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Chromosome territories

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...
October 19, 2016: Gene
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
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...
October 6, 2016: International Journal of Cancer. Journal International du Cancer
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...
September 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
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
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
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
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
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
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
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
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
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...
July 29, 2016: Hong Kong Medical Journal, Xianggang Yi Xue za Zhi
Vasili Pankratov, Sergei Litvinov, Alexei Kassian, Dzmitry Shulhin, Lieve Tchebotarev, Bayazit Yunusbayev, Märt Möls, Hovhannes Sahakyan, Levon Yepiskoposyan, Siiri Rootsi, Ene Metspalu, Maria Golubenko, Natalia Ekomasova, Farida Akhatova, Elza Khusnutdinova, Evelyne Heyer, Phillip Endicott, Miroslava Derenko, Boris Malyarchuk, Mait Metspalu, Oleg Davydenko, Richard Villems, Alena Kushniarevich
Medieval era encounters of nomadic groups of the Eurasian Steppe and largely sedentary East Europeans had a variety of demographic and cultural consequences. Amongst these outcomes was the emergence of the Lipka Tatars-a Slavic-speaking Sunni-Muslim minority residing in modern Belarus, Lithuania and Poland, whose ancestors arrived in these territories via several migration waves, mainly from the Golden Horde. Our results show that Belarusian Lipka Tatars share a substantial part of their gene pool with Europeans as indicated by their Y-chromosomal, mitochondrial and autosomal DNA variation...
2016: Scientific Reports
Mugdha Kulashreshtha, Ishita S Mehta, Pradeep Kumar, Basuthkar J Rao
During DNA damage response (DDR), certain gene rich chromosome territories (CTs) relocate to newer positions within interphase nuclei and revert to their native locations following repair. Such dynamic relocation of CTs has been observed under various cellular conditions, however, the underlying mechanistic basis of the same has remained largely elusive. In this study, we aim to understand the temporal and molecular details of such crosstalk between DDR signaling and CT relocation dynamics. We demonstrate that signaling at DNA double strand breaks (DSBs) by the phosphorylated histone variant (ϒ-H2AX) is a pre-requisite for damage induced CT relocation, as cells deficient in ϒ-H2AX signaling fail to exhibit such a response...
September 30, 2016: Nucleic Acids Research
B Hervé, A Coussement, T Gilbert, F Dumont, S Jacques, L Cuisset, M Chicard, S Hizem, P Bourdoncle, F Letourneur, C Dupont, F Vialard, A Choiset, J-M Dupont
The organization and dynamics of chromatin within the interphase nucleus as chromosome territories (CTs) and the relationship with transcriptional regulation are not fully understood. We studied a natural example of chromosomal disorganization: aneuploidy due to trisomies 13, 18 and 21. We hypothesized that the presence of an extra copy of one chromosome alters the CT distribution, which perturbs transcriptional activity. We used 3D-FISH to study the position of the chromosomes of interest (18 and 21) in cultured amniocytes and chorionic villus cells from pregnancies with a normal or aneuploid karyotype...
July 2016: Clinical Genetics
Ezequiel Miron, Cassandravictoria Innocent, Sophia Heyde, Lothar Schermelleh
Recent advances in super-resolution microscopy enable the study of subchromosomal chromatin organization in single cells with unprecedented detail. Here we describe refined methods for pulse-chase replication labeling of individual chromosome territories (CTs) and replication domain units in mammalian cell nuclei, with specific focus on their application to three-dimensional structured illumination microscopy (3D-SIM). We provide detailed protocols for highly efficient electroporation-based delivery or scratch loading of cell impermeable fluorescent nucleotides for live cell studies...
2016: Methods in Molecular Biology
Lei Liu, Changbong Hyeon
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have territorial organization with signatures pointing to metastability, we analyzed the biomolecular structures deposited in the Protein Data Bank and found that the intrachain contact probabilities, P(s) as a function of the arc length s, decay in power-law ∼s(-γ) over the intermediate range of s, 10 ≲ s ≲ 110...
June 7, 2016: Biophysical Journal
Evelyn K Guevara, Jukka U Palo, Sonia Guillén, Antti Sajantila
OBJECTIVES: The ancient Chachapoya were an aggregate of several ethnic groups that shared a common language, religion, and material culture. They inhabited a territory at the juncture of the Andes and the Amazon basin. Their position between those ecozones most likely influenced their genetic composition. We attempted to better understand their population history by assessing the contemporary genetic diversity in the Chachapoya and three of their immediate neighbors (Huancas, Jivaro, and Cajamarca)...
June 6, 2016: American Journal of Human Biology: the Official Journal of the Human Biology Council
Haiyan Huang, Qiang Wu
The genomes are organized into ordered and hierarchical topological structures in interphase nuclei. Within discrete territories of each chromosome, topologically associated domains (TADs) play important roles in various nuclear processes such as gene regulation. Inside TADs separated by relatively constitutive boundaries, distal elements regulate their gene targets through specific chromatin-looping contacts such as long-distance enhancer-promoter interactions. High-throughput sequencing studies have revealed millions of potential regulatory DNA elements, which are much more abundant than the mere ∼20,000 genes they control...
May 20, 2016: Journal of Genetics and Genomics, Yi Chuan Xue Bao
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