Natural ageing in the rat liver correlates with progressive stabilisation of DNA-nuclear matrix interactions and withdrawal of genes from the nuclear substructure

Mechanisms of Ageing and Development

Volumn 126, Issue 6-7, 2005, Pages 767-782

  Maya Mendoza, Apolinar ^a,b,d   Hernández Muñoz, Rolando ^c   Gariglio, Patricio ^b   Aranda Anzaldo, Armando ^a  

^a UNIVERSIDAD AUTÓNOMA DEL ESTADO DE MÉXICO   (Mexico)

^b DEPARTAMENTO DE FÍSICA   (Mexico)

^c INSTITUTO DE FISIOLOGÍA CELULAR   (Mexico)

^d UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Cell differentiation; Cell proliferation; Cellular senescence; DNA loops; Mammalian liver

Indexed keywords

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CELL AGING; CELL DIFFERENTIATION; CELL NUCLEUS MATRIX; CELL PROLIFERATION; CONTROLLED STUDY; LIVER CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RAT; SENESCENCE;

AGING; ANIMALS; CELL AGING; CELL DIFFERENTIATION; DNA, SUPERHELICAL; HEPATOCYTES; LIVER; MACROMOLECULAR SUBSTANCES; MALE; NUCLEAR MATRIX; RATS; RATS, WISTAR;

EUKARYOTA; MAMMALIA;

EID: 18844378332     PISSN: 00476374     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mad.2005.01.011     Document Type: Article

References (80)

1. J.R. Abney, B. Cutler, M.L. Fillbach, D. Axelrod, and B.A. Scalettar Chromatin dynamics in interphase nuclei and its implications for nuclear structure J. Cell Biol. 137 1997 1459 1468
2. A. Aranda-Anzaldo On the role of chromatin higher-order structure and mechanical interactions in the regulation of gene expression Speculations Sci. Technol. 12 1989 163 176
3. A. Aranda-Anzaldo Altered chromatin higher-order structure in cells infected by herpes simplex virus type 1 Arch. Virol. 124 1992 245 253
4. A. Aranda-Anzaldo Early induction of DNA single-stranded breaks in cells infected by herpes simplex virus type 1 Arch. Virol. 122 1992 317 330
5. A. Aranda-Anzaldo, and M.A.R. Dent Loss of DNA-loop supercoiling and organization in cells infected by herpes simplex virus type 1 Res. Virol. 148 1997 397 408
6. A. Aranda-Anzaldo The normal association between newly-replicated DNA and the nuclear matrix is abolished in cells infected by herpes simplex virus type 1 Res. Virol. 149 1998 195 208
7. A. Aranda-Anzaldo, F. Orozco-Velasco, E. García-Villa, and P. Gariglio p53 is a rate-limiting factor in the repair of higher-order DNA structure Biochem. Biophys. Acta 1446 1999 181 192
8. P. Barboro, C. D'Arrigo, M. Mormino, R. Coradeghini, S. Parodi, E. Patrone, and C. Balbi An intranuclear frame for chromatin compartamentalization and higher-order folding J. Cell Biochem. 88 2003 113 120
9. F. Becker The Liver 1974 Marcel Dekker Inc. USA p. 152
10. R. Berezney, and D.S. Coffey Isolation and characterization of a framework structure from rat liver nuclei J. Cell Biol. 73 1977 616 637
11. R. Berezney, and L.A. Buchholtz Dynamic association of replicating DNA fragments with the nuclear matrix of regenerating liver Exp. Cell Res. 132 1981 1 13
12. R. Berezney Dynamic properties of the nuclear matrix H. Busch The Cell Nucleus 1979 Academic Press Orlando 413 456
13. J. Bode, Y. Kohwi, L. Dickinson, R.T. Joh, D. Klehr, C. Mielke, and T. Kohwi-Shigematsu Biological significance of unwinding capability of nuclear matrix-associating DNAs Science 255 1992 195 197
14. T. Boulikas Chromatin domains and prediction of MAR sequences Int. Rev. Cytol. 162A 1995 279 387
15. J.M. Bridger, S. Boyle, I.R. Kill, and W.A. Bickmore Re-modelling of nuclear architecture in quiescent and senescent human fibroblasts Curr. Biol. 10 2000 149 152
16. M. Buongiorno-Nardelli, G. Micheli, M.T. Carri, and M.A. Marilley A relationship between replicon size and supercoiled loop domains in the eukaryotic genome Nature 298 1982 100 102
17. J. Campisi From cells to organism: can we learn about aging from cells in culture? Exp. Gerontol. 36 2001 607 618
18. E.M. Ciejek, M.-J. Tsai, and B.W. O'Malley Actively transcribed genes are associated with the nuclear matrix Nature 306 1983 607 609
19. P.R. Cook, I. Brazell, and E. Jost Characterization of nuclear structures containing superhelical DNA J. Cell Sci. 22 1976 303 324
20. P.R. Cook, and I.A. Brazell Mapping sequences in loops of nuclear DNA by their progressive detachment from the nuclear cage Nucleic Acids Res. 8 1980 2895 2905
21. P.R. Cook, J. Lang, A. Hayday, L. Lania, M. Fried, D.J. Chiswell, and J. Wyke Active viral genes in transformed cells lie close to the nuclear cage EMBO J. 1 1982 447 452
22. P.R. Cook The nucleoskeleton and the topology of DNA replication Cell 66 1991 627 635
23. P.R. Cook The organization of replication and transcription Science 284 1999 1790 1795
24. T. Cremer, and C. Cremer Chromosome territories, nuclear architecture and gene regulation in mammalian cells Nat. Rev. Genet. 2 2001 292 300
25. J.A. Croft, J.M. Bridger, P. Perry, S. Boyle, P. Teague, and W.A. Bickmore Differences in the localization and morphology of chromosomes in the human nucleus J. Cell Biol. 145 1999 1119 1131
26. V.M. Factor, M.R. Jensen, and S.S. Thorgeirsson Coexpression of c-myc and transforming growth factor alpha in the liver promotes early replicative senescence and diminishes regenerative capacity after partial hepatectomy in transgenic mice Hepatology 26 1997 1434 1443
27. N. Fausto Hepatocytes break the rules of senescence in serial transplantation studies. Is there a limit to their replicative capacity? Am. J. Pathol. 151 1997 1187 1189
28. N. Fausto Liver regeneration J. Hepatol. 32 Suppl. 1 2000 19 31
29. M. Fontoulakis, M.-C. de Vera, F. Crameri, F. Boess, R. Gasser, S. Albertini, and L. Suter Modulation of gene and protein expression by carbon tetrachloride in the rat liver Toxicol. Appl. Pharm. 183 2002 71 80
30. A. Gandillet, E. Alexandre, V. Holl, C. Royer, P. Bischoff, J. Cinqualbre, P. Wolf, D. Jaeck, and L. Richert Hepatocyte ploidy in normal young rat Comp. Biochem. Physiol. A134 2003 665 673
31. K.S. Hatton, V. Dhar, E.H. Brown, M.A. Iqbal, S. Stuart, V.T. Didamo, and C.L. Schildkraut Replication program of active and inactive multigene families in mammalian cells Mol. Cell Biol. 8 1988 2149 2158
32. H.H.Q. Heng, S. Goetze, J.C. Ye, G. Liu, J.B. Stevens, S.W. Bremer, S.M. Wykes, J. Bode, and S.A. Krawetz Chromatin loops are selectively anchored using scaffold/matrix-attachment regions J. Cell Sci. 117 2004 999 1008
33. P. Hozák, A. Bassim-Hassan, D.A. Jackson, and P.R. Cook Visualization of replication factories attached to a nucleoskeleton Cell 73 1993 361 373
34. P. Hozák, A.M. Sasseville, Y. Raymond, and P.R. Cook Lamin proteins form an internal nucleoskeleton as well as a peripheral lamina in human cells J. Cell Sci. 108 1995 635 644
35. O.V. Iarovaia, A. Bystritsky, D. Ravcheev, R. Hancock, and S.V. Razin Visualization of individual loops and a map of loop domains in the human dystrophin gene Nucleic Acids Res. 32 2004 2079 2086
36. S. Ivanović-Matić, S. Dinić, M. Vujoš ević, and G. Poznanović The protein composition of the hepatocyte nuclear matrix is differentiation-stage specific IUBMB Life 49 2000 511 517
37. E.M. Jack, P. Bentley, F. Bieri, S.F. Muakkassah-Kelly, W. Staubli, J. Suter, F. Waechter, and L.M. Cruz-Orive Increase in hepatocyte and nuclear volume and decrease in the population of binucleated cells in preneoplastic foci of rat liver: a stereological study using the nucleator method Hepatology 11 1990 286 297
38. D.A. Jackson, P. Dickinson, and P.R. Cook The size of chromatin loops in HeLa cells EMBO J. 9 1990 567 571
39. D.A. Jackson, and P.R. Cook The structural basis of nuclear function Int. Rev. Cytol. 162B 1995 125 149
40. B.J. Jennings, S.E. Ozanne, M.W. Dorling, and C.N. Hales Early growth determines longevity in male rats and may be related to telomere shortening in the kidney FEBS Lett. 448 1999 4 8
41. B. Lewin Gene Expression 2 second ed. 1980 John Wiley and Sons New York pp. 360-362
42. F. Li, J. Chen, M. Izumi, M.C. Butler, S.M. Keezer, and D.M. Gilbert The replication timing program of the Chinese hamster beta-globin locus is established coincident with its repositioning near peripheral heterochromatin in early G1 phase J. Cell Biol. 154 2001 283 292
43. Martínez-Ramos, I., Maya-Mendoza, A., Gariglio, P., Aranda-Anzaldo, A. A global but stable change in HeLa cell morphology induces reorganization of DNA structural loop domains within the cell nucleus. J. Cell Biochem., in press.
44. W.F. Marshall, A. Straight, J.F. Marko, J. Swedlow, A. Dernburg, A. Belmont, A.W. Murray, D.A. Agard, and J.W. Sedat Interphase chromosomes undergo constrained diffusional motion in living cells Curr. Biol. 7 1997 930 939
45. M.R. Mattern The relation of three-dimensional DNA structure to DNA repair as studied by nucleoid sedimentation. A.S. Collins C.S. Downes R.T. Johnson DNA Repair and its Inhibition 1984 IRL Press Oxford 13 34
46. A. Maya-Mendoza, and A. Aranda-Anzaldo Positional mapping of specific DNA sequences relative to the nuclear substructure by direct polymerase chain reaction on nuclear matrix-bound templates Anal. Biochem. 313 2003 196 207
47. A. Maya-Mendoza, R. Hernández-Muñoz, P. Gariglio, and A. Aranda-Anzaldo Gene positional changes relative to the nuclear substructure correlate with the proliferating status of hepatocytes during liver regeneration Nucleic Acids Res. 31 2003 6168 6179
48. A. Maya-Mendoza, R. Hernández-Muñoz, P. Gariglio, and A. Aranda-Anzaldo Gene positional changes relative to the nuclear substructure during carbon tetrachloride-induced hepatic fibrosis in rats J. Cell Biochem. 93 2004 1084 1098
49. G.K. Michalopoulos, and M.C. DeFrances Liver Regen. Sci. 276 1997 60 66
50. T. Misteli Cell Biology of transcription and pre-mRNA splicing: nuclear architecture meets nuclear function J. Cell Sci. 113 2000 1841 1849
51. J.A. Nickerson Experimental observations of a nuclear matrix J. Cell Sci. 114 2001 463 474
52. R.T. O'Keefe, S.C. Henderson, and D.L. Spector Dynamic organization of DNA replication in mammalian cell nuclei; spatially and temporally defined replication of chromosome-specific alpha-satellite DNA sequences J. Cell Biol. 116 1992 1095 1110
53. K. Overturf, M. Al-Dhalimy, M. Finegold, and M. Grompe The repopulation potential of hepatocyte populations differing in size and prior mitotic expansion Am. J. Pathol. 155 1997 2135 2143
54. 4-induced hepatic fibrosis Hepatology 8 1988 259 266
55. L.A. Parada, and T. Misteli Chromosome positioning in the interphase nucleus Trends Cell Biol. 12 2002 425 432
56. K.J. Pienta, and D.S. Coffey A structural analysis of the role of the nuclear matrix and DNA loops in the organization of the nucleus and chromosome J. Cell Sci. Suppl. 1 1984 123 135
57. K.J. Pienta, R.H. Getzenberg, and D.S. Coffey Characterization of nuclear morphology and nuclear matrices in ageing human fibroblasts Mech. Ageing Dev. 62 1992 13 24
58. C.V. Ramana-Murty, M.A. Mancini, B. Chatterjee, and A.K. Roy Changes in transcriptional activity and matrix association of the α2μ-globulin gene family in the rat liver during maturation and aging Biochem. Biophys. Acta 949 1988 27 34
59. Rat Genome Sequencing Project Consortium Genome sequence of the Brown Norway rat yields insights into mammalian evolution Nature 428 2004 493 521
60. S.V. Razin, I.I. Gromova, and O.V. Iarovaia Specificity and functional significance of DNA interaction with the nuclear matrix: new approaches to clarify the old questions Int. Rev. Cytol. 162B 1995 405 448
61. S.V. Razin The nuclear matrix and chromosomal DNA loops: is there any correlation between partitioning of the genome into loops and functional domains? Cell Mol. Biol. Lett. 6 2001 59 69
62. S.I. Robinson, B.D. Nelkin, and B. Vogelstein The ovalbumin gene is associated with the nuclear matrix of chicken oviduct cells Cell 28 1982 99 106
63. J.L. Roti-Roti, W.D. Wright, and Y.C. Taylor DNA loop structure and radiation response Adv. Radiat. Biol. 17 1993 227 259
64. N. Sanz, C. Díez-Fernández, A. Alvarez, and M. Cascales Age-dependent modifications in rat hepatocyte antioxidant defense systems J. Hepatol. 27 1997 525 534
65. P.T. Saunders An Introduction to Catastrophe Theory 1995 Cambridge University Press Cambridge, UK p. 17
66. S.M. Sigal, S. Gupta, D.F. Gebhard Jr., P. Holst, D. Neufeld, and L.M. Reid Evidence for a terminal differentiation process in the rat liver Differentiation 59 1995 35 42
67. S.H. Sigal, P. Rajvanshi, G.R. Gorla, R.P. Sokhi, R. Saxena, D.R. Gebhard Jr., L.M. Reid, and S. Gupta Partial hepatectomy-induced polyploidy attenuates hepatocyte replication and activates cell aging events Am. J. Physiol. 276 1999 G1260 G1272
68. D.S. Small, B. Nelkin, and B. Vogelstein The association of transcribed genes with the nuclear matrix of Drosophila cells during heat shock Nucleic Acids Res. 7 1985 2413 2431
69. D.S. Small, and B. Vogelstein Anatomy of supercoiled loops in the Drosophila 7F locus Nucleic Acids Res. 13 1985 7703 7713
70. C.A. Smith, and E.J. Wood Cell Biology 1992 Chapman and Hall London p. 81
71. G.S. Stein, A.J. van Wijnen, J. Stein, J.B. Lian, and M. Montecino Contributions of nuclear architecture to transcriptional control Int. Rev. Cytol. 162A 1995 251 278
72. R. Thom Structural stability and morphogenesis: an outline of a general theory of models 1989 Addison-Wesley Reading, MA p. 14
73. I. Thomson, S. Gilchrist, W.A. Bickmore, and J.R. Chubb The radial positioning of chromatin is not inherited through mitosis but is established de novo in early G1 Curr. Biol. 14 2004 166 172
74. J. Vijg, and M.E.T. Dollé Large genome rearrangements as a primary cause of aging Mech. Ageing Dev. 123 2002 907 915
75. A.E. Visser, and J.A. Aten Chromosomes as well as chromosomal subdomains constitute distinct units in interphase nuclei J. Cell Sci. 112 1999 3353 3360
76. J. Walter, L. Schermelleh, M. Cremer, S. Tashiro, and T. Cremer Chromosome order in HeLA cells changes during mitosis and early G1, but is stably maintained during subsequent interphase stages J. Cell Biol. 160 2003 685 697
77. X. Wei, J. Samarabandu, R.S. Devdhar, A.J. Siegel, R. Acharya, and R. Berezney Segregation of transcription and replication sites into higher order domains Science 281 1998 1502 1505
78. L.L. Whyte The Unitary Principle in Physics and Biology 1949 The Cresset Press London pp. 17-21
79. H.K. Wolf, and G.K. Michalopoulos Hepatocyte regeneration in acute fulminant and non-fulminant hepatitis: a study of proliferating cell nuclear antigen expression Hepatology 15 1992 707 713
80. K. Woodfine, H. Fiegler, D.M. Beare, J.E. Collins, O.T. McCann, B.D. Young, S. Debernardi, R. Mott, I. Dunham, and N.P. Carter Replication timing of the human genome Hum. Mol. Genet. 13 2004 191 202