thousands of cells and positive identification of CLL cells based on their phenotype. This immuno-flowFISH method does not require any prior cell separation and is automated. It adds a new dimension to chromosomal analysis in CLL, both at diagnosis and for MRD monitoring. The high precision and specificity of immuno-flowFISH illustrates that this has a real place as a new MRD assessment tool for CLL. DisclosuresNo relevant conflicts of interest to declare.

The SC-35 Splicing Factor Interacts with RNA Pol II and A-Type Lamin Depletion Weakens This Interaction

The essential components of splicing are the splicing factors accumulated in nuclear speckles; thus, we studied how DNA damaging agents and A-type lamin depletion affect the properties of these regions, positive on the SC-35 protein. We observed that inhibitor of PARP (poly (ADP-ribose) polymerase), and more pronouncedly inhibitors of RNA polymerases, caused DNA damage and increased the SC-35 protein level. Interestingly, nuclear blebs, induced by PARP inhibitor and observed in A-type lamin-depleted or senescent cells, were positive on both the SC-35 protein and another component of the spliceosome, SRRM2. In the interphase cell nuclei, SC-35 interacted with the phosphorylated form of RNAP II, which was A-type lamin-dependent. In mitotic cells, especially in telophase, the SC-35 protein formed a well-visible ring in the cytoplasmic fraction and colocalized with β-catenin, associated with the plasma membrane. The antibody against the SRRM2 protein showed that nuclear speckles are already established in the cytoplasm of the late telophase and at the stage of early cytokinesis. In addition, we observed the occurrence of splicing factors in the nuclear blebs and micronuclei, which are also sites of both transcription and splicing. This conclusion supports the fact that splicing proceeds transcriptionally. According to our data, this process is A-type lamin-dependent. Lamin depletion also reduces the interaction between SC-35 and β-catenin in mitotic cells.

Monochorionic diamniotic twin with a Down syndrome in one of the fetuses

A clinical observation of monochorionic diamniotic twins with discordance of cytogenetic and clinical manifestations of Down syndrome is presented. Pregnancy was complicated by feto-fetal transfusion syndrome at 17 weeks of gestation. An ultrasound scan revealed a ventriculomegaly in a donor. Laser coagulation of anastomoses was performed. Karyotype 46, XY was established in the recipient amniocytes. The pregnancy ended in childbirth at 33 weeks with newborn boys weighing 1789 and 2080g. One of the newborns (donor) had phenotypic signs of Down syndrome. When karyotyping peripheral blood lymphocytes of a child with clinical manifestations of Down syndrome, karyotype mos 47,XY,+21[12]/46,XY [88] was established, and a child with a normal phenotype was mos 47,XY,+21[14]/46,XY [86]. No malformations of internal organs were found. When analyzing the buccal epithelium by the FISH method, it was found that in all the analyzed interphase nuclei obtained from a child without clinical manifestations (recipient fetus), trisomy 21 was not detected. In 78% of the interphase nuclei of cells of a child with Down syndrome (fetus-donor), trisomy 21 was established. Thus, the presence of a clone of cells with trisomy 21 in the recipient is associated with twin chimerism.

3D Immuno-DNA Fluorescence In Situ Hybridization (FISH) for Detection of HIV-1 and Cellular Genes in Primary CD4+ T Cells.

Fluorescence in situ hybridization (FISH) is a powerful, broadly used microscopy-based technique that leverages fluorescently labeled nucleic acid probes to detect parts of the genome inside metaphase or interphase cell nuclei. In recent years, different methodologies developed to visualize genome topology and spatial relationships between genes have gained much attention as instruments to decode the relationship between chromatin structure and function. In addition to chromosome conformation capture-based techniques, highly multiplexed forms of FISH combined with high-throughput and super-resolution microscopy are used to map and spatially define contact frequencies between different genomic regions. All these approaches have strongly contributed to our knowledge of how the human genome is packed in the cell nucleus.In this chapter, we describe detailed step-by-step protocols for 3D immuno-DNA FISH detection of genes and Human immunodeficiency virus 1 (HIV-1) provirus in primary CD4+ T cells from healthy donors, or cells infected in vitro with the virus. Our multicolor 3D-FISH technique allows, by using up to three fluorophores, visualization of spatial positioning of loci inside a 3D cell nucleus.

Mitotic Chromosome Mechanics: How Cells Segregate Their Genome.

During mitosis, replicated chromosomes segregate such that each daughter cell receives one copy of the genome. Faithful mechanical transport during mitosis requires that chromosomes undergo extensive structural changes as the cell cycle progresses, resulting in the formation of compact, cylindrical bodies. Such structural changes encompass a range of different activities, including longitudinal condensation of the chromosome axis, global chromatin compaction, resolution of sister chromatids, and individualisation of chromosomes into separate bodies. After mitosis, chromosomes undergo further reorganisation to rebuild interphase cell nuclei. Here we review the requirements for mitotic chromosomes to successfully transmit genetic information to daughter cells and the biophysical principles that underpin such requirements.

A cell-by-cell Monte Carlo simulation for assessing radiation-induced DNA double strand breaks

This paper presents a cell-by-cell Monte Carlo simulation study that combines charged particle track structure data with an interphase cell nucleus model to quantify DNA double strand breaks (DSBs), spatial distribution of DSBs in a cell nucleus, and resulting potentially lethal or mutagenic events (PLMEs) between DSBs in close proximity. Cell nucleus is simulated according to the chromosome territory-interchromatin compartment (CT-IC) model in that chromatin content is unevenly distributed in chromatin domains (CDs) and IC with a chromatin compaction ratio of 22:1. A particle track structure coordinate (PTSC) library was first generated for each particle type, energy, and dose based on a large number of particle track data obtained by running the Monte Carlo track structure code Geant4-DNA. To assess the DNA DSBs of a cell for a specific particle type, energy, and dose, the corresponding PTSC was selected and “map overlaid” onto 960 unique cell nucleus data sets containing chromatin fiber (CF) locations. Clustering algorithm DBSCAN was next used to identify the clustered energy deposition events occurring inside the CF. These events were then converted to DNA DSBs using a probabilistic approach. The locations of the DSBs thus obtained were, in turn, used to calculate PLMEs within the cell nucleus that can result from DSB proximity and complexity. The results obtained from this simulation study are correctly correlated to the experimental data of DSB yield and the RBE-LET relationships for various types of charged particles and of various energies. The results show agreement with other published radiobiological models.

Evidence for the nuclear import of histones H3.1 and H4 as monomers

Newly synthesised histones are thought to dimerise in the cytosol and undergo nuclear import in complex with histone chaperones. Here, we provide evidence that human H3.1 and H4 are imported into the nucleus as monomers. Using a tether‐and‐release system to study the import dynamics of newly synthesised histones, we find that cytosolic H3.1 and H4 can be maintained as stable monomeric units. Cytosolically tethered histones are bound to importin‐alpha proteins (predominantly IPO4), but not to histone‐specific chaperones NASP, ASF1a, RbAp46 (RBBP7) or HAT1, which reside in the nucleus in interphase cells. Release of monomeric histones from their cytosolic tether results in rapid nuclear translocation, IPO4 dissociation and incorporation into chromatin at sites of replication. Quantitative analysis of histones bound to individual chaperones reveals an excess of H3 specifically associated with sNASP, suggesting that NASP maintains a soluble, monomeric pool of H3 within the nucleus and may act as a nuclear receptor for newly imported histone. In summary, we propose that histones H3 and H4 are rapidly imported as monomeric units, forming heterodimers in the nucleus rather than the cytosol.

A rice class-XIV kinesin enters the nucleus in response to cold

Higher plants possess a large number of kinesins, but lack the minus-end directed dynein motors. However, the kinesin class XIV has strongly expanded, and minus-end directed motors from this class may have taken over functions of cytoplasmic dyneins. In this study, we address the functional aspects of a novel rice homologue of the Arabidopsis class-XIV kinesins ATK1 and ATK5. Since a loss-of-function rice mutant of this kinesin is not viable, the function was studied in tobacco BY-2 as heterologous system. OsDLK-GFP stably expressed in BY-2 cells decorates cortical microtubules, but also can shift into the nucleus of interphase cells. Because of this peculiar localisation, we coined the name Dual Localisation Kinesin (DLK). The nuclear import of this protein is strongly and reversibly promoted in response to cold. During mitosis, OsDLK is repartitioned between spindle and phragmoplast. Motility assays in vitro using show that OsDLK can convey mutual sliding of microtubules and moves at a velocity comparable to other class-XIV kinesins. When tobacco cells overexpressing OsDLK are synchronised, they exhibit a delayed entry into metaphase, while the later phases of mitosis are accelerated. The data are discussed in relation to additional functions of this kinesin type, beyond their transport along microtubules.

Mouse chromocenters DNA content: sequencing and in silico analysis

BackgroundChromocenters are defined as a punctate condensed blocks of chromatin in the interphase cell nuclei of certain cell types with unknown biological significance. In recent years a progress in revealing of chromocenters protein content has been made although the details of DNA content within constitutive heterochromatin still remain unclear. It is known that these regions are enriched in tandem repeats (TR) and transposable elements. Quick improvement of genome sequencing does not help to assemble the heterochromatic regions due to lack of appropriate bioinformatics techniques.ResultsChromocenters DNA have been isolated by a biochemical approach from mouse liver cells nuclei and sequenced on the Illumina MiSeq resulting in ChrmC dataset. Analysis of ChrmC dataset by the bioinformatics tools available revealed that the major component of chromocenter DNA are TRs: ~ 66% MaSat and ~ 4% MiSat. Other previously classified TR families constitute ~ 1% of ChrmC dataset. About 6% of chromocenters DNA are mostly unannotated sequences. In the contigs assembled with IDBA_UD there are many fragments of heterochromatic Y-chromosome, rDNA and other pseudo-genes and non-coding DNA. A protein coding sfi1 homolog gene fragment was also found in contigs. The Sfi1 homolog gene is located on the chromosome 11 in the reference genome very close to the Golden Pass Gap (a ~ 3 Mb empty region reserved to the pericentromeric region) and proves the purity of chromocenters isolation. The second major fraction are non-LTR retroposons (SINE and LINE) with overwhelming majority of LINE - ~ 11% of ChrmC. Most of the LINE fragments are from the ~ 2 kb region at the end of the 2nd ORF and its’ flanking region. The precise LINEs’ segment of ~ 2 kb is the necessary mouse constitutive heterohromatin component together with TR. The third most abundant fraction are ERVs. The ERV distribution in chromocenters differs from the whole genome: IAP (ERV2 class) is the most numerous in ChrmC while MaLR (ERV3 class) prevails in the reference genome. IAP and its LTR also prevail in TR containing contigs extracted from the WGS dataset. In silico prediction of IAP and LINE fragments in chromocenters was confirmed by direct fluorescent in situ hybridization (FISH).ConclusionOur data of chromocenters’ DNA (ChrmC) sequencing demonstrate that IAP with LTR and a precise ~ 2 kb fragment of LINE represent a substantial fraction of mouse chromocenters (constitutive heteroсhromatin) along with TRs.

Spatial organization of chromosome territories in the interphase nucleus of trisomy 21 cells.

In the interphase cell nucleus, chromosomes adopt a conserved and non-random arrangement in subnuclear domains called chromosome territories (CTs). Whereas chromosome translocation can affect CT organization in tumor cell nuclei, little is known about how aneuploidies can impact CT organization. Here, we performed 3D-FISH on control and trisomic 21 nuclei to track the patterning of chromosome territories, focusing on the radial distribution of trisomic HSA21 as well as 11 disomic chromosomes. We have established an experimental design based on cultured chorionic villus cells which keep their original mesenchymal features including a characteristic ellipsoid nuclear morphology and a radial CT distribution that correlates with chromosome size. Our study suggests that in trisomy 21 nuclei, the extra HSA21 induces a shift of HSA1 and HSA3 CTs out toward a more peripheral position in nuclear space and a higher compaction of HSA1 and HSA17 CTs. We posit that the presence of a supernumerary chromosome 21 alters chromosome compaction and results in displacement of other chromosome territories from their usual nuclear position.

Cloning of canine Ku80 and its localization and accumulation at DNA damage sites.

Molecularly targeted therapies have high specificity and significant cancer‐killing effect. However, their antitumor effect might be greatly diminished by variation in even a single amino acid in the target site, as it occurs, for example, as a consequence of SNPs. Increasing evidence suggests that the DNA repair protein Ku80 is an attractive target molecule for the development of next‐generation radiosensitizers for human cancers. However, the localization, post‐translational modifications (PTMs), and complex formation of Ku80 have not been elucidated in canines. In this study, for the first time, we cloned, sequenced, and characterized canine Ku80 cDNA. Our data show that canine Ku80 localizes in the nuclei of interphase cells and is quickly recruited at laser‐induced double‐strand break sites. Comparative analysis shows that canine Ku80 had only 82.3% amino acid identity with the homologous human protein, while the nuclear localization signal (NLS) in human and canine Ku80 is evolutionarily conserved. Notably, some predicted PTM sites, including one acetylation site and one sumoylation site within the NLS, are conserved in the two species. These findings suggest that the spatial and temporal regulation of Ku80 might be conserved in humans and canines. However, our data indicate that the expression of Ku80 is considerably lower in the canine cell lines examined than in human cell lines. These important findings might be useful to better understand the mechanism of the Ku80‐dependent DNA repair and for the development of potential next‐generation radiosensitizers targeting common targets in human and canine cancers.

Non-equilibrium forces drive the anomalous diffusion of telomeres in the nucleus of mammalian cells

Telomeres are vital nucleotide sequences at both ends of each chromosome, and their motion reports on the local dynamics of decondensed chromatin in the nucleus of interphase cells. Here, we show that the previously reported subdiffusive motion of telomeres is driven by non-equilibrium cytoskeletal forces. In particular, breaking down microtubules leads to a significantly reduced generalized diffusion coefficient of telomeres. This translates into a markedly reduced effective temperature in the stochastic forces that govern the telomeres’ random walk. Moreover, telomere motion in cells that lack microtubules is well described by the monomer dynamics of a Rouse polymer that is embeddded in a viscoelastic medium. In contrast, active cytoskeletal forces in untreated cells override the environment’s elastic contributions, resulting in the well-known scaling for conventional Rouse dynamics in viscous media. Our data highlight that even subdiffusive motion in cells in most cases may not be a simple thermal transport process but rather is driven by non-equilibrium events.

Genome organization: A vision of 3D chromatin organization.

A new imaging technique (ChromEMT) enables the visualization of the local polymer structure and global 3D organization of chromatin in the nucleus of intact interphase and mitotic human cells.

Formation of a nucleoplasmic reticulum requires de novo assembly of nascent phospholipids and shows preferential incorporation of nascent lamins

Structure of interphase cell nuclei remains dynamic and can undergo various changes of shape and organisation, in health and disease. The double-membraned envelope that separates nuclear genetic material from the rest of the cell frequently includes deep, branching tubular invaginations that form a dynamic nucleoplasmic reticulum (NR). This study addresses mechanisms by which NR can form in interphase nuclei. We present a combination of Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS) approach and light microscopy techniques to follow formation of NR by using pulse-chase experiments to examine protein and lipid delivery to nascent NR in cultured cells. Lamina protein incorporation was assessed using precursor accumulation (for lamin A) or a MAPLE3 photoconvertible tag (for lamin B1) and membrane phospholipid incorporation using stable isotope labelling with deuterated precursors followed by high resolution NanoSIMS. In all three cases, nascent molecules were selectively incorporated into newly forming NR tubules; thus strongly suggesting that NR formation is a regulated process involving a focal assembly machine, rather than simple physical perturbation of a pre-existing nuclear envelope.

Cloning, localization and focus formation at DNA damage sites of canine Ku70

Understanding the molecular mechanisms of DNA double-strand break (DSB) repair machinery, specifically non-homologous DNA-end joining (NHEJ), is crucial for developing next-generation radiotherapies and common chemotherapeutics for human and animal cancers. The localization, protein-protein interactions and post-translational modifications of core NHEJ factors, might play vital roles for regulation of NHEJ activity. The human Ku heterodimer (Ku70/Ku80) is a core NHEJ factor in the NHEJ pathway and is involved in sensing of DSBs. Companion animals, such as canines, have been proposed to be an excellent model for cancer research, including development of chemotherapeutics. However, the post-translational modifications, localization and complex formation of canine Ku70 have not been clarified. Here, we show that canine Ku70 localizes in the nuclei of interphase cells and that it is recruited quickly at laser-microirradiated DSB sites. Structurally, two DNA-PK phosphorylation sites (S6 and S51), an ubiquitination site (K114), two canonical sumoylation consensus motifs, a CDK phosphorylation motif, and a nuclear localization signal (NLS) in the human Ku70 are evolutionarily conserved in canine and mouse species, while the acetylation sites in human Ku70 are partially conserved. Intriguingly, the primary candidate nucleophile (K31) required for 5’dRP/AP lyase activity of human and mouse Ku70 is not conserved in canines, suggesting that canine Ku does not possess this activity. Our findings provide insights into the molecular mechanisms of Ku-dependent NHEJ in a canine model and form a platform for the development of next-generation common chemotherapeutics for human and animal cancers.