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1
Grutzner, F., A. Casey, and T. Daish. "105. MEIOTIC ACROBATS: MONOTREME SEX CHROMOSOME ORGANISATION DURING SPERMATOGENESIS." Reproduction, Fertility and Development 22, no. 9 (2010): 23. http://dx.doi.org/10.1071/srb10abs105.
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Monotremes feature an extraordinarily complex sex chromosome system which shares extensive homology with bird sex chromosomes but no homology to sex chromosomes of other mammals (1,2,3). At meiotic prophase I the ten sex chromosomes in platypus (nine in echidna) assemble in a sex chromosome chain. We previously identified the multiple sex chromosomes in platypus and echidna that form the meiotic chain in males (1,2,4). We showed that sex chromosomes assembly in the chain in a specific order (5) and that they segregate alternately (1). In secondary spermatocytes we observed clustering of X and Y chromosomes in sperm (6). Our current research investigates the formation of the synaptonemal complex, recombination and meiotic silencing of monotreme sex chromosomes. Meiotic sex chromosome inactivation (MSCI) has been observed in eutherian mammals, marsupials and birds but has so far not been investigated experimentally in monotremes. We found that during pachytene the X5Y5 end of the chain closely associates with the nucleolus and accumulates repressive chromatin marks (e.g. histone variant mH2A). In contrast to the differential accumulation of mH2A we observe extensive loading of the cohesin SMC3 on sex chromosomes in particular during the pachytene stage of meiotic prophase I. We have also used markers of active transcription and gene expression analysis to investigate gene activity in platypus meiotic cells. I will discuss how these findings contribute to our current understanding of the meiotic organisation of monotreme sex chromosomes and the evolution of MSCI in birds and mammals. (1) Grützner et al. (2004), Nature 432: 913–917.(2) Rens et al. (2007), Genome Biology 16;8(11): R243.(3) Veyrunes et al. (2008), Genome Research, 18(6): 995–1004.(4) Rens et al. (2004), Proceedings of the National Academy of Sciences USA. 101 (46): 16 257–16 261.(5) Daish et al. (2009), Reprod Fertil Dev. 21(8): 976–84.(6) Tsend-Ayush et al. (2009), Chromosoma 118(1): 53–69.
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Joseph, Sunitha, Rebecca O’Connor, Abdullah Al Mutery, Mick Watson, Denis Larkin, and Darren Griffin. "Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation." Diversity 10, no. 4 (October 18, 2018): 113. http://dx.doi.org/10.3390/d10040113.
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Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, which can then be linked to the whole genome sequence to generate a so-called chromosome-level assembly. Chromosome-level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes, as well as determining patterns of gross genomic evolution. To date, only two falcon species have been sequenced and neither initially were assembled to the chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date, however, published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made. The purposes of this study were to generate analyzable karyotypes and ideograms of peregrine, saker, and gyr falcons, report on our recent generation of chromosome level sequence assemblies of peregrine and saker falcons, and for the first time, sequence the gyr falcon genome. Finally, we aimed to generate comparative genomic data between all three species and the reference chicken genome. Results revealed a diploid number of 2n = 50 for peregrine falcon and 2n = 52 for saker and gyr through high quality banded chromosomes. Standard ideograms that are generated here helped to map predicted chromosomal fragments (PCFs) from the genome sequences directly to chromosomes and thus generate chromosome level sequence assemblies for peregrine and saker falcons. Whole genome sequencing was successful in gyr falcon, but read depth and coverage was not sufficient to generate a chromosome level assembly. Nonetheless, comparative genomics revealed no differences in genome organization between gyr and saker falcons. When compared to peregrine falcon, saker/gyr differed by one interchromosomal and seven intrachromosomal rearrangements (a fusion plus seven inversions), whereas peregrine and saker/gyr differ from the reference chicken genome by 14/13 fusions (11 microchromosomal) and six fissions. The chromosomal differences between the species could potentially provide the basis of a screening test for hybrid animals.
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Fowler, Katie E., Anjali A. Mandawala, and Darren K. Griffin. "The role of chromosome segregation and nuclear organisation in human subfertility." Biochemical Society Transactions 47, no. 1 (February 7, 2019): 425–32. http://dx.doi.org/10.1042/bst20180231.
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Abstract Spermatogenesis is central to successful sexual reproduction, producing large numbers of haploid motile male gametes. Throughout this process, a series of equational and reductional chromosome segregation precedes radical repackaging of the haploid genome. Faithful chromosome segregation is thus crucial, as is an ordered spatio-temporal ‘dance’ of packing a large amount of chromatin into a very small space. Ergo, when the process goes wrong, this is associated with an improper chromosome number, nuclear position and/or chromatin damage in the sperm head. Generally, screening for overall DNA damage is relatively commonplace in clinics, but aneuploidy assessment is less so and nuclear organisation studies form the basis of academic research. Several studies have focussed on the role of chromosome segregation, nuclear organisation and analysis of sperm morphometry in human subfertility observing significant alterations in some cases, especially of the sex chromosomes. Importantly, sperm DNA damage has been associated with infertility and both extrinsic (e.g. lifestyle) and intrinsic (e.g. reactive oxygen species levels) factors, and while some DNA-strand breaks are repaired, unexpected breaks can cause differential chromatin packaging and further breakage. A ‘healthy’ sperm nucleus (with the right number of chromosomes, nuclear organisation and minimal DNA damage) is thus an essential part of reproduction. The purpose of this review is to summarise state of the art in the fields of sperm aneuploidy assessment, nuclear organisation and DNA damage studies.
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Nasiri, F., F. Mahjoubi, F. Manouchehry, F. Razazian, F. Mortezapour, and M. Rahnama. "Cytogenetic Findings in Mentally Retarded Iranian Patients." Balkan Journal of Medical Genetics 15, no. 2 (December 1, 2012): 29–34. http://dx.doi.org/10.2478/bjmg-2013-0004.
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ABSTRACT We conducted a cytogenetic study on 865 individuals with idiopathic mental retardation (MR) who were admitted to the Cytogenetics Department of the Iran Blood Transfusion Organisation (IBTO) Research Centre, Tehran, Iran; these were performed on blood samples using conventional staining methods. Chromosome anomalies were identified in 205 of the patients (23.6%). The majority were Down’s syndrome cases (n = 138). In 33 males, a positive fragile X anomaly was found .The remainder (n = 34) had other chromosomal abnormalities including structural chromosome aberrations (n = 23), marker chromosomes with an unknown origin (n = 3), sex chromosome aneuploidy (n = 6) and trisomy 18 (n = 2). The contribution of chromosome aberrations to the cause of MR in this group of patients is discussed.
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Sandery, Michael J., John W. Forster, Richard Blunden, and R. Neil Jones. "Identification of a family of repeated sequences on the rye B chromosome." Genome 33, no. 6 (December 1, 1990): 908–13. http://dx.doi.org/10.1139/g90-137.
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A novel family of highly repeated sequences on the B chromosome of rye (Secale cereale) has been identified. The D1100 family has not been detected on the rye A chromosomes and shows little or no homology to any previously described repeat sequence in rye. In addition, different rye species, and different B chromosomes within the same species, show significant heterogeneity in the arrangement of the D1100 sequences. An EcoRI clone of a member of the family has been obtained. These results provide direct evidence for the organisation and nature of the B-chromosome DNA in rye, and they are discussed in relation to the origin and evolution of rye B chromosomes.Key words: B chromosome, Secale cereale, repeated sequences.
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Heslop-Harrison, J. S. Pat, and Trude Schwarzacher. "Organisation of the plant genome in chromosomes." Plant Journal 66, no. 1 (March 28, 2011): 18–33. http://dx.doi.org/10.1111/j.1365-313x.2011.04544.x.
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Cintra, Leonardo Adabo, Thaíssa Boldieri de Souza, Letícia Maria Parteka, Lucas Mesquita Barreto, Luiz Filipe Protasio Pereira, Marcos Letaif Gaeta, Romain Guyot, and André Luís Laforga Vanzela. "An 82 bp tandem repeat family typical of 3′ non-coding end of Gypsy/TAT LTR retrotransposons is conserved in Coffea spp. pericentromeres." Genome 65, no. 3 (March 2022): 137–51. http://dx.doi.org/10.1139/gen-2021-0045.
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Coffea spp. chromosomes are very small and accumulate a variety of repetitive DNA families around the centromeres. However, the proximal regions of Coffea chromosomes remain poorly understood, especially regarding the nature and organisation of the sequences. Taking advantage of the genome sequences of C. arabica (2n = 44), C. canephora, and C. eugenioides (C. arabica progenitors with 2n = 22) and good coverage genome sequencing of dozens of other wild Coffea spp., repetitive DNA sequences were identified, and the genomes were compared to decipher particularities of pericentromeric structures. The searches revealed a short tandem repeat (82 bp length) typical of Gypsy/TAT LTR retrotransposons, named Coffea_sat11. This repeat organises clusters with fragments of other transposable elements, comprising regions of non-coding RNA production. Cytogenomic analyses showed that Coffea_sat11 extends from the pericentromeres towards the middle of the chromosomal arms. This arrangement was observed in the allotetraploid C. arabica chromosomes, as well as in its progenitors. This study improves our understanding of the role of the Gypsy/TAT LTR retrotransposon lineage in the organisation of Coffea pericentromeres, as well as the conservation of Coffea_sat11 within the genus. The relationships between fragments of other transposable elements and the functional aspects of these sequences on the pericentromere chromatin were also evaluated. Highlights: A scattered short tandem repeat, typical of Gypsy/TAT LTR retrotransposons, associated with several fragments of other transposable elements, accumulates in the pericentromeres of Coffea chromosomes. This arrangement is preserved in all clades of the genus and appears to have a strong regulatory role in the organisation of chromatin around centromeres.
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Agashe, Bhavna, Chellapilla Krishna Prasad, and Imran Siddiqi. "Identification and analysis ofDYAD: a gene required for meiotic chromosome organisation and female meiotic progression inArabidopsis." Development 129, no. 16 (August 15, 2002): 3935–43. http://dx.doi.org/10.1242/dev.129.16.3935.
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The dyad mutant of Arabidopsis was previously identified as being defective in female meiosis. We report here the analysis of the DYAD gene. In ovules and anthers DYAD RNA is detected specifically in female and male meiocytes respectively, in premeiotic interphase/meiotic prophase. Analysis of chromosome spreads in female meiocytes showed that in the mutant, chromosomes did not undergo synapsis and formed ten univalents instead of five bivalents. Unlike mutations in AtDMC1 and AtSPO11 which also affect bivalent formation as the univalent chromosomes segregate randomly, the dyad univalents formed an ordered metaphase plate and underwent an equational division. This suggests a requirement for DYAD for chromosome synapsis and centromere configuration in female meiosis. The dyad mutant showed increased and persistent expression of a meiosis-specific marker, pAtDMC1::GUS during female meiosis, indicative of defective meiotic progression. The sequence of the putative protein encoded by DYAD did not reveal strong similarity to other proteins. DYAD is therefore likely to encode a novel protein required for meiotic chromosome organisation and female meiotic progression.
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Hasterok, Robert, Natalia Borowska-Zuchowska, and Ewa Robaszkiewicz. "Cytomolecular Organisation of the Nuclear Genome." International Journal of Molecular Sciences 23, no. 21 (October 27, 2022): 13028. http://dx.doi.org/10.3390/ijms232113028.
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Modern molecular cytogenetics allows many aspects of the nuclear genome structure, function, and evolution to be analysed within the topographic context of mitotic and meiotic chromosomes and interphase nuclei [...]
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Mishra, Sujeet Kumar, Kunhe Li, Simon Brauburger, Arnab Bhattacherjee, Nestor Norio Oiwa, and Dieter W. Heermann. "Superstructure Detection in Nucleosome Distribution Shows Common Pattern within a Chromosome and within the Genome." Life 12, no. 4 (April 6, 2022): 541. http://dx.doi.org/10.3390/life12040541.
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Nucleosome positioning plays an important role in crucial biological processes such as replication, transcription, and gene regulation. It has been widely used to predict the genome’s function and chromatin organisation. So far, the studies of patterns in nucleosome positioning have been limited to transcription start sites, CTCFs binding sites, and some promoter and loci regions. The genome-wide organisational pattern remains unknown. We have developed a theoretical model to coarse-grain nucleosome positioning data in order to obtain patterns in their distribution. Using hierarchical clustering on the auto-correlation function of this coarse-grained nucleosome positioning data, a genome-wide clustering is obtained for Candida albicans. The clustering shows the existence beyond hetero- and eu-chromatin inside the chromosomes. These non-trivial clusterings correspond to different nucleosome distributions and gene densities governing differential gene expression patterns. Moreover, these distribution patterns inside the chromosome appeared to be conserved throughout the genome and within species. The pipeline of the coarse grain nucleosome positioning sequence to identify underlying genomic organisation used in our study is novel, and the classifications obtained are unique and consistent.
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Sepsi, Adél, and Trude Schwarzacher. "Chromosome–nuclear envelope tethering – a process that orchestrates homologue pairing during plant meiosis?" Journal of Cell Science 133, no. 15 (August 1, 2020): jcs243667. http://dx.doi.org/10.1242/jcs.243667.
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ABSTRACTDuring prophase I of meiosis, homologous chromosomes pair, synapse and exchange their genetic material through reciprocal homologous recombination, a phenomenon essential for faithful chromosome segregation. Partial sequence identity between non-homologous and heterologous chromosomes can also lead to recombination (ectopic recombination), a highly deleterious process that rapidly compromises genome integrity. To avoid ectopic exchange, homology recognition must be extended from the narrow position of a crossover-competent double-strand break to the entire chromosome. Here, we review advances on chromosome behaviour during meiotic prophase I in higher plants, by integrating centromere- and telomere dynamics driven by cytoskeletal motor proteins, into the processes of homologue pairing, synapsis and recombination. Centromere–centromere associations and the gathering of telomeres at the onset of meiosis at opposite nuclear poles create a spatially organised and restricted nuclear state in which homologous DNA interactions are favoured but ectopic interactions also occur. The release and dispersion of centromeres from the nuclear periphery increases the motility of chromosome arms, allowing meiosis-specific movements that disrupt ectopic interactions. Subsequent expansion of interstitial synapsis from numerous homologous interactions further corrects ectopic interactions. Movement and organisation of chromosomes, thus, evolved to facilitate the pairing process, and can be modulated by distinct stages of chromatin associations at the nuclear envelope and their collective release.
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McClelland, Sarah E. "Single-cell approaches to understand genome organisation throughout the cell cycle." Essays in Biochemistry 63, no. 2 (May 15, 2019): 209–16. http://dx.doi.org/10.1042/ebc20180043.
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Abstract Mammalian genomes are ordered at several scales, ranging from nucleosomes (beads on a string), to topologically associated domains (TADs), laminar associated domains (LADs), and chromosome territories. These are described briefly below and we refer the reader to some recent comprehensive reviews on genome architecture summarising the current state of knowledge of the organisational principles of the nucleus [1,2]. Biological observations from populations of millions of individual cells can reveal consensus behaviour. New methods to study and interpret biological data at the single-cell level have recently been instrumental in revealing new understanding of cell-to-cell variation and novel biology. Here we will summarise the recent advances in single-cell technology that have provided insights into the behaviour of the mammalian genome during a cell cycle. We will focus on the interphase domain structure of chromosomes, including TADs and LADs, and how chromosome architecture changes during the cell cycle. The role of genome architecture relating to gene expression has been reviewed elsewhere [3].
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Aiumsumang, Surachest, Patcharaporn Chaiyasan, Kan Khoomsab, Weerayuth Supiwong, Alongklod Tanomtong, and Sumalee Phimphan. "Comparative chromosome mapping of repetitive DNA in four minnow fishes (Cyprinidae, Cypriniformes)." Caryologia 75, no. 2 (September 21, 2022): 71–80. http://dx.doi.org/10.36253/caryologia-1523.
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The present study focused on the repetitive DNA of the chromosome in four minnow fishes from the genera Danio Hamilton, 1822, Devario Heckel, 1843 and Rasbora Bleeker, 1859. Chromosomes were analysed using fluorescence in situ hybridization (FISH) with microsatellite probes including (CA)15, (CAC)10, (CGG)10, (GC)15 and (TA)15 staining. All species retained the diploid chromosome number 2n = 50 in male and female. The microsatellite sequences were mapped in the chromosomes of Danio albolineatus (Blyth, 1860), Devario regina (Fowler, 1934), Rasbora aurotaenia Tirant, 1885 and R. paviana Tirant, 1885. In most cases, the microsatellite was dispersed in the chromosome with conspicuous markings in the telomeric region and the whole genome, which suggests that sequences contribute to chromosome structure and may have played a role in the relationship of this fish group. The comparative genome mapping data presented here provide novel information on the structure and organisation of the repetitive DNA region of the minnow’s genome and contribute to a better understanding of the genomes of these minnows.
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A. Eidelman, Yu, and S. G. Andreev. "Biophysical Study of the Globular Organisation of Interphase Chromosomes." Radiation Protection Dosimetry 99, no. 1 (June 1, 2002): 217–18. http://dx.doi.org/10.1093/oxfordjournals.rpd.a006766.
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Ingram, Samuel P., Nicholas T. Henthorn, John W. Warmenhoven, Norman F. Kirkby, Ranald I. Mackay, Karen J. Kirkby, and Michael J. Merchant. "Hi-C implementation of genome structure for in silico models of radiation-induced DNA damage." PLOS Computational Biology 16, no. 12 (December 16, 2020): e1008476. http://dx.doi.org/10.1371/journal.pcbi.1008476.
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Developments in the genome organisation field has resulted in the recent methodology to infer spatial conformations of the genome directly from experimentally measured genome contacts (Hi-C data). This provides a detailed description of both intra- and inter-chromosomal arrangements. Chromosomal intermingling is an important driver for radiation-induced DNA mis-repair. Which is a key biological endpoint of relevance to the fields of cancer therapy (radiotherapy), public health (biodosimetry) and space travel. For the first time, we leverage these methods of inferring genome organisation and couple them to nano-dosimetric radiation track structure modelling to predict quantities and distribution of DNA damage within cell-type specific geometries. These nano-dosimetric simulations are highly dependent on geometry and are benefited from the inclusion of experimentally driven chromosome conformations. We show how the changes in Hi-C contract maps impact the inferred geometries resulting in significant differences in chromosomal intermingling. We demonstrate how these differences propagate through to significant changes in the distribution of DNA damage throughout the cell nucleus, suggesting implications for DNA repair fidelity and subsequent cell fate. We suggest that differences in the geometric clustering for the chromosomes between the cell-types are a plausible factor leading to changes in cellular radiosensitivity. Furthermore, we investigate changes in cell shape, such as flattening, and show that this greatly impacts the distribution of DNA damage. This should be considered when comparing in vitro results to in vivo systems. The effect may be especially important when attempting to translate radiosensitivity measurements at the experimental in vitro level to the patient or human level.
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Lv, H., J. C. Wang, K. L. Wu, X. Gao, L. C. Wang, L. You, and Z. J. Chen. "Numb regulates meiotic spindle organisation in mouse oocytes." Reproduction, Fertility and Development 22, no. 4 (2010): 664. http://dx.doi.org/10.1071/rd09236.
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Numb is an adaptor protein that controls the fate of cells in different species through asymmetrical inheritance by sibling cells during division. It has been investigated extensively in mitosis, mostly in neural progenitor cells, but its function in meiosis remains unknown. The present study was designed to investigate the expression, subcellular localisation and functional roles of Numb during mouse oocyte meiotic maturation. Using real-time polymerase chain reaction and western blotting, we found that the expression of Numb increased from the germinal vesicle (GV) to MII stages. Immunofluorescent staining revealed that Numb was mainly concentrated in the GV before meiosis resumption, aggregated in the vicinity of the chromosomes after GV breakdown and then localised to the spindle poles from prometaphase I to MII. Nocodazole treatment resulted in spindle destruction and Numb diffusion into the cytoplasm. However, Numb appeared at the spindle poles again once the spindles had formed when nocodazole-treated oocytes were washed and cultured for spindle recovery. Depletion of Numb by RNA interference resulted in chromosome misalignment, spindle deformation and even doubled spindle formation. Our results suggest that Numb is critical for spindle organisation during mouse oocytes meiosis. The present study provides evidence of a new function for Numb in addition to its action as a cell fate-determining factor.
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Volkov, A. N., and L. V. Nacheva. "Сytogenetic techniques in current biomedical research. part i: history and theoretical basis of human cytogenetics." Fundamental and Clinical Medicine 6, no. 4 (December 28, 2021): 142–50. http://dx.doi.org/10.23946/2500-0764-2021-6-4-142-150.
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Cytogenetics is an essential part of human genetics which studies the structure of chromosomes and their collection which is called karyotype. Cytogenetic techniques are employed while interrogating DNA organisation and compaction. Analysis of the chromosomal structure contributes to uncovering the molecular basis of various cellular processes in normal and pathological conditions. Furthermore, spectrum and frequency of chromosome abnormalities serves as an indicator of mutagenic effects. Cytogenetic techniques became indispensable for discovering the genetic causes of human diseases at different stages of ontogenesis. Genetic abnormalities are a common cause of impaired reproductive function, abnormal pregnancy, and neonatal malformations. Genetic screening for chromosomal abnormalities and congenital anomalies is a powerful tool for reducing the genetic load in human populations as well as disease, psychological and social burden on families and societies. This paper begins the cycle of lectures on molecular basis of human cytogenetics, cytogenetic techniques, and the corresponding research and clinical applications. The lecture is primarily aimed at biomedical students and physicians who often have an unmet need to analyse and interpret the results of cytogenetic analyses.
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Hall, Elliott C. R., Christopher Murgatroyd, Georgina K. Stebbings, Brian Cunniffe, Lee Harle, Matthew Salter, Aroul Ramadass, et al. "The Prospective Study of Epigenetic Regulatory Profiles in Sport and Exercise Monitored Through Chromosome Conformation Signatures." Genes 11, no. 8 (August 7, 2020): 905. http://dx.doi.org/10.3390/genes11080905.
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The integration of genetic and environmental factors that regulate the gene expression patterns associated with exercise adaptation is mediated by epigenetic mechanisms. The organisation of the human genome within three-dimensional space, known as chromosome conformation, has recently been shown as a dynamic epigenetic regulator of gene expression, facilitating the interaction of distal genomic regions due to tight and regulated packaging of chromosomes in the cell nucleus. Technological advances in the study of chromosome conformation mean a new class of biomarker—the chromosome conformation signature (CCS)—can identify chromosomal interactions across several genomic loci as a collective marker of an epigenomic state. Investigative use of CCSs in biological and medical research shows promise in identifying the likelihood that a disease state is present or absent, as well as an ability to prospectively stratify individuals according to their likely response to medical intervention. The association of CCSs with gene expression patterns suggests that there are likely to be CCSs that respond, or regulate the response, to exercise and related stimuli. The present review provides a contextual background to CCS research and a theoretical framework discussing the potential uses of this novel epigenomic biomarker within sport and exercise science and medicine.
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Caperta, Ana D., Nuno Neves, Leonor Morais-Cecílio, Rui Malhó, and Wanda Viegas. "Genome restructuring in rye affects the expression, organization and disposition of homologous rDNA loci." Journal of Cell Science 115, no. 14 (July 15, 2002): 2839–46. http://dx.doi.org/10.1242/jcs.115.14.2839.
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The standard rye cultivar `Imperial' and a structural variant carrying an intact 1R chromosome and two telocentric 1R chromosomes (short and long arms)were used to investigate expression patterns of homologous rDNA loci, and the influence of chromosome structural change on their interphase organisation and relative disposition. Sequential silver staining and in situ hybridization with the rDNA probe pTa71, established a correspondence between the expression and organization patterns of rDNA domains in metaphase and interphase cells. In most cells of the cultivar Imperial, nucleolar organizer region (NOR)silver staining on metaphase chromosomes with equivalent numbers of rDNA genes revealed a size heteromorphism between homologous rDNA loci, resulting from their differential expression. NOR heteromorphism in the structural variant line was significantly reduced. The preferential activity of one NOR over its homologue was found to be random within cells and independent of parental origin. Nucleotypic modifications mediated by changes in the 1R chromosome structure include increased proximity between homologous rDNA loci in interphase, and an increase in the frequency of cells with intra-nucleolar ribosomal condensed chromatin. These results seem to indicate a `sequence recognition' process for the regulation of homologous loci.
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Millan, N. M., P. Lau, M. Hann, D. Ioannou, D. Hoffman, M. Barrionuevo, W. Maxson, S. Ory, and H. G. Tempest. "Hierarchical radial and polar organisation of chromosomes in human sperm." Chromosome Research 20, no. 7 (October 2012): 875–87. http://dx.doi.org/10.1007/s10577-012-9323-y.
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Narayan, R. K. J. "Constraints upon the organisation and evolution of chromosomes in Allium." Theoretical and Applied Genetics 75, no. 2 (January 1988): 319–29. http://dx.doi.org/10.1007/bf00303971.
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Kuipers, Anja GJ, Pat JS Heslop-Harrison, and Evert Jacobsen. "Characterisation and physical localisation of Ty1-copia-like retrotransposons in four Alstroemeria species." Genome 41, no. 3 (June 1, 1998): 357–67. http://dx.doi.org/10.1139/g98-048.
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The genus Alstroemeria contains species with large genomes (2C = 36.5-78.9 pg (17 600 - 38 000 Mb) in those species with 2n = 2x = 16). We investigated the diversity and genomic and chromosomal organisation of Ty1-copia-like retrotransposons in four Alstroemeria species. Analysis of 33 PCR-amplified sequences corresponding to a conserved domain of the Ty1-copia reverse transcriptase (rt) gene showed high heterogeneity among predicted amino acid sequences; no two sequences were identical, but most fell into one of five subgroups. Levels of inter- and intra-specific heterogeneity of sequences were similar. HaeIII-digested genomic DNA of various Alstroemeria species contained distinct bands upon hybridisation with individual rt gene fragments. Hybridisation with the heterogeneous PCR pool of rt fragments (retrotransposon pool) revealed additional bands; some minor bands were characteristic of either Brazilian or Chilean species. In situ hybridisation of the retrotransposon pool from three species to metaphase chromosomes from the same species showed a dispersed distribution of the retrotransposon pool with exclusion from rDNA and other chromosomal sites.Alstroemeria pelegrina, which is without major heterochromatic sites, showed some clustering and small negative bands. The retrotransposon pool was excluded from major DAPI-staining bands in Alstroemeria aurea, but in contrast, the sites of the major tandemly repeated sequences in Alstroemeria inodora showed a hybridisation signal similar to that in the rest of the chromosomes. The data are discussed in the context of the contribution of Ty1-copia-like retrotransposons to plant genome size, their evolution, and their value for phylogenetic and biodiversity studies.Key words: Alstroemeria, in situ hybridisation, genome organisation, retrotransposable elements, Ty1-copia.
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Rashid, Fatema-Zahra M., Eike Mahlandt, Michiel van der Vaart, Daphne E. C. Boer, Monica Varela Alvarez, Bram Henneman, Daan J. W. Brocken, et al. "HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein." Nucleic Acids Research 50, no. 2 (November 4, 2021): e10-e10. http://dx.doi.org/10.1093/nar/gkab993.
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Abstract The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS — a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.
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Makałowski, W. "The human genome structure and organization." Acta Biochimica Polonica 48, no. 3 (September 30, 2001): 587–98. http://dx.doi.org/10.18388/abp.2001_3893.
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Genetic information of human is encoded in two genomes: nuclear and mitochondrial. Both of them reflect molecular evolution of human starting from the beginning of life (about 4.5 billion years ago) until the origin of Homo sapiens species about 100,000 years ago. From this reason human genome contains some features that are common for different groups of organisms and some features that are unique for Homo sapiens. 3.2 x 10(9) base pairs of human nuclear genome are packed into 23 chromosomes of different size. The smallest chromosome - 21st contains 5 x 10(7) base pairs while the biggest one -1st contains 2.63 x 10(8) base pairs. Despite the fact that the nucleotide sequence of all chromosomes is established, the organisation of nuclear genome put still questions: for example: the exact number of genes encoded by the human genome is still unknown giving estimations from 30 to 150 thousand genes. Coding sequences represent a few percent of human nuclear genome. The majority of the genome is represented by repetitiVe sequences (about 50%) and noncoding unique sequences. This part of the genome is frequently wrongly called "junk DNA". The distribution of genes on chromosomes is irregular, DNA fragments containing low percentage of GC pairs code lower number of genes than the fragments of high percentage of GC pairs.
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Loginova, Dina B., Anastasia A. Zhuravleva, and Olga G. Silkova. "Random chromosome distribution in the first meiosis of F1 disomic substitution line 2R(2D) x rye hybrids (ABDR, 4× = 28) occurs without bipolar spindle assembly." Comparative Cytogenetics 14, no. 4 (October 9, 2020): 453–82. http://dx.doi.org/10.3897/compcytogen.v14.i4.55827.
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The assembly of the microtubule-based spindle structure in plant meiosis remains poorly understood compared with our knowledge of mitotic spindle formation. One of the approaches in our understanding of microtubule dynamics is to study spindle assembly in meiosis of amphyhaploids. Using immunostaining with phH3Ser10, CENH3 and α-tubulin-specific antibodies, we studied the chromosome distribution and spindle organisation in meiosis of F1 2R(2D)xR wheat-rye hybrids (genome structure ABDR, 4× = 28), as well as in wheat and rye mitosis and meiosis. At the prometaphase of mitosis, spindle assembly was asymmetric; one half of the spindle assembled before the other, with simultaneous chromosome alignment in the spindle mid-zone. At diakinesis in wheat and rye, microtubules formed a pro-spindle which was subsequently disassembled followed by a bipolar spindle assembly. In the first meiosis of hybrids 2R(2D)xR, a bipolar spindle was not found and the kinetochore microtubules distributed the chromosomes. Univalent chromosomes are characterised by a monopolar orientation and maintenance of sister chromatid and centromere cohesion. Presence of bivalents did not affect the formation of a bipolar spindle. Since the central spindle was absent, phragmoplast originates from “interpolar” microtubules generated by kinetochores. Cell plate development occurred with a delay. However, meiocytes in meiosis II contained apparently normal bipolar spindles. Thus, we can conclude that: (1) cohesion maintenance in centromeres and between arms of sister chromatids may negatively affect bipolar spindle formation in the first meiosis; (2) 2R/2D rye/wheat chromosome substitution affects the regulation of the random chromosome distribution in the absence of a bipolar spindle.
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Kartout-Benmessaoud, Yasmine, Siham Ouchia-Benissad, Leila Mahiddine-Aoudjit, and Kafia Ladjali-Mohammedi. "Highlighting chromosomal rearrangements of five species of Galliformes (Domestic fowl, Common and Japanese quail, Barbary and Chukar partridge) and the Houbara bustard, an endangered Otidiformes: banding cytogenetic is a powerful tool." Comparative Cytogenetics 18 (December 3, 2024): 213–37. https://doi.org/10.3897/compcytogen.18.135056.
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Birds are one of the most diverse groups among terrestrial vertebrates. They evolved from theropod dinosaurs, are closely related to the sauropsid group and separated from crocodiles about 240 million years ago. According to the IUCN, 12% of bird populations are threatened with potential extinction. Classical cytogenetics remains a powerful tool for comparing bird genomes and plays a crucial role in the preservation populations of endangered species. It thus makes it possible to detect chromosomal abnormalities responsible for early embryonic mortalities. Thus, in this work, we have provided new information on part of the evolutionary history by analysing high-resolution GTG-banded chromosomes to detect inter- and intrachromosomal rearrangements in six species. Indeed, the first eight autosomal pairs and the sex chromosomes of the domestic fowl Gallus gallus domesticus Linnaeus, 1758 were compared with five species, four of which represent the order Galliformes (Common and Japanese quail, Gambras and Chukar partridge) and one Otidiformes species (Houbara bustard). Our findings suggest a high degree of conservation of the analysed ancestral chromosomes of the four Galliformes species, with the exception of (double, terminal, para and pericentric) inversions, deletion and the formation of neocentromeres (1, 2, 4, 7, 8, Z and W chromosomes). In addition to the detected rearrangements, reorganisation of the Houbara bustard chromosomes mainly included fusions and fissions involving both macro- and microchromosomes (especially on 2, 4 and Z chromosomes). We also found interchromosomal rearrangements involving shared microchromosomes (10, 11, 13, 14 and 19) between the two analysed avian orders. These rearrangements confirm that the structure of avian karyotypes will be more conserved at the interchromosomal but not at intrachromosomal scale. The appearance ofa small number of inter- and intrachromosomal rearrangements that occurred during evolution suggests a high degree of conservatism of genome organisation in these six species studied. A summary diagram of the rearrangements detected in this study is proposed to explain the chronology of the appearance of various evolutionary events starting from the ancestral karyotype.
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Mudrak, Olga, Rajeev Chandra, Estella Jones, Earl Godfrey, and Andrei Zalensky. "Reorganisation of human sperm nuclear architecture during formation of pronuclei in a model system." Reproduction, Fertility and Development 21, no. 5 (2009): 665. http://dx.doi.org/10.1071/rd08269.
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By fertilisation, two terminally differentiated cells, namely the egg and spermatozoon, are combined to create a totipotent zygote. During this process, the inactive sperm nucleus is transformed into a functional male pronucleus. Recent studies demonstrate that human sperm chromatin has an elaborate multilevel organisation, but almost nothing is known about how sperm chromosomes are transformed during fertilisation. Because of ethical reasons and technical complications, experimentation with human embryos is generally unworkable and adequate model systems are necessary to study the formation of male pronuclei. Here, we analyse remodelling of human sperm chromatin and chromosome architecture in Xenopus egg extracts using immunofluorescent localisation of protamines and centromere protein A, as well as fluorescence in situ hybridisation localisation of major α-satellite DNA and whole chromosome territory (CT). We demonstrate noticeable relocalisation of centromeres and remodelling of CT during the decondensation–recondensation cycle, mimicking cellular events that occur in the paternal genome in vivo during fertilisation.
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Guinet, F., and D. Labie. "La subtile organisation des chromosomes du Plasmodium pour échapper à la reconnaissance immunitaire." médecine/sciences 13, no. 6-7 (1997): 858. http://dx.doi.org/10.4267/10608/472.
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MacGregor, Isobel A., Ian R. Adams, and Nick Gilbert. "Large-scale chromatin organisation in interphase, mitosis and meiosis." Biochemical Journal 476, no. 15 (August 5, 2019): 2141–56. http://dx.doi.org/10.1042/bcj20180512.
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Abstract The spatial configuration of chromatin is fundamental to ensure any given cell can fulfil its functional duties, from gene expression to specialised cellular division. Significant technological innovations have facilitated further insights into the structure, function and regulation of three-dimensional chromatin organisation. To date, the vast majority of investigations into chromatin organisation have been conducted in interphase and mitotic cells leaving meiotic chromatin relatively unexplored. In combination, cytological and genome-wide contact frequency analyses in mammalian germ cells have recently demonstrated that large-scale chromatin structures in meiotic prophase I are reminiscent of the sequential loop arrays found in mitotic cells, although interphase-like segmentation of transcriptionally active and inactive regions are also evident along the length of chromosomes. Here, we discuss the similarities and differences of such large-scale chromatin architecture, between interphase, mitotic and meiotic cells, as well as their functional relevance and the proposed modulatory mechanisms which underlie them.
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Bougoutaia, Youcef, Sònia Garcia, Teresa Garnatje, Meriem Kaid-Harche, and Joan Vallès. "Genome size, chromosome number, and rDNA organisation in Algerian populations of Artemisia herba-alba (Asteraceae), a basic plant for animal feeding facing overgrazing erosion." Anales del Jardín Botánico de Madrid 73, no. 2 (November 23, 2016): 043. http://dx.doi.org/10.3989/ajbm.2415.
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Artemisia herba-alba is a largely-distributed and often landscape-dominating taxon in arid areas of the Mediterranean and Irano-Turanian regions. In Algeria, in 2010 its communities covered 10% of the steppe territory, but its populations have been subjected to overgrazing. A karyological study based on 22 populations together with a cytogenetic characterisation of this species has been performed for the first time in Algerian materials, through genome size and chromosome number determination. Fluorescence in situ hybridisation (FISH) was also used to assess the rDNA loci number and distribution in the two ploidy levels detected. The studied accessions are diploid (2n = 2x = 18 chromosomes, 6 populations) or tetraploid (2n = 4x = 36 chromosomes, 15 populations). One population, occupying a more or less central geographic position among the studied area, presented both cytotypes. Genome size reflects well the two ploidy levels, with no evidence of downsizing with polyploidy. The karyotypes are rather symmetric (2A Stebbins’ class). FISH analyses detected four signals (2 loci) in diploid and eight signals (4 loci) in tetraploid cytotypes for both ribosomal DNA genes, which present an L-type (linked) organisation, i.e. with loci from both rDNA genes colocalised. The presence of two ploidy levels suggest a genomic dynamism and even a possible differentiation underlying the morphological uniformity and despite the dramatic decrease experienced by this plant in Algeria in terms of surface coverage.
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Glans, Hedvig, Gabriel M. Matos, Maria Bradley, Tim Downing, and Björn Andersson. "Genetic coping mechanisms observed in Leishmania tropica, from the Middle East region, enhance the survival of the parasite after drug exposure." PLOS ONE 19, no. 12 (December 3, 2024): e0310821. https://doi.org/10.1371/journal.pone.0310821.
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Introduction Cutaneous leishmaniasis caused by L. tropica is common in the Middle East and treatment failure and drug resistance are known to occur. Several genetic mechanisms: aneuploidy, recombination and loss of heterozygosity, single nucleotide polymorphism (SNP) changes, copy number variation (CNV), and mutation of the H locus associated with drug resistance have been described. Materials and methods We studied SNP and CNV patterns in 22 isolates of L. tropica from Afghanistan, Iran and Syria in a geographic, phylogenetic and antimony exposure context. Results A high SNP frequency was observed in isolates from Syria on chromosome 23, including the H locus, linked to different ancestry at that chromosome segment. Among the isolates from Afghanistan and Iran, an elevated frequency of nonsynonymous SNPs was observed on several chromosomes. Changes in CNV patterns were seen in isolates exposed to drug pressure, especially for the ferric iron reductase gene. Expanded genes were categorised into five functional categories: translational elongation, mitochondrial transmembrane transport, positive regulation of cellular component organisation, response to stimulus and response to hypoxia. No CNV was identified at the H locus, the MAPK1 gene, the APQ1 gene, nor chromosomes 23, 31 or 36 regardless of previous antimonial exposure. Discussion In our study, Leishmania tropica had a jump in the nonsynonymous SNP rates at chromosome 23, including the H locus. CNV was observed among isolates exposed to antimonials, especially involving the gene encoding a ferric iron reductase. Several essential genetic coping mechanisms in the cell were enhanced when exposed to antimony, possibly for the survival of the parasite. Our work supports the perspective that Leishmania uses several mechanisms to adapt to environmental changes and drug exposure.
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Ou, Xiang-Hong, Sen Li, Bao-Zeng Xu, Lei-Ning Chen, Man-Xi Jiang, Shao-Qin Chen, and Nan-Qiao Chen. "Mitogen-activated protein kinase-activated protein kinase 2 is a critical regulator of pig oocyte meiotic maturation." Reproduction, Fertility and Development 29, no. 2 (2017): 223. http://dx.doi.org/10.1071/rd15150.
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Mitogen-activated protein kinase (MAPK)-activated protein kinase 2 (MK2), a direct substrate of p38 MAPK, plays key roles in multiple cellular processes. In the present study, we showed that MK2 affected not only cumulus expansion, but also the oocyte meiotic cell cycle in porcine oocytes. Inhibition of MK2 arrested oocytes at the germinal vesicle (GV) stage or the prometaphase I/metaphase I stage. Unlike in mouse oocytes, where phosphorylated (p-) MK2 was localised at the minus end of spindle microtubules and close to the spindle poles, in porcine oocytes p-MK2 was concentrated at the spindle equator and localised at the plus end of spindle microtubules. Knockdown or inhibition of MK2 resulted in spindle defects: spindles were surrounded by irregular chromosome non-disjunction or by chromosomes detached from the spindles. MK2 regulated spindle organisation and chromosome alignment by connecting microtubules with kinetochores. In addition, unlike in mitotic cells and meiotic mouse oocytes, the MK2–p38 MAPK pathway may not play an important role during meiotic cell cycle in porcine oocytes. In conclusion, MK2 is an important regulator of porcine oocyte meiotic maturation.
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Madi, Katombe. "Revisiting the Organisational DNA Metaphor: Unlocking Genetic Potential." European Journal of Business and Innovation Research 13, no. 2 (February 15, 2025): 39–55. https://doi.org/10.37745/ejbir.2013/vol13n23955.
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Strategic management researchers reckon that the combination of the biology and genetics reality with the management science, could provide effective steps in improving and developing organizations; hence, the initiative paradigm shift of organisational DNA metaphor. This study embarks on an in-depth review of both the organisational DNA concept and the DNA knowledge frontier - firstly, to assess whether the organisational DNA metaphor and academic discussions are warranted; secondly, if advanced DNA knowledge could be integrated into the organisational DNA concept for the betterment of operations management; and if so, thirdly, provide a spectrum of organisational DNA model. The review of DNA knowledge frontier reveals that the genome (DNA) has two components - the “coding DNA” (or Genes) and “non-coding DNA”. Their integration into organisational concept has enabled to establish an analogy: The “coding DNA” (or Genes) that contains the instructions needed for an organism to grow and survive, – translates into unique organizational traits (“structure, decision rights, motivators, and information”); The “non-coding DNA” that controls genes activity (“transcription, and hence, translation, or can switch genes on and off”) and ensures correct chromosomes bundling, which is vital for cell survival, – translates into renewal and innovation without which an organisation survival is compromised. The study proposes a spectrum of organisational DNA model and establishes a pivotal point for re-alignment between internal and external environments.
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Ruggeri, E., D. Albertini, and E. Carnevale. "181 CYTOSKELETAL AND CHROMOSOMAL ORGANIZATION IN DEVELOPMENTALLY ARRESTED EQUINE ZYGOTES AFTER INTRACYTOPLASMIC SPERM INJECTION." Reproduction, Fertility and Development 26, no. 1 (2014): 205. http://dx.doi.org/10.1071/rdv26n1ab181.
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Intracytoplasmic sperm injection (ICSI) has been developed as a clinical procedure in the equine industry. Not all sperm-injected oocytes develop into embryos; however, the causes of developmental failure after equine ICSI have not been studied. Our objective was to use confocal microscopy to evaluate sperm-injected equine oocytes from young and old mares that did not cleave in a clinical ICSI program, to study the hypothesis that cleavage failure is associated with cytoskeletal and chromosomal alterations and affected by mare age. Oocytes were collected from the dominant follicles of young (Y; 5–15 years old) and old (O; 20–24 years old) oestrous mares approximately 24 h after administration of deslorelin and hCG. At approximately 44 h after deslorelin and hCG administration, oocytes were injected using frozen-thawed sperm from various stallions. Injected oocytes (n = 15) that failed to cleave by 24 to 48 h were fixed in microtubule stabilization buffer extraction fixative (MTSB-XF) and stained for DNA, α/β tubulin, acetylated α-tubulin, and f-actin. Confocal z-stacks were obtained using a Zeiss LSM 5 microscope (Carl Zeiss Microscopy LLC, Thornwood, NY), and images were assessed for cytoskeletal structures and chromosome organisation using the Zeiss LSM image browser. Potential zygotes (Y: n = 6 and O: n = 9) were categorized for (1) 2 sets of chromosomes, (2) misaligned chromosomes, (3) oversized spindles (approximately twice the size of an MII spindle), and (4) actin bubbling. The number of zygotes in each category for Y and O mares were compared by Fisher's exact test. Some samples were included in more than 1 morphological category. Two separate sets of chromosomes were observed in 1 of 6 and 4 of 9 injected oocytes from Y and O mares, respectively (P = 0.58), with development stopping before fusion of male and female pronuclei. Misaligned chromosomes were present in 2 of 6 and 7 of 9 oocytes from Y and O mares, respectively (P = 0.14). Oversized spindles were observed in more Y than O potential zygotes (5 of 6 and 2 of 9, respectively, P = 0.04), representing fusion of male and female pronuclei before developmental arrest. Multiasters were associated with the oversized spindles in potential zygotes from Y (2 of 6) and O (2 of 9) mares (P = 1), with microtubule activity potentially associated with the first mitotic division. Structures associated with actin bubbling tended (P = 0.12) to be higher in uncleaved zygotes from Y than O mares (5 of 6 and 3 of 9, respectively). Of the 15 injected oocytes, 10 arrested after fusion of male and female pronuclei. We have previously observed a high incidence of chromosomal misalignment in metaphase II oocytes from old mares. In the small number of potential zygotes that were studied, chromosomal misalignment tended (P = 0.14) to be higher for old mares. Other observations, such as oversized spindles and actin bubbling, appeared to be more prevalent in the potential zygotes of Y than O mares; these observations could be associated with normal development or post-ovulatory aging of the oocyte. Additional work will focus on the roles of actin and microtubules in remodelling the cytoplasm and organizing the chromosomes after fertilization in the horse and on the role of maternal aging in fertilization failure.
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Baez, M., Y. T. Kuo, Y. Dias, T. Souza, A. Boudichevskaia, J. Fuchs, V. Schubert, A. L. L. Vanzela, A. Pedrosa-Harand, and A. Houben. "Analysis of the small chromosomal Prionium serratum (Cyperid) demonstrates the importance of reliable methods to differentiate between mono- and holocentricity." Chromosoma 129, no. 3-4 (November 9, 2020): 285–97. http://dx.doi.org/10.1007/s00412-020-00745-6.
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AbstractFor a long time, the Cyperid clade (Thurniceae-Juncaceae-Cyperaceae) was considered a group of species possessing holocentromeres exclusively. The basal phylogenetic position of Prionium serratum (Thunb.) Drège (Thurniceae) within Cyperids makes this species an important specimen to understand the centromere evolution within this clade. In contrast to the expectation, the chromosomal distribution of the centromere-specific histone H3 (CENH3), alpha-tubulin and different centromere-associated post-translational histone modifications (H3S10ph, H3S28ph and H2AT120ph) demonstrate a monocentromeric organisation of P. serratum chromosomes. Analysis of the high-copy repeat composition resulted in the identification of two centromere-localised satellite repeats. Hence, monocentricity was the ancestral condition for the Juncaceae-Cyperaceae-Thurniaceae Cyperid clade, and holocentricity in this clade has independently arisen at least twice after differentiation of the three families, once in Juncaceae and the other one in Cyperaceae. In this context, methods suitable for the identification of holocentromeres are discussed.
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Aagaard, L., M. Schmid, P. Warburton, and T. Jenuwein. "Mitotic phosphorylation of SUV39H1, a novel component of active centromeres, coincides with transient accumulation at mammalian centromeres." Journal of Cell Science 113, no. 5 (March 1, 2000): 817–29. http://dx.doi.org/10.1242/jcs.113.5.817.
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Centromeres of eukaryotes are frequently associated with constitutive heterochromatin and their activity appears to be coregulated by epigenetic modification of higher order chromatin. Recently, we isolated murine (Suv39h1) and human (SUV39H1) homologues of the dominant Drosophila suppressor of position effect variegation Su(var)3-9, which is also related to the S. pombe silencing factor Clr4. We have shown that mammalian Su(var)3-9 homologues encode novel centromeric proteins on metaphase-arrested chromosomes. Here, we describe a detailed analysis of the chromatin distribution of human SUV39H1 during the cell cycle. Although there is significant heterochromatic overlap between SUV39H1 and M31 (HP1(beta)) during interphase, mitotic SUV39H1 displays a more restricted spatial and temporal association pattern with metaphase chromosomes than M31 (HP1(beta)), or the related HP1(α) gene product. SUV39H1 specifically accumulates at the centromere during prometaphase but dissociates from centromeric positions at the meta- to anaphase transition. In addition, SUV39H1 selectively associates with the active centromere of a dicentric chromosome and also with a neocentromere. Interestingly, SUV39H1 is shown to be a phosphoprotein with modifications at serine and, to a lesser degree, also at threonine residues. Whereas SUV39H1 steady-state protein levels appear constant during the cell cycle, two additional phosphorylated isoforms are detected in mitotic extracts. This intriguing localisation and modification pattern would be consistent with a regulatory role(s) for SUV39H1 in participating in higher order chromatin organisation at mammalian centromeres.
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Barbieri, M., A. Scialdone, A. Gamba, A. Pombo, and M. Nicodemi. "Polymer physics, scaling and heterogeneity in the spatial organisation of chromosomes in the cell nucleus." Soft Matter 9, no. 36 (2013): 8631. http://dx.doi.org/10.1039/c3sm51436f.
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Narayan, R. K. J. "Molecular organisation of the plant genome: Its relation to structure, recombination and evolution of chromosomes." Journal of Genetics 70, no. 1 (April 1991): 43–61. http://dx.doi.org/10.1007/bf02923577.
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Yordanov, Romeo V. "Effects of gamma-radiation on the organisation of polytene chromosomes ofGlyptotendipes salinus Michailova (Chironomidae, Diptera)." Netherlands Journal of Aquatic Ecology 26, no. 2-4 (June 1992): 581–85. http://dx.doi.org/10.1007/bf02255293.
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Najer, Tomáš, Jorge Doña, Aleš Buček, Andrew D. Sweet, Oldřich Sychra, and Kevin P. Johnson. "Mitochondrial genome fragmentation is correlated with increased rates of molecular evolution." PLOS Genetics 20, no. 5 (May 3, 2024): e1011266. http://dx.doi.org/10.1371/journal.pgen.1011266.
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While mitochondrial genome content and organization is quite diverse across all Eukaryotes, most bilaterian animal mitochondrial genomes (mitogenomes) exhibit highly conserved gene content and organisation, with genes typically encoded on a single circular chromosome. However, many species of parasitic lice (Insecta: Phthiraptera) are among the notable exceptions, having mitogenomes fragmented into multiple circular chromosomes. To better understand the process of mitogenome fragmentation, we conducted a large-scale genomic study of a major group of lice, Amblycera, with extensive taxon sampling. Analyses of the evolution of mitogenome structure across a phylogenomic tree of 90 samples from 53 genera revealed evidence for multiple independent origins of mitogenome fragmentation, some inferred to have occurred less than five million years ago. We leveraged these many independent origins of fragmentation to compare the rates of DNA substitution and gene rearrangement, specifically contrasting branches with fragmented and non-fragmented mitogenomes. We found that lineages with fragmented mitochondrial genomes had significantly higher rates of mitochondrial sequence evolution. In addition, lineages with fragmented mitochondrial genomes were more likely to have mitogenome gene rearrangements than those with single-chromosome mitochondrial genomes. By combining phylogenomics and mitochondrial genomics we provide a detailed portrait of mitogenome evolution across this group of insects with a remarkably unstable mitogenome structure, identifying processes of molecular evolution that are correlated with mitogenome fragmentation.
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Bancroft, Ian. "Insights into the Structural and Functional Evolution of Plant Genomes Afforded by the Nucleotide Sequences of Chromosomes 2 and 4 ofArabidopsis thaliana." Yeast 1, no. 1 (2000): 1–5. http://dx.doi.org/10.1002/(sici)1097-0061(200004)17:1<1::aid-yea3>3.0.co;2-v.
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The rapidly accumulating genome sequence data from the plantArabidopsis thalianaallows more detailed analysis of genome content and organisation than ever bafore possible in plants. The genome shows a surprisingly high level of genetic redundancy, with as many as 75% of gene products showing signficant homology to another protien ofA. thaliana.Many duplicated genes occur in arrays of conserved order and indicate thatA. thalianais likely to have had a tetraploid ancestor. Analysis of the divergence of duplicated genome segments leads to the prediction of two major modes of plant genome evolution: macro-scale duplication and rearrangement of chromosomes and micro-scale translocation, duplication and loss of individual genes or small groups of genes.
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Bancroft, Ian. "Insights into the Structural and Functional Evolution of Plant Genomes Afforded by the Nucleotide Sequences of Chromosomes 2 and 4 of Arabidopsis thaliana." Yeast 1, no. 1 (January 1, 2000): 1–5. http://dx.doi.org/10.1155/2000/365024.
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The rapidly accumulating genome sequence data from the plant Arabidopsis thaliana allows more detailed analysis of genome content and organisation than ever bafore possible in plants. The genome shows a surprisingly high level of genetic redundancy, with as many as 75% of gene products showing signficant homology to another protien of A. thaliana. Many duplicated genes occur in arrays of conserved order and indicate that A. thaliana is likely to have had a tetraploid ancestor. Analysis of the divergence of duplicated genome segments leads to the prediction of two major modes of plant genome evolution: macro-scale duplication and rearrangement of chromosomes and micro-scale translocation, duplication and loss of individual genes or small groups of genes.
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Pearce, Stephen R., Gill Harrison, Pat (J S. ). Heslop-Harrison, Andrew J. Flavell, and Amar Kumar. "Characterization and genomic organization of Ty1-copia group retrotransposons in rye (Secale cereale)." Genome 40, no. 5 (October 1, 1997): 617–25. http://dx.doi.org/10.1139/g97-081.
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The genomic organisation of the Ty1-copia retrotransposons in rye (Secale cereale) has been studied. We have used the polymerase chain reaction (PCR) to amplify sequences from a conserved domain of the reverse transcriptase gene of the Ty1-copia retrotransposons in this species. Sequence analysis of 26 of these PCR products shows them to be a highly heterogeneous population, a feature that is common in plants. Slot blot analysis shows that there are about 100 000 individual Ty1-copia retrotransposons in rye. In situ hybridization of a heterogeneous probe, representing the whole population of rye Ty1-copia retrotransposon sequences, to chromosome spreads of triticale (×Triticosecale), a rye–wheat hybrid, shows that these sequences are present throughout all the rye chromosomes but absent from the centromeric regions and, in particular, from the terminal heterochromatin. Southern analysis of oat, barley, wheat, and rye, using as a probe R9, one of the rye sequences that is closely similar to the BARE-1 element of barley, shows that close relatives of this retrotransposon subgroup are present in all these species in high copy number. Northern analysis on RNAs from seedlings shows that the BARE-1 subgroup is transcribed in all these cereal plants but in variable amounts: high in barley, moderate in wheat and rye, and extremely low in oat.Key words: retrotransposons, Secale cereale, plant genome, Ty1-copia, in situ hybridization.
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Gurzau, Alexandra D., Marnie E. Blewitt, Peter E. Czabotar, James M. Murphy, and Richard W. Birkinshaw. "Relating SMCHD1 structure to its function in epigenetic silencing." Biochemical Society Transactions 48, no. 4 (August 11, 2020): 1751–63. http://dx.doi.org/10.1042/bst20200242.
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The structural maintenance of chromosomes hinge domain containing protein 1 (SMCHD1) is a large multidomain protein involved in epigenetic gene silencing. Variations in the SMCHD1 gene are associated with two debilitating human disorders, facioscapulohumeral muscular dystrophy (FSHD) and Bosma arhinia microphthalmia syndrome (BAMS). Failure of SMCHD1 to silence the D4Z4 macro-repeat array causes FSHD, yet the consequences on gene silencing of SMCHD1 variations associated with BAMS are currently unknown. Despite the interest due to these roles, our understanding of the SMCHD1 protein is in its infancy. Most knowledge of SMCHD1 function is based on its similarity to the structural maintenance of chromosomes (SMC) proteins, such as cohesin and condensin. SMC proteins and SMCHD1 share similar domain organisation and affect chromatin conformation. However, there are important differences between the domain architectures of SMC proteins and SMCHD1, which distinguish SMCHD1 as a non-canonical member of the family. In the last year, the crystal structures of the two key domains crucial to SMCHD1 function, the ATPase and hinge domains, have emerged. These structures reveal new insights into how SMCHD1 may bind and regulate chromatin structure, and address how amino acid variations in SMCHD1 may contribute to BAMS and FSHD. Here, we contrast SMCHD1 with canonical SMC proteins, and relate the ATPase and hinge domain structures to their roles in SMCHD1-mediated epigenetic silencing and disease.
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Ortiz-Hernandez, R., G. H. Vázquez-Nin, O. Echeverría-Martínez, C. Höög, and A. Hernández-Hernández. "Crio-fixation of Pachytene Cells." Microscopy and Microanalysis 26, S1 (March 2020): 43. http://dx.doi.org/10.1017/s1431927620000458.
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AbstractGenetic variability in organisms with sexual reproduction is produced by a complex mechanism of cell division of the germ line cells known as meiosis. During meiosis, homologous chromosomes pair and exchange genetic material (meiotic recombination), process that is essential to complete the meiotic division and to produce variability. Homologous chromosome pairing is mediated by the synaptonemal complex (SC). The SC is a proteinaceous structure composed of two lateral elements (LEs) and a central region (CR). Any defect in SC structure impairs meiotic recombination leading to blockage of the cell division process and infertility1. The SC has been observed since the introduction of the electron microscope (EM) in the biological field and it has been reported to be present in almost all the organisms with sexual reproduction, conserving a very similar structure and organisation along the different species2,3. The classic approach to study the SC structure is to chemically fixate the sexual tissues (gonads), dehydrate and embedded them in plastic resins that provide a support for sample sectioning and observation under the EM. However, chemical fixation followed by dehydration is well known to produce artefacts in the structure of many biological samples. Recently, we have combined fluorescence activated cell sorting of cells with SCs with high-pressure freezing and freeze- substitution and have found that the structure of the CR looks different from that observed in chemically fixated samples. These data have prompted us to analyse the organization of the CR components under cryo-processing.
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Minocherhomji, Sheroy, Prochi F. Madon, and Firuza R. Parikh. "Epigenetic Regulatory Mechanisms Associated with Infertility." Obstetrics and Gynecology International 2010 (2010): 1–7. http://dx.doi.org/10.1155/2010/198709.
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Infertility is a complex human condition and is known to be caused by numerous factors including genetic alterations and abnormalities. Increasing evidence from studies has associated perturbed epigenetic mechanisms with spermatogenesis and infertility. However, there has been no consensus on whether one or a collective of these altered states is responsible for the onset of infertility. Epigenetic alterations involve changes in factors that regulate gene expression without altering the physical sequence of DNA. Understanding these altered epigenetic states at the genomic level along with higher order organisation of chromatin in genes associated with infertility and pericentromeric regions of chromosomes, particularly 9 and Y, could further identify causes of idiopathic infertility. Determining the association between DNA methylation, chromatin state, and noncoding RNAs with the phenotype could further determine what possible mechanisms are involved. This paper reviews certain mechanisms of epigenetic regulation with particular emphasis on their possible role in infertility.
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Kovalyshyn, Stepan. "Study of structural changes in the cells of the stimulated seed sprouts." International Agrophysics 30, no. 4 (October 1, 2016): 545–50. http://dx.doi.org/10.1515/intag-2016-0012.
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AbstractThe paper emphasises that one of the easiest and effective methods of pre-treatment of seed is by industrial electrical power frequency. In order to select the most effective treatment regime it is necessary to reveal the mechanism of the impact of electromagnetic fields on biological structures, including plants. In this regard, electron microscopy studies at the cellular level of seedlings of perennial ryegrass seed treated with electric field corona discharge were conducted. It was found that in seedlings of treated seeds the intracellular organisation of the plant varies, resulting in changes during cell division. This is apparently due to a reduction in interphase, including S-phase, resulting in disrupted normal DNA synthesis, chromatin formation and, consequently, the collection of chromosomes. As a result, the cell division is faster, which leads to increased sowing quality of seeds of studied plants. While maintaining the characteristics of the studied cell division of seedling seed which was subjected to electrical stimulation, there is the prospect of a significant increase of seed germination of ryegrass in the future generations.
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Gentric, Géraldine, Chantal Desdouets, and Séverine Celton-Morizur. "Hepatocytes Polyploidization and Cell Cycle Control in Liver Physiopathology." International Journal of Hepatology 2012 (2012): 1–8. http://dx.doi.org/10.1155/2012/282430.
Full textAbstract:
Most cells in mammalian tissues usually contain a diploid complement of chromosomes. However, numerous studies have demonstrated a major role of “diploid-polyploid conversion” during physiopathological processes in several tissues. In the liver parenchyma, progressive polyploidization of hepatocytes takes place during postnatal growth. Indeed, at the suckling-weaning transition, cytokinesis failure events induce the genesis of binucleated tetraploid liver cells. Insulin signalling, through regulation of the PI3K/Akt signalling pathway, is essential in the establishment of liver tetraploidization by controlling cytoskeletal organisation and consequently mitosis progression. Liver cell polyploidy is generally considered to indicate terminal differentiation and senescence, and both lead to a progressive loss of cell pluripotency associated to a markedly decreased replication capacity. Although adult liver is a quiescent organ, it retains a capacity to proliferate and to modulate its ploidy in response to various stimuli or aggression (partial hepatectomy, metabolic overload (i.e., high copper and iron hepatic levels), oxidative stress, toxic insult, and chronic hepatitis etc.). Here we review the mechanisms and functional consequences of hepatocytes polyploidization during normal and pathological liver growth.
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Senderowicz, Magdalena, Teresa Nowak, Hanna Weiss-Schneeweiss, Laszlo Papp, and Bozena Kolano. "Molecular and Cytogenetic Analysis of rDNA Evolution in Crepis Sensu Lato." International Journal of Molecular Sciences 23, no. 7 (March 26, 2022): 3643. http://dx.doi.org/10.3390/ijms23073643.
Full textAbstract:
Although Crepis was the first model plant group in which chromosomal changes were considered to play an important role in speciation, their chromosome structure and evolution have been barely investigated using molecular cytogenetic methods. The aim of the study was to provide a better understanding of the patterns and directions of Crepis chromosome evolution, using comparative analyses of rDNA loci number and localisation. The chromosome base number and chromosomal organisation of 5S and 35S rDNA loci were analysed in the phylogenetic background for 39 species of Crepis, which represent the evolutionary lineages of Crepis sensu stricto and Lagoseris, including Lapsana communis. The phylogenetic relationships among all the species were inferred from nrITS and newly obtained 5S rDNA NTS sequences. Despite high variations in rDNA loci chromosomal organisation, most species had a chromosome with both rDNA loci within the same (usually short) chromosomal arm. The comparative analyses revealed several independent rDNA loci number gains and loci repositioning that accompanied diversification and speciation in Crepis. Some of the changes in rDNA loci patterns were reconstructed for the same evolutionary lineages as descending dysploidy.
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Besse, P., and C. L. McIntyre. "Isolation and characterisation of repeated DNA sequences from Erianthus spp. (Saccharinae: Andropogoneae)." Genome 41, no. 3 (June 1, 1998): 408–16. http://dx.doi.org/10.1139/g98-034.
Full textAbstract:
Four anonymous noncoding sequences were isolated from Erianthus arundinaceus. The four sequences were selected because they were specific to the genusErianthus section Ripidium, relative to Saccharum spp. These sequences, designated Eracsi 294, 228, 153, and 34, showed various degrees of repetitiveness and different patterns of distribution. Eracsi 34 and 153 were low- and medium-copy repeated sequences, respectively, and appeared to be present at discrete locations in the Erianthus genome. By contrast, Eracsi 294, also a low-copy sequence, appeared to be more dispersed in location, with some tandem arrays identified. Eracsi 228 was highly repeated and dispersed. The location of Eracsi 228 was more precisely determined by FISH and was found to be distributed along the length of, but not at the telomeres of, most chromosomes in two Erianthus species. The distribution of the four sequences was investigated in a sample of 65 Erianthus (representing 9 species) and 14 Saccharum (2 species) accessions. The usefulness of these sequences for phylogenetic and genome organisation studies in sugarcane and for assessing the genetic structure of Saccharum x Erianthus intergeneric hybrids is discussed.Key words: Erianthus, FISH, repetitive sequences, Saccharum, sugarcane.