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Chromosome territory

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https://www.readbyqxmd.com/read/29721254/chromosome-positioning-in-interphase-nuclei-of-hematopoietic-stem-cell-and-myeloid-precursor
#1
Mariana Lomiento, Fabiana Mammoli, Emilia Maria Cristina Mazza, Silvio Bicciato, Sergio Ferrari
Human myelopoiesis is an intriguing biological process during which multipotent stem cells limit their differentiation potential generating precursors that evolve into terminally differentiated cells. The differentiation process is correlated with differential gene expression and changes in nuclear architecture. In interphase, chromosomes are distinct entities known as chromosome territories and they show a radial localization that could result in a constrain of inter-homologous distance. This element plays a role in genome stability and gene expression...
March 2, 2018: Hematology Reports
https://www.readbyqxmd.com/read/29703667/entering-the-next-dimension-plant-genomes-in-3d
#2
REVIEW
Mariana Sotelo-Silveira, Ricardo A Chávez Montes, Jose R Sotelo-Silveira, Nayelli Marsch-Martínez, Stefan de Folter
After linear sequences of genomes and epigenomic landscape data, the 3D organization of chromatin in the nucleus is the next level to be explored. Different organisms present a general hierarchical organization, with chromosome territories at the top. Chromatin interaction maps, obtained by chromosome conformation capture (3C)-based methodologies, for eight plant species reveal commonalities, but also differences, among them and with animals. The smallest structures, found in high-resolution maps of the Arabidopsis genome, are single genes...
April 24, 2018: Trends in Plant Science
https://www.readbyqxmd.com/read/29684168/emerin-modulates-spatial-organization-of-chromosome-territories-in-cells-on-softer-matrices
#3
Roopali Pradhan, Devika Ranade, Kundan Sengupta
Cells perceive and relay external mechanical forces into the nucleus through the nuclear envelope. Here we examined the effect of lowering substrate stiffness as a paradigm to address the impact of altered mechanical forces on nuclear structure-function relationships. RNA sequencing of cells on softer matrices revealed significant transcriptional imbalances, predominantly in chromatin associated processes and transcriptional deregulation of human Chromosome 1. Furthermore, 3-Dimensional fluorescence in situ hybridization (3D-FISH) analyses showed a significant mislocalization of Chromosome 1 and 19 Territories (CT) into the nuclear interior, consistent with their transcriptional deregulation...
April 19, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29660196/genome-wide-hi-c-analysis-reveals-extensive-hierarchical-chromatin-interactions-in-rice
#4
Qianli Dong, Ning Li, Xiaochong Li, Zan Yuan, Dejian Xie, Xiaofei Wang, Jianing Li, Yanan Yu, Jinbin Wang, Baoxu Ding, Zhibin Zhang, Changping Li, Yao Bian, Ai Zhang, Ying Wu, Bao Liu, Lei Gong
The non-random spatial packing of chromosomes in the nucleus plays critical roles in orchestrating gene expression and genome function. Here, we present a Hi-C analysis of the chromatin interaction patterns in rice (Oryza sativa L.) at hierarchical architectural levels. We confirm that rice chromosomes occupy their own territories with certain preferential inter-chromosomal associations. Moderate compartment delimitation and extensive TADs (Topologically Associated Domains) were determined to be associated with heterogeneous genomic compositions and epigenetic marks in the rice genome...
April 16, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29626919/the-4d-nucleome-genome-compartmentalization-in-an-evolutionary-context
#5
REVIEW
T Cremer, M Cremer, C Cremer
4D nucleome research aims to understand the impact of nuclear organization in space and time on nuclear functions, such as gene expression patterns, chromatin replication, and the maintenance of genome integrity. In this review we describe evidence that the origin of 4D genome compartmentalization can be traced back to the prokaryotic world. In cell nuclei of animals and plants chromosomes occupy distinct territories, built up from ~1 Mb chromatin domains, which in turn are composed of smaller chromatin subdomains and also form larger chromatin domain clusters...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29607481/ancient-dna-reveals-temporal-population-structure-within-the-south-central-andes-area
#6
M Gabriela Russo, Fanny Mendisco, Sergio A Avena, Cristian M Crespo, Valeria Arencibia, Cristina B Dejean, Verónica Seldes
OBJECTIVES: The main aim of this work was to contribute to the knowledge of pre-Hispanic genetic variation and population structure among the South-central Andes Area by studying individuals from Quebrada de Humahuaca, North-western (NW) Argentina. MATERIALS AND METHODS: We analyzed 15 autosomal STRs in 19 individuals from several archaeological sites in Quebrada de Humahuaca, belonging to the Regional Developments Period (900-1430 AD). Compiling autosomal, mitochondrial, and Y-chromosome data, we evaluated population structure and differentiation among eight South-central Andean groups from the current territories of NW Argentina and Peru...
April 1, 2018: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/29596530/establishment-and-characterization-of-pygmy-killer-whale-feresa-attenuata-dermal-fibroblast-cell-line
#7
Sun Yajing, Imran Rashid Rajput, Huang Ying, Yu Fei, Edmond Sanganyado, Li Ping, Wang Jingzhen, Liu Wenhua
The pygmy killer whale (Feresa attenuata) (PKW) is a tropical and subtropical marine mammal commonly found in the Atlantic, Indian and Pacific oceans. Since the PKWs live in offshore protected territories, they are rarely seen onshore. Hence, PKW are one of the most poorly understood oceanic species of odontocetes. The dermal tissue comes primarily from stranding events that occur along the coast of the Shantou, Guangdong, China. The sampled tissues were immediately processed and attached on collagen-coated 6-well tissue culture plate...
2018: PloS One
https://www.readbyqxmd.com/read/29581440/three-dimensional-epigenome-statistical-model-genome-wide-chromatin-looping-prediction
#8
Ziad Al Bkhetan, Dariusz Plewczynski
This study aims to understand through statistical learning the basic biophysical mechanisms behind three-dimensional folding of epigenomes. The 3DEpiLoop algorithm predicts three-dimensional chromatin looping interactions within topologically associating domains (TADs) from one-dimensional epigenomics and transcription factor profiles using the statistical learning. The predictions obtained by 3DEpiLoop are highly consistent with the reported experimental interactions. The complex signatures of epigenomic and transcription factors within the physically interacting chromatin regions (anchors) are similar across all genomic scales: genomic domains, chromosomal territories, cell types, and different individuals...
March 26, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29573605/expanded-croatian-12-x-str-loci-database-with-an-overview-of-anomalous-profiles
#9
Gordan Mršić, Petar Ozretić, Josip Crnjac, Siniša Merkaš, Viktorija Sukser, Ivana Račić, Sara Rožić, Lucija Barbarić, Maja Popović, Marina Korolija
In order to implement X-chromosome short tandem repeat (X-STR) typing into routine forensic practice, reference database of a given population should be established. Therefore we extended already published data with additional 397 blood samples from unrelated Croatian citizens, and analyzed the total of 995 samples (549 male and 446 female) typed by Investigator® Argus X-12 Kit. To test genetic homogeneity of consecutively processed five historic-cultural regions covering the entire national territory, we calculated pairwise Fst genetic distances between regions based on allele and full haplotype frequencies...
March 9, 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29568981/three-dimensional-organization-and-dynamics-of-the-genome
#10
REVIEW
Przemyslaw Szalaj, Dariusz Plewczynski
Genome is a complex hierarchical structure, and its spatial organization plays an important role in its function. Chromatin loops and topological domains form the basic structural units of this multiscale organization and are essential to orchestrate complex regulatory networks and transcription mechanisms. They also form higher-order structures such as chromosomal compartments and chromosome territories. Each level of this intrinsic architecture is governed by principles and mechanisms that we only start to understand...
March 22, 2018: Cell Biology and Toxicology
https://www.readbyqxmd.com/read/29496978/practice-guideline-joint-ccmg-sogc-recommendations-for-the-use-of-chromosomal-microarray-analysis-for-prenatal-diagnosis-and-assessment-of-fetal-loss-in-canada
#11
Christine M Armour, Shelley Danielle Dougan, Jo-Ann Brock, Radha Chari, Bernie N Chodirker, Isabelle DeBie, Jane A Evans, William T Gibson, Elena Kolomietz, Tanya N Nelson, Frédérique Tihy, Mary Ann Thomas, Dimitri J Stavropoulos
BACKGROUND: The aim of this guideline is to provide updated recommendations for Canadian genetic counsellors, medical geneticists, maternal fetal medicine specialists, clinical laboratory geneticists and other practitioners regarding the use of chromosomal microarray analysis (CMA) for prenatal diagnosis. This guideline replaces the 2011 Society of Obstetricians and Gynaecologists of Canada (SOGC)-Canadian College of Medical Geneticists (CCMG) Joint Technical Update. METHODS: A multidisciplinary group consisting of medical geneticists, genetic counsellors, maternal fetal medicine specialists and clinical laboratory geneticists was assembled to review existing literature and guidelines for use of CMA in prenatal care and to make recommendations relevant to the Canadian context...
April 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29408376/hictmap-detection-and-analysis-of-chromosome-territory-structure-and-position-by-high-throughput-imaging
#12
Ziad Jowhar, Prabhakar R Gudla, Sigal Shachar, Darawalee Wangsa, Jill L Russ, Gianluca Pegoraro, Thomas Ried, Armin Raznahan, Tom Misteli
The spatial organization of chromosomes in the nuclear space is an extensively studied field that relies on measurements of structural features and 3D positions of chromosomes with high precision and robustness. However, no tools are currently available to image and analyze chromosome territories in a high-throughput format. Here, we have developed High-throughput Chromosome Territory Mapping (HiCTMap), a method for the robust and rapid analysis of 2D and 3D chromosome territory positioning in mammalian cells...
February 10, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29357905/chromosome-nuclear-envelope-attachments-affect-interphase-chromosome-territories-and-entanglement
#13
Nicholas Allen Kinney, Igor V Sharakhov, Alexey V Onufriev
BACKGROUND: It is well recognized that the interphase chromatin of higher eukaryotes folds into non-random configurations forming territories within the nucleus. Chromosome territories have biologically significant properties, and understanding how these properties change with time during lifetime of the cell is important. Chromosome-nuclear envelope (Chr-NE) interactions play a role in epigenetic regulation of DNA replication, repair, and transcription. However, their role in maintaining chromosome territories remains unclear...
January 22, 2018: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29327450/the-black-legend-on-the-spanish-presence-in-the-low-countries-verifying-shared-beliefs-on-genetic-ancestry
#14
Maarten H D Larmuseau, Francesc Calafell, Sarah A Princen, Ronny Decorte, Violet Soen
OBJECTIVES: War atrocities committed by the Spanish army in the Low Countries during the 16th century are so ingrained in the collective memory of Belgian and Dutch societies that they generally assume a signature of this history to be present in their genetic ancestry. Historians claim this assumption is a consequence of the so-called "Black Legend" and negative propaganda portraying and remembering Spanish soldiers as extreme sexual aggressors. The impact of the presence of Spaniards during the Dutch Revolt on the genetic variation in the Low Countries has been verified in this study...
January 11, 2018: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/29238858/spatial-organization-of-chromosome-territories-in-the-interphase-nucleus-of-trisomy-21-cells
#15
Stephan Kemeny, Christophe Tatout, Gaelle Salaun, Céline Pebrel-Richard, Carole Goumy, Natasha Ollier, Eugenie Maurin, Bruno Pereira, Philippe Vago, Laetitia Gouas
In the interphase cell nucleus, chromosomes adopt a conserved and non-random arrangement in subnuclear domains called chromosome territories (CTs). Whereas chromosome translocation can affect CT organization in tumor cell nuclei, little is known about how aneuploidies can impact CT organization. Here, we performed 3D-FISH on control and trisomic 21 nuclei to track the patterning of chromosome territories, focusing on the radial distribution of trisomic HSA21 as well as 11 disomic chromosomes. We have established an experimental design based on cultured chorionic villus cells which keep their original mesenchymal features including a characteristic ellipsoid nuclear morphology and a radial CT distribution that correlates with chromosome size...
December 14, 2017: Chromosoma
https://www.readbyqxmd.com/read/29237819/condensins-promote-chromosome-individualization-and-segregation-during-mitosis-meiosis-and-amitosis-in-tetrahymena-thermophila
#16
Rachel Howard-Till, Josef Loidl
Condensin is a protein complex with diverse functions in chromatin packaging and chromosome condensation and segregation. We studied condensin in the evolutionarily distant protist model Tetrahymena , which features noncanonical nuclear organization and divisions. In Tetrahymena , the germline and soma are partitioned into two different nuclei within a single cell. Consistent with their functional specializations in sexual reproduction and gene expression, condensins of the germline nucleus and the polyploid somatic nucleus are composed of different subunits...
February 15, 2018: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/29190286/nucleolar-sub-compartments-in-motion-during-rrna-synthesis-inhibition-contraction-of-nucleolar-condensed-chromatin-and-gathering-of-fibrillar-centers-are-concomitant
#17
Pavel Tchelidze, Aassif Benassarou, Hervé Kaplan, Marie-Françoise O'Donohue, Laurent Lucas, Christine Terryn, Levan Rusishvili, Giorgi Mosidze, Nathalie Lalun, Dominique Ploton
The nucleolus produces the large polycistronic transcript (47S precursor) containing the 18S, 5.8S and 28S rRNA sequences and hosts most of the nuclear steps of pre-rRNA processing. Among numerous components it contains condensed chromatin and active rRNA genes which adopt a more accessible conformation. For this reason, it is a paradigm of chromosome territory organization. Active rRNA genes are clustered within several fibrillar centers (FCs), in which they are maintained in an open configuration by Upstream Binding Factor (UBF) molecules...
2017: PloS One
https://www.readbyqxmd.com/read/29148554/modelling-direct-dna-damage-for-gold-nanoparticle-enhanced-proton-therapy
#18
Marios Sotiropoulos, Nicholas T Henthorn, John W Warmenhoven, Ranald I Mackay, Karen J Kirkby, Michael J Merchant
Gold nanoparticles have been proven as potential radiosensitizer when combined with protons. Initially the radiosensitization effect was attributed to the physical interactions of radiation with the gold and the production of secondary electrons that induce DNA damage. However, emerging data challenge this hypothesis, supporting the existence of alternative or supplementary radiosensitization mechanisms. In this work we incorporate a realistic cell model with detailed DNA geometry and a realistic gold nanoparticle biodistribution based on experimental data...
November 30, 2017: Nanoscale
https://www.readbyqxmd.com/read/29141034/structure-of-the-human-chromosome-interaction-network
#19
Sergio Sarnataro, Andrea M Chiariello, Andrea Esposito, Antonella Prisco, Mario Nicodemi
New Hi-C technologies have revealed that chromosomes have a complex network of spatial contacts in the cell nucleus of higher organisms, whose organisation is only partially understood. Here, we investigate the structure of such a network in human GM12878 cells, to derive a large scale picture of nuclear architecture. We find that the intensity of intra-chromosomal interactions is power-law distributed. Inter-chromosomal interactions are two orders of magnitude weaker and exponentially distributed, yet they are not randomly arranged along the genomic sequence...
2017: PloS One
https://www.readbyqxmd.com/read/29037558/monozygotic-twins-discordant-for-trisomy-21-discussion-of-etiological-events-involved
#20
Yao-Lung Chang, Wu-Pei Yi, An-Shine Chao, Kuan-Ju Chen, Po-Jen Cheng, Tzu-Hao Wang, Shuenn-Dyh Chang
OBJECTIVE: To elucidate the etiologies of discordant trisomy 21 in monozygotic twin pregnancy. CASE REPORT: A monochorionic diamniotic twin pregnancy with hydrops and cleft lip (twin 1) found in one fetus presented at gestational age of 17 weeks. Amniotic fluid karyotyping showed nonmosaic trisomy 21 in twin 1 (47, XY, +21 [20]) and a normal karyotype in twin 2 (46, XY [20]). Short tandem repeat (STR) polymorphism markers revealed that the two fetuses were monozygotic, and the two chromosomes 21 were maternal isodisomy in the trisomy fetus...
October 2017: Taiwanese Journal of Obstetrics & Gynecology
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