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1
Liehr, Thomas. "From Human Cytogenetics to Human Chromosomics." International Journal of Molecular Sciences 20, no. 4 (February 14, 2019): 826. http://dx.doi.org/10.3390/ijms20040826.
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Background: The concept of “chromosomics” was introduced by Prof. Uwe Claussen in 2005. Herein, the growing insights into human chromosome structure finally lead to a “chromosomic view” of the three-dimensional constitution and plasticity of genes in interphase nuclei are discussed. This review is dedicated to the memory of Prof. Uwe Claussen (30 April 1945–20 July 2008). Recent findings: Chromosomics is the study of chromosomes, their three-dimensional positioning in the interphase nucleus, the consequences from plasticity of chromosomal subregions and gene interactions, the influence of chromatin-modification-mediated events on cells, and even individuals, evolution, and disease. Progress achieved in recent years is summarized, including the detection of chromosome-chromosome-interactions which, if damaged, lead to malfunction and disease. However, chromosomics in the Human Genetics field is not progressing presently, as research interest has shifted from single cell to high throughput, genomic approaches. Conclusion: Chromosomics and its impact were predicted correctly in 2005 by Prof. Claussen. Although some progress was achieved, present reconsiderations of the role of the chromosome and the single cell in Human Genetic research are urgently necessary.
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Pelttari, Jeanette, Mary-Rose Hoja, Li Yuan, Jian-Guo Liu, Eva Brundell, Peter Moens, Sabine Santucci-Darmanin, et al. "A Meiotic Chromosomal Core Consisting of Cohesin Complex Proteins Recruits DNA Recombination Proteins and Promotes Synapsis in the Absence of an Axial Element in Mammalian Meiotic Cells." Molecular and Cellular Biology 21, no. 16 (August 15, 2001): 5667–77. http://dx.doi.org/10.1128/mcb.21.16.5667-5677.2001.
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ABSTRACT The behavior of meiotic chromosomes differs in several respects from that of their mitotic counterparts, resulting in the generation of genetically distinct haploid cells. This has been attributed in part to a meiosis-specific chromatin-associated protein structure, the synaptonemal complex. This complex consist of two parallel axial elements, each one associated with a pair of sister chromatids, and a transverse filament located between the synapsed homologous chromosomes. Recently, a different protein structure, the cohesin complex, was shown to be associated with meiotic chromosomes and to be required for chromosome segregation. To explore the functions of the two different protein structures, the synaptonemal complex and the cohesin complex, in mammalian male meiotic cells, we have analyzed how absence of the axial element affects early meiotic chromosome behavior. We find that the synaptonemal complex protein 3 (SCP3) is a main determinant of axial-element assembly and is required for attachment of this structure to meiotic chromosomes, whereas SCP2 helps shape the in vivo structure of the axial element. We also show that formation of a cohesin-containing chromosomal core in meiotic nuclei does not require SCP3 or SCP2. Our results also suggest that the cohesin core recruits recombination proteins and promotes synapsis between homologous chromosomes in the absence of an axial element. A model for early meiotic chromosome pairing and synapsis is proposed.
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Spell, R. M., and C. Holm. "Nature and distribution of chromosomal intertwinings in Saccharomyces cerevisiae." Molecular and Cellular Biology 14, no. 2 (February 1994): 1465–76. http://dx.doi.org/10.1128/mcb.14.2.1465-1476.1994.
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To elucidate yeast chromosome structure and behavior, we examined the breakage of entangled chromosomes in DNA topoisomerase II mutants by hybridization to chromosomal DNA resolved by pulsed-field gel electrophoresis. Our study reveals that large and small chromosomes differ in the nature and distribution of their intertwinings. Probes to large chromosomes (450 kb or larger) detect chromosome breakage, but probes to small chromosomes (380 kb or smaller) reveal no breakage products. Examination of chromosomes with one small arm and one large arm suggests that the two arms behave independently. The acrocentric chromosome XIV breaks only on the long arm, and its preferred region of breakage is approximately 200 kb from the centromere. When the centromere of chromosome XIV is relocated, the preferred region of breakage shifts accordingly. These results suggest that large chromosomes break because they have long arms and small chromosomes do not break because they have small arms. Indeed, a small metacentric chromosome can be made to break if it is rearranged to form a telocentric chromosome with one long arm or a ring with an "infinitely" long arm. These results suggest a model of chromosomal intertwining in which the length of the chromosome arm prevents intertwinings from passively resolving off the end of the arm during chromosome segregation.
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Spell, R. M., and C. Holm. "Nature and distribution of chromosomal intertwinings in Saccharomyces cerevisiae." Molecular and Cellular Biology 14, no. 2 (February 1994): 1465–76. http://dx.doi.org/10.1128/mcb.14.2.1465.
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To elucidate yeast chromosome structure and behavior, we examined the breakage of entangled chromosomes in DNA topoisomerase II mutants by hybridization to chromosomal DNA resolved by pulsed-field gel electrophoresis. Our study reveals that large and small chromosomes differ in the nature and distribution of their intertwinings. Probes to large chromosomes (450 kb or larger) detect chromosome breakage, but probes to small chromosomes (380 kb or smaller) reveal no breakage products. Examination of chromosomes with one small arm and one large arm suggests that the two arms behave independently. The acrocentric chromosome XIV breaks only on the long arm, and its preferred region of breakage is approximately 200 kb from the centromere. When the centromere of chromosome XIV is relocated, the preferred region of breakage shifts accordingly. These results suggest that large chromosomes break because they have long arms and small chromosomes do not break because they have small arms. Indeed, a small metacentric chromosome can be made to break if it is rearranged to form a telocentric chromosome with one long arm or a ring with an "infinitely" long arm. These results suggest a model of chromosomal intertwining in which the length of the chromosome arm prevents intertwinings from passively resolving off the end of the arm during chromosome segregation.
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S. Ramos, Ana Carolina, and Samara Cao Paixão. "Montando cromossomos: o ensino das alterações cromossômicas estruturais de maneira inovadora." Revista Científica Faesa 16, no. 2 (August 1, 2020): 07–27. http://dx.doi.org/10.5008/1809.7367.174.
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Dooner, H. K., and A. Belachew. "Chromosome breakage by pairs of closely linked transposable elements of the Ac-Ds family in maize." Genetics 129, no. 3 (November 1, 1991): 855–62. http://dx.doi.org/10.1093/genetics/129.3.855.
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Abstract Chromosome breaks and hence chromosomal rearrangements often occur in maize stocks harboring transposable elements (TEs), yet it is not clear what types of TE structures promote breakage. We have shown previously that chromosomes containing a complex transposon structure consisting of an Ac (Activator) element closely linked in direct orientation to a terminally deleted or fractured Ac (fAc) element have a strong tendency to break during endosperm development. Here we show that pairs of closely linked transposons with intact ends, either two Ac elements--a common product of Ac transposition--or an Ac and a Ds (Dissociation) element, can constitute chromosome-breaking structures, and that the frequency of breakage is inversely related to intertransposon distance. Similar structures may also be implicated in chromosome breaks in other eukaryotic TE systems known to produce chromosomal rearrangements. The present findings are discussed in light of a model of chromosome breakage that is based on the transposition of a partially replicated macrotransposon delimited by the outside ends of the two linked TEs.
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Uchida, Tetsuya, Naoto Ishihara, Hiroyuki Zenitani, Keiichiro Hiratsu, and Haruyasu Kinashi. "Circularized Chromosome with a Large Palindromic Structure in Streptomyces griseus Mutants." Journal of Bacteriology 186, no. 11 (June 1, 2004): 3313–20. http://dx.doi.org/10.1128/jb.186.11.3313-3320.2004.
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ABSTRACT Streptomyces linear chromosomes display various types of rearrangements after telomere deletion, including circularization, arm replacement, and amplification. We analyzed the new chromosomal deletion mutants Streptomyces griseus 301-22-L and 301-22-M. In these mutants, chromosomal arm replacement resulted in long terminal inverted repeats (TIRs) at both ends; different sizes were deleted again and recombined inside the TIRs, resulting in a circular chromosome with an extremely large palindrome. Short palindromic sequences were found in parent strain 2247, and these sequences might have played a role in the formation of this unique structure. Dynamic structural changes of Streptomyces linear chromosomes shown by this and previous studies revealed extraordinary strategies of members of this genus to keep a functional chromosome, even if it is linear or circular.
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Eidelman, Yuri, Ilya Salnikov, Svetlana Slanina, and Sergey Andreev. "Chromosome Folding Promotes Intrachromosomal Aberrations under Radiation- and Nuclease-Induced DNA Breakage." International Journal of Molecular Sciences 22, no. 22 (November 10, 2021): 12186. http://dx.doi.org/10.3390/ijms222212186.
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The long-standing question in radiation and cancer biology is how principles of chromosome organization impact the formation of chromosomal aberrations (CAs). To address this issue, we developed a physical modeling approach and analyzed high-throughput genomic data from chromosome conformation capture (Hi-C) and translocation sequencing (HTGTS) methods. Combining modeling of chromosome structure and of chromosomal aberrations induced by ionizing radiation (IR) and nuclease we made predictions which quantitatively correlated with key experimental findings in mouse chromosomes: chromosome contact maps, high frequency of cis-translocation breakpoints far outside of the site of nuclease-induced DNA double-strand breaks (DSBs), the distinct shape of breakpoint distribution in chromosomes with different 3D organizations. These correlations support the heteropolymer globule principle of chromosome organization in G1-arrested pro-B mouse cells. The joint analysis of Hi-C, HTGTS and physical modeling data offers mechanistic insight into how chromosome structure heterogeneity, globular folding and lesion dynamics drive IR-recurrent CAs. The results provide the biophysical and computational basis for the analysis of chromosome aberration landscape under IR and nuclease-induced DSBs.
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Gunawardena, S., E. Heddle, and M. C. Rykowski. "‘Chromosomal puffing’ in diploid nuclei of Drosophila melanogaster." Journal of Cell Science 108, no. 5 (May 1, 1995): 1863–72. http://dx.doi.org/10.1242/jcs.108.5.1863.
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In situ hybridization has become a powerful technique for dissecting nuclear structure. By localizing nucleic acids with high precision, it is possible to infer the native structure of chromosomes, replication factories and transcript processing complexes. To increase the value of this technique, we have established the limits of resolution of two-color in situ hybridization to chromosomal DNA in diploid chromosomes of Drosophila embryonic nuclei. Using high-resolution 3-dimensional optical microscopy and computational image analysis, we establish that we can distinguish the location of chromosomal sequences that lie 27–29 kb apart within a 40 kb transcription unit with an accuracy of about 100 nm. Contrary to observations made in mammalian tissue culture cells, we find that when the gene is expressed, it assumes an open configuration, and that the extent of decondensation is variable from chromosome to chromosome. Further experiments suggest that variation in gene structure results from asynchrony in transcriptional elongation. We suggest that the phenomenon we observe is the diploid analog to chromosomal puffing that occurs in the transcriptionally active regions of Drosophila polytene chromosomes.
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Anderson, Lorinda K., Naser Salameh, Hank W. Bass, Lisa C. Harper, W. Z. Cande, Gerd Weber, and Stephen M. Stack. "Integrating Genetic Linkage Maps With Pachytene Chromosome Structure in Maize." Genetics 166, no. 4 (April 1, 2004): 1923–33. http://dx.doi.org/10.1093/genetics/166.4.1923.
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Abstract Genetic linkage maps reveal the order of markers based on the frequency of recombination between markers during meiosis. Because the rate of recombination varies along chromosomes, it has been difficult to relate linkage maps to chromosome structure. Here we use cytological maps of crossing over based on recombination nodules (RNs) to predict the physical position of genetic markers on each of the 10 chromosomes of maize. This is possible because (1) all 10 maize chromosomes can be individually identified from spreads of synaptonemal complexes, (2) each RN corresponds to one crossover, and (3) the frequency of RNs on defined chromosomal segments can be converted to centimorgan values. We tested our predictions for chromosome 9 using seven genetically mapped, single-copy markers that were independently mapped on pachytene chromosomes using in situ hybridization. The correlation between predicted and observed locations was very strong (r2 = 0.996), indicating a virtual 1:1 correspondence. Thus, this new, high-resolution, cytogenetic map enables one to predict the chromosomal location of any genetically mapped marker in maize with a high degree of accuracy. This novel approach can be applied to other organisms as well.
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Sajid, Atiqa, El-Nasir Lalani, Bo Chen, Teruo Hashimoto, Darren K. Griffin, Archana Bhartiya, George Thompson, Ian K. Robinson, and Mohammed Yusuf. "Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus." International Journal of Molecular Sciences 22, no. 11 (June 1, 2021): 5987. http://dx.doi.org/10.3390/ijms22115987.
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Three dimensional (3D) ultra-structural imaging is an important tool for unraveling the organizational structure of individual chromosomes at various stages of the cell cycle. Performing hitherto uninvestigated ultra-structural analysis of the human genome at prophase, we used serial block-face scanning electron microscopy (SBFSEM) to understand chromosomal architectural organization within 3D nuclear space. Acquired images allowed us to segment, reconstruct, and extract quantitative 3D structural information about the prophase nucleus and the preserved, intact individual chromosomes within it. Our data demonstrate that each chromosome can be identified with its homolog and classified into respective cytogenetic groups. Thereby, we present the first 3D karyotype built from the compact axial structure seen on the core of all prophase chromosomes. The chromosomes display parallel-aligned sister chromatids with familiar chromosome morphologies with no crossovers. Furthermore, the spatial positions of all 46 chromosomes revealed a pattern showing a gene density-based correlation and a neighborhood map of individual chromosomes based on their relative spatial positioning. A comprehensive picture of 3D chromosomal organization at the nanometer level in a single human lymphocyte cell is presented.
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Brinkley, B. R., and R. P. Zinkowski. "Scleroderma crest autoantibodies as fluorescent and Immuno-Electron Microscopic probes: Keys to a chromosomal black box." Proceedings, annual meeting, Electron Microscopy Society of America 49 (August 1991): 12–13. http://dx.doi.org/10.1017/s0424820100084363.
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The mammalian kinetochore is a highly differentiated structure found at the centromere (primary constriction) of chromosomes that serves as an attachment site for spindle microtubules. Ultrastructurally, the kinetochore typically appears as a tri-layered plate or disc situated at the sides of the centromere (Fig.1). Recent evidence demonstrates that kinetochores have the ability to capture and stabilize microtubules that grow from the spindle poles. Moreover, the motor(s) for chromosome movement appear to be located in or near the kinetochore which actively participates in the generation of forces necessary for chromosome movement in mitosis and meiosis. To understand how the precise ballet-like movements of chromosomes on the mitotic spindle occur, attention has focused on the “black box” of the chromosome; the centromere-kinetochore complex.The fortuitous discovery that serum from individuals with the CREST variant of scleroderma contain autoantibodies that bind to components of the centromere-kinetochore complex has led to major advancements in the understanding of this chromosomal black box. Indirect immunofluorescence has demonstrated the presence of paired fluorescent structures (Fig.2) at the centromeres of both mammalian and plant chromosomes.
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Albert, Patrice S., Tao Zhang, Kassandra Semrau, Jean-Marie Rouillard, Yu-Hsin Kao, Chung-Ju Rachel Wang, Tatiana V. Danilova, Jiming Jiang, and James A. Birchler. "Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships." Proceedings of the National Academy of Sciences 116, no. 5 (January 17, 2019): 1679–85. http://dx.doi.org/10.1073/pnas.1813957116.
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Whole-chromosome painting probes were developed for each of the 10 chromosomes of maize by producing amplifiable libraries of unique sequences of oligonucleotides that can generate labeled probes through transcription reactions. These paints allow identification of individual homologous chromosomes for many applications as demonstrated in somatic root tip metaphase cells, in the pachytene stage of meiosis, and in interphase nuclei. Several chromosomal aberrations were examined as proof of concept for study of various rearrangements using probes that cover the entire chromosome and that label diverse varieties. The relationship of the supernumerary B chromosome and the normal chromosomes was examined with the finding that there is no detectable homology between any of the normal A chromosomes and the B chromosome. Combined with other chromosome-labeling techniques, a complete set of whole-chromosome oligonucleotide paints lays the foundation for future studies of the structure, organization, and evolution of genomes.
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Pizzaia, Daniel, Vanessa M. Oliveira-Maekawa, Aline R. Martins, Mateus Mondin, and Margarida L. R. Aguiar-Perecin. "Karyotype structure and NOR activity in Brazilian Smilax Linnaeus, 1753 species (Smilacaceae)." Comparative Cytogenetics 13, no. 3 (August 22, 2019): 245–63. http://dx.doi.org/10.3897/compcytogen.v13i3.35775.
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The genus Smilax Linnaeus, 1753 (Smilacaceae) is a large genus of dioecious plants distributed in tropical, subtropical and temperate regions. Some Smilax species have medicinal importance and their identification is important for the control of raw material used in the manufacture of phytotherapeutical products. The karyotypes of seven Brazilian Smilax species were investigated. Mitotic metaphases of roots from young plants were analysed in Feulgen-stained preparations. The karyotypes were asymmetric and modal with 2n = 2x = 32 chromosomes gradually decreasing in size. In S. goyazana A De Candolle & C De Candolle, 1878, a polyploid species, 2n = 4x = 64. In all the species, the large and medium-sized chromosomes were subtelocentric and submetacentric and the small chromosomes were submetacentric or metacentric. Their karyotypes were quite similar, with differences in the arm ratio of some chromosomes. S. fluminensis Steudel, 1841 differed from the other species by having a large metacentric chromosome 1. These findings suggest that evolution occurred without drastic changes in the chromosomal structure in the species analyzed. Terminal secondary constrictions were visualized on the short arm of some chromosomes, but they were detected only in one homologue of each pair. Due to the terminal location and the degree of chromosome condensation, secondary constrictions were not visualized in some species. The nucleolus organizer regions (NORs) were mapped by silver-staining and fluorescent in situ hybridization (FISH) in S. rufescens Grisebach, 1842 and S. fluminensis. Silver-staining and FISH signals were colocalized on the short arms of six chromosomes in S. rufescens and four chromosomes in S. fluminensis. In FISH preparations, one of the largest chromosomes had the secondary constrictions highly decondensed in some cells. This finding and the heteromorphism observed in Feulgen-stained chromosomes suggest that differential rRNA gene expression between homologous rDNA loci can occur in some cells, resulting in different degrees of ribosomal chromatin decondensation. The presence of a heteromorphic chromosome pair in S. rufescens, S. polyantha Grisebach, 1842 and S. goyazana suggests a chromosomal sex determination in these dioecious species.
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Runge, K. W., R. J. Wellinger, and V. A. Zakian. "Effects of excess centromeres and excess telomeres on chromosome loss rates." Molecular and Cellular Biology 11, no. 6 (June 1991): 2919–28. http://dx.doi.org/10.1128/mcb.11.6.2919-2928.1991.
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The linear chromosomes of eukaryotes contain specialized structures to ensure their faithful replication and segregation to daughter cells. Two of these structures, centromeres and telomeres, are limited, respectively, to one and two copies per chromosome. It is possible that the proteins that interact with centromere and telomere DNA sequences are present in limiting amounts and could be competed away from the chromosomal copies of these elements by additional copies introduced on plasmids. We have introduced excess centromeres and telomeres into Saccharomyces cerevisiae and quantitated their effects on the rates of loss of chromosome III and chromosome VII by fluctuation analysis. We show that (i) 600 new telomeres have no effect on chromosome loss; (ii) an average of 25 extra centromere DNA sequences increase the rate of chromosome III loss from 0.4 x 10(-4) events per cell division to 1.3 x 10(-3) events per cell division; (iii) centromere DNA (CEN) sequences on circular vectors destabilize chromosomes more effectively than do CEN sequences on 15-kb linear vectors, and transcribed CEN sequences have no effect on chromosome stability. We discuss the different effects of extra centromere and telomere DNA sequences on chromosome stability in terms of how the cell recognizes these two chromosomal structures.
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Runge, K. W., R. J. Wellinger, and V. A. Zakian. "Effects of excess centromeres and excess telomeres on chromosome loss rates." Molecular and Cellular Biology 11, no. 6 (June 1991): 2919–28. http://dx.doi.org/10.1128/mcb.11.6.2919.
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The linear chromosomes of eukaryotes contain specialized structures to ensure their faithful replication and segregation to daughter cells. Two of these structures, centromeres and telomeres, are limited, respectively, to one and two copies per chromosome. It is possible that the proteins that interact with centromere and telomere DNA sequences are present in limiting amounts and could be competed away from the chromosomal copies of these elements by additional copies introduced on plasmids. We have introduced excess centromeres and telomeres into Saccharomyces cerevisiae and quantitated their effects on the rates of loss of chromosome III and chromosome VII by fluctuation analysis. We show that (i) 600 new telomeres have no effect on chromosome loss; (ii) an average of 25 extra centromere DNA sequences increase the rate of chromosome III loss from 0.4 x 10(-4) events per cell division to 1.3 x 10(-3) events per cell division; (iii) centromere DNA (CEN) sequences on circular vectors destabilize chromosomes more effectively than do CEN sequences on 15-kb linear vectors, and transcribed CEN sequences have no effect on chromosome stability. We discuss the different effects of extra centromere and telomere DNA sequences on chromosome stability in terms of how the cell recognizes these two chromosomal structures.
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Li, Ziang, Yunfei Bi, Xing Wang, Yunzhu Wang, Shuqiong Yang, Zhentao Zhang, Jinfeng Chen, and Qunfeng Lou. "Chromosome identification in Cucumis anguria revealed by cross-species single-copy gene FISH." Genome 61, no. 6 (June 2018): 397–404. http://dx.doi.org/10.1139/gen-2017-0235.
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Cucumis anguria is a potential genetic resource for improving crops of the genus Cucumis, owing to its broad-spectrum resistance. However, few cytogenetic studies on C. anguria have been reported because of its small metaphase chromosomes and the scarcity of distinguished chromosomal landmarks. In this study, 14 single-copy genes from cucumber and rDNAs were used as probes for FISH to identify the individual chromosomes of C. anguria. The distinctive signal distribution patterns of the probes allowed us to distinguish each chromosome of C. anguria (A01–A12). Further, detailed chromosome characteristics were obtained through pachytene chromosome FISH. The lengths of pachytene chromosomes varied from 54.80 to 143.41 μm. The proportion of heterochromatin regions varied from 13.56% to 63.86%. Finally, the chromosomal homeologous relationship between C. anguria and cucumber (C1–C7) was analyzed. The results showed that A06 + A09, A03 + A12, A02 + A04, and A01 + A11 were homeologs of C1, C2, C3, and C6, respectively. Furthemore, chromosomes A08, A10, and A05 were homeologs of C4, C5, and C7, respectively. Chromosome identification and homeologous relationship analysis between C. anguria and cucumber lay the foundation for further research of genome structure evolution in species of Cucumis.
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Shopland, Lindsay S., Christopher R. Lynch, Kevin A. Peterson, Kathleen Thornton, Nick Kepper, Johann von Hase, Stefan Stein, et al. "Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence." Journal of Cell Biology 174, no. 1 (July 3, 2006): 27–38. http://dx.doi.org/10.1083/jcb.200603083.
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Specific mammalian genes functionally and dynamically associate together within the nucleus. Yet, how an array of many genes along the chromosome sequence can be spatially organized and folded together is unknown. We investigated the 3D structure of a well-annotated, highly conserved 4.3-Mb region on mouse chromosome 14 that contains four clusters of genes separated by gene “deserts.” In nuclei, this region forms multiple, nonrandom “higher order” structures. These structures are based on the gene distribution pattern in primary sequence and are marked by preferential associations among multiple gene clusters. Associating gene clusters represent expressed chromatin, but their aggregation is not simply dependent on ongoing transcription. In chromosomes with aggregated gene clusters, gene deserts preferentially align with the nuclear periphery, providing evidence for chromosomal region architecture by specific associations with functional nuclear domains. Together, these data suggest dynamic, probabilistic 3D folding states for a contiguous megabase-scale chromosomal region, supporting the diverse activities of multiple genes and their conserved primary sequence organization.
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Visser, A. E., and J. A. Aten. "Chromosomes as well as chromosomal subdomains constitute distinct units in interphase nuclei." Journal of Cell Science 112, no. 19 (October 1, 1999): 3353–60. http://dx.doi.org/10.1242/jcs.112.19.3353.
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Fluorescence in situ hybridization has demonstrated that chromosomes form individual territories in interphase nuclei. However, this technique is not suitable to determine whether territories are mutually exclusive or interwoven. This notion, however, is essential for understanding functional organizations in the cell nucleus. Here, we analyze boundary areas of individual chromosomes during interphase using a sensitive method based on replication labeling and immunocytochemistry. Thymidine analogues IdUrd and CldUrd were incorporated during S-phase into DNA of Chinese Hamster fibroblasts. Cells labeled with IdUrd were fused with cells labeled with CldUrd. Fused nuclei contained both IdUrd or CldUrd labeled chromosomes. Alternatively, the two labels were incorporated sequentially during successive S-phases and segregated to separate chromosomes by culturing the cells one more cell cycle. Metaphase spreads showed IdUrd-, CldUrd- and unlabeled chromosomes. Some chromatids were divided sharply in differently labeled subdomains by sister chromatid exchanges. With both methods, confocal imaging of interphase nuclei revealed labeled chromosomal domains containing fiber-like structures and unlabeled areas. At various sites, fiber-like structures were embedded in other territories. Even so, essentially no overlap between chromosome territories or between subdomains within a chromosome was observed. These observations indicate that chromosome territories and chromosomal subdomains in G(1)-phase are mutually exclusive at the resolution of the light microscope.
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Matsunaga, Sachihiro, and Kiichi Fukui. "The chromosome peripheral proteins play an active role in chromosome dynamics." BioMolecular Concepts 1, no. 2 (August 1, 2010): 157–64. http://dx.doi.org/10.1515/bmc.2010.018.
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AbstractThe chromosome periphery is a chromosomal structure that covers the surface of mitotic chromosomes. The structure and function of the chromosome periphery has been poorly understood since its first description in 1882. It has, however, been proposed to be an insulator or barrier to protect chromosomes from subcellular substances and to act as a carrier of nuclear and nucleolar components to direct their equal distribution to daughter cells because most chromosome peripheral proteins (CPPs) are derived from the nucleolus or nucleus. Until now, more than 30 CPPs were identified in mammalians. Recent immunostaining analyses of CPPs have revealed that the chromosome periphery covers the centromeric region of mitotic chromosomes in addition to telomeres and regions between two sister chromatids. Knockdown analyses of CPPs using RNAi have revealed functions in chromosome dynamics, including cohesion of sister chromatids, kinetochore-microtubule attachments, spindle assembly and chromosome segregation. Because most CPPs are involved in various subcellular events in the nucleolus or nuclear at interphase, a temporal and spatial-specific knockdown method of CPPs in the chromosome periphery will be useful to understand the function of chromosome periphery in cell division.
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Machado, Cristina, Claudio E. Sunkel, and Deborah J. Andrew. "Human Autoantibodies Reveal Titin as a Chromosomal Protein." Journal of Cell Biology 141, no. 2 (April 20, 1998): 321–33. http://dx.doi.org/10.1083/jcb.141.2.321.
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Assembly of the higher-order structure of mitotic chromosomes is a prerequisite for proper chromosome condensation, segregation and integrity. Understanding the details of this process has been limited because very few proteins involved in the assembly of chromosome structure have been discovered. Using a human autoimmune scleroderma serum that identifies a chromosomal protein in human cells and Drosophila embryos, we cloned the corresponding Drosophila gene that encodes the homologue of vertebrate titin based on protein size, sequence similarity, developmental expression and subcellular localization. Titin is a giant sarcomeric protein responsible for the elasticity of striated muscle that may also function as a molecular scaffold for myofibrillar assembly. Molecular analysis and immunostaining with antibodies to multiple titin epitopes indicates that the chromosomal and muscle forms of titin may vary in their NH2 termini. The identification of titin as a chromosomal component provides a molecular basis for chromosome structure and elasticity.
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Ye, Jing, Yunlin Wu, and Eric Gilson. "Dynamics of telomeric chromatin at the crossroads of aging and cancer." Essays in Biochemistry 48 (September 20, 2010): 147–64. http://dx.doi.org/10.1042/bse0480147.
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Telomeres are nucleoprotein structures that protect the ends of human chromosomes through the formation of a ‘cap’, thus preventing exonucleolytic degradation, inter- and intra-chromosomal fusion, and subsequent chromosomal instability. During aging, telomere shortening correlates with tissue dysfunction and loss of renewal capacity. In human cancer, telomere dysfunction is involved in early chromosome instability, long-term cellular proliferation, and possibly other processes related to cell survival and microenvironment. Telomeres constitute an attractive target for the development of novel small-molecule anti-cancer drugs. In particular, individual protein components of the core telomere higher-order chromatin structure (known as the telosome or ‘shelterin’ complex) are promising candidate targets for cancer therapy.
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Al-Ardi, Musafer. "Illumination on the structure and characteristics of Entamoeba histolytica genome." Al-Qadisiyah Journal Of Pure Science 26, no. 4 (July 5, 2021): 19–26. http://dx.doi.org/10.29350/qjps.2021.26.4.1311.
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Entamoeba histolytica, likes other Organismes, is characterized by diversity and heterogeneity in its genetic content, which is one of the most paramount reasons for survival, and the increase in susceptibility to infection. Non-condensation of chromosomes during the process of cell division and the ambiguity of the chromosomal ploidy makes predicting the exact chromosomal numeral difficult. Genes distributed across 14 chromosomes as well as many extra-chromosome elements. Most Genes compose of one axon only, with Introns in 25% of Genes. This genome is characterized by the presence of Polymorphic internal repeat regions, and several gene families, one of these large families encoding Transmembrane kinas, Cysteine protease (CP), SREHP protein, and others.
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Yen, Jui-Hung, Shao-Yin Chu, Yann-Jang Chen, Yi-Chieh Su, Chun-Ching Chien, Chun-Ying Weng, and Pei-Yi Chen. "A Maternally Inherited Rare Case with Chromoanagenesis-Related Complex Chromosomal Rearrangements and De Novo Microdeletions." Diagnostics 12, no. 8 (August 5, 2022): 1900. http://dx.doi.org/10.3390/diagnostics12081900.
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Chromoanagenesis is a phenomenon of highly complex rearrangements involving the massive genomic shattering and reconstitution of chromosomes that has had a great impact on cancer biology and congenital anomalies. Complex chromosomal rearrangements (CCRs) are structural alterations involving three or more chromosomal breakpoints between at least two chromosomes. Here, we present a 3-year-old boy exhibiting multiple congenital malformations and developmental delay. The cytogenetic analysis found a highly complex CCR inherited from the mother involving four chromosomes and five breakpoints due to forming four derivative chromosomes (2, 3, 6 and 11). FISH analysis identified an ultrarare derivative chromosome 11 containing three parts that connected the 11q telomere to partial 6q and 3q fragments. We postulate that this derivative chromosome 11 is associated with chromoanagenesis-like phenomena by which DNA repair can result in a cooccurrence of inter-chromosomal translocations. Additionally, chromosome microarray studies revealed that the child has one subtle maternal-inherited deletion at 6p12.1 and two de novo deletions at 6q14.1 and 6q16.1~6q16.3. Here, we present a familial CCR case with rare rearranged chromosomal structures and the use of multiple molecular techniques to delineate these genomic alterations. We suggest that chromoanagenesis may be a possible mechanism involved in the repair and reconstitution of these rearrangements with evidence for increasing genomic imbalances such as additional deletions in this case.
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Wolf, Klaus Werner, Karel Novák, and František Marec. "Chromosome structure in spermatogenesis of Anabolia furcata (Trichoptera)." Genome 35, no. 1 (February 1, 1992): 46–52. http://dx.doi.org/10.1139/g92-008.
Full textAbstract:
The structure of metaphase chromosomes was analysed in spermatogonia and spermatocytes of the caddis-fly, Anabolia furcata (Trichoptera: Limnephilidae), using ultrathin serial sections and electron microscopy. In metaphase spermatogonia, about 40% of the chromosomal length was covered with a compact kinetochore plate. Subjectively estimated, secondary spermatocytes were not significantly different in this respect. However, in primary spermatocytes, each bivalent showed four kinetochores, two at each poleward surface, connected with the chromosome. The kinetochores were not located at the chromosome portions most proximal to the spindle poles, but attached laterally in a more equatorial position. When the orientation of individual kinetochore plates in metaphase I bivalents was not roughly at right angles with respect to the spindle axis, gaps and holes were visible in the plates. This possibly indicates the presence of compound kinetochores in A. furcata. The center of the bivalents contains less dense material than the periphery. The structural features of chromosomes in this Trichoptera species are very similar to those described in Lepidotera species with a comparable chromosome number. Taken together with similarities in other karyotype characteristics, such as female heterogamety and the lack of chiasmata in female meiosis, this further corroborates the notion that Lepidoptera and Trichoptera have strong phylogenetic affinities.Key words: caddis-fly, metaphase chromosomes, kinetochore, microtubules, spindle.
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Meng, Zhuang, Xiaoxu Hu, Zhiliang Zhang, Zhanjie Li, Qingfang Lin, Mei Yang, Pingfang Yang, Ray Ming, Qingyi Yu, and Kai Wang. "Chromosome Nomenclature and Cytological Characterization of Sacred Lotus." Cytogenetic and Genome Research 153, no. 4 (2017): 223–31. http://dx.doi.org/10.1159/000486777.
Full textAbstract:
Sacred lotus is a basal eudicot plant that has been cultivated in Asia for over 7,000 years for its agricultural, ornamental, religious, and medicinal importance. A notable characteristic of lotus is the seed longevity. Extensive endeavors have been devoted to dissect its genome assembly, including the variety China Antique, which germinated from a 1,300-year-old seed. Here, cytogenetic markers representing the 10 largest megascaffolds, which constitute approximately 70% of the lotus genome assembly, were developed. These 10 megascaffolds were then anchored to the corresponding lotus chromosomes by fluorescence in situ hybridization using these cytogenetic markers, and a set of chromosome-specific cytogenetic markers that could unambiguously identify each of the 8 chromosomes was generated. Karyotyping was conducted, and a nomenclature based on chromosomal length was established for the 8 chromosomes of China Antique. Comparative karyotyping revealed relatively conserved chromosomal structures between China Antique and 3 modern cultivars. Interestingly, significant variations in the copy number of 45S rDNA were detected between China Antique and modern cultivars. Our results provide a comprehensive view on the chromosomal structure of sacred lotus and will facilitate further studies and the genome assembly of lotus.
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Howe, Mary, Kent L. McDonald, Donna G. Albertson, and Barbara J. Meyer. "Him-10 Is Required for Kinetochore Structure and Function on Caenorhabditis elegans Holocentric Chromosomes." Journal of Cell Biology 153, no. 6 (June 11, 2001): 1227–38. http://dx.doi.org/10.1083/jcb.153.6.1227.
Full textAbstract:
Macromolecular structures called kinetochores attach and move chromosomes within the spindle during chromosome segregation. Using electron microscopy, we identified a structure on the holocentric mitotic and meiotic chromosomes of Caenorhabditis elegans that resembles the mammalian kinetochore. This structure faces the poles on mitotic chromosomes but encircles meiotic chromosomes. Worm kinetochores require the evolutionarily conserved HIM-10 protein for their structure and function. HIM-10 localizes to the kinetochores and mediates attachment of chromosomes to the spindle. Depletion of HIM-10 disrupts kinetochore structure, causes a failure of bipolar spindle attachment, and results in chromosome nondisjunction. HIM-10 is related to the Nuf2 kinetochore proteins conserved from yeast to humans. Thus, the extended kinetochores characteristic of C. elegans holocentric chromosomes provide a guide to the structure, molecular architecture, and function of conventional kinetochores.
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Sharbel, Timothy F., David M. Green, and Andreas Houben. "B-chromosome origin in the endemic New Zealand frog Leiopelma hochstetteri through sex chromosome devolution." Genome 41, no. 1 (February 1, 1998): 14–22. http://dx.doi.org/10.1139/g97-091.
Full textAbstract:
The endemic New Zealand frog Leiopelma hochstetteri has variable numbers of mitotically stable B chromosomes. To assess whether the B chromosomes were derived from the autosome complement, they were isolated by micromanipulation and their DNA amplified by degenerate oligonucleotide primed PCR. Southern hybridizations of B chromosome DNA probes to genomic DNA from males and females characterized by differing numbers of B chromosomes demonstrated that the B chromosomes were derived from the univalent W sex chromosome characteristic of North Island populations. The presence of homologous B chromosome specific sequences from geographically distinct populations indicates a single origin of the B chromosomes. Furthermore, a primitive homology shared by B chromosomes and the W sex chromosome from an ancestral WZ/ZZ karyotype, which is still present in frogs from Great Barrier Island, shows that the B chromosomes originated soon after the univalent W sex chromosome had originated. Sequence analysis revealed that B chromosome DNA is composed of repeat sequences and has the potential to form stable hairpin structures. The molecular dynamics of these structures may reflect an inherent propensity to undergo rapid change in nucleotide sequence and chromosome structure.
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Hołówka, Joanna, and Małgorzata Płachetka. "Structure of bacterial chromosome: An analysis of DNA-protein interactions in vivo." Postępy Higieny i Medycyny Doświadczalnej 71 (December 8, 2017): 0. http://dx.doi.org/10.5604/01.3001.0010.6696.
Full textAbstract:
According to recent reports, bacterial chromosomes exhibit a hierarchical organization. The number of proteins that bind DNA are responsible for local and global organization of the DNA ensuring proper chromosome compaction. Advanced molecular biology techniques combined with high-throughput DNA sequencing methods allow a precise analysis of bacterial chromosome structures on a local and global scale. Methods such as in vivo footprinting and ChIP-seq allow to map binding sites of analyzed proteins in certain chromosomal regions or along the whole chromosome while analysis of the spatial interactions on global scale could be performed by 3C techniques. Additional insight into complex structures created by chromosome-organizing proteins is provided by high-resolution fluorescence microscopy techniques.
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Bazaz, Asim Iqbal, Irfan Ahmad, Tasaduq H. Shah, and Nafath-ul-Arab Arab. "Karyomorphometric analysis of fresh water fish species of India, with special reference to cold water fishes of Kashmir Himalayas. A Mini Review." Caryologia 75, no. 1 (July 7, 2022): 109–21. http://dx.doi.org/10.36253/caryologia-1362.
Full textAbstract:
Cytogenetics is the diagnostic study of chromosomal structure and properties, as well as cell division, using a variety of methods, one of which is “karyotyping.” It refers to a method of photographing a stained preparation in which the chromosomes are organised in a uniform pattern. The advent of modern techniques such as “karyotyping” has made it feasible to visualize undetected chromosomal abnormalities such as short chromosome segments and chromosome translocations. Because such techniques enabled each pair of chromosomes to be identified separately, they have further aided our understanding of the chromosomal basis of a certain significant genetic diseases. Every organism has its own unique karyotype, which is defined by its number and shape. Karyotypic variation, on the other hand, occurs in different individuals of the same species, as well as between different species. Monitoring cytogenetic data of economically significant fishes as well as threatened fishes can hold importance of the succeeding generations. This review article highlights the variation in the chromosomal number & classification, methods of chromosome preparation and karyotypic analysis of various fish species of India with a special reference to fishes of Kashmir Himalayas.
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Strehl, S., J. M. LaSalle, and M. Lalande. "High-resolution analysis of DNA replication domain organization across an R/G-band boundary." Molecular and Cellular Biology 17, no. 10 (October 1997): 6157–66. http://dx.doi.org/10.1128/mcb.17.10.6157.
Full textAbstract:
Establishing how mammalian chromosome replication is regulated and how groups of replication origins are organized into replication bands will significantly increase our understanding of chromosome organization. Replication time bands in mammalian chromosomes show overall congruency with structural R- and G-banding patterns as revealed by different chromosome banding techniques. Thus, chromosome bands reflect variations in the longitudinal structure and function of the chromosome, but little is known about the structural basis of the metaphase chromosome banding pattern. At the microscopic level, both structural R and G bands and replication bands occupy discrete domains along chromosomes, suggesting separation by distinct boundaries. The purpose of this study was to determine replication timing differences encompassing a boundary between differentially replicating chromosomal bands. Using competitive PCR on replicated DNA from flow-sorted cell cycle fractions, we have analyzed the replication timing of markers spanning roughly 5 Mb of human chromosome 13q14.3/q21.1. This is only the second report of high-resolution analysis of replication timing differences across an R/G-band boundary. In contrast to previous work, however, we find that band boundaries are defined by a gradient in replication timing rather than by a sharp boundary separating R and G bands into functionally distinct chromatin compartments. These findings indicate that topographical band boundaries are not defined by specific sequences or structures.
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Zakian, V. A., H. M. Blanton, L. Wetzel, and G. M. Dani. "Size threshold for Saccharomyces cerevisiae chromosomes: generation of telocentric chromosomes from an unstable minichromosome." Molecular and Cellular Biology 6, no. 3 (March 1986): 925–32. http://dx.doi.org/10.1128/mcb.6.3.925-932.1986.
Full textAbstract:
A 9-kilobase pair CEN4 linear minichromosome constructed in vitro transformed Saccharomyces cerevisiae with high frequency but duplicated or segregated inefficiently in most cells. Stable transformants were only produced by events which fundamentally altered the structure of the minichromosome: elimination of telomeres, alteration of the centromere, or an increase of fivefold or greater in its size. Half of the stable transformants arose via homologous recombination between an intact chromosome IV and the CEN4 minichromosome. This event generated a new chromosome from each arm of chromosome IV. The other "arm" of each new chromosome was identical to one "arm" of the unstable minichromosome. Unlike natural yeast chromosomes, these new chromosomes were telocentric: their centromeres were either 3.9 or 5.4 kilobases from one end of the chromosome. The mitotic stability of the telocentric chromosome derived from the right arm of chromosome IV was determined by a visual assay and found to be comparable to that of natural yeast chromosomes. Both new chromosomes duplicated, paired, and segregated properly in meiosis. Moreover, their structure, as deduced from mobilities in orthogonal field gels, did not change with continued mitotic growth or after passage through meiosis, indicating that they did not give rise to isochromosomes or suffer large deletions or additions. Thus, in S. cerevisiae the close spacing of centromeres and telomeres on a DNA molecule of chromosomal size does not markedly alter the efficiency with which it is maintained. Taken together these data suggest that there is a size threshold below which stable propagation of linear chromosomes is no longer possible.
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Zakian, V. A., H. M. Blanton, L. Wetzel, and G. M. Dani. "Size threshold for Saccharomyces cerevisiae chromosomes: generation of telocentric chromosomes from an unstable minichromosome." Molecular and Cellular Biology 6, no. 3 (March 1986): 925–32. http://dx.doi.org/10.1128/mcb.6.3.925.
Full textAbstract:
A 9-kilobase pair CEN4 linear minichromosome constructed in vitro transformed Saccharomyces cerevisiae with high frequency but duplicated or segregated inefficiently in most cells. Stable transformants were only produced by events which fundamentally altered the structure of the minichromosome: elimination of telomeres, alteration of the centromere, or an increase of fivefold or greater in its size. Half of the stable transformants arose via homologous recombination between an intact chromosome IV and the CEN4 minichromosome. This event generated a new chromosome from each arm of chromosome IV. The other "arm" of each new chromosome was identical to one "arm" of the unstable minichromosome. Unlike natural yeast chromosomes, these new chromosomes were telocentric: their centromeres were either 3.9 or 5.4 kilobases from one end of the chromosome. The mitotic stability of the telocentric chromosome derived from the right arm of chromosome IV was determined by a visual assay and found to be comparable to that of natural yeast chromosomes. Both new chromosomes duplicated, paired, and segregated properly in meiosis. Moreover, their structure, as deduced from mobilities in orthogonal field gels, did not change with continued mitotic growth or after passage through meiosis, indicating that they did not give rise to isochromosomes or suffer large deletions or additions. Thus, in S. cerevisiae the close spacing of centromeres and telomeres on a DNA molecule of chromosomal size does not markedly alter the efficiency with which it is maintained. Taken together these data suggest that there is a size threshold below which stable propagation of linear chromosomes is no longer possible.
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Hovenga, Van, and Oluwatosin Oluwadare. "CBCR: A Curriculum Based Strategy For Chromosome Reconstruction." International Journal of Molecular Sciences 22, no. 8 (April 16, 2021): 4140. http://dx.doi.org/10.3390/ijms22084140.
Full textAbstract:
In this paper, we introduce a novel algorithm that aims to estimate chromosomes’ structure from their Hi-C contact data, called Curriculum Based Chromosome Reconstruction (CBCR). Specifically, our method performs this three dimensional reconstruction using cis-chromosomal interactions from Hi-C data. CBCR takes intra-chromosomal Hi-C interaction frequencies as an input and outputs a set of xyz coordinates that estimate the chromosome’s three dimensional structure in the form of a .pdb file. The algorithm relies on progressively training a distance-restraint-based algorithm with a strategy we refer to as curriculum learning. Curriculum learning divides the Hi-C data into classes based on contact frequency and progressively re-trains the distance-restraint algorithm based on the assumed importance of each curriculum in predicting the underlying chromosome structure. The distance-restraint algorithm relies on a modification of a Gaussian maximum likelihood function that scales probabilities based on the importance of features. We evaluate the performance of CBCR on both simulated and actual Hi-C data and perform validation on FISH, HiChIP, and ChIA-PET data as well. We also compare the performance of CBCR to several current methods. Our analysis shows that the use of curricula affects the rate of convergence of the optimization while decreasing the computational cost of our distance-restraint algorithm. Also, CBCR is more robust to increases in data resolution and therefore yields superior reconstruction accuracy of higher resolution data than all other methods in our comparison.
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Umezu, Keiko, Mina Hiraoka, Masaaki Mori, and Hisaji Maki. "Structural Analysis of Aberrant Chromosomes That Occur Spontaneously in Diploid Saccharomyces cerevisiae: Retrotransposon Ty1 Plays a Crucial Role in Chromosomal Rearrangements." Genetics 160, no. 1 (January 1, 2002): 97–110. http://dx.doi.org/10.1093/genetics/160.1.97.
Full textAbstract:
Abstract The structural analysis of aberrant chromosomes is important for our understanding of the molecular mechanisms underlying chromosomal rearrangements. We have identified a number of diploid Saccharomyces cerevisiae clones that have undergone loss of heterozygosity (LOH) leading to functional inactivation of the hemizygous URA3 marker placed on the right arm of chromosome III. Aberrant-sized chromosomes derived from chromosome III were detected in ~8% of LOH clones. Here, we have analyzed the structure of the aberrant chromosomes in 45 LOH clones with a PCR-based method that determines the ploidy of a series of loci on chromosome III. The alterations included various deletions and amplifications. Sequencing of the junctions revealed that all the breakpoints had been made within repeat sequences in the yeast genome, namely, MAT-HMR, which resulted in intrachromosomal deletion, and retrotransposon Ty1 elements, which were involved in various translocations. Although the translocations involved different breakpoints on different chromosomes, all breakpoints were exclusively within Ty1 elements. Some of the resulting Ty1 elements left at the breakpoints had a complex construction that indicated the involvement of other Ty1 elements not present at the parental breakpoints. These indicate that Ty1 elements are crucially involved in the generation of chromosomal rearrangements in diploid yeast cells.
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Danieli, Adi, and Argyris Papantonis. "Spatial genome architecture and the emergence of malignancy." Human Molecular Genetics 29, R2 (July 3, 2020): R197—R204. http://dx.doi.org/10.1093/hmg/ddaa128.
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Abstract Human chromosomes are large spatially and hierarchically structured entities, the integrity of which needs to be preserved throughout the lifespan of the cell and in conjunction with cell cycle progression. Preservation of chromosomal structure is important for proper deployment of cell type-specific gene expression programs. Thus, aberrations in the integrity and structure of chromosomes will predictably lead to disease, including cancer. Here, we provide an updated standpoint with respect to chromatin misfolding and the emergence of various cancer types. We discuss recent studies implicating the disruption of topologically associating domains, switching between active and inactive compartments, rewiring of promoter–enhancer interactions in malignancy as well as the effects of single nucleotide polymorphisms in non-coding regions involved in long-range regulatory interactions. In light of these findings, we argue that chromosome conformation studies may now also be useful for patient diagnosis and drug target discovery.
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Heldrich, Jonna, Xiaoji Sun, Luis A. Vale-Silva, Tovah E. Markowitz, and Andreas Hochwagen. "Topoisomerases Modulate the Timing of Meiotic DNA Breakage and Chromosome Morphogenesis in Saccharomyces cerevisiae." Genetics 215, no. 1 (March 9, 2020): 59–73. http://dx.doi.org/10.1534/genetics.120.303060.
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During meiotic prophase, concurrent transcription, recombination, and chromosome synapsis place substantial topological strain on chromosomal DNA, but the role of topoisomerases in this context remains poorly defined. Here, we analyzed the roles of topoisomerases I and II (Top1 and Top2) during meiotic prophase in Saccharomyces cerevisiae. We show that both topoisomerases accumulate primarily in promoter-containing intergenic regions of actively transcribing genes, including many meiotic double-strand break (DSB) hotspots. Despite the comparable binding patterns, top1 and top2 mutations have different effects on meiotic recombination. TOP1 disruption delays DSB induction and shortens the window of DSB accumulation by an unknown mechanism. By contrast, temperature-sensitive top2-1 mutants exhibit a marked delay in meiotic chromosome remodeling and elevated DSB signals on synapsed chromosomes. The problems in chromosome remodeling were linked to altered Top2 binding patterns rather than a loss of Top2 catalytic activity, and stemmed from a defect in recruiting the chromosome remodeler Pch2/TRIP13 to synapsed chromosomes. No chromosomal defects were observed in the absence of TOP1. Our results imply independent roles for Top1 and Top2 in modulating meiotic chromosome structure and recombination.
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Shaw, David D., David J. Coates, and Michael L. Arnold. "Complex patterns of chromosomal variation along a latitudinal cline in the grasshopper Caledia captiva." Genome 30, no. 2 (April 1, 1988): 108–17. http://dx.doi.org/10.1139/g88-019.
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An analysis of chromosomal variation along a 1500-km latitudinal cline in the Moreton subspecies of Caledia captiva has revealed the existence of complex and systemic changes to genome structure. These changes involved variation in the position of the centromere on every chromosome, from medial locations in northern populations to more distal or terminal locations in the southern populations. At the ends of this genomic cline, two contrasting chromosomal patterns were evident. In the north, the genome was fixed for metacentric chromosomes whereas at the southern limit, the genome was homozygous for acrocentric and telocentric chromosomes. Intermediate populations showed highly complex patterns of chromosomal polymorphisms. All populations along the cline were homogeneous for mitochondrial DNA restriction fragment length polymorphisms, highly repeated DNA sequences, and allozyme variation, with no evidence of genetic differentiation or inhibition of gene flow. It is argued that these complex patterns of genomic change reveal evidence of an adaptive role for both fixed and polymorphic chromosomal rearrangements within the same taxon.Key words: chromosome variation, natural selection, Caledia, grasshopper.
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Gasser, Susan M. "Chromosome Structure: Coiling up chromosomes." Current Biology 5, no. 4 (April 1995): 357–60. http://dx.doi.org/10.1016/s0960-9822(95)00071-6.
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Marec, František, and Walther Traut. "Sex chromosome pairing and sex chromatin bodies in W–Z translocation strains of Ephestia kuehniella (Lepidoptera)." Genome 37, no. 3 (June 1, 1994): 426–35. http://dx.doi.org/10.1139/g94-060.
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Structure and pairing behavior of sex chromosomes in females of four T(W;Z) lines of the Mediterranean flour moth, Ephestia kuehniella, were investigated using light and electron microscopic techniques and compared with the wild type. In light microscopic preparations of pachytene oocytes of wild-type females, the WZ bivalent stands out by its heterochromatic W chromosome strand. In T(W;Z) females, the part of the Z chromosome that was translated onto the W chromosome was demonstrated as a distal segment of the neo-W chromosome, displaying a characteristic non-W chromosomal chromomere–interchromomere pattern. This segment is homologously paired with the corresponding part of a complete Z chromosome. In contrast with the single ball of heterochromatic W chromatin in highly polyploid somatic nuclei of wild-type females, the translocation causes the formation of deformed or fragmented W chromatin bodies, probably owing to opposing tendencies of the Z and W chromosomal parts of the neo-W. In electron microscopic preparations of microspread nuclei, sex chromosome bivalents were identified by the remnants of electron-dense heterochromatin tangles decorating the W chromosome axis, by the different lengths of the Z and W chromosome axes, and by incomplete pairing. No heterochromatin tangles were attached to the translocated segment of the Z chromosome at one end of the neo-W chromosome. Because of the homologous pairing between the translocation and the structurally normal Z chromosome, pairing affinity of sex chromosomes in T(W;Z) females is significantly improved. Specific differences observed among T(W;Z)1–4 translocations are probably due to the different lengths of the translocated segments.Key words: Mediterranean flour moth, sex chromosomes, sex chromatin, translocations, synaptonemal complexes, microspreading.
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Chen, Bo-Wei, Ming-Hsing Lin, Chen-Hsi Chu, Chia-En Hsu, and Yuh-Ju Sun. "Insights into ParB spreading from the complex structure of Spo0J and parS." Proceedings of the National Academy of Sciences 112, no. 21 (May 11, 2015): 6613–18. http://dx.doi.org/10.1073/pnas.1421927112.
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Spo0J (stage 0 sporulation protein J, a member of the ParB superfamily) is an essential component of the ParABS (partition system of ParA, ParB, and parS)-related bacterial chromosome segregation system. ParB (partition protein B) and its regulatory protein, ParA, act cooperatively through parS (partition S) DNA to facilitate chromosome segregation. ParB binds to chromosomal DNA at specific parS sites as well as the neighboring nonspecific DNA sites. Various ParB molecules can associate together and spread along the chromosomal DNA. ParB oligomer and parS DNA interact together to form a high-order nucleoprotein that is required for the loading of the structural maintenance of chromosomes proteins onto the chromosome for chromosomal DNA condensation. In this report, we characterized the binding of parS and Spo0J from Helicobacter pylori (HpSpo0J) and solved the crystal structure of the C-terminal domain truncated protein (Ct-HpSpo0J)-parS complex. Ct-HpSpo0J folds into an elongated structure that includes a flexible N-terminal domain for protein–protein interaction and a conserved DNA-binding domain for parS binding. Two Ct-HpSpo0J molecules bind with one parS. Ct-HpSpo0J interacts vertically and horizontally with its neighbors through the N-terminal domain to form an oligomer. These adjacent and transverse interactions are accomplished via a highly conserved arginine patch: RRLR. These interactions might be needed for molecular assembly of a high-order nucleoprotein complex and for ParB spreading. A structural model for ParB spreading and chromosomal DNA condensation that lead to chromosome segregation is proposed.
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Boroń, Alicja, Anna Grabowska, Aneta Spóz, and Anna Przybył. "B Chromosomes and Cytogenetic Characteristics of the Common Nase Chondrostoma nasus (Linnaeus, 1758)." Genes 11, no. 11 (November 6, 2020): 1317. http://dx.doi.org/10.3390/genes11111317.
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Supernumerary B chromosomes (Bs) are very promising structures, among others, in that they are an additional genomic compartment for evolution. In this study, we tested the presence and frequency of B chromosomes and performed the first cytogenetic examination of the common nase (Chondrostoma nasus). We investigated the individuals from two populations in the Vistula River basin, in Poland, according to the chromosomal distribution of the C-bands and silver nucleolar organizer regions (Ag-NORs), using sequential staining with AgNO3 and chromomycin A3 (CMA3). Furthermore, we analyzed the chromosomal localization of two rDNA families (45S and 5S rDNA) using fluorescence in situ hybridization (FISH) with rDNA probes. Chondrostoma nasus individuals showed a standard (A) chromosome set consisting of 2n = 50: 12 metacentric, 32 submetacentric, and 6 acrocentric chromosomes (NF = 94). Fourteen out of the 20 analyzed individuals showed 1–2 mitotically unstable submetacentric B chromosomes of different sizes. Six of them, in 14.1% of the analyzed metaphase plates, had a single, medium-sized submetacentric B (Bsm) chromosome (2n = 51) with a heterochromatic block located in its pericentromeric region. The other seven individuals possessed a Bsm (2n = 51) in 19.4% of the analyzed metaphase plates, and a second Bsm chromosome (2n = 52), the smallest in the set, in 15.5% of metaphase plates, whereas one female was characterized by both Bsm chromosomes (2n = 52) in 14.3% of the analyzed metaphase plates. AgNORs, GC-rich DNA sites, and 28S rDNA hybridization sites were observed in the short arms of two submetacentric chromosome pairs of A set. The constitutive heterochromatin was visible as C bands in the centromeric regions of almost all Chondrostoma nasus chromosomes and in the pericentromeric region of several chromosome pairs. Two 5S rDNA hybridization sites in the pericentromeric position of the largest acrocentric chromosome pair were observed, whereas two other such sites in co-localization on a smaller pair of NOR chromosomes indicate a species-specific character. The results herein broaden our knowledge in the field of B chromosome distribution and molecular cytogenetics of Chondrostoma nasus: a freshwater species from the Leuciscidae family.
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Scherthan, H., J. Bähler, and J. Kohli. "Dynamics of chromosome organization and pairing during meiotic prophase in fission yeast." Journal of Cell Biology 127, no. 2 (October 15, 1994): 273–85. http://dx.doi.org/10.1083/jcb.127.2.273.
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Interactions between homologous chromosomes (pairing, recombination) are of central importance for meiosis. We studied entire chromosomes and defined chromosomal subregions in synchronous meiotic cultures of Schizosaccharomyces pombe by fluorescence in situ hybridization. Probes of different complexity were applied to spread nuclei, to delineate whole chromosomes, to visualize repeated sequences of centromeres, telomeres, and ribosomal DNA, and to study unique sequences of different chromosomal regions. In diploid nuclei, homologous chromosomes share a joint territory even before entry into meiosis. The centromeres of all chromosomes are clustered in vegetative and meiotic prophase cells, whereas the telomeres cluster near the nucleolus early in meiosis and maintain this configuration throughout meiotic prophase. Telomeres and centromeres appear to play crucial roles for chromosome organization and pairing, both in vegetative cells and during meiosis. Homologous pairing of unique sequences shows regional differences and is most frequent near centromeres and telomeres. Multiple homologous interactions are formed independently of each other. Pairing increases during meiosis, but not all chromosomal regions become closely paired in every meiosis. There is no detectable axial compaction of chromosomes in meiotic prophase. S. pombe does not form mature synaptonemal complexes, but axial element-like structures (linear elements), which were analyzed in parallel. Their appearance coincides with pairing of interstitial chromosomal regions. Axial elements may define minimal structures required for efficient pairing and recombination of meiotic chromosomes.
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Dwiranti, Astari, Hideaki Takata, and Kiichi Fukui. "Reversible Changes of Chromosome Structure upon Different Concentrations of Divalent Cations." Microscopy and Microanalysis 25, no. 3 (April 17, 2019): 817–21. http://dx.doi.org/10.1017/s1431927619000266.
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AbstractThe structural details of chromosomes have been of interest to researchers for many years, but how the metaphase chromosome is constructed remains unsolved. Divalent cations have been suggested to be required for the organization of chromosomes. However, detailed information about the role of these cations in chromosome organization is still limited. In the current study, we investigated the effects of Ca2+ and Mg2+ depletion and the reversibility upon re-addition of one of the two ions. Human chromosomes were treated with different concentrations of Ca2+and Mg2+. Depletion of Ca2+ and both Ca2+ and Mg2+ were carried out using 1, 2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid and ethylenediaminetetraacetic acid (EDTA), respectively. Chromosome structure was examined by fluorescence microscopy and scanning electron microscopy. The results indicated that chromosome structures after treatment with a buffer without Mg2+, after Ca2+ depletion, as well as after depletion of both Mg2+, and Ca2+, yielded fewer compact structures with fibrous chromatin than those without cation depletion. Interestingly, the chromatin of EDTA-treated chromosomes reversed to their original granular diameters after re-addition of either Mg2+ or Ca2+ only. These findings signify the importance of divalent cations on the chromosome structure and suggest the interchangeable role of Ca2+ and Mg2+.
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Ryu, Je-Kyung, Da-Eun Hwang, and Jeong-Mo Choi. "Current Understanding of Molecular Phase Separation in Chromosomes." International Journal of Molecular Sciences 22, no. 19 (October 4, 2021): 10736. http://dx.doi.org/10.3390/ijms221910736.
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Biomolecular phase separation denotes the demixing of a specific set of intracellular components without membrane encapsulation. Recent studies have found that biomolecular phase separation is involved in a wide range of cellular processes. In particular, phase separation is involved in the formation and regulation of chromosome structures at various levels. Here, we review the current understanding of biomolecular phase separation related to chromosomes. First, we discuss the fundamental principles of phase separation and introduce several examples of nuclear/chromosomal biomolecular assemblies formed by phase separation. We also briefly explain the experimental and computational methods used to study phase separation in chromosomes. Finally, we discuss a recent phase separation model, termed bridging-induced phase separation (BIPS), which can explain the formation of local chromosome structures.
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Strukov, Yuri G., Yan Wang, and Andrew S. Belmont. "Engineered chromosome regions with altered sequence composition demonstrate hierarchical large-scale folding within metaphase chromosomes." Journal of Cell Biology 162, no. 1 (June 30, 2003): 23–35. http://dx.doi.org/10.1083/jcb.200303098.
Full textAbstract:
Mitotic chromosome structure and DNA sequence requirements for normal chromosomal condensation remain unknown. We engineered labeled chromosome regions with altered scaffold-associated region (SAR) sequence composition as a formal test of the radial loop and other chromosome models. Chinese hamster ovary cells were isolated containing high density insertions of a transgene containing lac operator repeats and a dihydrofolate reductase gene, with or without flanking SAR sequences. Lac repressor staining provided high resolution labeling with good preservation of chromosome ultrastructure. No evidence emerged for differential targeting of SAR sequences to a chromosome axis within native chromosomes. SAR sequences distributed uniformly throughout the native chromosome cross section and chromosome regions containing a high density of SAR transgene insertions showed normal diameter and folding. Ultrastructural analysis of two different transgene insertion sites, both spanning less than the full chromatin width, clearly contradicted predictions of simple radial loop models while providing strong support for hierarchical models of chromosome architecture. Specifically, an ∼250-nm-diam folding subunit was visualized directly within fully condensed metaphase chromosomes. Our results contradict predictions of simple radial loop models and provide the first unambiguous demonstration of a hierarchical folding subunit above the level of the 30-nm fiber within normally condensed metaphase chromosomes.
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Muratova, E. N., T. S. Sedel’nikova, A. V. Pimenov, and O. V. Goryachkina. "Karyological and cytogenetic research of the conifers of boreal zone by classic and new methods." Faktori eksperimental'noi evolucii organizmiv 25 (August 30, 2019): 74–79. http://dx.doi.org/10.7124/feeo.v25.1142.
Full textAbstract:
Aim. Establishing of karyological features and conducting of cytogenetic analysis on conifer plants for biological diversity studies, solving of problems of taxonomics, evolutionary and population genetics. Methods. Classic methods with acetohematoxylin staining of slides and fluorescent in situ hybridization (FISH). Results. More than 150 populations and provenances of representatives of different conifer genera from the Pinaceae and Cupressaceae families were studied. The studies were carried out in natural populations and during the introduction, in optimal and extreme conditions, in disturbed ecosystems, botanical gardens and parks; in addition, various intraspecific forms have been studied. The variability of chromosome numbers and a wide range of chromosomal mutations have been revealed. Fluorescence in situ hybridization (FISH) with the 45S and 5S ribosomal RNA gene probes and DAPI staining allows to identify of homologous chromosome pairs in the karyotypes of conifers and to facilitate the comparative karyotype analysis of these species. Conclusions. The studies of chromosomes in species of the Pinaceae and Cupressaceae families showed a karyotypic diversity and chromosomal anomalies in extreme conditions and under introduction. The use of molecular cytogenetic markers made it possible to obtain new information on the structure of conifer chromosomes.
Keywords: chromosomes, nucleolar loci, chromosome mutations, Pinaceae, Cupressaceae.
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Semeshin, V. F., I. F. Zhimulev, D. Kritikou, and A. Zacharopoulou. "Electron microscope investigation of polytene chromosomes in the Mediterranean fruit fly Ceratitis capitata." Genome 38, no. 4 (August 1, 1995): 652–60. http://dx.doi.org/10.1139/g95-083.
Full textAbstract:
Ultrastructural analyses of polytene chromosomes from male pupal orbital bristle cells and from larval salivary glands of Ceratitis capitata were carried out. It was shown that chromatin complexes corresponding to the X chromosome heterochromatic network are surrounded by material containing ribonucleoprotein (RNP) granules 250–300 Å (1 Å = 0.1 nm) in diameter. RNP granules of similar size surround the spherical Y chromosome. These data point out the presence of transcriptional activity in both of these chromosomes. The absence of clear structure in chromosomal regions situated between large bands in both types of tissues was observed. These results support the hypothesis of weak synapsis between chromatids or small chromomeres of polytene chromosomes in this species. In addition, we describe a specific puff revealed in both orbital trichogen cells and salivary glands that is morphologically similar to the 93D puff of Drosophila melanogaster.Key words: Ceratitis capitata, polytene chromosomes, electron microscopy.
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Typylo, K. "Karyotype variability of the Ukrainian Mountain-Carpathian sheep breed." Agricultural Science and Technology 12, no. 1 (March 2020): 3–5. http://dx.doi.org/10.15547/ast.2020.01.001.
Full textAbstract:
Abstract. The main purpose of this work was to describe the karyotype variability of the Ukrainian Mountain-Carpathian sheep breed. Cytogenetic studies were carried out on a group of 25 sheep from that breed. The cultivation of lymphocytes, preparing the cytogenetic samples, classification and registration of chromosome aberrations were held using conventional methods. It was established that the number and structure of the chromosomes of sheep of the Ukrainian Mountain-Carpathian breed correspond to the norm typical for this species of animals. Chromosomal variability of the studied population includes 19.22% of numerical and structural aberrations. By the number and structure of the chromosome set the Ukrainian Mountain-Carpathian sheep breed does not differ from other breeds of sheep. Accurate identification of individual chromosomes with routine coloring allows using cytogenetic studies in breeding practice in sheep breeding.
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Vieira, Cristina P., Paula A. Coelho, and Jorge Vieira. "Inferences on the Evolutionary History of theDrosophila americanaPolymorphicX/4Fusion From Patterns of Polymorphism at theX-LinkedparalyticandelavGenes." Genetics 164, no. 4 (August 1, 2003): 1459–69. http://dx.doi.org/10.1093/genetics/164.4.1459.
Full textAbstract:
AbstractIn Drosophila there is limited evidence on the nature of evolutionary forces affecting chromosomal arrangements other than inversions. The study of the X/4 fusion polymorphism of Drosophila americana is thus of interest. Polymorphism patterns at the paralytic (para) gene, located at the base of the X chromosome, suggest that there is suppressed crossing over in this region between fusion and nonfusion chromosomes but not within fusion and nonfusion chromosomes. These data are thus compatible with previous claims that within fusion chromosomes the amino acid clines found at fused1 (also located at the base of the X chromosome) are likely maintained by local selection. The para data set also suggests a young age of the X/4 fusion. Polymorphism data on para and elav (located at the middle region of the X chromosome) suggest that there is no population structure other than that caused by the X/4 fusion itself. These findings are therefore compatible with previous claims that selection maintains the strong association observed between the methionine/threonine variants at fused1 and the status of the X chromosome as fused or unfused to the fourth chromosome.