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Nuclear spatial organisation

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https://www.readbyqxmd.com/read/27861863/exploring-the-role-of-pgc-1%C3%AE-in-defining-nuclear-organisation-in-skeletal-muscle-fibres
#1
Jacob A Ross, Adam Pearson, Yotam Levy, Bettina Cardel, Christoph Handschin, Julien Ochala
Muscle fibres are multinucleated cells, with each nucleus controlling the protein synthesis in a finite volume of cytoplasm termed the myonuclear domain (MND). What determines MND size remains unclear. In the present study, we aimed to test the hypothesis that the level of expression of the transcriptional coactivator PGC-1α and subsequent activation of the mitochondrial biogenesis are major contributors. Hence, we used two transgenic mouse models with varying expression of PGC-1α in skeletal muscles. We isolated myofibres from the fast twitch extensor digitorum longus (EDL) and slow twitch diaphragm muscles...
November 7, 2016: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/27614293/disruption-of-the-ubf-gene-induces-aberrant-somatic-nucleolar-bodies-and-disrupts-embryo-nucleolar-precursor-bodies
#2
Nourdine Hamdane, Michel G Tremblay, Stefan Dillinger, Victor Y Stefanovsky, Attila Németh, Tom Moss
The nucleolus is the site of ribosome biogenesis and forms around the actively transcribed ribosomal RNA (rRNA) genes. However, the nucleolus is also implicated in cell cycle regulation, tumour suppression and chromosome segregation and nucleolar disfunction is linked to a wide range of human diseases. Interestingly, the nucleolus is also required for genome reprogramming and the establishment of heterochromatin in the mammalian embryo. Mammalian oocytes contain a subnuclear structure that is believed to be the precursor of the functional nucleolus, the Nucleolar Precursor Body (NPB)...
September 7, 2016: Gene
https://www.readbyqxmd.com/read/26982524/multicolor-detection-of-every-chromosome-as-a-means-of-detecting-mosaicism-and-nuclear-organization-in-human-embryonic-nuclei
#3
Kara Turner, Katie Fowler, Gothami Fonseka, Darren Griffin, Dimitrios Ioannou
Fluorescence in-situ hybridization (FISH) revolutionized cytogenetics using fluorescently labelled probes with high affinity with target (nuclear) DNA. By the early 1990s FISH was adopted as a means of preimplantation genetic diagnosis (PGD) sexing for couples at risk of transmitting X-linked disorders and later for detection of unbalanced translocations. Following a rise in popularity of PGD by FISH for sexing and the availability of multicolor probes (5-8 colors), the use of FISH was expanded to the detection of aneuploidy and selective implantation of embryos more likely to be euploid, the rationale being to increase pregnancy rates (referral categories were typically advanced maternal age, repeated IVF failure, repeated miscarriage or severe male factor infertility)...
June 2016: Panminerva Medica
https://www.readbyqxmd.com/read/26949251/the-cell-proliferation-antigen-ki-67-organises-heterochromatin
#4
Michal Sobecki, Karim Mrouj, Alain Camasses, Nikolaos Parisis, Emilien Nicolas, David Llères, François Gerbe, Susana Prieto, Liliana Krasinska, Alexandre David, Manuel Eguren, Marie-Christine Birling, Serge Urbach, Sonia Hem, Jérôme Déjardin, Marcos Malumbres, Philippe Jay, Vjekoslav Dulic, Denis Lj Lafontaine, Robert Feil, Daniel Fisher
Antigen Ki-67 is a nuclear protein expressed in proliferating mammalian cells. It is widely used in cancer histopathology but its functions remain unclear. Here, we show that Ki-67 controls heterochromatin organisation. Altering Ki-67 expression levels did not significantly affect cell proliferation in vivo. Ki-67 mutant mice developed normally and cells lacking Ki-67 proliferated efficiently. Conversely, upregulation of Ki-67 expression in differentiated tissues did not prevent cell cycle arrest. Ki-67 interactors included proteins involved in nucleolar processes and chromatin regulators...
2016: ELife
https://www.readbyqxmd.com/read/26728621/resetting-a-functional-g1-nucleus-after-mitosis
#5
REVIEW
Ines J de Castro, Ezgi Gokhan, Paola Vagnarelli
The maintenance of the correct cellular information goes beyond the simple transmission of an intact genetic code from one generation to the next. Epigenetic changes, topological cues and correct protein-protein interactions need to be re-established after each cell division to allow the next cell cycle to resume in the correct regulated manner. This process begins with mitotic exit and re-sets all the changes that occurred during mitosis thus restoring a functional G1 nucleus in preparation for the next cell cycle...
September 2016: Chromosoma
https://www.readbyqxmd.com/read/26673895/a-deep-proteomics-perspective-on-crm1-mediated-nuclear-export-and-nucleocytoplasmic-partitioning
#6
Koray Kırlı, Samir Karaca, Heinz Jürgen Dehne, Matthias Samwer, Kuan Ting Pan, Christof Lenz, Henning Urlaub, Dirk Görlich
CRM1 is a highly conserved, RanGTPase-driven exportin that carries proteins and RNPs from the nucleus to the cytoplasm. We now explored the cargo-spectrum of CRM1 in depth and identified surprisingly large numbers, namely >700 export substrates from the yeast S. cerevisiae, ≈1000 from Xenopus oocytes and >1050 from human cells. In addition, we quantified the partitioning of ≈5000 unique proteins between nucleus and cytoplasm of Xenopus oocytes. The data suggest new CRM1 functions in spatial control of vesicle coat-assembly, centrosomes, autophagy, peroxisome biogenesis, cytoskeleton, ribosome maturation, translation, mRNA degradation, and more generally in precluding a potentially detrimental action of cytoplasmic pathways within the nuclear interior...
2015: ELife
https://www.readbyqxmd.com/read/26630398/two-stages-of-xrcc1-recruitment-and-two-classes-of-xrcc1-foci-formed-in-response-to-low-level-dna-damage-induced-by-visible-light-or-stress-triggered-by-heat-shock
#7
Kamil J Solarczyk, Magdalena Kordon, Krzysztof Berniak, Jurek W Dobrucki
Induction of local photosensitised DNA damage has been used to study recruitment of repair factors, spatial organisation and subsequent stages of the repair processes. However, the damage induced by a focused laser beam interacting with a photosensitiser may not fully reflect the types of damage and repair encountered in cells of an animal under typical conditions in vivo. We report on two characteristic stages of recruitment of XRCC1 (a protein engaged in BER and SSB repair pathways), in response to low level DNA damage induced by visible light...
January 2016: DNA Repair
https://www.readbyqxmd.com/read/26260408/taxonomy-phylogeny-and-molecular-epidemiology-of-echinococcus-multilocularis-from-fundamental-knowledge-to-health-ecology
#8
Jenny Knapp, Bruno Gottstein, Urmas Saarma, Laurence Millon
Alveolar echinococcosis, caused by the tapeworm Echinococcus multilocularis, is one of the most severe parasitic diseases in humans and represents one of the 17 neglected diseases prioritised by the World Health Organisation (WHO) in 2012. Considering the major medical and veterinary importance of this parasite, the phylogeny of the genus Echinococcus is of considerable importance; yet, despite numerous efforts with both mitochondrial and nuclear data, it has remained unresolved. The genus is clearly complex, and this is one of the reasons for the incomplete understanding of its taxonomy...
October 30, 2015: Veterinary Parasitology
https://www.readbyqxmd.com/read/26220581/inferring-3d-chromatin-structure-using-a-multiscale-approach-based-on-quaternions
#9
Claudia Caudai, Emanuele Salerno, Monica Zoppè, Anna Tonazzini
BACKGROUND: The knowledge of the spatial organisation of the chromatin fibre in cell nuclei helps researchers to understand the nuclear machinery that regulates DNA activity. Recent experimental techniques of the type Chromosome Conformation Capture (3C, or similar) provide high-resolution, high-throughput data consisting in the number of times any possible pair of DNA fragments is found to be in contact, in a certain population of cells. As these data carry information on the structure of the chromatin fibre, several attempts have been made to use them to obtain high-resolution 3D reconstructions of entire chromosomes, or even an entire genome...
July 29, 2015: BMC Bioinformatics
https://www.readbyqxmd.com/read/25274422/the-elastin-peptide-vgvapg-3-induces-the-3d-reorganisation-of-pml-nbs-and-sc35-speckles-architecture-and-accelerates-proliferation-of-fibroblasts-and-melanoma-cells
#10
Aurore Chatron-Colliet, Nathalie Lalun, Christine Terryn, Sandrine Kurdykowski, Marianne Lorenzato, Anthony Rusciani, Dominique Ploton, Laurent Duca, Hélène Bobichon
During melanoma tumour growth, cancerous cells are exposed to the immediate surrounding the micro- and macro environment, which is largely modified through the degradation of the extracellular matrix by fibroblast-derived metalloproteinases. Among the degradation products, (VGVAPG)3, an elastin peptide is known to stimulate the proliferation of both fibroblasts and cancerous cells by binding to the elastin-binding receptor and activating the MEK/ERK signal transduction pathway. As this process strongly modifies mRNA synthesis, we investigated its effect on the relative three-dimensional organisation of the major partners of the mRNA splicing machinery: promyelocytic nuclear bodies (PML-NBs ) and splicing component 35 speckles (SC35) of normal fibroblasts and melanoma SK-MEL-28 cells...
March 2015: Histochemistry and Cell Biology
https://www.readbyqxmd.com/read/25139492/monitoring-the-response-of-bone-metastases-to-treatment-with-magnetic-resonance-imaging-and-nuclear-medicine-techniques-a-review-and-position-statement-by-the-european-organisation-for-research-and-treatment-of-cancer-imaging-group
#11
REVIEW
F E Lecouvet, J N Talbot, C Messiou, P Bourguet, Y Liu, N M de Souza
Assessment of the response to treatment of metastases is crucial in daily oncological practice and clinical trials. For soft tissue metastases, this is done using computed tomography (CT), Magnetic Resonance Imaging (MRI) or Positron Emission Tomography (PET) using validated response evaluation criteria. Bone metastases, which frequently represent the only site of metastases, are an exception in response assessment systems, because of the nature of the fixed bony defects, their complexity, which ranges from sclerotic to osteolytic and because of the lack of sensitivity, specificity and spatial resolution of the previously available bone imaging methods, mainly bone scintigraphy...
October 2014: European Journal of Cancer
https://www.readbyqxmd.com/read/24974018/transcriptional-regulatory-functions-of-nuclear-long-noncoding-rnas
#12
REVIEW
Keith W Vance, Chris P Ponting
Several nuclear localised intergenic long noncoding RNAs (lncRNAs) have been ascribed regulatory roles in transcriptional control and their number is growing rapidly. Initially, these transcripts were shown to function locally, near their sites of synthesis, by regulating the expression of neighbouring genes. More recently, lncRNAs have been demonstrated to interact with chromatin at several thousand different locations across multiple chromosomes and to modulate large-scale gene expression programs. Although the molecular mechanisms involved in targeting lncRNAs to distal binding sites remain poorly understood, the spatial organisation of the genome may have a role in specifying lncRNA function...
August 2014: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/24973960/distribution-of-segmental-duplications-in-the-context-of-higher-order-chromatin-organisation-of-human-chromosome-7
#13
Grit Ebert, Anne Steininger, Robert Weißmann, Vivien Boldt, Allan Lind-Thomsen, Jana Grune, Stefan Badelt, Melanie Heßler, Matthias Peiser, Manuel Hitzler, Lars R Jensen, Ines Müller, Hao Hu, Peter F Arndt, Andreas W Kuss, Katrin Tebel, Reinhard Ullmann
BACKGROUND: Segmental duplications (SDs) are not evenly distributed along chromosomes. The reasons for this biased susceptibility to SD insertion are poorly understood. Accumulation of SDs is associated with increased genomic instability, which can lead to structural variants and genomic disorders such as the Williams-Beuren syndrome. Despite these adverse effects, SDs have become fixed in the human genome. Focusing on chromosome 7, which is particularly rich in interstitial SDs, we have investigated the distribution of SDs in the context of evolution and the three dimensional organisation of the chromosome in order to gain insights into the mutual relationship of SDs and chromatin topology...
2014: BMC Genomics
https://www.readbyqxmd.com/read/24929041/a-computational-model-of-nuclear-self-organisation-in-syncytial-embryos
#14
Christoph Koke, Takuma Kanesaki, Jörg Grosshans, Ulrich S Schwarz, Carina M Dunlop
Syncytial embryos develop through cycles of nuclear division and rearrangement within a common cytoplasm. A paradigm example is Drosophila melanogaster in which nuclei form an ordered array in the embryo surface over cell cycles 10-13. This ordering process is assumed to be essential for subsequent cellularisation. Using quantitative tissue analysis, it has previously been shown that the regrowth of actin and microtubule networks after nuclear division generates reordering forces that counteract its disordering effect (Kanesaki et al...
October 21, 2014: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/24330859/chromosome-territories-reposition-during-dna-damage-repair-response
#15
Ishita S Mehta, Mugdha Kulashreshtha, Sandeep Chakraborty, Ullas Kolthur-Seetharam, Basuthkar J Rao
BACKGROUND: Local higher-order chromatin structure, dynamics and composition of the DNA are known to determine double-strand break frequencies and the efficiency of repair. However, how DNA damage response affects the spatial organization of chromosome territories is still unexplored. RESULTS: Our report investigates the effect of DNA damage on the spatial organization of chromosome territories within interphase nuclei of human cells. We show that DNA damage induces a large-scale spatial repositioning of chromosome territories that are relatively gene dense...
2013: Genome Biology
https://www.readbyqxmd.com/read/24305250/67-correlation-of-architectural-and-functional-reprogramming-of-nuclei-during-embryonic-genome-activation-of-early-bovine-embryos-generated-by-ivf-and-scnt
#16
J Popken, D Koehler, A Brero, A Wuensch, T Thormeyer, T Guengoer, E Wolf, V Zakhartchenko, T Cremer
Development of mammalian pre-implantation embryos provides an excellent model to explore interactions of nuclear organisation and nuclear functions. Based on light optical sectioning with confocal laser scanning microscopy and structured illumination microscopy, we performed a quantitative three-dimensional image analysis of nuclei in early bovine embryos generated by in vitro fertilization (IVF) and somatic cell nuclear transfer (SCNT) of bovine fibroblast nuclei. The same sequence of changes was observed in nuclei of both IVF and SCNT embryos during embryonic genome activation (EGA) is that typically achieved in embryos between 8 and 16 cells...
December 2013: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/24205348/a-phylogenetic-study-of-spbp-and-rai1-evolutionary-conservation-of-chromatin-binding-modules
#17
Sagar Darvekar, Cecilie Rekdal, Terje Johansen, Eva Sjøttem
Our genome is assembled into and array of highly dynamic nucleosome structures allowing spatial and temporal access to DNA. The nucleosomes are subject to a wide array of post-translational modifications, altering the DNA-histone interaction and serving as docking sites for proteins exhibiting effector or "reader" modules. The nuclear proteins SPBP and RAI1 are composed of several putative "reader" modules which may have ability to recognise a set of histone modification marks. Here we have performed a phylogenetic study of their putative reader modules, the C-terminal ePHD/ADD like domain, a novel nucleosome binding region and an AT-hook motif...
2013: PloS One
https://www.readbyqxmd.com/read/24019912/characterisation-of-nuclear-architectural-alterations-during-in-vitro-differentiation-of-human-stem-cells-of-myogenic-origin
#18
Natalia Rozwadowska, Tomasz Kolanowski, Ewa Wiland, Marcin Siatkowski, Piotr Pawlak, Agnieszka Malcher, Tomasz Mietkiewski, Marta Olszewska, Maciej Kurpisz
Cell differentiation is based on a synchronised orchestra of complex pathways of intrinsic and extrinsic signals that manifest in the induced expression of specific transcription factors and pivotal genes within the nucleus. One cannot ignore the epigenetic status of differentiating cells, comprising not only histones and DNA modifications but also the spatial and temporal intranuclear chromatin organisation, which is an important regulator of nuclear processes. In the present study, we investigated the nuclear architecture of human primary myoblasts and myocytes in an in vitro culture, with reference to global changes in genomic expression...
2013: PloS One
https://www.readbyqxmd.com/read/24018840/nema-nu-4-2008-validation-and-applications-of-the-pet-sorteo-monte-carlo-simulations-platform-for-the-geometry-of-the-inveon-pet-preclinical-scanner
#19
F Boisson, C J Wimberley, W Lehnert, D Zahra, T Pham, G Perkins, H Hamze, M-C Gregoire, A Reilhac
Monte Carlo-based simulation of positron emission tomography (PET) data plays a key role in the design and optimization of data correction and processing methods. Our first aim was to adapt and configure the PET-SORTEO Monte Carlo simulation program for the geometry of the widely distributed Inveon PET preclinical scanner manufactured by Siemens Preclinical Solutions. The validation was carried out against actual measurements performed on the Inveon PET scanner at the Australian Nuclear Science and Technology Organisation in Australia and at the Brain & Mind Research Institute and by strictly following the NEMA NU 4-2008 standard...
October 7, 2013: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/23874217/fgf-signalling-regulates-chromatin-organisation-during-neural-differentiation-via-mechanisms-that-can-be-uncoupled-from-transcription
#20
Nishal S Patel, Muriel Rhinn, Claudia I Semprich, Pamela A Halley, Pascal Dollé, Wendy A Bickmore, Kate G Storey
Changes in higher order chromatin organisation have been linked to transcriptional regulation; however, little is known about how such organisation alters during embryonic development or how it is regulated by extrinsic signals. Here we analyse changes in chromatin organisation as neural differentiation progresses, exploiting the clear spatial separation of the temporal events of differentiation along the elongating body axis of the mouse embryo. Combining fluorescence in situ hybridisation with super-resolution structured illumination microscopy, we show that chromatin around key differentiation gene loci Pax6 and Irx3 undergoes both decompaction and displacement towards the nuclear centre coincident with transcriptional onset...
2013: PLoS Genetics
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