Epigenetic regulation of the mammalian cell

PLoS ONE

Volumn 3, Issue 6, 2008, Pages

  Baverstock, Keith ^a   Rönkkö, Mauno ^a  

^a UNIVERSITY OF EASTERN FINLAND   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; GENOMIC DNA; MICRORNA;

ARTICLE; CARCINOGENESIS; CONTROLLED STUDY; DNA DEGRADATION; EPIGENETICS; GENE CONTROL; GENETIC CONSERVATION; GENETIC VARIABILITY; GENOMIC INSTABILITY; HUMAN; HUMAN CELL; LOGIC; MAMMAL CELL; MICROENVIRONMENT; MOLECULAR BIOLOGY; PHENOTYPE; PREDICTION; PROTEOMICS; ANIMAL; GENETIC EPIGENESIS; GENETICS; MAMMAL;

MAMMALIA;

ANIMALS; EPIGENESIS, GENETIC; MAMMALS;

EID: 48449102277     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0002290     Document Type: Article

References (63)

1. Nanney DL (1958) Epigenetic Control Systems. Proc Natl Acad Sci USA 44: 712-717.
2. Delbruck M (1919) translation of discussion following a paper by Sonneborn, T. M. and Beale, G.H. Unites Biologiques Douees de Continute Genetique: 33-35.
3. Schrödinger E (1944) What is life? Cambridge: Cambridge University Press.
4. Weinhold B (2006) Epigenetics: the science of change. Environ Health Perspect 114: a160-167.
5. Jacnisch R, Bird A (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33 Suppl: 245-254.
6. Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16: 6-21.
7. Bird A (2007) Perceptions of epigenetics. Nature 447: 396-398.
8. O'Malley MA, Dupre J (2005) Fundamental issues in systems biology. Bioessays 27: 1270-1276.
9. Bertalanffy L von (1950) An outline of general systems theory. British Journal for the Philosophy of Science 1: 134-165.
10. Huang S (2004) Back to the biology in systems biology: what can we learn from biomolecular networks? Brief Funct Genomic Proteomic 2: 279-297.
11. Felsenfeld G (1992) Chromatin as an essential part of the transcriptional mechanism. Nature 355: 219-224.
12. Greener T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2: 292-301.
13. Cremer M, von Hasc J, Volm T, Brero A, Kreth G, et al. (2001) Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. Chromosome Res 9: 541-567.
14. Bolzer A, Kreth G, Solovci I, Koehler D, Saracoglu K, et al. (2005) Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol 3: c157.
15. Fraser P, Bickmore W (2007) Nuclear organization of the genome and the potential for gene regulation. Nature 147: 413-417.
16. Kosak ST, Scalzo D, Alworth SV, Li F, Palmer S, et al. (2007) Coordinate gene regulation during hematopoiesis is related to genomic organization. PLoS Biol 5: c309.
17. Kadhim MA, Macdonald DA, Goodhead DT, Lorimore SA, Marsden SJ, et al. (1992) Transmission of chromosomal instability after plutonium alpha-particle irradiation. Nature 355: 738-740.
18. Baverstock KF (1991) DNA instability, paternal irradiation and leukaemia in children around Sellafield. Int J Radiat Biol 60: 581-595.
19. Baverstock K (2000) Radiation-induced genomic instability: a paradigm-breaking phenomenon and its relevance to environmentally induced cancer. Mutat Res 454: 89-109.
20. Huang S, Eichler G, Bar-Yam Y, Ingber DE (2005) Cell fates as high-dimensional attractor states of a complex gene regulatory network. Phys Rev Lett 94: 128701.
21. Chang HH, Oh PY, Ingber DE, Huang S (2006) Multistable and multistep dynamics in neutrophil differentiation. BMC Cell Biol 7: 11.
22. Morgan WF (2003) Non-targeted and delayed effects of exposure to ionizing radiation: I. Radiation-induced genomic instability and bystander effects in vitro. Radiat Res 159: 567-580.
23. Morgan WF (2003) Non-targeted and delayed effects of exposure to ionizing radiation: II. Radiation-induced genomic instability and bystander effects in vivo, clastogenic factors and transgenerational effects. Radiat Res 159: 581-596.
24. McFall-Ngai MJ (2002) Unseen forces: the influence of bacteria on animal development. Dev Biol 242: 1-14.
25. Rosen R (1991) Life Itself: a Comprehensive Inquiry into the Nature, Origin and Fabrication of Life. Allen THF, Roberts DW, eds. New York: Columbia University Press.
26. Rosen R (2000) Essays of Life Itself; Timothy EH, Roberts A, Roberts DW, eds. New York: Columbia University Press.
27. Kauffman SA (1993) The Origins of Order: Self Organisation and Selection in Evolution. Oxford: Oxford University Press.
28. Aldana M, Cluzel P (2003) A natural class of robust networks. Proc Natl Acad Sci USA 100: 8710-8714.
29. Aldana M, Balleza E, Kauffman S, Resendiz O (2007) Robustness and evolvability in genetic regulatory networks. J Theor Biol 245: 433-448.
30. Kashiwagi A, Urabe I, Kaneko K, Yomo T (2006) Adaptive response of a gene network to environmental changes by fitness-induced attractor selection. PLoS ONE 1: c49.
31. Davidich MI, Bornholdt S (2008) Boolean network model predicts cell cycle sequence of fission yeast. PLoS ONE 3: e1672.
32. Li F, Long T, Lu Y, Ouyang Q, Tang C (2004) The yeast cell-cycle network is robustly designed. Proc Natl Acad Sci USA 101: 4781-4786.
33. Falt S, Holmberg K, Lambert B, Wennberg A (2003) Long-term global gene expression patterns in irradiated human lymphocytes. Carcinogenesis 24: 1823-1845.
34. Shiloh Y (2003) ATM and related protein kinases: safeguarding genome integrity. Nat Rev Cancer 3: 155-168.
35. Zhou BB, Elledge SJ (2000) The DNA damage response: putting checkpoints in perspective. Nature 408: 433-439.
36. Rogakou EP, Boon C, Redon C, Bonner WM (1999) Megabase chromatin domains involved in DNA double-strand breaks in vivo. J Cell Biol 146: 905-916.
37. Watson A, Mata J, Bahler J, Carr A, Humphrey T (2004) Global gene expression responses of fission yeast to ionizing radiation. Mol Biol Cell 15: 851-860.
38. Krawetz SA (2005) Paternal contribution: new insights and future challenges. Nat Rev Genet 6: 633-642.
39. Rousseaux S, Caron C, Govin J, Lestrat C, Faure AK, et al. (2005) Establishment of male-specific epigenetic information. Gene 345: 139-153.
40. Miller D, Ostermeier GC, Krawetz SA (2005) The controversy, potential and roles of spermatozoal RNA. Trends Mol Med 11: 156-163.
41. Wykes SM, Krawetz SA (2003) The structural organization of sperm chromatin. J Biol Chem 278: 29471-29477.
42. Barber RC, Dubrova YE (2006) The offspring of irradiated parents, are they stable? Mutat Res 598: 50-60.
43. Bouffler SD, Bridges BA, Cooper DN, Dubrova Y, McMillan TJ, et al. (2006) Assessing radiation-associated mutational risk to the germline: repetitive DNA sequences as mutational targets and biomarkers. Radiat Res 165: 249-268.
44. Chen JW, Romero P, Uversky VN, Dunker AK (2006) Conservation of intrinsic disorder in protein domains and families: II. functions of conserved disorder. J Proteome Res 5: 888-898.
45. Romero P, Obradovic Z, Dunker AK (2004) Natively disordered proteins: functions and predictions. Appl Bioinformatics 3: 105-113.
46. Stgase K, Dyson HJ, Wright PE (2007) Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447: 1021-1025.
47. Back R, Wright von J (1998) Refinement Calculus: A Systematic Introduction. New York: Springer-Verlag.
48. Tarski AA (1955) Lattice-Theoretical Fixed-point Theorem and Its Applications. Pacific J Math 5: 285-309.
49. Kitano H (2002) Computational systems biology. Nature 420: 206-210.
50. Krishnan A, Giuliani A, Tomita M (2007) Indeterminacy of reverse engineering of Gene Regulatory Networks: the curse of gene elasticity. PLoS ONE 2: e562.
51. Gould SJ (2002) The Structure of Evolutionary Theory. Cambridge Mass.: Harvard University Press. 1433 p.
52. Mayr E (2002) What Evolution Is. London: Weidenfeld and Nicholson. 318 p.
53. Gould SJ, Eldredge N (1993) Punctuated equilibrium comes of age. Nature 366: 223-227.
54. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
55. Li WH, Saunders MA (2005) News and views: the chimpanzee and us. Nature 437: 50-51.
56. Bateson P (2002) William Bateson: a biologist ahead of his time. J Genet 81: 49-58.
57. Biclas JH, Loeb KR, Rubin BP, True LD, Locb LA (2006) Human cancers express a mutator phenotype. Proc Natl Acad Sci USA 103: 18238-18242.
58. Mintz B, Illmensee K (1975) Normal genetically mosaic mice produced from malignant teratocarcinoma cells. Proc Natl Acad Sci USA 72: 3585-3589.
59. Illmensee K, Mintz B (1976) Totipotency and normal differentiation of single teratocarcinoma cells cloned by injection into blastocysts. Proc Natl Acad Sci USA 73: 549-553.
60. Li L, Connelly MC, Wetmore C, Curran T, Morgan JI (2003) Mouse embryos cloned from brain tumors. Cancer Res 63: 2733-2736.
61. Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100: 57-70.
62. Dupre J (2008) The Constituents of Life. Amsterdam: Van Gorcum.
63. Elsasser WM (1981) Principles of a new biological theory: a summary. J Theor Biol 89: 131-150.