keyword
https://read.qxmd.com/read/24127217/whole-genome-screening-identifies-proteins-localized-to-distinct-nuclear-bodies
#21
JOURNAL ARTICLE
Ka-Wing Fong, Yujing Li, Wenqi Wang, Wenbin Ma, Kunpeng Li, Robert Z Qi, Dan Liu, Zhou Songyang, Junjie Chen
The nucleus is a unique organelle that contains essential genetic materials in chromosome territories. The interchromatin space is composed of nuclear subcompartments, which are defined by several distinctive nuclear bodies believed to be factories of DNA or RNA processing and sites of transcriptional and/or posttranscriptional regulation. In this paper, we performed a genome-wide microscopy-based screening for proteins that form nuclear foci and characterized their localizations using markers of known nuclear bodies...
October 14, 2013: Journal of Cell Biology
https://read.qxmd.com/read/22102035/crystallization-of-a-paraspeckle-protein-pspc1-nono-heterodimer
#22
JOURNAL ARTICLE
Daniel M Passon, Mihwa Lee, Archa H Fox, Charles S Bond
The paraspeckle component 1 (PSPC1) and non-POU-domain-containing octamer-binding protein (NONO) heterodimer is an essential structural component of paraspeckles, ribonucleoprotein bodies found in the interchromatin space of mammalian cell nuclei. PSPC1 and NONO both belong to the Drosophila behaviour and human splicing (DBHS) protein family, which has been implicated in many aspects of RNA processing. A heterodimer of the core DBHS conserved region of PSPC1 and NONO comprising two tandemly arranged RNA-recognition motifs (RRMs), a NONA/paraspeckle (NOPS) domain and part of a predicted coiled-coil domain has been crystallized in space group C2, with unit-cell parameters a = 90...
October 1, 2011: Acta Crystallographica. Section F, Structural Biology and Crystallization Communications
https://read.qxmd.com/read/22078878/ncrna-and-pc2-methylation-dependent-gene-relocation-between-nuclear-structures-mediates-gene-activation-programs
#23
JOURNAL ARTICLE
Liuqing Yang, Chunru Lin, Wen Liu, Jie Zhang, Kenneth A Ohgi, Jonathan D Grinstein, Pieter C Dorrestein, Michael G Rosenfeld
Although eukaryotic nuclei contain distinct architectural structures associated with noncoding RNAs (ncRNAs), their potential relationship to regulated transcriptional programs remains poorly understood. Here, we report that methylation/demethylation of Polycomb 2 protein (Pc2) controls relocation of growth-control genes between Polycomb bodies (PcGs) and interchromatin granules (ICGs) in response to growth signals. This movement is the consequence of binding of methylated and unmethylated Pc2 to the ncRNAs TUG1 and MALAT1/NEAT2, located in PcGs and ICGs, respectively...
November 11, 2011: Cell
https://read.qxmd.com/read/22023725/early-apoptotic-reorganization-of-spliceosomal-proteins-involves-caspases-cad-and-rearrangement-of-numa
#24
JOURNAL ARTICLE
Jürgen Dieker, Victoria Iglesias-Guimarais, Marion Décossas, James Stevenin, Johan van der Vlag, Victor J Yuste, Sylviane Muller
The reorganization of nuclear structures is an important early feature of apoptosis and involves the activity of specific proteases and nucleases. Well-known is the condensation and fragmentation of chromatin; however, much less is understood about the mechanisms involved in the reorganization of structures from the interchromatin space, such as interchromatin granule clusters (IGCs). In this study, we show that the initial enlargement and rounding-up of IGCs correlate with a decrease in mRNA transcription and are caspase-independent, but involve protein phosphatases PP1/PP2A...
February 2012: Traffic
https://read.qxmd.com/read/21467142/functional-nuclear-organization-of-transcription-and-dna-replication-a-topographical-marriage-between-chromatin-domains-and-the-interchromatin-compartment
#25
JOURNAL ARTICLE
Y Markaki, M Gunkel, L Schermelleh, S Beichmanis, J Neumann, M Heidemann, H Leonhardt, D Eick, C Cremer, T Cremer
We studied the nuclear topography of RNA transcription and DNA replication in mammalian cell types with super-resolution fluorescence microscopy, which offers a resolution beyond the classical Abbe/Raleigh limit. Three-dimensional structured illumination microscopy (3D-SIM) demonstrated a network of channels and wider lacunas, called the interchromatin compartment (IC). The IC starts at nuclear pores and expands throughout the nuclear space. It is demarcated from the compact interior of higher-order chromatin domains (CDs) by a 100-200-nm thick layer of decondensed chromatin, termed the perichromatin region (PR)...
2010: Cold Spring Harbor Symposia on Quantitative Biology
https://read.qxmd.com/read/21289045/structure-and-function-of-the-perinucleolar-compartment-in-cancer-cells
#26
JOURNAL ARTICLE
A Slusarczyk, R Kamath, C Wang, D Anchel, C Pollock, M A Lewandowska, T Fitzpatrick, D P Bazett-Jones, S Huang
The perinucleolar compartment (PNC) is a subnuclear body that forms in cancer cells. In vivo analyses using human tumor tissues demonstrate a close correlation between PNC prevalence and disease progress in colorectal carcinoma, and a high PNC prevalence is associated with poor patient outcome. These findings are consistent with previous observations in breast cancer and cancer cell lines in vitro. The PNC is composed of thick strands that form a filamental meshwork often extending into the nucleolus. Although it appears to be electron dense as observed by transmission electron microscopy (TEM), the actual density of the structure imaged by electron spectroscopy is much lower, similar to that of the interchromatin space, and is lined with ribonucleoproteins (RNPs)...
2010: Cold Spring Harbor Symposia on Quantitative Biology
https://read.qxmd.com/read/21079985/nucleocytoplasmic-mrnp-export-is-an-integral-part-of-mrnp-biogenesis
#27
REVIEW
Petra Björk, Lars Wieslander
Nucleocytoplasmic export and biogenesis of mRNPs are closely coupled. At the gene, concomitant with synthesis of the pre-mRNA, the transcription machinery, hnRNP proteins, processing, quality control and export machineries cooperate to release processed and export competent mRNPs. After diffusion through the interchromatin space, the mRNPs are translocated through the nuclear pore complex and released into the cytoplasm. At the nuclear pore complex, defined compositional and conformational changes are triggered, but specific cotranscriptionally added components are retained in the mRNP and subsequently influence the cytoplasmic fate of the mRNP...
February 2011: Chromosoma
https://read.qxmd.com/read/21056558/transcribed-dna-is-preferentially-located-in-the-perichromatin-region-of-mammalian-cell-nuclei
#28
JOURNAL ARTICLE
Janusz Niedojadlo, Cécile Perret-Vivancos, Karl-Henning Kalland, Dusan Cmarko, Thomas Cremer, Roel van Driel, Stanislav Fakan
The precise localization of transcribed DNA and resulting RNA is an important aspect of the functional architecture of the nucleus. To this end we have developed a novel in situ hybridization approach in combination with immunoelectron microscopy, using sense and anti-sense RNA probes that are derived from total cellular or cytoplasmic poly(A+) RNA. This new technology is much more gentle than classical in situ hybridization using DNA probes and shows excellent preservation of nuclear structure. Carried out on ultrathin sections of fixed and resin-embedded COS-7 cells, it revealed at high resolution the localization of the genes that code for the cellular mRNAs...
February 15, 2011: Experimental Cell Research
https://read.qxmd.com/read/20573717/paraspeckles
#29
REVIEW
Archa H Fox, Angus I Lamond
Paraspeckles are a relatively new class of subnuclear bodies found in the interchromatin space of mammalian cells. They are RNA-protein structures formed by the interaction between a long nonprotein-coding RNA species, NEAT1/Men epsilon/beta, and members of the DBHS (Drosophila Behavior Human Splicing) family of proteins: P54NRB/NONO, PSPC1, and PSF/SFPQ. Paraspeckles are critical to the control of gene expression through the nuclear retention of RNA containing double-stranded RNA regions that have been subject to adenosine-to-inosine editing...
July 2010: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/20302859/remodeling-of-nuclear-architecture-by-the-thiodioxoxpiperazine-metabolite-chaetocin
#30
JOURNAL ARTICLE
Doris Illner, Roman Zinner, Violet Handtke, Jacques Rouquette, Hilmar Strickfaden, Christian Lanctôt, Marcus Conrad, Alexander Seiler, Axel Imhof, Thomas Cremer, Marion Cremer
Extensive changes of higher order chromatin arrangements can be observed during prometaphase, terminal cell differentiation and cellular senescence. Experimental systems where major reorganization of nuclear architecture can be induced under defined conditions, may help to better understand the functional implications of such changes. Here, we report on profound chromatin reorganization in fibroblast nuclei by chaetocin, a thiodioxopiperazine metabolite. Chaetocin induces strong condensation of chromosome territories separated by a wide interchromatin space largely void of DNA...
June 10, 2010: Experimental Cell Research
https://read.qxmd.com/read/19866688/electron-microscopic-examination-of-the-sites-of-nuclear-rna-synthesis-during-amphibian-embryogenesis
#31
JOURNAL ARTICLE
S Karasaki
The site of H(3)-uridine incorporation and the fate of labeled RNA during early embryo-genesis of the newt Triturus pyrrhogaster were studied with electron microscopic autoradiography. Isolated ectodermal and mesodermal tissues from the embryos were treated in H(3)-uridine for 3 hours and cultured in cold solution for various periods before fixation with OsO(4) and embedding in Epon. At the blastula stage, the only structural component of the nucleus seen in electron micrographs is a mass of chromatin fibrils...
September 1, 1965: Journal of Cell Biology
https://read.qxmd.com/read/19763862/induction-of-chromatin-condensation-by-nuclear-expression-of-a-novel-arginine-rich-cationic-protein-genetically-engineered-from-the-enhanced-green-fluorescent-protein
#32
JOURNAL ARTICLE
Yukihiro Higashiyama, Akinori Takahashi, Yasunori Fukumoto, Yuji Nakayama, Naoto Yamaguchi
In the interphase nuclei of cultured cells, chromatin is compacted and organized in higher-order structures through the condensation and decondensation processes. Chromosomes in the interphase nucleus are known to occupy distinct territories. The chromosome territory-interchromatin compartment model premises that the interchromatin compartment is separated from compact higher-order chromatin domains and expands in between these chromatin-organized territories. Chromatin in cultured cells is compacted under some conditions, such as the stress of heat shock and high osmolarity, and Src-mediated nuclear tyrosine phosphorylation...
July 2009: Cytotechnology
https://read.qxmd.com/read/19731052/revealing-the-high-resolution-three-dimensional-network-of-chromatin-and-interchromatin-space-a-novel-electron-microscopic-approach-to-reconstructing-nuclear-architecture
#33
JOURNAL ARTICLE
Jacques Rouquette, Christel Genoud, Gerardo H Vazquez-Nin, Bernd Kraus, Thomas Cremer, Stanislav Fakan
The nuclear architecture is considered an important contributor to genome function. Although the fine structural features of the cell nucleus have been investigated extensively by means of ultrastructural cytochemistry, mainly on ultrathin sections in two dimensions (2D), there was a of lack routine methods for a rapid reconstruction of three-dimensional (3D) distribution of different structural constituents throughout the nuclear volume. We have now filled this gap by the application of a novel approach associating a pre-embedding selective visualization of nuclear components with a method making use of ultramicrotomy combined with scanning electron microscopy (microtome serial block face scanning electron microscopy--'3View')...
2009: Chromosome Research
https://read.qxmd.com/read/19720872/paraspeckles-nuclear-bodies-built-on-long-noncoding-rna
#34
REVIEW
Charles S Bond, Archa H Fox
Paraspeckles are ribonucleoprotein bodies found in the interchromatin space of mammalian cell nuclei. These structures play a role in regulating the expression of certain genes in differentiated cells by nuclear retention of RNA. The core paraspeckle proteins (PSF/SFPQ, P54NRB/NONO, and PSPC1 [paraspeckle protein 1]) are members of the DBHS (Drosophila melanogaster behavior, human splicing) family. These proteins, together with the long nonprotein-coding RNA NEAT1 (MEN-epsilon/beta), associate to form paraspeckles and maintain their integrity...
September 7, 2009: Journal of Cell Biology
https://read.qxmd.com/read/19274654/universal-nuclear-domains-of-somatic-and-germ-cells-some-lessons-from-oocyte-interchromatin-granule-cluster-and-cajal-body-structure-and-molecular-composition
#35
REVIEW
Dmitry Bogolyubov, Irina Stepanova, Vladimir Parfenov
It is now clear that two prominent nuclear domains, interchromatin granule clusters (IGCs) and Cajal bodies (CBs), contribute to the highly ordered organization of the extrachromosomal space of the cell nucleus. These functional domains represent structurally stable but highly dynamic nuclear organelles enriched in factors that are required for different nuclear activities, especially RNA biogenesis. IGCs are considered to be the main sites for storage, assembly, and/or recycling of the essential spliceosome components...
April 2009: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/19052240/enhancing-nuclear-receptor-induced-transcription-requires-nuclear-motor-and-lsd1-dependent-gene-networking-in-interchromatin-granules
#36
JOURNAL ARTICLE
Qidong Hu, Young-Soo Kwon, Esperanza Nunez, Maria Dafne Cardamone, Kasey R Hutt, Kenneth A Ohgi, Ivan Garcia-Bassets, David W Rose, Christopher K Glass, Michael G Rosenfeld, Xiang-Dong Fu
Although the role of liganded nuclear receptors in mediating coactivator/corepressor exchange is well-established, little is known about the potential regulation of chromosomal organization in the 3-dimensional space of the nucleus in achieving integrated transcriptional responses to diverse signaling events. Here, we report that ligand induces rapid interchromosomal interactions among specific subsets of estrogen receptor alpha-bound transcription units, with a dramatic reorganization of nuclear territories, which depends on the actions of nuclear actin/myosin-I machinery and dynein light chain 1...
December 9, 2008: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/18606154/dynamic-relocation-of-nuclear-proteins-during-the-execution-phase-of-apoptosis
#37
JOURNAL ARTICLE
Anna Ivana Scovassi, Maria Grazia Bottone, Marco Biggiogera, Carlo Pellicciari
In the apoptotic program of controlled cell dismantling, the most characteristic nuclear changes involve chromatin, which condenses and often collapses against the nuclear envelope in the form of crescents. A severe reorganization also occurs in ribonucleoprotein (RNP)-containing structures which are involved in the synthesis and processing of transcripts: already during early apoptosis, the nucleoplasmic RNPs (namely, perichromatin fibrils, perichromatin granules, and interchromatin granules) coalesce in the interchromatin space where they associate with segregated nucleolar components, to ectopically form fibro-granular heterogeneous clusters...
December 1, 2008: Biochemical Pharmacology
https://read.qxmd.com/read/18370015/purification-and-proteomic-analysis-of-a-nuclear-insoluble-protein-fraction
#38
JOURNAL ARTICLE
Tsuneyoshi Horigome, Kazuhiro Furukawa, Kohei Ishii
We describe here a method for analyzing a rat liver nuclear-insoluble protein fraction to determine candidate proteins participating in nuclear architecture formation. Rat liver nuclei are purified by sucrose density gradient centrifugation. The purified nuclei are treated with DNase and RNase and then washed with high salt and detergent solutions. The residual nuclear-insoluble protein fraction is separated by reversed-phase high-performance liquid chromatography (HPLC) in 60% formic acid on a polystyrene resin column...
2008: Methods in Molecular Biology
https://read.qxmd.com/read/18358812/nuclear-receptor-enhanced-transcription-requires-motor-and-lsd1-dependent-gene-networking-in-interchromatin-granules
#39
JOURNAL ARTICLE
Esperanza Nunez, Young-Soo Kwon, Kasey R Hutt, Qidong Hu, Maria Dafne Cardamone, Kenneth A Ohgi, Ivan Garcia-Bassets, David W Rose, Christopher K Glass, Michael G Rosenfeld, Xiang-Dong Fu
While the transcriptional machinery has been extensively dissected at the molecular level, little is known about regulation of chromosomal organization in the three-dimensional space of the nucleus to achieve integrated transcriptional responses to diverse signaling events. Here, we report that ligand induces rapid interchromosomal interactions among subsets of estrogen receptor alpha-bound transcription units, with a dramatic reorganization of nuclear territories requiring nuclear actin/myosin-I transport machinery, dynein light chain 1 (DLC1), and a specific subset of transcriptional coactivators and chromatin remodeling complexes...
March 21, 2008: Cell
https://read.qxmd.com/read/18325909/subnuclear-localization-and-mobility-are-key-indicators-of-pax3-dysfunction-in-waardenburg-syndrome
#40
JOURNAL ARTICLE
Gareth N Corry, Michael J Hendzel, D Alan Underhill
Mutations in the transcription factor PAX3 cause Waardenburg syndrome (WS) in humans and the mouse Splotch mutant, which display similar neural crest-derived defects. Previous characterization of disease-causing mutations revealed pleiotropic effects on PAX3 DNA binding and transcriptional activity. In this study, we evaluated the impact of disease alleles on PAX3 localization and mobility. Immunofluorescence analyses indicated that the majority of PAX3 occupies the interchromatin space, with only sporadic colocalization with sites of transcription...
June 15, 2008: Human Molecular Genetics
keyword
keyword
61320
2
3
Fetch more papers »
Fetching more papers... Fetching...
Remove bar
Read by QxMD icon Read
×

Save your favorite articles in one place with a free QxMD account.

×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"

We want to hear from doctors like you!

Take a second to answer a survey question.