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https://www.readbyqxmd.com/read/28923964/repeat-e-anchors-xist-rna-to-the-inactive-x-chromosomal-compartment-through-cdkn1a-interacting-protein-ciz1
#1
Hongjae Sunwoo, David Colognori, John E Froberg, Yesu Jeon, Jeannie T Lee
X chromosome inactivation is an epigenetic dosage compensation mechanism in female mammals driven by the long noncoding RNA, Xist. Although recent genomic and proteomic approaches have provided a more global view of Xist's function, how Xist RNA localizes to the inactive X chromosome (Xi) and spreads in cis remains unclear. Here, we report that the CDKN1-interacting zinc finger protein CIZ1 is critical for localization of Xist RNA to the Xi chromosome territory. Stochastic optical reconstruction microscopy (STORM) shows a tight association of CIZ1 with Xist RNA at the single-molecule level...
September 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28919969/karyotypic-differentiation-of-populations-of-the-common-shrew-sorex-araneus-l-mammalia-in-belarus
#2
Yury M Borisov, Iryna A Kryshchuk, Helen S Gaiduchenko, Elena V Cherepanova, Svetlana V Zadyra, Elena S Levenkova, Dmitriy V Lukashov, Victor N Orlov
The common shrews, Sorex araneus Linnaeus, 1758, inhabiting the territory of Belarus, are characterized by a significant variation in the frequency of Robertsonian (Rb) translocations. The frequency clines for translocations specific of three chromosome races: the West Dvina (gm, hk, ip, no, qr), Kiev (g/m, hi, k/o, n, p, q, r), and Białowieża (g/r, hn, ik, m/p, o, q) have already been studied in this territory. In this communication we report new data on polymorphic populations with Rb metacentrics specific of the Neroosa race (go, hi, kr, mn, p/q) in south-eastern Belarus, analyse the distribution of karyotypes in southern and central Belarus and draw particular attention to the fixation of the acrocentric variants of chromosomes in this area...
2017: Comparative Cytogenetics
https://www.readbyqxmd.com/read/28910577/subnuclear-distribution-of-proteins-links-with-genome-architecture
#3
Fouziya R Shah, Younus A Bhat, Ajazul H Wani
Metazoan genomes have a hierarchal 3-dimensional (3D) organization scaling from nucleosomes, loops, topologically associating domains (TADs), compartments, to chromosome territories. The 3D organization of genome has been linked with development, differentiation and disease. However, the principles governing the 3D chromatin architecture are just beginning to get unraveled. The nucleus has very high concentration of proteins and these proteins are either diffusely distributed throughout the nucleus, or aggregated in the form of foci/bodies/clusters/speckles or in combination of both...
September 14, 2017: Nucleus
https://www.readbyqxmd.com/read/28853923/the-yeast-genomes-in-three-dimensions-mechanisms-and-functions
#4
Ken-Ichi Noma
The three-dimensional (3D) genome structure is highly ordered by a hierarchy of organizing events ranging from enhancer-promoter or gene-gene contacts to chromosomal territorial arrangement. It is becoming clear that the cohesin and condensin complexes are key molecular machines that organize the 3D genome structure. These complexes are highly conserved from simple systems, e.g., yeast cells, to the much more complex human system. Therefore, knowledge from the budding and fission yeast systems illuminates highly conserved molecular mechanisms of how cohesin and condensin establish the functional 3D genome structures...
August 30, 2017: Annual Review of Genetics
https://www.readbyqxmd.com/read/28831272/pain-reporting-and-analgesia-management-in-270-children-with-a-progressive-neurologic-metabolic-or-chromosomally-based-condition-with-impairment-of-the-central-nervous-system-cross-sectional-baseline-results-from-an-observational-longitudinal-study
#5
Stefan J Friedrichsdorf, Andrea C Postier, Gail S Andrews, Karen Es Hamre, Rose Steele, Harold Siden
Little is known about the prevalence, characterization and treatment of pain in children with progressive neurologic, metabolic or chromosomal conditions with impairment of the central nervous system. The primary aims of this study were to explore the differences between parental and clinical pain reporting in children with life-limiting conditions at the time of enrollment into an observational, longitudinal study and to determine if differences in pain experiences were associated with patient- or treatment-related factors...
2017: Journal of Pain Research
https://www.readbyqxmd.com/read/28780612/invisible-cities-segregated-domains-in-the-yeast-genome-with-distinct-structural-and-functional-attributes
#6
Christoforos Nikolaou
Recent advances in our understanding of the three-dimensional organization of the eukaryotic nucleus have rendered the spatial distribution of genes increasingly relevant. In a recent work (Tsochatzidou et al., Nucleic Acids Res 45:5818-5828, 2017), we proposed the existence of a functional compartmentalization of the yeast genome according to which, genes occupying the chromosomal regions at the nuclear periphery have distinct structural, functional and evolutionary characteristics compared to their centromeric-proximal counterparts...
August 5, 2017: Current Genetics
https://www.readbyqxmd.com/read/28776025/three-dimensional-positioning-and-structure-of-chromosomes-in-a-human-prophase-nucleus
#7
Bo Chen, Mohammed Yusuf, Teruo Hashimoto, Ana Katrina Estandarte, George Thompson, Ian Robinson
The human genetic material is packaged into 46 chromosomes. The structure of chromosomes is known at the lowest level, where the DNA chain is wrapped around a core of eight histone proteins to form nucleosomes. Around a million of these nucleosomes, each about 11 nm in diameter and 6 nm in thickness, are wrapped up into the complex organelle of the chromosome, whose structure is mostly known at the level of visible light microscopy to form a characteristic cross shape in metaphase. However, the higher-order structure of human chromosomes, between a few tens and hundreds of nanometers, has not been well understood...
July 2017: Science Advances
https://www.readbyqxmd.com/read/28767705/changes-in-chromosome-territory-position-within-the-nucleus-reflect-alternations-in-gene-expression-related-to-embryonic-lineage-specification
#8
Maciej Orsztynowicz, Dorota Lechniak, Piotr Pawlak, Beata Kociucka, Svatava Kubickova, Halina Cernohorska, Zofia Eliza Madeja
Loss of totipotentcy in an early embryo is directed by molecular processes responsible for cell fate decisions. Three dimensional genome organisation is an important factor linking chromatin architecture with stage specific gene expression patterns. Little is known about the role of chromosome organisation in gene expression regulation of lineage specific factors in mammalian embryos. Using bovine embryos as a model we have described these interactions at key developmental stages. Three bovine chromosomes (BTA) that differ in size, number of carried genes, and contain loci for key lineage regulators OCT4, NANOG and CDX2, were investigated...
2017: PloS One
https://www.readbyqxmd.com/read/28757389/spatial-organization-of-genome-architecture-in-neuronal-development-and-disease
#9
REVIEW
Yuki Fujita, Toshihide Yamashita
Although mammalian genomes encode genetic information in their linear sequences, their fundamental function with regard to gene expression depends on the higher-order structure of chromosomes. Current techniques for the evaluation of chromosomal structure have revealed that genomes are arranged at several hierarchical levels in three-dimensional space. The spatial organization of genomes involves the formation of chromatin loops that bypass a wide range of genomic distances, providing a connection between enhancers and chromosomal domains...
July 28, 2017: Neurochemistry International
https://www.readbyqxmd.com/read/28696859/nucleoporins-redistribute-inside-the-nucleus-after-cell-cycle-arrest-induced-by-histone-deacetylases-inhibition
#10
Miguel Pérez-Garrastachu, Jon Arluzea, Ricardo Andrade, Alejandro Díez-Torre, Marta Urtizberea, Margarita Silió, Juan Aréchaga
Nucleoporins are the main components of the nuclear-pore complex (NPC) and were initially considered as mere structural elements embedded in the nuclear envelope, being responsible for nucleocytoplasmic transport. Nevertheless, several recent scientific reports have revealed that some nucleoporins participate in nuclear processes such as transcription, replication, DNA repair and chromosome segregation. Thus, the interaction of NPCs with chromatin could modulate the distribution of chromosome territories relying on the epigenetic state of DNA...
July 11, 2017: Nucleus
https://www.readbyqxmd.com/read/28640660/chromosome-territory-relocation-paradigm-during-dna-damage-response-some-insights-from-molecular-biology-to-physics
#11
Sarosh N Fatakia, Mugdha Kulashreshtha, Ishita S Mehta, Basuthkar J Rao
Among the many facets of DNA damage response (DDR), relocation of chromosome territories (CTs) is most intriguing. We have previously reported that cisplatin induced DDR in human dermal fibroblasts led to relocation of CTs 12, 15 from the nuclear periphery to its interior while CTs 19, 17 repositioned from the interior to its periphery. Studies of CT relocation remain nascent as we begin unraveling the role of key players in DDR to demonstrate its mechanistic basis. Consolidating our recent reports, we argue that γH2AX-signaling leads to enhanced recruitment of nuclear myosin 1 (NM1) to chromatin, which via its motor function, results in CT repositioning...
June 22, 2017: Nucleus
https://www.readbyqxmd.com/read/28627755/labeling-dna-replication-foci-to-visualize-chromosome-territories-in-vivo
#12
Apolinar Maya-Mendoza, Dean A Jackson
While a detailed understanding of chromatin dynamics is needed to explain how higher-order chromatin organization influences nuclear function, the molecular principles that regulate chromatin mobility in mammalian nuclei remain largely unknown. Here we describe experimental tools to follow chromatin dynamics by labeling DNA during S phase. Using these methods, we have found that foci labeled during early and mid/late S phase have significantly different dynamic behavior. Spatially constrained heterochromatic foci restrict long-range transformations of the chromosome territory (CT) structure while providing a structural framework on which highly mobile euchromatic foci undergo positional oscillations that drive local changes in the chromosome shape...
June 19, 2017: Current Protocols in Cell Biology
https://www.readbyqxmd.com/read/28615317/orientation-and-repositioning-of-chromosomes-correlate-with-cell-geometry-dependent-gene-expression
#13
Yejun Wang, Mallika Nagarajan, Caroline Uhler, G V Shivashankar
Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries...
July 7, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28615069/regulatory-landscape-fusion-in-rhabdomyosarcoma-through-interactions-between-the-pax3-promoter-and-foxo1-regulatory-elements
#14
Cristina Vicente-García, Barbara Villarejo-Balcells, Ibai Irastorza-Azcárate, Silvia Naranjo, Rafael D Acemel, Juan J Tena, Peter W J Rigby, Damien P Devos, Jose L Gómez-Skarmeta, Jaime J Carvajal
BACKGROUND: The organisation of vertebrate genomes into topologically associating domains (TADs) is believed to facilitate the regulation of the genes located within them. A remaining question is whether TAD organisation is achieved through the interactions of the regulatory elements within them or if these interactions are favoured by the pre-existence of TADs. If the latter is true, the fusion of two independent TADs should result in the rewiring of the transcriptional landscape and the generation of ectopic contacts...
June 14, 2017: Genome Biology
https://www.readbyqxmd.com/read/28546514/the-nuclear-matrix-protein-ciz1-facilitates-localization-of-xist-rna-to-the-inactive-x-chromosome-territory
#15
Rebeca Ridings-Figueroa, Emma R Stewart, Tatyana B Nesterova, Heather Coker, Greta Pintacuda, Jonathan Godwin, Rose Wilson, Aidan Haslam, Fred Lilley, Renate Ruigrok, Sumia A Bageghni, Ghadeer Albadrani, William Mansfield, Jo-An Roulson, Neil Brockdorff, Justin F X Ainscough, Dawn Coverley
The nuclear matrix protein Cip1-interacting zinc finger protein 1 (CIZ1) promotes DNA replication in association with cyclins and has been linked to adult and pediatric cancers. Here we show that CIZ1 is highly enriched on the inactive X chromosome (Xi) in mouse and human female cells and is retained by interaction with the RNA-dependent nuclear matrix. CIZ1 is recruited to Xi in response to expression of X inactive-specific transcript (Xist) RNA during the earliest stages of X inactivation in embryonic stem cells and is dependent on the C-terminal nuclear matrix anchor domain of CIZ1 and the E repeats of Xist CIZ1-null mice, although viable, display fully penetrant female-specific lymphoproliferative disorder...
May 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28494440/nuclear-architecture-of-mouse-spermatocytes-chromosome-topology-heterochromatin-and-nucleolus
#16
REVIEW
Soledad Berrios
The nuclear organization of spermatocytes in meiotic prophase I is primarily determined by the synaptic organization of the bivalents that are bound by their telomeres to the nuclear envelope and described as arc-shaped trajectories through the 3D nuclear space. However, over this basic meiotic organization, a spermatocyte nuclear architecture arises that is based on higher-ordered patterns of spatial associations among chromosomal domains from different bivalents that are conditioned by the individual characteristics of chromosomes and the opportunity for interactions between their domains...
2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28479596/the-x-chromosome-in-space
#17
REVIEW
Teddy Jégu, Eric Aeby, Jeannie T Lee
Extensive 3D folding is required to package a genome into the tiny nuclear space, and this packaging must be compatible with proper gene expression. Thus, in the well-hierarchized nucleus, chromosomes occupy discrete territories and adopt specific 3D organizational structures that facilitate interactions between regulatory elements for gene expression. The mammalian X chromosome exemplifies this structure-function relationship. Recent studies have shown that, upon X-chromosome inactivation, active and inactive X chromosomes localize to different subnuclear positions and adopt distinct chromosomal architectures that reflect their activity states...
June 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28463980/transcription-facilitated-genome-wide-recruitment-of-topoisomerase-i-and-dna-gyrase
#18
Wareed Ahmed, Claudia Sala, Shubhada R Hegde, Rajiv Kumar Jha, Stewart T Cole, Valakunja Nagaraja
Movement of the transcription machinery along a template alters DNA topology resulting in the accumulation of supercoils in DNA. The positive supercoils generated ahead of transcribing RNA polymerase (RNAP) and the negative supercoils accumulating behind impose severe topological constraints impeding transcription process. Previous studies have implied the role of topoisomerases in the removal of torsional stress and the maintenance of template topology but the in vivo interaction of functionally distinct topoisomerases with heterogeneous chromosomal territories is not deciphered...
May 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28415805/regulatory-functional-territory-of-plk-1-and-their-substrates-beyond-mitosis
#19
REVIEW
Shiv Kumar, Garima Sharma, Chiranjib Chakraborty, Ashish Ranjan Sharma, Jaebong Kim
Polo-like kinase 1 (PLK-1) is a well-known (Ser/Thr) mitotic protein kinase and is considered as a proto-oncogene. As hyper-activation of PLK-1 is broadly associated with poor prognosis and cancer progression, it is one of the most extensively studied mitotic kinases. During mitosis, PLK-1 regulates various cell cycle events, such as spindle pole maturation, chromosome segregation and cytokinesis. However, studies have demonstrated that the role of PLK-1 is not only restricted to mitosis, but PLK-1 can also regulate other vital events beyond mitosis, including transcription, translation, ciliogenesis, checkpoint adaptation and recovery, apoptosis, chromosomes dynamics etc...
June 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28411854/the-molecular-revolution-in-cutaneous-biology-chromosomal-territories-higher-order-chromatin-remodeling-and-the-control-of%C3%A2-gene-expression-in-keratinocytes
#20
REVIEW
Vladimir A Botchkarev
Three-dimensional organization of transcription in the nucleus and mechanisms controlling the global chromatin folding, including spatial interactions between the genes, noncoding genome elements, and epigenetic and transcription machinery, are essential for establishing lineage-specific gene expression programs during cell differentiation. Spatial chromatin interactions in the nucleus involving gene promoters and distal regulatory elements are currently considered major forces that drive cell differentiation and genome evolution in general, and such interactions are substantially reorganized during many pathological conditions...
May 2017: Journal of Investigative Dermatology
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