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Chromosome territories

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https://www.readbyqxmd.com/read/28343235/transcription-dependent-radial-distribution-of-tcf7l2-regulated-genes-in-chromosome-territories
#1
Keyvan Torabi, Darawalee Wangsa, Immaculada Ponsa, Markus Brown, Anna Bosch, Maria Vila-Casadesús, Tatiana S Karpova, Maria Calvo, Antoni Castells, Rosa Miró, Thomas Ried, Jordi Camps
Human chromosomes occupy distinct territories in the interphase nucleus. Such chromosome territories (CTs) are positioned according to gene density. Gene-rich CTs are generally located in the center of the nucleus, while gene-poor CTs are positioned more towards the nuclear periphery. However, the association between gene expression levels and the radial positioning of genes within the CT is still under debate. In the present study, we performed three-dimensional fluorescence in situ hybridization experiments in the colorectal cancer cell lines DLD-1 and LoVo using whole chromosome painting probes for chromosomes 8 and 11 and BAC clones targeting four genes with different expression levels assessed by gene expression arrays and RT-PCR...
March 25, 2017: Chromosoma
https://www.readbyqxmd.com/read/28323041/quantitative-analyses-of-the-3d-nuclear-landscape-recorded-with-super-resolved-fluorescence-microscopy
#2
Volker J Schmid, Marion Cremer, Thomas Cremer
Recent advancements of super-resolved fluorescence microscopy have revolutionized microscopic studies of cells, including the exceedingly complex structural organization of cell nuclei in space and time. In this paper we describe and discuss tools for (semi-) automated, quantitative 3D analyses of the spatial nuclear organization. These tools allow the quantitative assessment of highly resolved different chromatin compaction levels in individual cell nuclei, which reflect functionally different regions or sub-compartments of the 3D nuclear landscape, and measurements of absolute distances between sites of different chromatin compaction...
March 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28284913/higher-order-assembly-folding-the-chromosome
#3
REVIEW
Sven A Sewitz, Zahra Fahmi, Karen Lipkow
The linear molecules of DNA that constitute a eukaryotic genome have to be carefully organised within the nucleus to be able to correctly direct gene expression. Microscopy and chromosome capture methods have revealed a hierarchical organisation into territories, domains and subdomains that ensure the accessibility of expressed genes and eventually chromatin loops that serve to bring gene enhancers into proximity of their target promoters. A rapidly growing number of genome-wide datasets and their analyses have given detailed information into the conformation of the entire genome, allowing evolutionary insights, observations of genome rearrangements during development and the identification of new gene-to-disease associations...
March 8, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28190810/visualization-of-the-spatial-arrangement-of-nuclear-organization-using-three-dimensional-fluorescence-in-situ-hybridization-in-early-mouse-embryos-a-new-easi-fish-chamber-glass-for-mammalian-embryos
#4
Masataka Nakaya, Hideyuki Tanabe, Shingo Takamatsu, Misaki Hosokawa, Tasuku Mitani
The fertilized oocyte begins cleavage, leading to zygotic gene activation (ZGA), which re-activates the resting genome to acquire totipotency. In this process, genomic function is regulated by the dynamic structural conversion in the nucleus. Indeed, a considerable number of genes that are essential for embryonic development are located near the pericentromeric regions, wherein the heterochromatin is formed. These genes are repressed transcriptionally in somatic cells. Three-dimensional fluorescence in situ hybridization (3D-FISH) enables the visualization of the intranuclear spatial arrangement, such as gene loci, chromosomal domains, and chromosome territories (CTs)...
February 11, 2017: Journal of Reproduction and Development
https://www.readbyqxmd.com/read/28161540/genome-organization-in-the-nucleus-from-dynamic-measurements-to-a-functional-model
#5
REVIEW
Anat Vivante, Eugene Brozgol, Irena Bronshtein, Yuval Garini
A biological system is by definition a dynamic environment encompassing kinetic processes that occur at different length scales and time ranges. To explore this type of system, spatial information needs to be acquired at different time scales. This means overcoming significant hurdles, including the need for stable and precise labeling of the required probes and the use of state of the art optical methods. However, to interpret the acquired data, biophysical models that can account for these biological mechanisms need to be developed...
February 1, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28158219/tissue-specific-features-of-the-x-chromosome-and-nucleolus-spatial-dynamics-in-a-malaria-mosquito-anopheles-atroparvus
#6
Semen M Bondarenko, Gleb N Artemov, Igor V Sharakhov, Vladimir N Stegniy
Spatial organization of chromosome territories is important for maintenance of genomic stability and regulation of gene expression. Recent studies have shown tissue-specific features of chromosome attachments to the nuclear envelope in various organisms including malaria mosquitoes. However, other spatial characteristics of nucleus organization, like volume and shape of chromosome territories, have not been studied in Anopheles. We conducted a thorough analysis of tissue-specific features of the X chromosome and nucleolus volume and shape in follicular epithelium and nurse cells of the Anopheles atroparvus ovaries using a modern open-source software...
2017: PloS One
https://www.readbyqxmd.com/read/28138773/revisiting-the-male-genetic-landscape-of-china-a-multi-center-study-of-almost-38-000-y-str-haplotypes
#7
REVIEW
Michael Nothnagel, Guangyao Fan, Fei Guo, Yongfeng He, Yiping Hou, Shengping Hu, Jiang Huang, Xianhua Jiang, Wook Kim, Kicheol Kim, Chengtao Li, Hui Li, Liming Li, Shilin Li, Zhao Li, Weibo Liang, Chao Liu, Di Lu, Haibo Luo, Shengjie Nie, Meisen Shi, Hongyu Sun, Jianpin Tang, Lei Wang, Chuan-Chao Wang, Dan Wang, Shao-Qing Wen, Hongyan Wu, Weiwei Wu, Jiaxin Xing, Jiangwei Yan, Shi Yan, Hongbing Yao, Yi Ye, Libing Yun, Zhaoshu Zeng, Lagabaiyila Zha, Suhua Zhang, Xiufen Zheng, Sascha Willuweit, Lutz Roewer
China has repeatedly been the subject of genetic studies to elucidate its prehistoric and historic demography. While some studies reported a genetic distinction between Northern and Southern Han Chinese, others showed a more clinal picture of small differences within China. Here, we investigated the distribution of Y chromosome variation along administrative as well as ethnic divisions in the mainland territory of the People's Republic of China, including 28 administrative regions and 19 recognized Chinese nationalities, to assess the impact of recent demographic processes...
January 30, 2017: Human Genetics
https://www.readbyqxmd.com/read/28101915/early-medieval-stone-lined-graves-in-southern-germany-analysis-of-an-emerging-noble-class
#8
Andreas Rott, Nils Turner, Ulrike Scholz, Kristin von Heyking, Franziska Immler, Joris Peters, Jochen Haberstroh, Michaela Harbeck
OBJECTIVES: Stone-lined graves, which first appear in Bavarian territory during the 7(th) century AD, are assumed to be tombs of emerging nobility. While previous research on stone-lined grave goods supports their status as elite burials, an important factor defining nobility-kinship-has not been examined so far. MATERIALS AND METHODS: Morphological analysis of the commingled skeletal remains of 21 individuals from three archaeological sites was carried out. Radiocarbon dating was conducted on these individuals to gain information on usage intervals of these graves...
January 19, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28048349/we-h-bra-04-biological-geometries-for-the-monte-carlo-simulation-toolkit-topasnbio
#9
A McNamara, J Perl, P Piersimoni, J Ramos-Mendez, B Faddegon, K Held, H Paganetti, J Schuemann
PURPOSE: New advances in radiation therapy are most likely to come from the complex interface of physics, chemistry and biology. Computational simulations offer a powerful tool for quantitatively investigating radiation interactions with biological tissue and can thus help bridge the gap between physics and biology. The aim of TOPAS-nBio is to provide a comprehensive tool to generate advanced radiobiology simulations. METHODS: TOPAS wraps and extends the Geant4 Monte Carlo (MC) simulation toolkit...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28034957/a-three-dimensional-parf-meshwork-assembles-through-the-nucleoid-to-mediate-plasmid-segregation
#10
Brett N McLeod, Gina E Allison-Gamble, Madhuri T Barge, Nam K Tonthat, Maria A Schumacher, Finbarr Hayes, Daniela Barillà
Genome segregation is a fundamental step in the life cycle of every cell. Most bacteria rely on dedicated DNA partition proteins to actively segregate chromosomes and low copy-number plasmids. Here, by employing super resolution microscopy, we establish that the ParF DNA partition protein of the ParA family assembles into a three-dimensional meshwork that uses the nucleoid as a scaffold and periodically shuttles between its poles. Whereas ParF specifies the territory for plasmid trafficking, the ParG partner protein dictates the tempo of ParF assembly cycles and plasmid segregation events by stimulating ParF adenosine triphosphate hydrolysis...
December 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/28006965/nucleolus-like-compartmentalization-of-the-transcription-machinery-in-fast-growing-bacterial-cells
#11
Ding Jun Jin, Carmen Mata Martin, Zhe Sun, Cedric Cagliero, Yan Ning Zhou
We have learned a great deal about RNA polymerase (RNA Pol), transcription factors, and the transcriptional regulation mechanisms in prokaryotes for specific genes, operons, or transcriptomes. However, we have only begun to understand how the transcription machinery is three-dimensionally (3D) organized into bacterial chromosome territories to orchestrate the transcription process and to maintain harmony with the replication machinery in the cell. Much progress has been made recently in our understanding of the spatial organization of the transcription machinery in fast-growing Escherichia coli cells using state-of-the-art superresolution imaging techniques...
December 23, 2016: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/27994579/intraclonal-genome-stability-of-the-metallo-%C3%AE-lactamase-spm-1-producing-pseudomonas-aeruginosa-st277-an-endemic-clone-disseminated-in-brazilian-hospitals
#12
Ana P B Nascimento, Mauro F Ortiz, Willames M B S Martins, Guilherme L Morais, Lorena C C Fehlberg, Luiz G P Almeida, Luciane P Ciapina, Ana C Gales, Ana T R Vasconcelos
Carbapenems represent the mainstay therapy for the treatment of serious P. aeruginosa infections. However, the emergence of carbapenem resistance has jeopardized the clinical use of this important class of compounds. The production of SPM-1 metallo-β-lactamase has been the most common mechanism of carbapenem resistance identified in P. aeruginosa isolated from Brazilian medical centers. Interestingly, a single SPM-1-producing P. aeruginosa clone belonging to the ST277 has been widely spread within the Brazilian territory...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27919068/capturing-pairwise-and-multi-way-chromosomal-conformations-using-chromosomal-walks
#13
Pedro Olivares-Chauvet, Zohar Mukamel, Aviezer Lifshitz, Omer Schwartzman, Noa Oded Elkayam, Yaniv Lubling, Gintaras Deikus, Robert P Sebra, Amos Tanay
Chromosomes are folded into highly compacted structures to accommodate physical constraints within nuclei and to regulate access to genomic information. Recently, global mapping of pairwise contacts showed that loops anchoring topological domains (TADs) are highly conserved between cell types and species. Whether pairwise loops synergize to form higher-order structures is still unclear. Here we develop a conformation capture assay to study higher-order organization using chromosomal walks (C-walks) that link multiple genomic loci together into proximity chains in human and mouse cells...
December 8, 2016: Nature
https://www.readbyqxmd.com/read/27899641/3d-genome-structure-modeling-by-lorentzian-objective-function
#14
Tuan Trieu, Jianlin Cheng
The 3D structure of the genome plays a vital role in biological processes such as gene interaction, gene regulation, DNA replication and genome methylation. Advanced chromosomal conformation capture techniques, such as Hi-C and tethered conformation capture, can generate chromosomal contact data that can be used to computationally reconstruct 3D structures of the genome. We developed a novel restraint-based method that is capable of reconstructing 3D genome structures utilizing both intra-and inter-chromosomal contact data...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27873269/the-use-of-3d-telomere-fish-for-the-characterization-of-the-nuclear-architecture-in-ebv-positive-hodgkin-s-lymphoma
#15
Hans Knecht, Sabine Mai
The 3D nuclear architecture is closely related to cellular functions and chromosomes are organized in distinct territories. Quantitative 3D telomere FISH analysis (3D Q-FISH) and 3D super-resolution imaging (3D-SIM) at a resolution up to 80 nm as well as the recently developed combined quantitative 3D TRF2-telomere immune FISH technique (3D TRF2/Telo-Q-FISH) have substantially contributed to elucidate molecular pathogenic mechanisms of hematological diseases. Here we report the methods we applied to uncover major molecular steps involved in the pathogenesis of EBV-associated Hodgkin's lymphoma...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27871318/reference-curves-of-birth-weight-length-and-head-circumference-for-gestational-ages-in-yogyakarta-indonesia
#16
Ekawaty L Haksari, Harrie N Lafeber, Mohammad Hakimi, Endy P Pawirohartono, Lennarth Nyström
BACKGROUND: The birth weight reference curve to estimate the newborns at risk in need of assessment and monitoring has been established. The previous reference curves from Indonesia, approximately 8 years ago, were based on the data collected from teaching hospitals only with limited gestational ages. The aims of the study were to update the reference curves for birth weight, supine length and head circumference for Indonesia, and to compare birth weight curves of boys and girls, first child and later children, and the ones in the previous studies...
November 21, 2016: BMC Pediatrics
https://www.readbyqxmd.com/read/27845379/systems-level-chromosomal-parameters-represent-a-suprachromosomal-basis-for-the-non-random-chromosomal-arrangement-in-human-interphase-nuclei
#17
Sarosh N Fatakia, Ishita S Mehta, Basuthkar J Rao
Forty-six chromosome territories (CTs) are positioned uniquely in human interphase nuclei, wherein each of their positions can range from the centre of the nucleus to its periphery. A non-empirical basis for their non-random arrangement remains unreported. Here, we derive a suprachromosomal basis of that overall arrangement (which we refer to as a CT constellation), and report a hierarchical nature of the same. Using matrix algebra, we unify intrinsic chromosomal parameters (e.g., chromosomal length, gene density, the number of genes per chromosome), to derive an extrinsic effective gene density matrix, the hierarchy of which is dominated largely by extrinsic mathematical coupling of HSA19, followed by HSA17 (human chromosome 19 and 17, both preferentially interior CTs) with all CTs...
November 15, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27826995/molecular-diversity-of-23-y-chromosome-short-tandem-repeat-loci-in-the-population-of-tuzla-canton-bosnia-and-herzegovina
#18
Naida Babić, Serkan Dogan, Jasmina Čakar, Amela Pilav, Damir Marjanović, Vesna Hadžiavdić
BACKGROUND: Tuzla Canton is the most populated region in the ethnically mixed territory of Bosnia and Herzegovina, whose genetic analysis could provide an insight into past demographic events. AIM: Analysis of 23 Y-chromosome STR markers in the population of Tuzla Canton and investigation of the genetic relationship of the male population of the Tuzla Canton and that of the larger Bosnian and Herzegovinian population as well as neighbouring and other European populations...
November 30, 2016: Annals of Human Biology
https://www.readbyqxmd.com/read/27802612/computer-simulations-of-melts-of-randomly-branching-polymers
#19
Angelo Rosa, Ralf Everaers
Randomly branching polymers with annealed connectivity are model systems for ring polymers and chromosomes. In this context, the branched structure represents transient folding induced by topological constraints. Here we present computer simulations of melts of annealed randomly branching polymers of 3 ≤ N ≤ 1800 segments in d = 2 and d = 3 dimensions. In all cases, we perform a detailed analysis of the observed tree connectivities and spatial conformations. Our results are in excellent agreement with an asymptotic scaling of the average tree size of R ∼ N(1/d), suggesting that the trees behave as compact, territorial fractals...
October 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27771449/the-nuclear-higher-order-structure-defined-by-the-set-of-topological-relationships-between-dna-and-the-nuclear-matrix-is-species-specific-in-hepatocytes
#20
COMPARATIVE STUDY
Evangelina Silva-Santiago, Juan Pablo Pardo, Rolando Hernández-Muñoz, Armando Aranda-Anzaldo
During the interphase the nuclear DNA of metazoan cells is organized in supercoiled loops anchored to constituents of a nuclear substructure or compartment known as the nuclear matrix. The stable interactions between DNA and the nuclear matrix (NM) correspond to a set of topological relationships that define a nuclear higher-order structure (NHOS). Current evidence suggests that the NHOS is cell-type-specific. Biophysical evidence and theoretical models suggest that thermodynamic and structural constraints drive the actualization of DNA-NM interactions...
January 15, 2017: Gene
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