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Chromosome territories

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https://www.readbyqxmd.com/read/27919068/capturing-pairwise-and-multi-way-chromosomal-conformations-using-chromosomal-walks
#1
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...
November 30, 2016: Nature
https://www.readbyqxmd.com/read/27899641/3d-genome-structure-modeling-by-lorentzian-objective-function
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/27716032/expressed-alleles-of-imprinted-igf2-dlk1-and-meg3-colocalize-in-3d-preserved-nuclei-of-porcine-fetal-cells
#9
Yvette Lahbib-Mansais, Harmonie Barasc, Maria Marti-Marimon, Florence Mompart, Eddie Iannuccelli, David Robelin, Juliette Riquet, Martine Yerle-Bouissou
BACKGROUND: To explore the relationship between spatial genome organization and gene expression in the interphase nucleus, we used a genomic imprinting model, which offers parental-specific gene expression. Using 3D FISH in porcine fetal liver cells, we compared the nuclear organization of the two parental alleles (expressed or not) of insulin-like growth factor 2 (IGF2), a paternally imprinted gene located on chromosome 2. We investigated whether its nuclear positioning favors specific locus associations...
October 1, 2016: BMC Cell Biology
https://www.readbyqxmd.com/read/27711972/distinct-and-shared-three-dimensional-chromosome-organization-patterns-in-lymphocytes-monoclonal-gammopathy-of-undetermined-significance-and-multiple-myeloma
#10
Chirawadee Sathitruangsak, Christiaan H Righolt, Ludger Klewes, Doris Tung Chang, Rami Kotb, Sabine Mai
The consistent appearance of specific chromosomal translocations in multiple myeloma has suggested that the positioning of chromosomes in the interphase nucleus might play a role in the occurrence of particular chromosomal rearrangements associated with malignant transformation. Using fluorescence in situ hybridization, we have determined the positions of selected chromosome pairs (18 and 19, 9 and 22, 4 and 14, 14 and 16, 11 and 14) in interphase nuclei of myeloma cells compared to normal lymphocytes of treatment-naïve patients...
January 15, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27688758/transferable-model-for-chromosome-architecture
#11
Michele Di Pierro, Bin Zhang, Erez Lieberman Aiden, Peter G Wolynes, José N Onuchic
In vivo, the human genome folds into a characteristic ensemble of 3D structures. The mechanism driving the folding process remains unknown. We report a theoretical model for chromatin (Minimal Chromatin Model) that explains the folding of interphase chromosomes and generates chromosome conformations consistent with experimental data. The energy landscape of the model was derived by using the maximum entropy principle and relies on two experimentally derived inputs: a classification of loci into chromatin types and a catalog of the positions of chromatin loops...
October 25, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27627454/molecular-genealogy-of-a-mongol-queen-s-family-and-her-possible-kinship-with-genghis-khan
#12
Gavaachimed Lkhagvasuren, Heejin Shin, Si Eun Lee, Dashtseveg Tumen, Jae-Hyun Kim, Kyung-Yong Kim, Kijeong Kim, Ae Ja Park, Ho Woon Lee, Mi Jin Kim, Jaesung Choi, Jee-Hye Choi, Na Young Min, Kwang-Ho Lee
Members of the Mongol imperial family (designated the Golden family) are buried in a secret necropolis; therefore, none of their burial grounds have been found. In 2004, we first discovered 5 graves belonging to the Golden family in Tavan Tolgoi, Eastern Mongolia. To define the genealogy of the 5 bodies and the kinship among them, SNP and/or STR profiles of mitochondria, autosomes, and Y chromosomes were analyzed. Four of the 5 bodies were determined to carry the mitochondrial DNA haplogroup D4, while the fifth carried haplogroup CZ, indicating that this individual had no kinship with the others...
2016: PloS One
https://www.readbyqxmd.com/read/27604033/a-decade-of-understanding-spatio-temporal-regulation-of-dna-repair-by-the-nuclear-architecture
#13
Hicham Saad, Jennifer A Cobb
The nucleus is a hub for gene expression and is a highly organized entity. The nucleoplasm is heterogeneous, owing to the preferential localization of specific metabolic factors, which lead to the definition of nuclear compartments or bodies. The genome is organized into chromosome territories, as well as heterochromatin and euchromatin domains. Recent observations have indicated that nuclear organization is important for maintaining genomic stability. For example, nuclear organization has been implicated in stabilizing damaged DNA, repair-pathway choice, and in preventing chromosomal rearrangements...
October 2016: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
https://www.readbyqxmd.com/read/27588463/the-arrangement-of-brachypodium-distachyon-chromosomes-in-interphase-nuclei
#14
Ewa Robaszkiewicz, Dominika Idziak-Helmcke, Magdalena A Tkacz, Kornel Chrominski, Robert Hasterok
The spatial organization of chromatin within the interphase nucleus and the interactions between chromosome territories (CTs) are essential for various biological processes, such as DNA replication, transcription, and repair. However, detailed data about the CT arrangement in monocotyledonous plants are scarce. In this study, chromosome painting was used to analyse the distribution and associations of individual chromosomes in the 3-D preserved nuclei of Brachypodium distachyon root cells in order to determine the factors that may have an impact on the homologous CT arrangement...
October 2016: Journal of Experimental Botany
https://www.readbyqxmd.com/read/27580967/genomic-features-of-human-limb-specific-enhancers
#15
Shahid Ali, Bibi Amina, Saneela Anwar, Rashid Minhas, Nazia Parveen, Uzma Nawaz, Syed Sikandar Azam, Amir Ali Abbasi
To elucidate important cellular and molecular interactions that regulate patterning and skeletal development, vertebrate limbs served as a model organ. A growing body of evidence from detailed studies on a subset of limb regulators like the HOXD cluster or SHH, reveals the importance of enhancers in limb related developmental and disease processes. Exploiting the recent genome-wide availability of functionally confirmed enhancer dataset, this study establishes regulatory interactions for dozens of human limb developmental genes...
August 28, 2016: Genomics
https://www.readbyqxmd.com/read/27555585/hedgehog-dependent-e3-ligase-midline1-regulates-ubiquitin-mediated-proteasomal-degradation-of-pax6-during-visual-system-development
#16
Thorsten Pfirrmann, Enrico Jandt, Swantje Ranft, Ashwin Lokapally, Herbert Neuhaus, Muriel Perron, Thomas Hollemann
Pax6 is a key transcription factor involved in eye, brain, and pancreas development. Although pax6 is expressed in the whole prospective retinal field, subsequently its expression becomes restricted to the optic cup by reciprocal transcriptional repression of pax6 and pax2 However, it remains unclear how Pax6 protein is removed from the eyestalk territory on time. Here, we report that Mid1, a member of the RBCC/TRIM E3 ligase family, which was first identified in patients with the X-chromosome-linked Opitz BBB/G (OS) syndrome, interacts with Pax6...
September 6, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27526631/the-use-of-dapi-fluorescence-lifetime-imaging-for-investigating-chromatin-condensation-in-human-chromosomes
#17
Ana Katrina Estandarte, Stanley Botchway, Christophe Lynch, Mohammed Yusuf, Ian Robinson
Chromatin undergoes dramatic condensation and decondensation as cells transition between the different phases of the cell cycle. The organization of chromatin in chromosomes is still one of the key challenges in structural biology. Fluorescence lifetime imaging (FLIM), a technique which utilizes a fluorophore's fluorescence lifetime to probe changes in its environment, was used to investigate variations in chromatin compaction in fixed human chromosomes. Fixed human metaphase and interphase chromosomes were labeled with the DNA minor groove binder, DAPI, followed by measurement and imaging of the fluorescence lifetime using multiphoton excitation...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27509849/fgfr3-preferentially-colocalizes-with-igh-in-the-interphase-nucleus-of-multiple-myeloma-patient-b-cells-when-fgfr3-is-located-outside-of-ct4
#18
Lorri D Martin, Jana Harizanova, Sabine Mai, Andrew R Belch, Linda M Pilarski
Many B-cell malignancies are characterized by chromosomal translocations involving IGH and a proto-oncogene. For translocations to occur, spatial proximity of translocation-prone genes is necessary. Currently, it is not known how such genes are brought into proximity with one another. Although decondensed chromosomes occupy definitive, non-random spaces in the interphase nucleus known as chromosome territories (CTs), chromatin at the edges of CTs can intermingle, and specific genomic regions from some chromosomes have been shown to "loop out" of their respective CTs...
December 2016: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/27505434/chromosome-territory-modeller-and-viewer
#19
Magdalena A Tkacz, Kornel Chromiński, Dominika Idziak-Helmcke, Ewa Robaszkiewicz, Robert Hasterok
This paper presents ChroTeMo, a tool for chromosome territory modelling, accompanied by ChroTeVi-a chromosome territory visualisation software that uses the data obtained by ChroTeMo. These tools have been developed in order to complement the molecular cytogenetic research of interphase nucleus structure in a model grass Brachypodium distachyon. Although the modelling tool has been initially created for one particular species, it has universal application. The proposed version of ChroTeMo allows for generating a model of chromosome territory distribution in any given plant or animal species after setting the initial, species-specific parameters...
2016: PloS One
https://www.readbyqxmd.com/read/27468965/silver-russell-syndrome-in-hong-kong
#20
H M Luk, K S Yeung, W L Wong, B Hy Chung, T Mf Tong, I Fm Lo
OBJECTIVES: To examine the molecular pathogenetic mechanisms, (epi)genotype-phenotype correlation, and the performance of the three clinical scoring systems-namely Netchine et al, Bartholdi et al, and Birmingham scores-for patients with Silver-Russell syndrome in Hong Kong. METHODS: This retrospective case series was conducted at two tertiary genetic clinics, the Clinical Genetic Service, Department of Health, and clinical genetic clinic in Queen Mary Hospital in Hong Kong...
December 2016: Hong Kong Medical Journal, Xianggang Yi Xue za Zhi
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