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Chromosome Research

Daniil A Maksimov, Petr P Laktionov, Stepan N Belyakin
Analysis of gene expression regulation typically requires identification of genomic sites bound by regulatory proteins. For this purpose, chromatin immunoprecipitation (ChIP) and Dam identification (DamID) methods can be applied to cell lines, whole organisms, or enriched cell populations. In this work, we present modifications to the experimental DamID protocol, as well as a custom data processing algorithm, that allow to confidently identify genomic sites enriched with the proteins of interest. This algorithm is implemented in Perl and is also available as executable files, thereby making DamID analysis relatively straightforward...
October 21, 2016: Chromosome Research
Dal-Hoe Koo, Hainan Zhao, Jiming Jiang
Tandemly repetitive DNA sequences, also named satellite repeats, are major DNA components of heterochromatin and are often organized as long arrays in the pericentromeric, centromeric, and subtelomeric regions of eukaryotic chromosomes. An increasing amount of evidence indicates that transcripts derived from some satellite repeats play important roles in various biological functions. We used a RNA-fluorescence in situ hybridization (RNA-FISH) technique to investigate the transcription of the four well-characterized satellite repeats of maize (Zea mays), including the 180-bp knob repeat, the telomeric (TTTAGGG)n repeat, the 156-bp centromeric repeat CentC, and a 350-bp subtelomeric repeat...
September 2, 2016: Chromosome Research
Lori L Sullivan, Kristin A Maloney, Aaron J Towers, Simon G Gregory, Beth A Sullivan
Centromeres are defined by a specialized chromatin organization that includes nucleosomes that contain the centromeric histone variant centromere protein A (CENP-A) instead of canonical histone H3. Studies in various organisms have shown that centromeric chromatin (i.e., CENP-A chromatin or centrochromatin) exhibits plasticity, in that it can assemble on different types of DNA sequences. However, once established on a chromosome, the centromere is maintained at the same position. In humans, this location is the highly homogeneous repetitive DNA alpha satellite...
August 31, 2016: Chromosome Research
Harmonie Barasc, Annabelle Congras, Nicolas Mary, Lidwine Trouilh, Valentine Marquet, Stéphane Ferchaud, Isabelle Raymond-Letron, Anne Calgaro, Anne-Marie Loustau-Dudez, Nathalie Mouney-Bonnet, Hervé Acloque, Alain Ducos, Alain Pinton
No abstract text is available yet for this article.
August 31, 2016: Chromosome Research
Jennifer N Cech, Catherine L Peichel
Having one and only one centromere per chromosome is essential for proper chromosome segregation during both mitosis and meiosis. Chromosomes containing two centromeres are known as dicentric and often mis-segregate during cell division, resulting in aneuploidy or chromosome breakage. Dicentric chromosome can be stabilized by centromere inactivation, a process which reestablishes monocentric chromosomes. However, little is known about this process in naturally occurring dicentric chromosomes. Using a combination of fluorescence in situ hybridization (FISH) and immunofluorescence combined with FISH (IF-FISH) on metaphase chromosome spreads, we demonstrate that centromere inactivation has evolved on a neo-Y chromosome fusion in the Japan Sea threespine stickleback fish (Gasterosteus nipponicus)...
August 23, 2016: Chromosome Research
Harmonie Barasc, Annabelle Congras, Nicolas Mary, Lidwine Trouilh, Valentine Marquet, Stéphane Ferchaud, Isabelle Raymond-Letron, Anne Calgaro, Anne-Marie Loustau-Dudez, Nathalie Mouney-Bonnet, Hervé Acloque, Alain Ducos, Alain Pinton
Individuals carrying balanced constitutional reciprocal translocations generally have a normal phenotype, but often present reproductive disorders. The aim of our research was to analyze the meiotic process in an oligoasthenoteratospermic boar carrying an asymmetric reciprocal translocation involving chromosomes 1 and 14. Different multivalent structures (quadrivalent and trivalent plus univalent) were identified during chromosome pairing analysis. Some of these multivalents were characterized by the presence of unpaired autosomal segments with histone γH2AX accumulation sometimes associated with the XY body...
August 2, 2016: Chromosome Research
William Ziccardi, Chongjian Zhao, Valery Shepelev, Lev Uralsky, Ivan Alexandrov, Tatyana Andreeva, Evgeny Rogaev, Christopher Bun, Emily Miller, Catherine Putonti, Jeffrey Doering
Human alpha satellite (AS) sequence domains that currently function as centromeres are typically flanked by layers of evolutionarily older AS that presumably represent the remnants of earlier primate centromeres. Studies on several human chromosomes reveal that these older AS arrays are arranged in an age gradient, with the oldest arrays farthest from the functional centromere and arrays progressively closer to the centromere being progressively younger. The organization of AS on human chromosome 21 (HC21) has not been well-characterized...
September 2016: Chromosome Research
Chie Murata, Yoko Kuroki, Issei Imoto, Asato Kuroiwa
Two species of the genus Tokudaia lack the Y chromosome and SRY, but several Y-linked genes have been rescued by translocation or transposition to other chromosomes. Tokudaia muenninki is the only species in the genus that maintains the Y owing to sex chromosome-autosome fusions. According to previous studies, many SRY pseudocopies and other Y-linked genes have evolved by excess duplication in this species. Using RNA-seq and RT-PCR, we found that ZFY, EIF2S3Y, TSPY, UTY, DDX3Y, USP9Y, and RBMY, but not UBA1Y, had high deduced amino acid sequence similarity and similar expression patterns with other rodents, suggesting that these genes were functional...
September 2016: Chromosome Research
Wei Ma, Veit Schubert, Mihaela Maria Martis, Gerd Hause, Zhaojun Liu, Yi Shen, Udo Conrad, Wenqing Shi, Uwe Scholz, Stefan Taudien, Zhukuan Cheng, Andreas Houben
Holocentric chromosomes occur in a number of independent eukaryotic lineages, and they form holokinetic kinetochores along the entire poleward chromatid surfaces. Due to this alternative chromosome structure, Luzula elegans sister chromatids segregate already in anaphase I followed by the segregation of the homologues in anaphase II. However, not yet known is the localization and dynamics of cohesin and the structure of the synaptonemal complex (SC) during meiosis. We show here that the α-kleisin subunit of cohesin localizes at the centromeres of both mitotic and meiotic metaphase chromosomes and that it, thus, may contribute to assemble the centromere in L...
September 2016: Chromosome Research
Florence Richard, Michèle Gerbault-Seureau, Bounneuang Douangboupha, Kham Keovichit, Jean-Pierre Hugot, Bernard Dutrillaux
Laonastes aenigmamus (Khanyou) is a recently described rodent species living in geographically separated limestone formations of the Khammuan Province in Lao PDR. Chromosomes of 21 specimens of L. aenigmamus were studied using chromosome banding as well as fluorescent in situ hybridization (FISH) techniques using human painting, telomere repeats, and 28S rDNA probes. Four different karyotypes were established. Study with human chromosome paints and FISH revealed that four large chromosomes were formed by multiple common tandem fusions, with persistence of some interstitial telomeres...
September 2016: Chromosome Research
Katarzyna Wyrwa, Michał Książkiewicz, Anna Szczepaniak, Karolina Susek, Jan Podkowiński, Barbara Naganowska
Narrow-leafed lupin (Lupinus angustifolius L.) has recently been considered a reference genome for the Lupinus genus. In the present work, genetic and cytogenetic maps of L. angustifolius were supplemented with 30 new molecular markers representing lupin genome regions, harboring genes involved in nitrogen fixation during the symbiotic interaction of legumes and soil bacteria (Rhizobiaceae). Our studies resulted in the precise localization of bacterial artificial chromosomes (BACs) carrying sequence variants for early nodulin 40, nodulin 26, nodulin 45, aspartate aminotransferase P2, asparagine synthetase, cytosolic glutamine synthetase, and phosphoenolpyruvate carboxylase...
September 2016: Chromosome Research
Adrienne Eastland, Jessica Hornick, Ryo Kawamura, Dhaval Nanavati, John F Marko
We have found that reagents that reduce oxidized cysteines lead to destabilization of metaphase chromosome folding, suggesting that chemically linked cysteine residues may play a structural role in mitotic chromosome organization, in accord with classical studies by Dounce et al. (J Theor Biol 42:275-285, 1973) and Sumner (J Cell Sci 70:177-188, 1984a). Human chromosomes isolated into buffer unfold when exposed to dithiothreitol (DTT) or tris(2-carboxyethyl)phosphine (TCEP). In micromanipulation experiments which allow us to examine the mechanics of individual metaphase chromosomes, we have found that the gel-like elastic stiffness of native metaphase chromosomes is dramatically suppressed by DTT and TCEP, even before the chromosomes become appreciably unfolded...
September 2016: Chromosome Research
Miluse Vozdova, Aurora Ruiz-Herrera, Jonathan Fernandez, Halina Cernohorska, Jan Frohlich, Hana Sebestova, Svatava Kubickova, Jiri Rubes
The recurrent occurrence of sex-autosome translocations during mammalian evolution suggests common mechanisms enabling a precise control of meiotic synapsis, recombination and inactivation of sex chromosomes. We used immunofluorescence and FISH to study the meiotic behaviour of sex chromosomes in six species of Bovidae with evolutionary sex-autosome translocations (Tragelaphus strepsiceros, Taurotragus oryx, Tragelaphus imberbis, Tragelaphus spekii, Gazella leptoceros and Nanger dama ruficollis). The autosomal regions of fused sex chromosomes showed normal synapsis with their homologous counterparts...
September 2016: Chromosome Research
Inna S Kuznetsova, Dmitrii I Ostromyshenskii, Alexei S Komissarov, Andrei N Prusov, Irina S Waisertreiger, Anna V Gorbunova, Vladimir A Trifonov, Malcolm A Ferguson-Smith, Olga I Podgornaya
Chromocenters are interphase nuclear landmark structures of constitutive heterochromatin. The tandem repeat (TR)-enriched parts of different chromosomes cluster together in chromocenters. There has been progress in recent years in determining the protein content of chromocenters, although it is not clear which DNA sequences underly constitutive heterochromatin apart from the TRs. The aim of the current work was to find out which DNA sequences besides TRs are involved in chromocenters' formation. Biochemically isolated chromocenters and microdissected centromeric regions were amplified by DOP-PCR, then cloned and sequenced...
September 2016: Chromosome Research
Susann Hesse, Antonio Manetto, Valentina Cassinelli, Jörg Fuchs, Lu Ma, Nada Raddaoui, Andreas Houben
In situ hybridisation is a powerful tool to investigate the genome and chromosome architecture. Nick translation (NT) is widely used to label DNA probes for fluorescence in situ hybridisation (FISH). However, NT is limited to the use of long double-stranded DNA and does not allow the labelling of single-stranded and short DNA, e.g. oligonucleotides. An alternative technique is the copper(I)-catalysed azide-alkyne cycloaddition (CuAAC), at which azide and alkyne functional groups react in a multistep process catalysed by copper(I) ions to give 1,4-distributed 1,2,3-triazoles at a high yield (also called 'click reaction')...
September 2016: Chromosome Research
Gabriela Barreto Dos Reis, Takayoshi Ishii, Joerg Fuchs, Andreas Houben, Lisete Chamma Davide
Genome instability is observed in several species hybrids. We studied the mechanisms underlying the genome instability in hexaploid hybrids of Napier grass (Pennisetum purpureum R.) and pearl millet (Pennisetum glaucum L.) using a combination of different methods. Chromosomes of both parental genomes are lost by micronucleation. Our analysis suggests that genome instability occurs preferentially in meristematic root tissue of hexaploid hybrids, and chromosome elimination is not only caused by centromere inactivation...
September 2016: Chromosome Research
Helder Maiato
No abstract text is available yet for this article.
May 2016: Chromosome Research
Daniel W Förster, Eleanor P Jones, Fríða Jóhannesdóttir, Sofia I Gabriel, Mabel D Giménez, Thadsin Panithanarak, Heidi C Hauffe, Jeremy B Searle
The importance of chromosomal rearrangements for speciation can be inferred from studies of genetic exchange between hybridising chromosomal races within species. Reduced fertility or recombination suppression in karyotypic hybrids has the potential to maintain or promote genetic differentiation in genomic regions near rearrangement breakpoints. We studied genetic exchange between two hybridising groups of chromosomal races of house mouse in Upper Valtellina (Lombardy, Italy), using microsatellites. These groups differ by Robertsonian fusions and/or whole-arm reciprocal translocations such that F1 hybrids have a chain-of-five meiotic configuration...
May 2016: Chromosome Research
Tao Zhang, James R Paulson, Muhammed Bakhrebah, Ji Hun Kim, Cameron Nowell, Paul Kalitsis, Damien F Hudson
Condensin is an integral component of the mitotic chromosome condensation machinery, which ensures orderly segregation of chromosomes during cell division. In metazoans, condensin exists as two complexes, condensin I and II. It is not yet clear what roles these complexes may play outside mitosis, and so we have examined their behaviour both in normal interphase and in premature chromosome condensation (PCC). We find that a small fraction of condensin I is retained in interphase nuclei, and our data suggests that this interphase nuclear condensin I is active in both gene regulation and chromosome condensation...
May 2016: Chromosome Research
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