A new look at the nuclear matrix

Chromosoma

Volumn 109, Issue 4, 2000, Pages 219-225

  Hancock, Ronald ^a  

^a LAVAL UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BINDING PROTEIN; GREEN FLUORESCENT PROTEIN; RIBONUCLEOPROTEIN;

CELL COMPARTMENTALIZATION; CELL NUCLEUS MATRIX; CELL STRUCTURE; CHROMATIN; CHROMOSOME ANALYSIS; DNA REPLICATION; DNA TRANSCRIPTION; GENE ACTIVITY; HUMAN; MOLECULAR INTERACTION; PROTEIN BINDING; PROTEIN PROCESSING; REVIEW;

EID: 0033930577     PISSN: 00095915     EISSN: None     Source Type: Journal    
DOI: 10.1007/s004120000077     Document Type: Review

References (90)

1. Aebi U, Cohn J, Buhle L, Gerace L (1986) The nuclear lamina is a meshwork of intermediate-type filaments. Nature 323:569-564
2. Amankwah KS, De Boni U (1994) Ultrastructural localization of filamentous actin within neuronal interphase nuclei in situ. Exp Cell Res 210:315-325
3. Belgrader P, Dey R, Berezney R (1991a) Molecular cloning of matrin 3. J Biol Chem 266:9893-9899
4. Belgrader P, Siegel AJ, Berezney R (1991b) A comprehensive study on the isolation and characterization of the HeLa S3 nuclear matrix. J Cell Sci 98:281-291
5. Benham C, Kohwi-Shigematsu T, Bode J (1997) Stress-induced duplex DNA destabilization in scaffold/matrix attachment regions. J Mol Biol 274:181-196
6. Benyajati C, Worcel A (1976) Isolation, characterization, and structure of the folded interphase genome of Drosophila melanogaster. Cell 9:393-407
7. Berrios M, Osheroff N, Fisher PA (1985) In situ localization of DNA topoisomerase II, a major polypeptide component of the Drosophila nuclear matrix fraction. Proc Natl Acad Sci USA 82:4142-4146
8. Bickel S, Pirrotta V (1990) Self-association of the Drosophila zeste protein is responsible for transvection affects. EMBO J 9:2959-2967
9. Blagoi IuP, Sorokin VA, Valeev VA, Gladchenko GO (1978) Effect of divalent copper ions on heat denaturation of DNA. Mol Biol (Mosk) 12:795-805
10. Blasquez VC, Sperry AO, Cockerill PN, Garrard WT (1989) Protein:DNA interactions at chromosomal loop attachment sites. Genome 31:503-509
11. Borochov N, Ausio J, Eisenberg H (1984) Interaction and conformational changes of chromatin with divalent ions. Nucleic Acids Res 12:3089-3096
12. Boulikas T (1995) Chromatin domains and prediction of MAR sequences. Int Rev Cytol 162A:279-386
13. Bridger JM, Kill IR, O'Farrell M, Hutchison CJ (1993) Internal lamin structures within G1 nuclei of human dermal fibroblasts. J Cell Sci 104:297-306
14. Chaly N, Little JE, Brown DL (1985) Localization of nuclear antigens during preparation of nuclear matrices in situ. Can J Biochem Cell Biol 63:644-653
15. Chiu SM, Xue LY, Friedman LR, Oleinick NL (1993) Copper ion-mediated sensitization of nuclear matrix attachment sites to ionizing radiation. Biochemistry 32:6214-6219
16. Ciejek EM, Nordstrom JL, Tsai MJ, O'Malley BW (1982) Ribonucleic acid precursors are associated with the chick oviduct nuclear matrix. Biochemistry 21:4945-4953
17. Clark P, Eichhorn GL (1995) A simple probe for DNA accessibility in chromatin. J Inorg Biochem 59:765-772
18. Cremer T, Kurz A, Zirbel R, Dietzel S, Rinke B, Schrock E, Speicher MR, Mathieu U, Jauch A, Emmerich P, Scherthan H, Ried T, Cremer C, Lichter P ( 1993) Role of chromosome territories in the functional compartmentalization of the cell nucleus. Cold Spring Harb Symp Quant Biol 58:777-792
19. Delpire E, Duchene C, Goessens G, Gilles R (1985) Effects of osmotic shock on the ultrastructure of different tissues and cell types. Exp Cell Res 160:106-116
20. Dennig J, Beato M, Suske G (1996) An inhibitor domain in Sp3 regulates its glutamine-rich activation domains. EMBO J 15: 5659-5667
21. Drake FH, Zimmerman JP, McCabe FL, Bartus HF, Per SR, Sullivan DM, Ross WE, Mattern MR, Johnson RK, Crooke ST, Mirabelli CK (1987) Purification of topoisomerase II from amsacrine-resistant P388 leukemia cells. J Biol Chem 262: 16739-16747
22. Eggert H, Jack RS (1991) An ectopic copy of the Drosophila ftz-associated SAR neither reorganizes local chromatin structure nor hinders elution of a chromatin fragment from isolated nuclei. EMBO J 10:1237-1243
23. Evan GI, Hancock DC (1985) Studies on the interaction of the human c-myc protein with cell nuclei: p62c-myc as a member of a discrete subset of nuclear proteins. Cell 43:253-261
24. Fernandes DJ, Danks MK, Beck WT (1990) Decreased nuclear matrix DNA topoisomerase II in human leukemia cells resistant to VM-26 and m-AMSA. Biochemistry 29:4235-4241
25. Fey EG, Krochmalnic G, Penman S (1986) The nonchromatin substructures of the nucleus: the ribonucleoprotein (RNP)-containing and RNP-depleted matrices analyzed by sequential fractionation and resinless section electron microscopy. J Cell Biol 102:1654-1665
26. Fields AP, Kaufmann SH, Shaper JH (1986) Analysis of the internal nuclear matrix. Oligomers of a 38 kD nucleolar polypeptide stabilized by disulfide bonds. Exp Cell Res 164:139-153
27. Finch RA, Chan PK (1996) ATP depletion affects NPM translocation and exportation of rRNA from nuclei. Biochem Biophys Res Commun 222:553-558
28. Fisher PA, Berrios M, Blobel G (1982) Isolation and characterization of a proteinaceous subnuclear fraction composed of nuclear matrix, peripheral lamina, and nuclear pore complexes from embryos of Drosophila melanogaster. J Cell Biol 92: 674-686
29. Fricker M, Hollinshead M, White N, Vaux D (1997) Interphase nuclei of many mammalian cell types contain deep, dynamic, tubular membrane-bound invaginations of the nuclear envelope. J Cell Biol 136:531-544
30. Gallinaro H, Puvion E, Kister L, Jacob M (1983) Nuclear matrix and hnRNP share a common structural constituent associated with premessenger RNA. EMBO J 2:953-960
31. Georgiev GP, Chentsov YuS (1960) On the structure of cell nuclei: experimental electron microscopic inverstigation of isolated nuclei. Dokl Akad Nauk 132:199-202
32. Gromova II, Nielsen OF, Razin SV (1995) Long-range fragmentation of the eukaryotic genome by exogenous and endogenous nucleases proceeds in a specific fashion via preferential DNA cleavage at matrix attachment sites. J Biol Chem 270:18685-18690
33. Hainaut P, Rolley N, Davies M, Milner J (1995) Modulation by copper of p53 conformation and sequence-specific DNA binding. Oncogene 10:27-32
34. Hancock R, Hughes ME (1982) Organisation of DNA in the interphase nucleus. Biol Cell 44:201-212
35. Harless J, Hewitt RR (1987) Intranuclear localization of UV-induced DNA repair in human VA13 cells. Mutat Res 183: 177-184
36. He DC, Nickerson JA, Penman S (1990) Core filaments of the nuclear matrix. J Cell Biol 110:569-580
37. Hempel K, Strätling WH (1996) The chicken lysozyme gene 5′ MAR and the Drosophila histone SAR are electroelutable from encapsulated and digested nuclei. J Cell Sci 109:1459-1469
38. Herrera JE, Correia JJ, Jones AE, Olson MO (1996) Sedimentation analyses of the salt- and divalent metal ion-induced oligomerization of nucleolar protein B23. Biochemistry 35:26682673
39. Hozak P, Sasseville AM, Raymond Y, Cook PR (1995) Lamin proteins form an internal nucleoskeleton as well as a peripheral lamina in human cells. J Cell Sci 108:635-644
40. Huang S, Deerinck TJ, Ellisman MH, Spector DL (1994) In vivo analysis of the stability and transport of nuclear poly(A)+ RNA. J Cell Biol 126:877-899
41. Humphrey GW, Pigiet V (1987) Protein disulfide crosslinking stabilizes a polyoma large T antigen-host protein complex on the nuclear matrix. Exp Cell Res 171:122-136
42. Jackson DA, Yuan J, Cook PR (1988) A gentle method for preparing cyto- and nucleo-skeletons and associated chromatin. J Cell Sci 90:365-378
43. Jagatheesan G, Thanumalayan S, Muralikrishna B, Rangaraj N, Karande AA, Parnaik VK (1999) Colocalization of intranuclear lamin foci with RNA splicing factors. J Cell Sci 112: 4651-4661
44. Johansson HO, Brooks DE, Haynes CA (2000) Macromolecular crowding and its consequences. Int Rev Cytol 192:155-170
45. Kabakov AE, Gabai VL (1994) Stress-induced insolubilization of certain proteins in ascites tumor cells. Arch Biochem Biophys 309:247-253
46. Kaufmann SH, Shaper JH (1991) Association of topoisomerase II with the hepatoma cell nuclear matrix: the role of intermolecular disulfide bond formation. Exp Cell Res 192:511-523
47. Kaufmann SH, Okret S, Wikstrom AC, Gustafsson JA, Shaper JH (1986) Binding of the glucocorticoid receptor to the rat liver nuclear matrix. The role of disulfide bond formation. J Biol Chem 261:11962-11967
48. Kaufmann SH, Brunet G, Talbot B, Lamarr D, Dumas C, Shaper JH, Poirier G (1991) Association of poly(ADP-ribose) polymerase with the nuclear matrix: the role of intermolecular disulfide bond formation, RNA retention, and cell type. Exp Cell Res 192:524-535
49. Kenar KT, Garcia-Moreno B, Freire E (1995) A calorimetric characterization of the salt dependence of the stability of the GCN4 leucine zipper. Protein Sci 4:1934-1938
50. Kraiss S, Lorenz A, Montenarh M (1992) Protein-protein interactions in high molecular weight forms of the transformation-related phosphoprotein p53. Biochim Biophys Acta 1119:11-18
51. Kuzmina S, Buldyaeva T, Troitskaya L, Zbarsky I (1981) Characterization and fractionation of rat liver nuclear matrix. Eur J Cell Biol 25:225-232
52. Lee LL, Lee JC (1987) Thermal stability of proteins in the presence of poly(ethylene glycols). Biochemistry 26:7813-7819
53. Lehner CF, Eppenberger HM, Fakan S, Nigg EA (1986) Nuclear substructure antigens. Monoclonal antibodies against components of nuclear matrix preparations. Exp Cell Res 162:205-219
54. Lewis CD, Lebkowski JS, Daly AK, Laemmli UK (1984) Interphase nuclear matrix and metaphase scaffolding structures. J Cell Sci Suppl 1:103-122
55. Loh SN, Dethlefsen LA, Newton GL, Aguilera JA, Fahey RC (1990) Nuclear thiols: technical limitations on the determination of endogenous nuclear glutathione and the potential importance of sulfhydryl proteins. Radiat Res 121:98-106
56. Loktionova SA, Kabakov AE (1998) Protein phosphatase inhibitors and heat preconditioning prevent Hsp27 dephosphorylation, F-actin disruption and deterioration of morphology in ATP-depleted endothelial cells. FEBS Lett 433:294-300
57. Lothstein L, Arenstorf HP, Chung SY, Walker BW, Wooley JC, LeStourgeon WM (1985) General organization of protein in HeLa 40S nuclear ribonucleoprotein particles. J Cell Biol 100:1570-1581
58. Malcolm DB, Sommerville J (1977) The structure of nuclear ribonucleoprotein of amphibian oocytes. J Cell Sci 24:143-165
59. Martelli AM, Cocco L, Riederer BM, Neri LM (1996) The nuclear matrix: a critical appraisal. Histol Histopathol 11:1035-1048
60. Michels AA, Nguyen VT, Konings AW, Kampinga HH, Bensaude O (1995) Thermostability of a nuclear-targeted luciferase expressed in mammalian cells. Destabilizing influence of the intranuclear microenvironment. Eur J Biochem 234:382-389
61. Minton AP (1992) Confinement as a determinant of macromolecular structure and reactivity. Biophys J 63:1090-1100
62. Moir RD, Montag-Lowy M, Goldman RD (1994) Dynamic properties of nuclear lamins: lamin B is associated with sites of DNA replication. J Cell Biol 125:1201-1212
63. Moulder KL, Onodera O, Burke JR, Strittmutter WJ, Johnson EM (1999) Generation of neuronal intranuclear inclusions by polyglutamine-GFP: analysis of inclusion clearance and toxicity as a function of polyglutamine length. J Neurosci 19:705-715
64. Neri LM, Fackelmayer FO, Zweyer M, Kohwi-Shigematsu T, Martelli AM (1997) Subnuclear localization of S/MAR-binding proteins is differently affected by in vitro stabilization with heat or Cu2+. Chromosoma 106:81-93
65. Neri LM, Raymond Y, Giordano A, Borgatti P, Marchisio M, Capitani S, Martelli AM (1999) Spatial distribution of lamin A and B1 in the K562 cell nuclear matrix stabilized with metal ions. J Cell Biochem 75:36-45
66. Pederson T (1998) Thinking about a nuclear matrix. J Mol Biol 277:147-159
67. Perez MK, Paulson HL, Pittman RN (1999) Ataxin-3 with an altered conformation that exposes the polyglutamine domain is associated with the nuclear matrix. Hum Mol Genet 8:2377-2385
68. Peterson MG, Tanese N, Pugh BF, Tjian R (1990) Functional domains and upstream activation properties of cloned human TATA binding protein. Science 248:1625-1630
69. Politz JC, Tuft RA, Pederson T, Singer RH (1999) Movement of nuclear poly(A)RNA throughout the interchromatin space in living cells. Curr Biol 9:285-291
70. Razin SV (1997) The nuclear matrix and spatial organisation of chromosomal DNA domains. Springer, Berlin, Heidelberg, New York
71. Razin SV, Gromova II (1995) The channels model of nuclear matrix structure. Bioessays 17:443-449
72. Razin SV, Gromova II, Iarovaia OV (1995) Specificity and functional significance of DNA interaction with the nuclear matrix: new approaches to clarify the old questions. Int Rev Cytol 162B:405-448
73. Rivas G, Fernandez JA, Minton AP (1999) Direct observation of the self-association of dilute proteins in the presence of inert macromolecules at high concentration via tracer sedimentation equilibrium: theory, experiment, and biological significance. Biochemistry 38:9379-9388
74. Roberge M, Dahmus ME, Bradbury EM (1988) Chromosomal loop/nuclear matrix organization of transcriptionally active and inactive RNA polymerases in HeLa nuclei. J Mol Biol 201:545-555
75. Saredi A, Howard L, Compton DA (1997) Phosphorylation regulates the assembly of NuMA in a mammalian mitotic extract. J Cell Sci 110:1287-1297
76. Schafer-Nielsen C, Rose C (1982) Separation of nucleic acids and chromatin proteins by hydrophobic interaction chromatography. Biochim Biophys Acta 696:323-331
77. Scovassi AI, Stivala LA, Rossi L, Bianchi L, Prosperi E (1997) Nuclear association of cyclin D1 in human fibroblasts: tight binding to nuclear structures and modulation by protein kinase inhibitors. Exp Cell Res 237:127-134
78. Singh OP, Bjorkroth B, Masich S, Wieslander L, Daneholt B (1999) The intranuclear movement of Balbiani ring premessenger ribonucleoprotein particles. Exp Cell Res 251:135-146
79. Skaer RJ, Whytock S, Emmines JP (1976) Intranuclear electrophoresis of the chromatin of living cells. J Cell Sci 21:479-496
80. Skinner PJ, Koshy BT, Cummings CJ, Klement IA, Helin K, Servadio A, Zoghbi HY, Orr HT (1997) Ataxin-1 with an expanded glutamine tract alters nuclear matrix-associated structures. Nature 389:971-974
81. Soboll S, Grundel S, Harris J, Kolb-Bachofen V, Ketterer B, Sies H (1995) The content of glutathione and glutathione S-transferases and the glutathione peroxidase activity in rat liver nuclei determined by a non-aqueous technique of cell fractionation. Biochem J 311:889-894
82. Stuurman N, Floore A, Colen A, de Jong L, van Driel R (1992) Stabilization of the nuclear matrix by disulfide bridges: identification of matrix polypeptides that form disulfides. Exp Cell Res 200:285-294
83. Tang Y, DeFranco DB (1996) ATP-dependent release of glucocorticoid receptors from the nuclear matrix. Mol Cell Biol 16: 1989-2001
84. Templeton DJ (1992) Nuclear binding of purified retinoblastoma gene product is determined by cell cycle-regulated phosphorylation. Mol Cell Biol 12:435-443
85. Valkov NI, Ivanova MI, Uscheva AA, Krachmarov CP (1989) Association of actin with DNA and nuclear matrix from Guerin ascites tumour cells. Mol Cell Biochem 87:47-56
86. Xing Y, Johnson CV, Dobner PR, Lawrence JB (1993) Higher level organization of individual gene transcription and RNA splicing. Science 259:1326-1330
87. Zachar Z, Kramer J, Mims IP, Bingham PM (1993) Evidence for channeled diffusion of pre-mRNAs during nuclear RNA transport in metazoans. J Cell Biol 121:729-742
88. Zeng C, He D, Brinkley BR (1994) Localization of NuMA protein isoforms in the nuclear matrix of mammalian cells. Cell Motil Cytoskeleton 29:167-76
89. Zini N, Martelli AM, Sabatelli P, Santi S, Negri C, Astaldi Ricotti GC, Maraldi NM (1992) The 180-kDa isoform of topoisomerase II is localized in the nucleolus and belongs to the structural elements of the nucleolar remnant. Exp Cell Res 200: 460-466
90. Zini N, Santi S, Ognibene A, Bavelloni A, Neri LM, Valmori A, Mariani E, Negri C (1994) Discrete localization of different DNA topoisomerases in HeLa and K562 cell nuclei and subnuclear fractions. Exp Cell Res 210:336-348