Genomes and Genes
Summary: The residual framework structure of the CELL NUCLEUS that maintains many of the overall architectural features of the cell nucleus including the nuclear lamina with NUCLEAR PORE complex structures, residual CELL NUCLEOLI and an extensive fibrogranular structure in the nuclear interior. (Advan. Enzyme Regul. 2002; 42:39-52)
Publications261 found, 100 shown here
- HA95 is a protein of the chromatin and nuclear matrix regulating nuclear envelope dynamicsS B Martins
Institute of Medical Biochemistry, University of Oslo, PO Box 1112 Blindern, Norway
J Cell Sci 113:3703-13. 2000..Biochemical and photobleaching data indicate that HA95 is tightly associated with chromatin and the nuclear matrix/lamina network in interphase, and bound to chromatin at mitosis...
- Anchoring the genomeDiego Ottaviani
Cancer Research UK London Research Institute, Lincoln s Inn Fields, London WC2A 3PX, UK
Genome Biol 9:201. 2008..is evidence that higher-order chromatin folding is mediated by the anchoring of specific DNA sequences to the nuclear matrix. These genome anchors are also crucial regulators of gene expression and DNA replication, and play a role in ..
- A hyperphosphorylated form of the large subunit of RNA polymerase II is associated with splicing complexes and the nuclear matrixM J Mortillaro
Department of Biological Sciences, State University of New York at Buffalo 14260, USA
Proc Natl Acad Sci U S A 93:8253-7. 1996..retained in a similar pattern following in situ extraction of cells and was quantitatively recovered in the nuclear matrix fraction...
- Nuclear matrix support of DNA replicationBoyka Anachkova
Institute of Molecular Biology, Bulgarian Academy of Sciences, Akad G Bonchev Street, Bl 21, Sofia 1113, Bulgaria
J Cell Biochem 96:951-61. 2005..To achieve this, DNA is organized into loops attached to the nuclear matrix. Each loop represents one individual replicon with the origin of replication localized within the loop and the ..
- Nuclear matrix association of insulin receptor and IRS-1 by insulin in osteoblast-like UMR-106 cellsKi Cheon Seol
Department of Pharmacology, School of Dentistry, Kyung Hee University, Seoul 130 701, Republic of Korea
Biochem Biophys Res Commun 306:898-904. 2003..The majority of insulin receptor and IRS-1 translocated to the nucleus appeared to associate with nuclear matrix. Tyrosine phosphorylation of a number of proteins with a molecular mass of 180, 95, 85, or 70 kDa in the ..
- Subnuclear proteomics in colorectal cancer: identification of proteins enriched in the nuclear matrix fraction and regulation in adenoma to carcinoma progressionJakob Albrethsen
OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center VUmc Cancer Center Amsterdam, The Netherlands
Mol Cell Proteomics 9:988-1005. 2010..in subnuclear domains in colorectal cancer tissues and apply this work flow to a comparative analysis of the nuclear matrix fraction in colorectal adenoma and carcinoma tissue samples...
- PDLIM2 suppresses human T-cell leukemia virus type I Tax-mediated tumorigenesis by targeting Tax into the nuclear matrix for proteasomal degradationPengrong Yan
University of Pittsburgh Cancer Institute, University of Pittsburgh Medical Center, PA, USA
Blood 113:4370-80. 2009..In addition, PDLIM2 recruited Tax from its functional sites into the nuclear matrix where the polyubiquitinated Tax was degraded by the proteasome...
- From DNA structure to gene expression: mediators of nuclear compartmentalization and dynamicsJ Bode
GBF German Research Center for Biotechnology Epigenetic Regulation, Mascheroder Weg 1, D 38124 Braunschweig
Chromosome Res 11:435-45. 2003..into chromatin domains by their attachment to a supporting structure that has traditionally been termed the nuclear matrix. Present evidence indicates the dynamics of this entity, which requires particular properties of the elements ..
- Differential nuclear scaffold/matrix attachment marks expressed genesAmelia K Linnemann
The Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, C S Mott Center, Detroit, MI48201, USA
Hum Mol Genet 18:645-54. 2009..The varied functions of the S/MARs as revealed by the different extraction methods highlights their unique functional contribution...
- Dynamics of association of origins of DNA replication with the nuclear matrix during the cell cycleV Djeliova
Institute of Molecular Biology, Bulgarian Academy of Sciences, Akad. G. Bonchev Street, Bl. 21, Sofia 1113, Bulgaria
Nucleic Acids Res 29:3181-7. 2001DNA of replication foci attached to the nuclear matrix was isolated from Chinese hamster ovary cells and human HeLa cells synchronized at different stages of the G(1) and S phases of the cell cycle...
- Interaction of EBV latent origin of replication with the nuclear matrix: identification of S/MAR sequences and protein componentsGiulia Mearini
Department of Public Health Sciences, University La Sapienza, Rome, Italy
FEBS Lett 547:119-24. 2003During latency, Epstein Barr virus (EBV) genome, as an episome, is attached to the nuclear matrix (NM) via the latent origin of replication ori P...
- Necdin interacts with the ribonucleoprotein hnRNP U in the nuclear matrixHideo Taniura
Division of Regulation of Macromolecular Functions, Institute for Protein Research, Osaka University, Yamadaoka 3 2, Suita, Osaka 565 0871, Japan
J Cell Biochem 84:545-55. 2002..contained cDNA encoding a carboxyl-terminal portion of heterogeneous nuclear ribonucleoprotein U (hnRNP U), a nuclear matrix-associated protein that interacts with chromosomal DNA...
- Fanconi anemia proteins localize to chromatin and the nuclear matrix in a DNA damage- and cell cycle-regulated mannerF Qiao
Departments of Microbiology and Pediatrics, University of Virginia and the University of Virginia Health System, Charlottesville, Virginia 22908, USA
J Biol Chem 276:23391-6. 2001..Biochemical fractionation reveals that the FA proteins are found in nuclear matrix and chromatin and that treatment with mitomycin C results in increase of the FA proteins in nuclear matrix and ..
- DNA damage-dependent interaction of the nuclear matrix protein C1D with Translin-associated factor X (TRAX)Tuba Erdemir
Bilkent University, Molecular Biology and Genetics Department, 06533, Bilkent, Ankara, Turkey
J Cell Sci 115:207-16. 2002The nuclear matrix protein C1D is an activator of the DNA-dependent protein kinase (DNA-PK), which is essential for the repair of DNA double-strand breaks (DSBs) and V(D)J recombination...
- Unraveling the organization of the internal nuclear matrix: RNA-dependent anchoring of NuMA to a lamin scaffoldPaola Barboro
Istituto Nazionale per la Ricerca sul Cancro, I 16132, Genova, Italy
Exp Cell Res 279:202-18. 2002Using quantitative immunoelectron microscopy we show here that when the nuclear matrix is isolated from rat hepatocytes in the presence of an inhibitor of RNase activity both lamins and the nuclear mitotic apparatus protein (NuMA) ..
- Aged and post-mitotic cells share a very stable higher-order structure in the cell nucleus in vivoJaneth Alva-Medina
Universidad Autonoma del Estado de Mexico, Toluca, Estado de Mexico, Mexico
Biogerontology 11:703-16. 2010..cells the nuclear DNA is organized in supercoiled loops anchored to a proteinaceous substructure known as the nuclear matrix (NM). The DNA-NM interactions define a higher-order structure in the cell nucleus (NHOS)...
- A new spectrin, beta IV, has a major truncated isoform that associates with promyelocytic leukemia protein nuclear bodies and the nuclear matrixW T Tse
Division of Hematology Oncology, Children s Hospital, and the Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
J Biol Chem 276:23974-85. 2001..Spectrin betaIV is the first beta-spectrin associated with a subnuclear structure and may be part of a nuclear scaffold to which gene regulatory machinery binds...
- A structural basis for cellular senescenceArmando Aranda-Anzaldo
Laboratorio de Biologia Molecular, Facultad de Medicina, Universidad Autonoma del Estado de Mexico, Paseo Tollocan y Jesús Carranza, Toluca, Edo Mex, Mexico
Aging (Albany NY) 1:598-607. 2009..and discuss evidence that the interactions between DNA and the nuclear substructure, commonly known as the nuclear matrix, define a higher-order structure within the cell nucleus that following thermodynamic constraints, ..
- Hcc-1 is a novel component of the nuclear matrix with growth inhibitory functionC L Leaw
Bioprocessing Technology Institute, Agency for Science, Technology and Research A STAR, Singapore
Cell Mol Life Sci 61:2264-73. 2004..0173) and an accumulation of cells at the G2/M phase (p = 0.0276 compared to control HEK293 cells). Taken together, these results suggest a role for Hcc-1 in growth regulation and nucleic acids metabolism...
- A novel CpG-free vertebrate insulator silences the testis-specific SP-10 gene in somatic tissues: role for TDP-43 in insulator functionMayuresh M Abhyankar
Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
J Biol Chem 282:36143-54. 2007..Here we report that the insulator tethers the SP-10 gene to the nuclear matrix in somatic tissues, sequestering the core promoter in the process, thus preventing transcription...
- Interactions of Epstein-Barr virus origins of replication with nuclear matrix in the latent and in the lytic phases of viral infectionE Mattia
Faculty of Medicine and Surgery, University of Roma La Sapienza, Rome, Italy
Virology 262:9-17. 1999Eukaryotic DNA is organized into domains or loops generated by the attachment of chromatin fibers to the nuclear matrix via specific regions called scaffold or matrix attachment regions...
- PIASy, a nuclear matrix-associated SUMO E3 ligase, represses LEF1 activity by sequestration into nuclear bodiesS Sachdev
Gene Center and Institute of Biochemistry, University of Munich, 81377 Munich, Germany
Genes Dev 15:3088-103. 2001..Moreover, PIASy binds to nuclear matrix-associated DNA sequences and targets LEF1 to nuclear bodies, suggesting that PIASy-mediated subnuclear ..
- c-Abl tyrosine kinase selectively regulates p73 nuclear matrix associationMerav Ben-Yehoyada
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
J Biol Chem 278:34475-82. 2003..that in response to ionizing radiation, p73 undergoes nuclear redistribution and becomes associated with the nuclear matrix. This association is c-Abl-dependent because it was not observed in cells that are defective in c-Abl kinase ..
- The newly identified human nuclear protein NXP-2 possesses three distinct domains, the nuclear matrix-binding, RNA-binding, and coiled-coil domainsYukio Kimura
Department of Life Science, Graduate School and Faculty of Science, Himeji Institute of Technology, Kamigori, Hyogo 678 1201, Japan
J Biol Chem 277:20611-7. 2002Using a monoclonal antibody that recognizes a nuclear matrix protein, we selected a cDNA clone from a lambdagt11 human placenta cDNA library. This cDNA encoded a 939-amino acid protein designated nuclear matrix protein NXP-2...
- Exploring the effects of a dysfunctional nuclear matrixLauren S Elcock
Laboratory of Nuclear and Genomic Health, Centre for Cell and Chromosome Biology, Brunel University, Uxbridge, UK
Biochem Soc Trans 36:1378-83. 2008The nuclear matrix has remained a contentious structure for decades; many believe that it is an artefact of harsh non-physiological procedures...
- Autosomal-dominant distal myopathy associated with a recurrent missense mutation in the gene encoding the nuclear matrix protein, matrin 3Jan Senderek
Institute of Cell Biology, ETH Zurich, 8093 Zurich, Switzerland
Am J Hum Genet 84:511-8. 2009..MATR3 is expressed in skeletal muscle and encodes matrin 3, a component of the nuclear matrix, which is a proteinaceous network that extends throughout the nucleus...
- Gene positional changes relative to the nuclear substructure during carbon tetrachloride-induced hepatic fibrosis in ratsApolinar Maya-Mendoza
, Facultad de Medicina, , Apdo. Postal 428, C.P. 50000, Toluca, ,
J Cell Biochem 93:1084-98. 2004..interphase nucleus the DNA of higher eukaryotes is organized in loops anchored to a substructure known as the nuclear matrix (NM)...
- Gene positional changes relative to the nuclear substructure correlate with the proliferating status of hepatocytes during liver regenerationApolinar Maya-Mendoza
, Facultad de Medicina, , Apartado Postal 428, C.P. 50000, Toluca, ,
Nucleic Acids Res 31:6168-79. 2003..is organised in loops anchored to a proteinaceous substructure variously named but commonly known as the nuclear matrix. Important processes of nuclear physiology, such as replication, transcription and processing of primary ..
- Re-defining the chromatin loop domainH H Heng
Center for Molecular Medicine and Genetics, Department of Pathology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit MI 48202, USA
Cytogenet Cell Genet 93:155-61. 2001..to target some long-standing issues regarding the structure and function of the chromatin loop domain and its relationship with the nuclear matrix. This new knowledge will have a profound impact for modern genetics and molecular medicine.
- Boundary element-associated factor 32B connects chromatin domains to the nuclear matrixRashmi U Pathak
Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
Mol Cell Biol 27:4796-806. 2007..In this report we show that BEAF is associated with the nuclear matrix and map the domain required for matrix association to the middle region of the protein...
- Acute-phase-dependent binding affinity of C/EBPbeta from the nuclear extract and nuclear matrix towards the hormone response element of the alpha2-macroglobulin gene in rat hepatocytesD Bogojevic
Molecular Biology Laboratory, Institute for Biological Research, 29 Novembra 142, 11000 Belgrade, Serbia and Montenegro
Gen Physiol Biophys 22:279-85. 2003Interactions of nuclear extract and nuclear matrix proteins from rat hepatocytes with the hormone response element of the alpha2-macroglobulin gene were studied...
- Hairless is translocated to the nucleus via a novel bipartite nuclear localization signal and is associated with the nuclear matrixK Djabali
Departments of Dermatology and Genetics and Development, Columbia University, College of Physicians and Surgeons, New York, New York, USA
J Cell Sci 114:367-76. 2001..Furthermore, nuclear fractionation analysis revealed that the hr protein is associated with components of the nuclear matrix.
- A novel alpha-helical protein, specific to and highly conserved in plants, is associated with the nuclear matrix fractionAnnkatrin Rose
Plant Biotechnology Center and Department of Plant Biology, Ohio State University, Columbus, OH 43210, USA
J Exp Bot 54:1133-41. 2003A cDNA for a novel plant protein was isolated from tomato. Nuclear Matrix Protein 1 (NMP1) is a ubiquitously expressed 36 kDa protein, which has no homologues in animals and fungi, but is highly conserved among flowering and non-flowering ..
- Functional domains of necdin for protein-protein interaction, nuclear matrix targeting, and cell growth suppressionHideo Taniura
Graduate School of Natural Science and Technology, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920 1192, Japan
J Cell Biochem 94:804-15. 2005..We here characterize the regions of necdin required for the protein-protein interaction, nuclear matrix targeting, and cell growth suppression...
- Metabolic stabilization of p53 by FE65 in the nuclear matrix of osmotically stressed cellsTadashi Nakaya
Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
FEBS J 276:6364-74. 2009..Within the nucleus, FE65 formed a patched structure at the nuclear matrix, which facilitated the induction of gammaH2AX [Nakaya T, Kawai T & Suzuki T (2008) J Biol Chem283, 19119-..
- Nuclear matrix localization of high mobility group protein I(Y) in a transgenic mouse model for prostate cancerEddy S Leman
Department of Urology, University of Pittsburgh School of Medicine, Pennsylvania 15232, USA
J Cell Biochem 88:599-608. 2003Nuclear shape and the underlying nuclear structure, the nuclear matrix in cancer cells. Since the NM composition is considered to maintain nuclear shape and architecture, nuclear matrix proteins (NMPs) may be involved in transformation...
- Accumulation of LANA at nuclear matrix fraction is important for Kaposi's sarcoma-associated herpesvirus replication in latencyEriko Ohsaki
Department of Infectious Diseases, University of Hamamatsu School of Medicine, 1 20 1 Handayama, Higashi ku, Hamamatsu, Shizuoka 431 3192, Japan
Virus Res 139:74-84. 2009..the KSHV genome, and a viral replication factor, latency-associated nuclear antigen (LANA) accumulate at the nuclear matrix fraction in the G1 phase...
- Localization of prohibitin in the nuclear matrix and alteration of its expression during differentiation of human neuroblastoma SK-N-SH cells induced by retinoic acidQi fu Li
The Key Laboratory of Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Science, Xiamen University, China
Cell Mol Neurobiol 31:203-11. 2011The nuclear matrix-intermediate filament system of human neuroblastoma SK-N-SH cells before and after retinoic acid (RA) treatment was selectively extracted and the distribution of prohibitin (PHB) in the nuclear matrix, as well as its ..
- The sperm nucleus: chromatin, RNA, and the nuclear matrixGraham D Johnson
The Center for Molecular Medicine and Genetics, C S Mott Center, Wayne State University of Medicine, 275 East Hancock, Detroit, MI 48201, USA
Reproduction 141:21-36. 2011..These regions may be necessary for organizing higher order genomic structure through interactions with the nuclear matrix. The promoters of this transcriptionally quiescent genome are differentially marked by modified histones that ..
- Chronic cyclophosphamide exposure alters the profile of rat sperm nuclear matrix proteinsAlexis M Codrington
Department of Pharmacology, McGill University, Montreal, Quebec, Canada H3G 1Y6
Biol Reprod 77:303-11. 2007..Sperm DNA is organized by the nuclear matrix into loop-domains in a sequence-specific manner...
- The conserved domain CR2 of Epstein-Barr virus nuclear antigen leader protein is responsible not only for nuclear matrix association but also for nuclear localizationA Yokoyama
Department of Tumor Virology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, 1-5-45, Yushima, Bunkyo-ku, 113-8510, Japan
Virology 279:401-13. 2001There is a growing body of evidence for the importance of the nuclear matrix in various nuclear events including gene expression and DNA replication...
- Identification of proteins immunologically related to vertebrate lamins in the nuclear matrix of the myxomycete Physarum polycephalumS Lang
Department of Microbiology, University of Innsbruck Medical School, Austria
Eur J Cell Biol 61:177-83. 1993Lamin-like proteins have been identified as components of the nuclear matrix of the myxomycete Physarum polycephalum...
- Nuclear matrix association: switching to the invasive cytotrophoblastK J Drennan
Department of Obstetrics and Gynecology, Wayne State University, 253 C S Mott Center, 275 E Hancock St, Detroit, MI 48201, USA
Placenta 31:365-72. 2010..well characterized invasive and non-invasive behavior, and to correlate the activity of the transcriptome with nuclear matrix attachment and cell phenotype. Comparison of the invasive to non-invasive HTR transcriptomes was unremarkable...
- Cloning and characterization of a novel zinc finger protein that associates with nuclear matrixJ Y Lee
Division of Chemotherapy, Chiba Cancer Center Research Institute, Japan
DNA Cell Biol 17:849-58. 1998..of 75 kDa (p75), which was distinct from Vn, existed in the nuclear fraction, and, more specifically, in the nuclear matrix fraction, of NIH3T3 cells...
- Recruitment of RNA polymerase II in the Ifng gene promoter correlates with the nuclear matrix association in activated T helper cellsElvira R Eivazova
Vanderbilt University School of Medicine, Department of Medicine, Nashville, TN 37232, USA
J Mol Biol 371:317-22. 2007..However, the interaction of the Ifng gene promoter with the nuclear matrix occurred differentially in a lineage-specific manner...
- Natural ageing in the rat liver correlates with progressive stabilisation of DNA-nuclear matrix interactions and withdrawal of genes from the nuclear substructureApolinar Maya-Mendoza
, Facultad de Medicina, , Toluca, Edo
Mech Ageing Dev 126:767-82. 2005In the interphase nucleus, the DNA of higher eukaryotes is organised in supercoiled loops anchored to a nuclear matrix (NM). Replication, transcription and splicing seem to occur at macromolecular complexes organised upon the NM...
- Characterization of SAF-A, a novel nuclear DNA binding protein from HeLa cells with high affinity for nuclear matrix/scaffold attachment DNA elementsH Romig
Department of Biology, University of Konstanz, Germany
EMBO J 11:3431-40. 1992..SAF-A is an abundant nuclear protein and a constituent of the nuclear matrix and scaffold...
- Mapping of the nuclear matrix-bound chromatin hubs by a new M3C experimental procedureAlexey A Gavrilov
Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology of the Russian Academy of Sciences, 34 5 Vavilov Street, 119334 Moscow, Russia
Nucleic Acids Res 38:8051-60. 2010We have developed an experimental procedure to analyze the spatial proximity of nuclear matrix-bound DNA fragments...
- Cell cycle dependent regulation of protein kinase CK2 signaling to the nuclear matrixHuamin Wang
Cellular and Molecular Biochemistry Research Laboratory (151, Minneapolis Veterans Affairs Medical Center and Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota 55417, USA
J Cell Biochem 88:812-22. 2003..b>Nuclear matrix is a key locus for CK2 signaling in the nucleus...
- 1alpha,25-dihydroxy vitamin D(3) induces nuclear matrix association of the 1alpha,25-dihydroxy vitamin D(3) receptor in osteoblasts independently of its ability to bind DNAGloria Arriagada
Facultad de Ciencias Biologicas, Departamento de Bioquimica y Biologia Molecular, Universidad de Concepcion, Concepcion, Chile
J Cell Physiol 222:336-46. 2010..Here, we demonstrate that in osteoblastic cells, the VDR binds to the nuclear matrix in a vitamin D(3)-dependent manner...
- Nuclear envelope and nuclear matrix: interactions and dynamicsS Vlcek
Department of Biochemistry and Molecular Cell Biology, Vienna Biocenter, University of Vienna, Austria
Cell Mol Life Sci 58:1758-65. 2001..filaments that connect to nuclear pore complexes, are proposed to be major structural elements of the internal nuclear matrix. We describe the structural links between the peripheral lamina and the internal nuclear matrix that are ..
- The nuclear matrix and chromosomal DNA loops: is their any correlation between partitioning of the genome into loops and functional domains?S V Razin
Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology of the Russian Academy of Sciences, Moscow
Cell Mol Biol Lett 6:59-69. 2001..Although the DNA loops attached to the nuclear matrix (chromosomal scaffold) are frequently considered as independent functional domains, this supposition lack ..
- NeuN/Fox-3 is an intrinsic component of the neuronal nuclear matrixMyrna A R Dent
Facultad de Medicina, Universidad Autonoma del Estado de Mexico, Toluca, Mexico, Mexico
FEBS Lett 584:2767-71. 2010..Here we provide evidence that NeuN/Fox-3 is an intrinsic component of the neuronal nuclear matrix and a reliable marker of nuclear speckles in neurons.
- Human satellite 3 (HS3) binding protein from the nuclear matrix: isolation and binding propertiesO Podgornaya
Institute of Cytology, Russian Academy of Sciences, St Petersburg 164064, Russia
Biochim Biophys Acta 1497:204-14. 2000Satellite DNA (satDNA) is the main component of residual DNA in nuclear matrix (NM) preparations. Gel mobility shift assay (GMSA) revealed specific human satellite 3 (HS3) binding activity in NM extracts...
- Involvement of the nuclear matrix in the control of skeletal genes: the NMP1 (YY1), NMP2 (Cbfa1), and NMP4 (Nmp4/CIZ) transcription factorsJ P Bidwell
Department of Anatomy and Cell Biology, Indiana University School of Dentistry, Indianapolis 46202, USA
Crit Rev Eukaryot Gene Expr 11:279-97. 2001The functional role of the osteoblast nuclear matrix has been a matter of supposition...
- Distinct LIM domains of Hic-5/ARA55 are required for nuclear matrix targeting and glucocorticoid receptor binding and coactivationJennifer Guerrero-Santoro
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
J Cell Biochem 92:810-9. 2004..LIM4 also functions as a nuclear matrix targeting sequence (NMTS) for Hic-5/ARA55, as it is both necessary and sufficient to target a heterologous ..
- Cell-type-specific organization of nuclear DNA into structural looped domainsClaudia Trevilla-García
Facultad de Medicina, Universidad Autonoma del Estado de Mexico, Toluca, Mexico, Mexico
J Cell Biochem 112:531-40. 2011..metazoan cells the DNA is organized in supercoiled loops anchored to a proteinaceous substructure known as the nuclear matrix (NM)...
- Differential nuclear localization and nuclear matrix association of the splicing factors PSF and PTBM Meissner
Institute of Tumor Biology Cancer Research, University of Vienna, A 1090 Vienna, Austria
J Cell Biochem 76:559-66. 2000A monoclonal antibody raised against nuclear matrix proteins detected a protein of basic pI in human nuclear matrix protein samples of various cellular origin...
- DNA moves sequentially towards the nuclear matrix during DNA replication in vivoJuan Carlos Rivera-Mulia
Laboratorio de Biologia Molecular, Facultad de Medicina, Universidad Autonoma del Estado de Mexico, Apartado Postal 428, CP 50000 Toluca, Edo Mex, Mexico
BMC Cell Biol 12:3. 2011In the interphase nucleus of metazoan cells DNA is organized in supercoiled loops anchored to a nuclear matrix (NM)...
- Association of the nuclear matrix component NuMA with the Cajal body and nuclear speckle compartments during transitions in transcriptional activity in lens cell differentiationChris Gribbon
School of Life Sciences, MSIWTB, University of Dundee, UK
Eur J Cell Biol 81:557-66. 2002..These data suggest the nuclear matrix is important in the concentration of Cajal body and speckle components into large, distinct spots in ..
- Positional mapping of specific DNA sequences relative to the nuclear substructure by direct polymerase chain reaction on nuclear matrix-bound templatesApolinar Maya-Mendoza
, Facultad de Medicina, , Apartado Postal 428, C.P. 50000, Toluca, , Mexico
Anal Biochem 313:196-207. 2003..eukaryotes is organized in supercoiled loops anchored to a proteinaceous substructure commonly known as the nuclear matrix. Current evidence suggests that important processes of nuclear physiology, such as replication, transcription, ..
- Induction of transcription within chromosomal DNA loops flanked by MAR elements causes an association of loop DNA with the nuclear matrixOlga V Iarovaia
Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology RAS, Vavilov Street 34/5, 117984 Moscow, Russia
Nucleic Acids Res 33:4157-63. 2005..It is likely that the loop observed was attached to the nuclear matrix via MAR elements present at the flanks of the area under study...
- Association of topoisomerase II with the hepatoma cell nuclear matrix: the role of intermolecular disulfide bond formationS H Kaufmann
Department of Pharmacology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland 21205
Exp Cell Res 192:511-23. 1991..in conflicting data regarding the recovery of the nuclear enzymes topoisomerase (topo) II and topo I in the nuclear matrix fraction...
- RIF-1, a novel nuclear receptor corepressor that associates with the nuclear matrixHui Joyce Li
Molecular Cardiology Research Institute, New England Medical Center, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
J Cell Biochem 102:1021-35. 2007..RIF1 is localized exclusively in the cell nucleus and specifically to the nuclear matrix. Mutation of the nuclear localization signal abolishes this nuclear localization and causes RIF1 to appear in ..
- Human matrix attachment regions insulate transgene expression from chromosomal position effects in Drosophila melanogasterS J Namciu
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
Mol Cell Biol 18:2382-91. 1998..In contrast, expression of white transgenes containing human DNA segments without matrix-binding activity was highly variable in Drosophila transformants. These data indicate that human MARs can function as insulator elements in vivo...
- Dynamic view of the nuclear matrixKimiko M Tsutsui
Department of Neuroanatomy and Neurobiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Japan
Acta Med Okayama 59:113-20. 2005The nuclear matrix is an operationally defined nuclear skeletal structure that is believed to be involved in many nuclear functions including DNA replication, transcription, repair, and prem RNA processing/transport...
- Identification and characterization of a silkgland-related matrix association region in Bombyx moriC Z Zhou
Department of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, PR China
Gene 277:139-44. 2001From DNA fragments in vivo attached to the nuclear matrix in silkglands of Bombyx mori 5th instar larvae, we have screened a matrix association region (MAR), termed BmMAR1, by means of in vitro binding assay...
- Genomewide identification of nuclear matrix attachment regions: an analysis of methodsA K Linnemann
Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
Biochem Soc Trans 35:612-7. 2007..Nevertheless, several interesting trends were revealed. We expect that these technologies will prove useful in systems approaches directed towards defining the role of MARs in various cell types and cellular processes...
- Nuclear matrix localization and SUMO-1 modification of adenovirus type 5 E1b 55K protein are controlled by E4 Orf6 proteinKatherine J Lethbridge
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
J Gen Virol 84:259-68. 2003..Thus, this modification is favoured when 55K remains associated with the matrix but does not correlate with its stable association with ND10, many components of which are modified by SUMO-1...
- S/MARt DB: a database on scaffold/matrix attached regionsInes Liebich
Research Group Bioinformatics, GBF, Mascheroder Weg 1, D 38124 Braunschweig, Germany
Nucleic Acids Res 30:372-4. 2002..S/MAR transaction database, is a relational database covering scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are involved in the chromosomal attachment to the nuclear scaffold...
- Sequences of DNA fragments contacting the nuclear lamina in vivoR Christova
Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia
DNA Cell Biol 11:627-36. 1992....
- A proteomic study of the arabidopsis nuclear matrixTomasz T Calikowski
Department of Plant Biology and Plant Biotechnology Center, Ohio State University, Columbus, Ohio 43210, USA
J Cell Biochem 90:361-78. 2003..to be organized by two interdependent nucleoprotein structures, the DNA-based chromatin and the RNA-dependent nuclear matrix. The functional composition and molecular organization of the second component have not yet been resolved...
- The transcriptional enhancer of the pea plastocyanin gene associates with the nuclear matrix and regulates gene expression through histone acetylationYii Leng Chua
Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
Plant Cell 15:1468-79. 2003..The PetE enhancer bound to isolated tobacco nuclear matrices in vitro and was associated with the nuclear matrix in nuclei isolated from transgenic tobacco plants...
- Human OGG1 undergoes serine phosphorylation and associates with the nuclear matrix and mitotic chromatin in vivoFrancoise Dantzer
Department of Molecular Biology, Institute of Medical Microbiology, University of Oslo, Rikshospitalet, Sognsvannveien 20, NO 0027 Oslo, Norway
Nucleic Acids Res 30:2349-57. 2002..It is shown that hOGG1 is preferentially associated with chromatin and the nuclear matrix during interphase and becomes associated with the condensed chromatin during mitosis...
- Tissue-specific association of the human tyrosine hydroxylase gene with the nuclear matrixRobert Lenartowski
N Copernicus University, Institute of General and Molecular Biology, Laboratory of Genetics, Gagarina 9, 87 100 Torun, Poland
Neurosci Lett 330:151-4. 2002Association of the human tyrosine hydroxylase (TH) gene with the nuclear matrix was studied using bovine matrices from tissues differing in expression of the gene...
- CpG-binding protein is a nuclear matrix- and euchromatin-associated protein localized to nuclear speckles containing human trithorax. Identification of nuclear matrix targeting signalsJeong Heon Lee
Herman B Wells Center for Pediatric Research, Section of Pediatric Hematology Oncology, Department of Pediatrics and Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis 46202, USA
J Biol Chem 277:42259-67. 2002..CGBP associates with the nuclear matrix, and fragments of CGBP that fail to associate with the nuclear matrix fail to localize to nuclear speckles and ..
- Dynamics of replication foci and nuclear matrix during S phase in Allium cepa L. cellsRafael Samaniego
Nuclear Matrix Laboratory, , CSIC, , 28006 Madrid, Spain
Planta 215:195-204. 2002..organisation of replication foci during S phase in onion ( Allium cepa) and their relationship to the nuclear matrix were investigated...
- Small heat shock protein p26 associates with nuclear lamins and HSP70 in nuclei and nuclear matrix fractions from stressed cellsJulia K Willsie
Section of Molecular and Cellular Biology, Bodega Marine Laboratory, University of California (Davis, Bodega Bay CA 94923, USA
J Cell Biochem 84:601-14. 2002..Nuclear fractionation shows that the majority of nuclear p26 and a nuclear lamin are associated with the nuclear matrix fraction...
- Germ-line transcripts of the immunoglobulin lambda J-C clusters in the mouse: characterization of the initiation sites and regulatory elementsH Engel
Department of Cellbiology and Immunobiology, GBF, German Research Centre for Biotechnology, Mascheroder Weg 1, 38124, Braunschweig, Germany
Mol Immunol 38:289-302. 2001..This region between the lambda1/lambda3 clusters binds to the nuclear matrix in vitro, and J-C lambda1 germ-line transcription initiates a short distance downstream from this S/MAR element...
- Sp2 localizes to subnuclear foci associated with the nuclear matrixK Scott Moorefield
Graduate Program in Genomic Sciences, Center for Comparative Medicine and Translational Research, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA
Mol Biol Cell 17:1711-22. 2006..We report that 1) Sp2 localizes largely within subnuclear foci associated with the nuclear matrix, and 2) these foci are distinct from promyelocytic oncogenic domains and appear to be stable during an 18-h ..
- The role of insulator elements in defining domains of gene expressionP K Geyer
Department of Biochemistry, University of Iowa College of Medicine, Iowa City, Iowa, 52242, USA
Curr Opin Genet Dev 7:242-8. 1997..Additionally, they suggest that the mechanism of insulation is related to that of enhancer function. Two models of insulator can be considered: a domain boundary and a transcriptional decoy model...
- Specific radial positions of centromeres of human chromosomes X, 1, and 19 remain unchanged in chromatin-depleted nuclei of primary human fibroblasts: evidence for the organizing role of the nuclear matrixNatalia V Petrova
Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology RAS, Vavilov Street 34/5, 119334 Moscow, Russia
J Cell Biochem 96:850-7. 2005..These results strongly suggest that the characteristic organization of interphase chromosomes is supported by the proteinous nuclear matrix and is not maintained by simple repulsing of negatively charged chromosomes.
- Stable chromosomal units determine the spatial and temporal organization of DNA replicationNicolas Sadoni
University of Munich (LMU, Department Biology II, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany
J Cell Sci 117:5353-65. 2004..These findings imply that the specific nuclear substructure of chromosomes and the order of their stable subunits determine the spatiotemporal organization of DNA replication...
- Ataxin-1 with an expanded glutamine tract alters nuclear matrix-associated structuresP J Skinner
Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis 55455, USA
Nature 389:971-4. 1997..Colocalization studies show that mutant ataxin-1 causes a specific redistribution of the nuclear matrix-associated domain containing promyelocytic leukaemia protein...
- Combinatorial organization of the transcriptional regulatory machinery in biological control and cancerGary S Stein
Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, 55 Lake Ave North, Worcester, MA 01655, USA
Adv Enzyme Regul 45:136-54. 2005....
- Distinct patterns of MCM protein binding in nuclei of S phase and rereplicating SV40-infected monkey kidney cellsThomas D Friedrich
Albany Medical College, Center for Immunology and Microbial Diseases, Albany, New York 12208, USA
Cytometry A 68:10-8. 2005..0 was associated with rebinding of the minichromosome maintenance (MCM) hexamer, the putative replicative helicase, to chromatin...
- Runx2: a master organizer of gene transcription in developing and maturing osteoblastsTania M Schroeder
Graduate Program in Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
Birth Defects Res C Embryo Today 75:213-25. 2005..including transcription factors and cofactors, is posttranslationally modified, and associates with the nuclear matrix to integrate a variety of signals and organize crucial events during osteoblast development and maturation...
- Interaction of the nuclear matrix protein NAKAP with HypA and huntingtin: implications for nuclear toxicity in Huntington's disease pathogenesisJonathan A Sayer
Neurological Sciences Institute, Oregon Health and Science University, Beaverton, OR 97006, USA
Neuromolecular Med 7:297-310. 2005..In cultured cells, NAKAP and HypA localize within the nucleus and copurify with the nuclear matrix. Furthermore, NAKAP associates with HypA from human brain and copurifies with huntingtin protein in brain ..
- Using molecular tethering to analyze the role of nuclear compartmentalization in the regulation of mammalian gene activityK L Reddy
Department of Molecular Genetics and Cell Biology, The University of Chicago, Howard Hughes Medical Institute, GCIS W522, 929 E 57th Street, Chicago, IL 60637, USA
Methods 45:242-51. 2008..This approach can be generalized and extended to position genes or chromosomal domains within other nuclear compartments thereby greatly facilitating the analysis of nuclear structure and its impact on genome activity...
- At the nucleus of the problem: nuclear proteins and diseaseNadir M Maraldi
ITOI-CNR, Unit of Bologna, c/o IOR, Bologna, Italy
Adv Enzyme Regul 43:411-43. 2003
- Mitotic accumulations of PML protein contribute to the re-establishment of PML nuclear bodies in G1Graham Dellaire
Programme in Cell Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, M5G 1X8, Canada
J Cell Sci 119:1034-42. 2006..The recycling of PML protein from one cell cycle to the next via mitotic accumulations may represent a common mechanism for the partitioning of other nuclear bodies during mitosis...
- Sub-nuclear localization of Rad51 in response to DNA damageEmil Mladenov
Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
Genes Cells 11:513-24. 2006..The results showed association of Rad51, Rad54, BRCA1 and BRCA2, but not Rad51C, with the nuclear matrix fraction in response to double-strand breaks induction...
- Genetic analysis of human Orc2 reveals specific domains that are required in vivo for assembly and nuclear localization of the origin recognition complexIlian Radichev
NICHD, National Institutes of Health, Bethesda, Maryland 20892 2753, USA
J Biol Chem 281:23264-73. 2006..Because this suppression required only the ORC assembly and NLS domains, these domains appear to constitute the functional domain of Orc2...
- [Nuclear organization and expression of milk protein genes]Eric Chanat
Unité Génomique et Physiologie de la Lactation, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy en Josas Cedex, France
J Soc Biol 200:181-92. 2006..Our goal is to make some progress into the understanding of the molecular and cellular mechanisms involved in the formation of these milk products...
- Activation of the S phase DNA damage checkpoint by mitomycin CEmil Mladenov
Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
J Cell Physiol 211:468-76. 2007..cell cycle distribution, formation of gamma-H2AX, and Rad51 nuclear foci and association of Rad51 with the nuclear matrix after treatment of HeLa cells with the interstrand crosslinking agent mitomycin C (MMC) in the presence of the ..
- Functional TFIIH is required for UV-induced translocation of CSA to the nuclear matrixMasafumi Saijo
Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1 3, Suita, Osaka 565 0871, Japan
Mol Cell Biol 27:2538-47. 2007..We have found that CSA protein is translocated to the nuclear matrix after UV irradiation and colocalized with the hyperphosphorylated form of RNA polymerase II and that the ..
- Cell cycle-dependent association of Rad51 with the nuclear matrixEmil Mladenov
Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
DNA Cell Biol 26:36-43. 2007..foci did not appear until middle S phase, and this was accompanied by an increase in the chromatin- and nuclear matrix-bound Rad51 in the middle to late S phase...
- Organization of transcriptional regulatory machinery in osteoclast nuclei: compartmentalization of Runx1Laura H Saltman
Department of Cell Biology, University of Massachusetts Medical School, Worcester, 01655, USA
J Cell Physiol 204:871-80. 2005....
- The insulator binding protein CTCF associates with the nuclear matrixKatherine L Dunn
Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Manitoba R3E 0V9, Canada
Exp Cell Res 288:218-23. 2003..At the base of these loops, matrix-associated regions (MARs) of the DNA interact with nuclear matrix proteins...
- SUMO modification of a novel MAR-binding protein, SATB2, modulates immunoglobulin mu gene expressionGergana Dobreva
Gene Center and Institute of Biochemistry, University of Munich, Munich 81377, Germany
Genes Dev 17:3048-61. 2003b>Nuclear matrix attachment regions (MARs) are regulatory DNA sequences that are important for higher-order chromatin organization, long-range enhancer function, and extension of chromatin modifications...
- Nuclear microenvironments support assembly and organization of the transcriptional regulatory machinery for cell proliferation and differentiationGary S Stein
Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, 55 Lake Ave N, Worcester, Massachusetts 01655, USA
J Cell Biochem 91:287-302. 2004....
- Preclinical assay development of a novel Colon Cancer Marker (CCSA-4)JACK CLEMENS; Fiscal Year: 2007..Onconome, Inc. has licensed these novel nuclear matrix proteins and is developing products for the detection of these biomarkers for research and clinical use...
- ISOLATION OF THE FANCONI ANEMIA NUCLEAR PROTEIN COMPLEXGary Kupfer; Fiscal Year: 2003..Within the nucleus the data reveal that these proteins localize to the DNA and nuclear matrix-containing fractions and have an appearance that parallels that of other nuclear matrix proteins...
- INTRACELLULAR MECHANISMS OF GLUCOCORTICOID ACTIONDonald Defranco; Fiscal Year: 1999..In ATP-depleted cells, GRs remain localized within the nucleus and, in fact, are associated with the nuclear matrix. The restoration of cellular ATP levels leads to the release of matrix-bound GR in vivo...
- Anaplasma regulation of host granulocyte functionJohn Stephen Dumler; Fiscal Year: 2010..reprograms the global neutrophil transcriptome by altering the epigenome through AnkA"s action on nuclear matrix, chromatin, and transcriptional apparatus recruitment. We propose the following aims: 1...
- Repair of oxidative damage in mammalian genomesTapas K Hazra; Fiscal Year: 2010..mutations in NEIL2-deficient cells, are consistent with this hypothesis, hnRNP-U, an abundant multifunctional nuclear matrix protein, has also been shown to regulate transcription. NEIL2 carries out a beta-delta-reaction like E...
- Repair of oxidative damage in mammalian genomesTAPAS HAZRA; Fiscal Year: 2009..mutations in NEIL2-deficient cells, are consistent with this hypothesis, hnRNP-U, an abundant multifunctional nuclear matrix protein, has also been shown to regulate transcription. NEIL2 carries out a beta-delta-reaction like E...
- Repair of oxidative damage in mammalian genomesTAPAS HAZRA; Fiscal Year: 2007..mutations in NEIL2-deficient cells, are consistent with this hypothesis, hnRNP-U, an abundant multifunctional nuclear matrix protein, has also been shown to regulate transcription. NEIL2 carries out a beta-delta-reaction like E...
- KSHV-Ori-Lyt-Dependent DNA ReplicationYan Yuan; Fiscal Year: 2010..Two cellular proteins that may involve origin DNA unwinding and nuclear matrix attachment will be further studied because these two events are believed to be antecedent steps before ..
- Proteomic Characterization of IC BladderPradeep Tyagi; Fiscal Year: 2006..The nuclear matrix is the structural scaffolding of the cell nucleus and plays a central role in the regulation of important ..
- NUCLEAR MATRIX STRUCTURE AND DNA REPLICATIONRonald Berezney; Fiscal Year: 1993..Our laboratory has been studying the nuclear matrix and its role in DNA replication for over 15 years...
- NUCLEAR PROTEIN CONTENT AND HEAT INDUCED CELL KILLINGJoseph Roti Roti; Fiscal Year: 1999The objective of the proposed work is to test 2 hypotheses regarding proteins whose nuclear matrix (NM) association is modified by heat shock (i.e., HMNMP, hyperthermia modifiable NM proteins)...
- CHROMATIN-TELOMERE STRUCTURE AND AT GENOMIC SENSITIVITYTEJ PANDITA; Fiscal Year: 2005..We demonstrated that altered telomere nuclear matrix interactions and nucleosomal periodicity observed in cells derived from individuals with ataxia telangiectasia ..
- ER Co-Repressor Function of SAFB in Breast CancerAdrian Lee; Fiscal Year: 2006The scaffold attachment factor/nuclear matrix protein SAFB maps to a locus with extremely high loss of heterozygosity in human breast cancer...
- ER Co-Repressor Function of SAFB in Breast CancerSteffi Oesterreich; Fiscal Year: 2005The scaffold attachment factor/nuclear matrix protein SAFB maps to a locus with extremely high loss of heterozygosity in human breast cancer...
- NUCLEAR MATRIX STRUCTURE AND DNA REPLICATIONRonald Berezney; Fiscal Year: 1992..1) What are the cell cycle relationships of different replicational components associated with the nuclear matrix? Various properties of DNA polymerase alpha, DNA primase, diadenosine tetraphosphate (AP4A) binding sites, DNA ..