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Chromosome Research

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https://www.readbyqxmd.com/read/30617621/the-chromatin-landscape-of-the-ribosomal-rna-genes-in-mouse-and-human
#1
REVIEW
Tom Moss, Jean-Clement Mars, Michel G Tremblay, Marianne Sabourin-Felix
The rRNA genes of mouse and human encode the three major RNAs of the ribosome and as such are essential for growth and development. These genes are present in high copy numbers and arranged as direct repeats at the Nucleolar Organizer Regions on multiple chromosomes. Not all the rRNA genes are transcriptionally active, but the molecular mechanisms that determine activity are complex and still poorly understood. Recent studies applying a novel Deconvolution Chromatin Immunoprecipitation (DChIP-Seq) technique in conjunction with conditional gene inactivation provide new insights into the structure of the active rRNA genes and question previous assumptions on the role of chromatin and histone modifications...
January 8, 2019: Chromosome Research
https://www.readbyqxmd.com/read/30610403/uva-irradiation-strengthened-an-interaction-between-ubf1-2-proteins-and-h4k20-di-tri-methylation
#2
Lenka Stixová, Denisa Komůrková, Alena Svobodová Kovaříková, Eva Bártová
Repair of ribosomal DNA (rDNA) is a very important nuclear process due to the most active transcription of ribosomal genes. Proper repair of rDNA is required for physiological biogenesis of ribosomes. Here, we analyzed the epigenetics of the DNA damage response in a nucleolar compartment, thus in the ribosomal genes studied in nonirradiated and UVA-irradiated mouse embryonic fibroblasts (MEFs). We found that the promoter of ribosomal genes is not abundant on H4K20me2, but it is densely occupied by H4K20me3...
January 4, 2019: Chromosome Research
https://www.readbyqxmd.com/read/30604344/cytogenetic-instability-of-chromosomal-nucleolar-organizer-regions-nors-in-cloned-mouse-l929-fibroblasts
#3
Olga V Zatsepina
Ribosomal DNA (rDNA) gene codes for 18S, 5.8S, and 28S rRNA form tandem repetitive clusters, which occupy distinct chromosomal loci called nucleolar organizer regions (NORs). The number and position of NORs on chromosomes are genetic characteristics of the species although within a cell, the NOR sizes can significantly vary due to loss or multiplication of rDNA copies. In the current study, we used mouse L929 fibroblasts, the aneuploid cells which differ in the FISH- and Ag-NOR numbers, to examine whether the parental NOR variability is inherited in clones...
January 3, 2019: Chromosome Research
https://www.readbyqxmd.com/read/30604343/ribosomal-dna-instability-and-genome-adaptability
#4
REVIEW
Devika Salim, Jennifer L Gerton
Ribosomes are large, multi-subunit ribonucleoprotein complexes, essential for protein synthesis. To meet the high cellular demand for ribosomes, all eukaryotes have numerous copies of ribosomal DNA (rDNA) genes that encode ribosomal RNA (rRNA), usually far in excess of the requirement for ribosome biogenesis. In all eukaryotes studied, rDNA genes are arranged in one or more clusters of tandem repeats localized to nucleoli. The tandem arrangement of repeats, combined with the high rates of transcription at the rDNA loci, and the difficulty of replicating repetitive sequences make the rDNA inherently unstable and particularly susceptible to large variations in repeat copy number...
January 3, 2019: Chromosome Research
https://www.readbyqxmd.com/read/30565005/heterochromatic-regions-in-japanese-quail-chromosomes-comprehensive-molecular-cytogenetic-characterization-and-3d-mapping-in-interphase-nucleus
#5
Anna Zlotina, Antonina Maslova, Nadezda Kosyakova, Ahmed B Hamid Al-Rikabi, Thomas Liehr, Alla Krasikova
Chromosomes of Japanese quail (Coturnix coturnix japonica, 2n=78), a galliform domestic species closely related to chicken, possess multiple heterochromatic segments. Due to the difficulties in careful analysis of such heterochromatic regions, there is a lack of data on their DNA composition, epigenetic status, as well as spatial distribution in interphase nucleus. In the present study, we applied giant lampbrush chromosome (LBC) microdissection for high-resolution analysis of quail centromeric regions of macrochromosomes and polymorphic short arms of submetacentric microchromosomes...
December 18, 2018: Chromosome Research
https://www.readbyqxmd.com/read/30556094/keeping-ribosomal-dna-intact-a-repeating-challenge
#6
REVIEW
Daniël O Warmerdam, Rob M F Wolthuis
More than half of the human genome consists of repetitive sequences, with the ribosomal DNA (rDNA) representing two of the largest repeats. Repetitive rDNA sequences may form a threat to genomic integrity and cellular homeostasis due to the challenging aspects of their transcription, replication, and repair. Predisposition to cancer, premature aging, and neurological impairment in ataxia-telangiectasia and Bloom syndrome, for instance, coincide with increased cellular rDNA repeat instability. However, the mechanisms by which rDNA instability contributes to these hereditary syndromes and tumorigenesis remain unknown...
December 17, 2018: Chromosome Research
https://www.readbyqxmd.com/read/30539407/the-nucleolar-transcriptome-regulates-piwi-shuttling-between-the-nucleolus-and-the-nucleoplasm
#7
Elena A Mikhaleva, Toomas A Leinsoo, Hirotsugu Ishizu, Vladimir A Gvozdev, Mikhail S Klenov
The nucleolus contains a lot of proteins unrelated to ribosome biogenesis. Some of these proteins shuttle between the nucleolus and the nucleoplasm regulating the cell cycle and stress response. The piRNA binding protein Piwi is involved in silencing of transposable elements (TEs) in the Drosophila gonads. Here we used cultured ovarian somatic cells (OSC) to characterize Piwi as a visitor to the nucleolus. Dynamic Piwi localization was shown to vary from its uniform distribution between the nucleoplasm and the nucleolus to pronounced nucleolar immobilization...
December 12, 2018: Chromosome Research
https://www.readbyqxmd.com/read/30539406/the-methylation-and-telomere-landscape-in-two-families-of-marsupials-with-different-rates-of-chromosome-evolution
#8
Emory D Ingles, Janine E Deakin
Two marsupial families exemplify divergent rates of karyotypic change. The Dasyurid family has an extremely conserved karyotype. In contrast, there is significant chromosomal variation within the Macropodidae family, best exemplified by members of the genus Petrogale (rock-wallabies). Both families are also distinguished by their telomere landscape (length and epigenetics), with the dasyurids having a unique telomere length dimorphism not observed in other marsupials and hypothesised to be regulated in a parent-of-origin fashion...
December 12, 2018: Chromosome Research
https://www.readbyqxmd.com/read/30511202/the-peculiar-genetics-of-the-ribosomal-dna-blurs-the-boundaries-of-transgenerational-epigenetic-inheritance
#9
REVIEW
Farah Bughio, Keith A Maggert
Our goal is to draw a line-hypothetical in its totality but experimentally supported at each individual step-connecting the ribosomal DNA and the phenomenon of transgenerational epigenetic inheritance of induced phenotypes. The reasonableness of this hypothesis is offset by its implication, that many (or most) (or all) of the cases of induced-and-inherited phenotypes that are seen to persist for generations are instead unmapped induced polymorphisms in the ribosomal DNA, and thus are the consequence of the peculiar and enduringly fascinating genetics of the highly transcribed repeat DNA structure at that locus...
December 4, 2018: Chromosome Research
https://www.readbyqxmd.com/read/30499043/distribution-of-cr1-like-transposable-element-in-woodpeckers-aves-piciformes-z-sex-chromosomes-can-act-as-a-refuge-for-transposable-elements
#10
Natasha Avila Bertocchi, Thays Duarte de Oliveira, Analía Del Valle Garnero, Rafael Luiz Buogo Coan, Ricardo José Gunski, Cesar Martins, Fabiano Pimentel Torres
Birds have relatively few repetitive sequences compared to other groups of vertebrates; however, the members of order Piciformes (woodpeckers) have more of these sequences, composed mainly of transposable elements (TE). The TE most often found in birds is a retrotransposon chicken repeat 1 (CR1). Piciformes lineages were subjected to an expansion of the CR1 elements, carrying a larger fraction of transposable elements. This study compared patterns of chromosome distribution among five bird species, through chromosome mapping of the CR1 sequence and reconstructed their phylogenetic tree...
November 29, 2018: Chromosome Research
https://www.readbyqxmd.com/read/30443803/a-combined-banding-method-that-allows-the-reliable-identification-of-chromosomes-as-well-as-differentiation-of-at-and-gc-rich-heterochromatin
#11
Natalya A Lemskaya, Anastasia I Kulemzina, Violetta R Beklemisheva, Larisa S Biltueva, Anastasia A Proskuryakova, John M Hallenbeck, Polina L Perelman, Alexander S Graphodatsky
Сonstitutive heterochromatin areas are revealed by differential staining as C-positive chromosomal regions. These C-positive bands may greatly vary by location, size, and nucleotide composition. CBG-banding is the most commonly used method to detect structural heterochromatin in animals. The difficulty in identification of individual chromosomes represents an unresolved problem of this method as the body of the chromosome is stained uniformly and does not have banding pattern beyond C-bands. Here, we present the method that we called CDAG for sequential heterochromatin staining after differential GTG-banding...
November 15, 2018: Chromosome Research
https://www.readbyqxmd.com/read/30406864/nucleoli-in-embryos-a-central-structural-platform-for-embryonic-chromatin-remodeling
#12
REVIEW
Helena Fulka, Alena Langerova
Nucleoli are the site of ribosomal RNA production and subunit assembly. In contrast to active nucleoli in somatic cells, where three basic sub-compartments can be observed, mammalian oocytes and early embryos contain atypical nucleoli termed "nucleolus-like bodies" or "nucleolus precursor bodies", respectively. Unlike their somatic counterparts, these structures are composed of dense homogenous fibrillar material and exhibit no polymerase activity. Irrespective of these unusual properties, they have been shown to be absolutely essential for embryonic development, as their microsurgical removal results in developmental arrest...
November 8, 2018: Chromosome Research
https://www.readbyqxmd.com/read/30343462/dosage-effects-of-human-ribosomal-genes-rdna-in-health-and-disease
#13
REVIEW
L N Porokhovnik, N A Lyapunova
Human ribosomal RNA genes encoding a pre-transcript of the three major ribosomal RNA (18S, 5.8S, and 28S rRNA) are tandemly repeated in human genome. Their total copy number varies from 250 to 670 per diploid genome with a mean of approximately 420 copies, but only a fraction of them is transcriptionally active. The functional consequences of human ribosomal RNA gene dosage are not widely known and often assumed to be negligible. Here, we review the facts of rRNA gene dosage effects on normal growth and aging, stress resistance of healthy individuals, and survivability of patients with chromosomal abnormalities, as well as on the risk and severity of some multifactorial diseases with proven genetic predisposition...
October 20, 2018: Chromosome Research
https://www.readbyqxmd.com/read/30343461/genes-involved-in-mirna-biogenesis-affect-meiosis-and-fertility
#14
REVIEW
Mónica Pradillo, Juan L Santos
MicroRNAs (miRNAs) are a class of small (containing about 22 nucleotides) single-stranded non-coding RNAs that regulate gene expression at the post-transcriptional level in plants and animals, being absent from unicellular organisms. They act on diverse key physiological and cellular processes, such as development and tissue differentiation, cell identity, cell cycle progression, and programmed cell death. They are also likely to be involved in a broad spectrum of human diseases. Particularly, this review examines and summarizes work characterizing the function of miRNAs in gametogenesis and fertility...
October 20, 2018: Chromosome Research
https://www.readbyqxmd.com/read/30276581/herbert-macgregor-1933-2018
#15
EDITORIAL
Joseph G Gall
No abstract text is available yet for this article.
October 1, 2018: Chromosome Research
https://www.readbyqxmd.com/read/30225548/but-where-did-the-centromeres-go-in-the-chicken-genome-models
#16
Benoît Piégu, Peter Arensburger, Florian Guillou, Yves Bigot
The chicken genome was the third vertebrate to be sequenced. To date, its sequence and feature annotations are used as the reference for avian models in genome sequencing projects developed on birds and other Sauropsida species, and in genetic studies of domesticated birds of economic and evolutionary biology interest. Therefore, an accurate description of this genome model is important to a wide number of scientists. Here, we review the location and features of a very basic element, the centromeres of chromosomes in the galGal5 genome model...
September 17, 2018: Chromosome Research
https://www.readbyqxmd.com/read/29974361/alpha-satellite-dna-biology-finding-function-in-the-recesses-of-the-genome
#17
REVIEW
Shannon M McNulty, Beth A Sullivan
Repetitive DNA, formerly referred to by the misnomer "junk DNA," comprises a majority of the human genome. One class of this DNA, alpha satellite, comprises up to 10% of the genome. Alpha satellite is enriched at all human centromere regions and is competent for de novo centromere assembly. Because of the highly repetitive nature of alpha satellite, it has been difficult to achieve genome assemblies at centromeres using traditional next-generation sequencing approaches, and thus, centromeres represent gaps in the current human genome assembly...
September 2018: Chromosome Research
https://www.readbyqxmd.com/read/29789973/chromosomal-distribution-of-soybean-retrotransposon-sore-1-suggests-its-recent-preferential-insertion-into-euchromatic-regions
#18
Kenta Nakashima, Jun Abe, Akira Kanazawa
Retrotransposons constitute a large portion of plant genomes. The chromosomal distribution of a wide variety of retrotransposons has been analyzed using genome sequencing data in several plants, but the evolutionary profile of transposition has been characterized for a limited number of retrotransposon families. Here, we characterized 96 elements of the SORE-1 family of soybean retrotransposons using genome sequencing data. Insertion time of each SORE-1 element into the genome was estimated on the basis of sequence differences between the 5' and 3' long terminal repeats (LTRs)...
September 2018: Chromosome Research
https://www.readbyqxmd.com/read/29679205/changes-in-the-position-and-volume-of-inactive-x-chromosomes-during-the-g0-g1-transition
#19
Guoliang Lyu, Tan Tan, Yiting Guan, Lei Sun, Qianjin Liang, Wei Tao
In female mammals, each cell silences one X chromosome by converting it into transcriptionally inert heterochromatin. The inactivation is concomitant with epigenetic changes including methylation of specific histone residues and incorporation of macroH2A. Such epigenetic changes may exert influence on the positioning of the inactive X chromosome (Xi) within the nucleus beyond the level of chromatin structure. However, the dynamic positioning of the inactive X chromosome during cell cycle remains unclear. Here, we show that H3K27me3 is a cell-cycle-independent marker for the inactivated X chromosomes in WI38 cells...
September 2018: Chromosome Research
https://www.readbyqxmd.com/read/29524007/insights-into-the-karyotype-evolution-and-speciation-of-the-beetle-euchroma-gigantea-coleoptera-buprestidae
#20
Crislaine Xavier, Rógean Vinícius Santos Soares, Igor Costa Amorim, Diogo Cavalcanti Cabral-de-Mello, Rita de Cássia de Moura
Euchroma Dejean, 1833 (Buprestidae: Coleoptera) is a monotypic genus comprising the species Euchroma gigantea, with populations presenting a degree of karyotypic variation/polymorphism rarely found within a single taxonomic (specific) unit, as well as drastically incompatible meiotic configurations in populations from extremes of the species range. To better understand the complex karyotypic evolution of E. gigantea, the karyotypes of specimens from five populations in Brazil were investigated using molecular cytogenetics and phylogenetic approaches...
September 2018: Chromosome Research
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