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Chromosome Research

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https://www.readbyqxmd.com/read/28091870/perspectives-using-polymer-modeling-to-understand-the-formation-and-function-of-nuclear-compartments
#1
REVIEW
N Haddad, D Jost, C Vaillant
Compartmentalization is a ubiquitous feature of cellular function. In the nucleus, early observations revealed a non-random spatial organization of the genome with a large-scale segregation between transcriptionally active-euchromatin-and silenced-heterochromatin-parts of the genome. Recent advances in genome-wide mapping and imaging techniques have strikingly improved the resolution at which nuclear genome folding can be analyzed and have revealed a multiscale spatial compartmentalization with increasing evidences that such compartment may indeed result from and participate to genome function...
January 14, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28078516/dense-gene-physical-maps-of-the-non-model-species-drosophila-subobscura
#2
Dorcas J Orengo, Eva Puerma, Montserrat Papaceit, Carmen Segarra, Montserrat Aguadé
The comparative analysis of genetic and physical maps as well as of whole genome sequences had revealed that in the Drosophila genus, most structural rearrangements occurred within chromosomal elements as a result of paracentric inversions. Genome sequence comparison would seem the best method to estimate rates of chromosomal evolution, but the high-quality reference genomes required for this endeavor are still scanty. Here, we have obtained dense physical maps for Muller elements A, C, and E of Drosophila subobscura, a species with an extensively studied rich and adaptive chromosomal polymorphism...
January 11, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28078515/capturing-genomic-relationships-that-matter
#3
REVIEW
Cameron S Osborne, Borbála Mifsud
There is a strong interrelationship within the cell nucleus between form and function of the genome. This connection is exhibited across multiple hierarchies, ranging from grand-scale positioning of chromosomes and their intersection with specific nuclear functional activities, the segregation of chromosome structure into distinct domains and long-range regulatory contacts that drive spatial and temporal expression patterns of genes. Fifteen years ago, the development of the chromosome conformation capture method placed the nature of specific, long-range regulatory interactions under scrutiny...
January 11, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28078514/the-molecular-basis-of-the-organization-of-repetitive-dna-containing-constitutive-heterochromatin-in-mammals
#4
REVIEW
Gohei Nishibuchi, Jérôme Déjardin
Constitutive heterochromatin is composed mainly of repetitive elements and represents the typical inert chromatin structure in eukaryotic cells. Approximately half of the mammalian genome is made of repeat sequences, such as satellite DNA, telomeric DNA, and transposable elements. As essential genes are not present in these regions, most of these repeat sequences were considered as junk DNA in the past. However, it is now clear that these regions are essential for chromosome stability and the silencing of neighboring genes...
January 11, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28070687/predicting-chromatin-architecture-from-models-of-polymer-physics
#5
REVIEW
Simona Bianco, Andrea M Chiariello, Carlo Annunziatella, Andrea Esposito, Mario Nicodemi
We review the picture of chromatin large-scale 3D organization emerging from the analysis of Hi-C data and polymer modeling. In higher mammals, Hi-C contact maps reveal a complex higher-order organization, extending from the sub-Mb to chromosomal scales, hierarchically folded in a structure of domains-within-domains (metaTADs). The domain folding hierarchy is partially conserved throughout differentiation, and deeply correlated to epigenomic features. Rearrangements in the metaTAD topology relate to gene expression modifications: in particular, in neuronal differentiation models, topologically associated domains (TADs) tend to have coherent expression changes within architecturally conserved metaTAD niches...
January 9, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28058543/genomic-profiling-of-canine-mast-cell-tumors-identifies-dna-copy-number-aberrations-associated-with-kit-mutations-and-high-histological-grade
#6
Hiroyuki Mochizuki, Rachael Thomas, Scott Moroff, Matthew Breen
Mast cell tumor (MCT) is the most common skin malignancy of domestic dogs and presents with a widely variable clinical behavior. Although activating KIT mutations are present in approximately 20% of canine MCTs, molecular etiology is largely unknown for the majority of this cancer. Characterization of genomic alterations in canine MCTs may identify genomic regions and/or genes responsible for their development and progression, facilitating the discovery of new therapeutic targets and improved clinical management of this heterogeneous cancer...
January 5, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28050734/sororin-is-enriched-at-the-central-region-of-synapsed-meiotic-chromosomes
#7
Philip W Jordan, Craig Eyster, Jingrong Chen, Roberto J Pezza, Susannah Rankin
During meiotic prophase, cohesin complexes mediate cohesion between sister chromatids and promote pairing and synapsis of homologous chromosomes. Precisely how the activity of cohesin is controlled to promote these events is not fully understood. In metazoans, cohesion establishment between sister chromatids during mitotic divisions is accompanied by recruitment of the cohesion-stabilizing protein Sororin. During somatic cell division cycles, Sororin is recruited in response to DNA replication-dependent modification of the cohesin complex by ESCO acetyltransferases...
January 3, 2017: Chromosome Research
https://www.readbyqxmd.com/read/27995349/the-essential-drosophila-clamp-protein-differentially-regulates-non-coding-rox-rnas-in-male-and-females
#8
Jennifer A Urban, Caroline A Doherty, William T Jordan, Jacob E Bliss, Jessica Feng, Marcela M Soruco, Leila E Rieder, Maria A Tsiarli, Erica N Larschan
Heterogametic species require chromosome-wide gene regulation to compensate for differences in sex chromosome gene dosage. In Drosophila melanogaster, transcriptional output from the single male X-chromosome is equalized to that of XX females by recruitment of the male-specific lethal (MSL) complex, which increases transcript levels of active genes 2-fold. The MSL complex contains several protein components and two non-coding RNA on the X ( roX) RNAs that are transcriptionally activated by the MSL complex. We previously discovered that targeting of the MSL complex to the X-chromosome is dependent on the chromatin-linked adapter for MSL proteins (CLAMP) zinc finger protein...
December 19, 2016: Chromosome Research
https://www.readbyqxmd.com/read/27987109/proliferating-cell-nuclear-antigen-pcna-contributes-to-the-high-order-structure-and-stability-of-heterochromatin-in-saccharomyces-cerevisiae
#9
Xin Bi, Yue Ren, Morgan Kath
Heterochromatin plays important roles in the structure, maintenance, and function of the eukaryotic genome. It is associated with special histone modifications and specialized non-histone proteins and assumes a more compact structure than euchromatin. Genes embedded in heterochromatin are generally transcriptionally silent. It was found previously that several mutations of proliferating cell nuclear antigen (PCNA), a DNA replication processivity factor, reduce transcriptional silencing at heterochromatin loci in Saccharomyces cerevisiae...
December 16, 2016: Chromosome Research
https://www.readbyqxmd.com/read/27924426/preditor-a-synthetic-biology-approach-to-removing-heterochromatin-from-cells
#10
Oscar Molina, Mar Carmena, Isabella E Maudlin, William C Earnshaw
It is widely accepted that heterochromatin is necessary to maintain genomic stability. However, direct experimental evidence supporting this is slim. Previous studies using either enzyme inhibitors, gene knockout or knockdown studies all are subject to the caveat that drugs may have off-target effects and enzymes that modify chromatin proteins to support heterochromatin formation may also have numerous other cellular targets as well. Here, we describe PREditOR (protein reading and editing of residues), a synthetic biology approach that allows us to directly remove heterochromatin from cells without either drugs or global interference with gene function...
December 2016: Chromosome Research
https://www.readbyqxmd.com/read/27766446/data-analysis-algorithm-for-damid-seq-profiling-of-chromatin-proteins-in-drosophila-melanogaster
#11
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...
December 2016: Chromosome Research
https://www.readbyqxmd.com/read/27590598/chromatin-associated-transcripts-of-tandemly-repetitive-dna-sequences-revealed-by-rna-fish
#12
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...
December 2016: Chromosome Research
https://www.readbyqxmd.com/read/27581771/human-centromere-repositioning-within-euchromatin-after-partial-chromosome-deletion
#13
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...
December 2016: Chromosome Research
https://www.readbyqxmd.com/read/27581770/erratum-to-meiotic-pairing-and-gene-expression-disturbance-in-germ-cells-from-an-infertile-boar-with-a-balanced-reciprocal-autosome-autosome-translocation
#14
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.
December 2016: Chromosome Research
https://www.readbyqxmd.com/read/27553478/centromere-inactivation-on-a-neo-y-fusion-chromosome-in-threespine-stickleback-fish
#15
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)...
December 2016: Chromosome Research
https://www.readbyqxmd.com/read/27484982/meiotic-pairing-and-gene-expression-disturbance-in-germ-cells-from-an-infertile-boar-with-a-balanced-reciprocal-autosome-autosome-translocation
#16
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...
December 2016: Chromosome Research
https://www.readbyqxmd.com/read/27430641/clusters-of-alpha-satellite-on-human-chromosome-21-are-dispersed-far-onto-the-short-arm-and-lack-ancient-layers
#17
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
https://www.readbyqxmd.com/read/27333765/ancestral-y-linked-genes-were-maintained-by-translocation-to-the-x-and-y-chromosomes-fused-to-an-autosomal-pair-in-the-okinawa-spiny-rat-tokudaia-muenninki
#18
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
https://www.readbyqxmd.com/read/27294972/the-distribution-of-%C3%AE-kleisin-during-meiosis-in-the-holocentromeric-plant-luzula-elegans
#19
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
https://www.readbyqxmd.com/read/27193170/karyotype-diversity-suggests-that-laonastes-aenigmamus-laotian-rock-rat-rodentia-diatomyidae-is-a-multi-specific-genus
#20
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
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