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Genes, Gene Products, and Transcription Factors

  • Philip T. Cagle
Part of the Molecular Pathology Library book series (MPLB, volume 1)

Abstract

Molecular pathology employs an ever-expanding array of special techniques to study nucleic acids, genes, gene products, receptors, signaling pathways, the cell cycle, and mutations. This chapter and the others in this section provide a quick review of basic terminology and concepts for the understanding of subsequent chapters.

Keywords

Microsatellite Instability Origin Recognition Complex Curr Opin Cell Biol Preinitiation Complex Curr Opin Struct Biol 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Coleman WB, Tsongalis GJ, eds. The Molecular Basis of Human Cancer. Totowa, NJ: Humana Press; 2002.Google Scholar
  2. 2.
    Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R, eds. Molecular Biology of the Gene, 5th ed. Menlo Park, CA: Benjamin Cummings; 2003.Google Scholar
  3. 3.
    Epstein RJ, ed. Human Molecular Biology: An Introduction to the Molecular Basis of Health and Disease. Cambridge UK: Cambridge University Press; 2003.Google Scholar
  4. 4.
    Strachan T, Read A, eds. Human Molecular Genetics, 3rd ed. New York: Garland Science/Taylor and Francis Group; 2003.Google Scholar
  5. 5.
    Swansbury J, ed. Cancer Cytogenetics: Methods and Protocols. Totowa, NJ: Humana Press; 2003.Google Scholar
  6. 6.
    Cooper GM, Hausman RE, eds. The Cell: A Molecular Approach, 3rd ed. Washington, DC: ASM Press/Sunderland, MA: Sinauer Associates; 2004.Google Scholar
  7. 7.
    Farkas DH, ed. DNA from A to Z. Washington, DC: AACC Press; 2004.Google Scholar
  8. 8.
    Killeen AA, ed. Principles of Molecular Pathology. Totowa, NJ: Humana Press; 2004.Google Scholar
  9. 9.
    Leonard DGB, Bagg A, Caliendo A, et al., eds. Molecular Pathology in Clinical Practice. New York: Springer-Verlag; 2005.Google Scholar
  10. 10.
    Watson JD, Crick FH. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 1953;171:737–738.PubMedCrossRefGoogle Scholar
  11. 11.
    Thoma F, Koller T. Influence of histone H1 on chromatin structure. Cell 1977;12:101–107.PubMedCrossRefGoogle Scholar
  12. 12.
    Varshavsky AJ, Bakayev VV, Nedospasov SA, Georgiev GP. On the structure of eukaryotic, prokaryotic, and viral chromatin. Cold Spring Harb Symp Quant Biol 1978;42 Pt 1:457–473.PubMedGoogle Scholar
  13. 13.
    Tyler-Smith C, Willard HF. Mammalian chromosome structure. Curr Opin Genet Dev 1993;3:390–397.PubMedCrossRefGoogle Scholar
  14. 14.
    Lamond AI, Earnshaw WC. Structure and function in the nucleus. Science 1998;280:547–553.PubMedCrossRefGoogle Scholar
  15. 15.
    Blow JJ, Laskey RA. A role for the nuclear envelope in controlling DNA replication within the cell cycle. Nature 1988;332:546–548.PubMedCrossRefGoogle Scholar
  16. 16.
    Nishitani H, Nurse P. p65cdc18 plays a major role controlling the initiation of DNA replication in fission yeast. Cell 1995;83:397–405.PubMedCrossRefGoogle Scholar
  17. 17.
    Cocker JH, Piatti S, Santocanale C, et al. An essential role for the Cdc6 protein in forming the pre-replicative complexes of budding yeast. Nature 1996;379:180–182.PubMedCrossRefGoogle Scholar
  18. 18.
    Coleman TR, Carpenter PB, Dunphy WG. The Xenopus Cdc6 protein is essential for the initiation of a single round of DNA replication in cell-free extracts. Cell 1996;87:53–63.PubMedCrossRefGoogle Scholar
  19. 19.
    Muzi Falconi M, Brown GW, Kelly TJ. cdc18+ regulates initiation of DNA replication in Schizosaccharomyces pombe. Proc Natl Acad Sci USA 1996;93:1566–1570.PubMedCrossRefGoogle Scholar
  20. 20.
    Owens JC, Detweiler CS, Li JJ. CDC45 is required in conjunction with CDC7/DBF4 to trigger the initiation of DNA replication. Proc Natl Acad Sci USA 1997;94:12521–12526.PubMedCrossRefGoogle Scholar
  21. 21.
    Tanaka T, Knapp D, Nasmyth K. Loading of an Mcm protein onto DNA replication origins is regulated by Cdc6p and CDKs. Cell 1997;90:649–660.PubMedCrossRefGoogle Scholar
  22. 22.
    Williams RS, Shohet RV, Stillman B. A human protein related to yeast Cdc6p. Proc Natl Acad Sci USA 1997;94:142–147.PubMedCrossRefGoogle Scholar
  23. 23.
    Hateboer G, Wobst A, Petersen BO, et al. Cell cycleregulated expression of mammalian CDC6 is dependent on E2F. Mol Cell Biol 1998;18:6679–6697.PubMedGoogle Scholar
  24. 24.
    Hua XH, Newport J. Identification of a preinitiation step in DNA replication that is independent of origin recognition complex and cdc6, but dependent on cdk2. J Cell Biol 1998;140:271–281.PubMedCrossRefGoogle Scholar
  25. 25.
    Leatherwood J. Emerging mechanisms of eukaryotic DNA replication initiation. Curr Opin Cell Biol 1998;10:742–748.PubMedCrossRefGoogle Scholar
  26. 26.
    McGarry TJ, Kirschner MW. Geminin, an inhibitor of DNA replication, is degraded during mitosis. Cell 1998;93:1043–1053.PubMedCrossRefGoogle Scholar
  27. 27.
    Mimura S, Takisawa H. Xenopus Cdc45-dependent loading of DNA polymerase onto chromatin under the control of S-phase Cdk. EMBO J 1998;17:5699–5707.PubMedCrossRefGoogle Scholar
  28. 28.
    Saha P, Chen J, Thome KC, et al. Human CDC6/Cdc18 associates with Orc1 and cyclin-cdk and is selectively eliminated from the nucleus at the onset of S phase. Mol Cell Biol 1998;18:2758–2767.PubMedGoogle Scholar
  29. 29.
    Williams GH, Romanowski P, Morris L, et al. Improved cervical smear assessment using antibodies against proteins that regulate DNA replication. Proc Natl Acad Sci USA 1998;95:14932–14937.PubMedCrossRefGoogle Scholar
  30. 30.
    Yan Z, DeGregori J, Shohet R, et al. Cdc6 is regulated by E2F and is essential for DNA replication in mammalian cells. Proc Natl Acad Sci USA 1998;95:3603–3608.PubMedCrossRefGoogle Scholar
  31. 31.
    Zou L, Stillman B. Formation of a preinitiation complex by S-phase cyclin CDK-dependent loading of Cdc45p onto chromatin. Science 1998;280:593–596.PubMedCrossRefGoogle Scholar
  32. 32.
    Donaldson AD, Blow JJ. The regulation of replication origin activation. Curr Opin Genet Dev 1999;9:62–68.PubMedCrossRefGoogle Scholar
  33. 33.
    Fujita M, Yamada C, Goto H, et al. Cell cycle regulation of human CDC6 protein. Intracellular localization, interaction with the human mcm complex, and CDC2 kinasemediated hyperphosphorylation. J Biol Chem 1999;274:25927–25932.PubMedCrossRefGoogle Scholar
  34. 34.
    Masai H, Sato N, Takeda T, Arai K. CDC7 kinase complex as a molecular switch for DNA replication. Front Biosci 1999;4:D834–D840.PubMedCrossRefGoogle Scholar
  35. 35.
    Petersen BO, Lukas J, Sorensen CS, et al. Phosphorylation of mammalian CDC6 by cyclin A/CDK2 regulates its subcellular localization. EMBO J 1999;18:396–410.PubMedCrossRefGoogle Scholar
  36. 36.
    Coverley D, Pelizon C, Trewick S, Laskey RA. Chromatinbound Cdc6 persists in S and G2 phases in human cells, while soluble Cdc6 is destroyed in a cyclin A-cdk2 dependent process. J Cell Sci 2000;113:1929–1938.PubMedGoogle Scholar
  37. 37.
    Homesley L, Lei M, Kawasaki Y, et al. Mcm10 and the MCM2-7 complex interact to initiate DNA synthesis and to release replication factors from origins. Genes Dev 2000;14:913–926.PubMedGoogle Scholar
  38. 38.
    Maiorano D, Moreau J, Mechali M. XCDT1 is required for the assembly of pre-replicative complexes in Xenopus laevis. Nature 2000;404:622–625.PubMedCrossRefGoogle Scholar
  39. 39.
    Nishitani H, Lygerou Z, Nishimoto T, Nurse P. The Cdt1 protein is required to license DNA for replication in fission yeast. Nature 2000;404:625–628.PubMedCrossRefGoogle Scholar
  40. 40.
    Petersen BO, Wagener C, Marinoni F, et al. Cell cycle-and cell growth-regulated proteolysis of mammalian CDC6 is dependent on APC-CDH1. Genes Dev 2000;14:2330–2343.PubMedCrossRefGoogle Scholar
  41. 41.
    Takisawa H, Mimura S, Kubota Y. Eukaryotic DNA replication: from pre-replication complex to initiation complex. Curr Opin Cell Biol 2000;12:690–696.PubMedCrossRefGoogle Scholar
  42. 42.
    Whittaker AJ, Royzman I, Orr-Weaver TL. Drosophila double parked: a conserved, essential replication protein that colocalizes with the origin recognition complex and links DNA replication with mitosis and the downregulation of S phase transcripts. Genes Dev 2000;14:1765–1776.PubMedGoogle Scholar
  43. 43.
    Wohlschlegel JA, Dwyer BT, Dhar SK, et al. Inhibition of eukaryotic DNA replication by geminin binding to Cdt1. Science 2000;290:2309–2312.PubMedCrossRefGoogle Scholar
  44. 44.
    Diffley JF. DNA replication: building the perfect switch. Curr Biol 2001;11:R367–R370.PubMedCrossRefGoogle Scholar
  45. 45.
    Lei M, Tye BK. Initiating DNA synthesis: from recruiting to activating the MCM complex. J Cell Sci 2001;114:1447–1454.PubMedGoogle Scholar
  46. 46.
    Nishitani H, Taraviras S, Lygerou Z, Nishimoto T. The human licensing factor for DNA replication Cdt1 accumulates in G1 and is destabilized after initiation of S-phase. J Biol Chem 2001;276:44905–44911.PubMedCrossRefGoogle Scholar
  47. 47.
    Tada S, Li A, Maiorano D, et al. Repression of origin assembly in metaphase depends on inhibition of RLF-B/Cdt1 by geminin. Nat Cell Biol 2001;3:107–113.PubMedCrossRefGoogle Scholar
  48. 48.
    Yanow SK, Lygerou Z, Nurse P. Expression of Cdc18/Cdc6 and Cdt1 during G2 phase induces initiation of DNA replication. EMBO J 2001;20:4648–4656.PubMedCrossRefGoogle Scholar
  49. 49.
    Arentson E, Faloon P, Seo J, et al. Oncogenic potential of the DNA replication licensing protein CDT1. Oncogene 2002;21:1150–1158.PubMedCrossRefGoogle Scholar
  50. 50.
    Bell SP, Dutta A. DNA replication in eukaryotic cells. Annu Rev Biochem 2002;71:333–374.PubMedCrossRefGoogle Scholar
  51. 51.
    Bermejo R, Vilaboa N, Cales C. Regulation of CDC6, geminin, and CDT1 in human cells that undergo polyploidization. Mol Biol Cell 2002;13:3989–4000.PubMedCrossRefGoogle Scholar
  52. 52.
    Bonds L, Baker P, Gup C, Shroyer KR. Immunohistochemical localization of cdc6 in squamous and glandular neoplasia of the uterine cervix. Arch Pathol Lab Med 2002;26:1164–1168.Google Scholar
  53. 53.
    Mihaylov IS, Kondo T, Jones L, et al. Control of DNA replication and chromosome ploidy by geminin and cyclin A. Mol Cell Biol 2002;22:1868–1880.PubMedCrossRefGoogle Scholar
  54. 54.
    Nishitani H, Lygerou Z. Control of DNA replication licensing in a cell cycle. Genes Cells 2002;7:523–534.PubMedCrossRefGoogle Scholar
  55. 55.
    Robles LD, Frost AR, Davila M, et al. Down-regulation of Cdc6, a cell cycle regulatory gene, in prostate cancer. J Biol Chem 2002;277:25431–2538.PubMedCrossRefGoogle Scholar
  56. 56.
    Shreeram S, Sparks A, Lane DP, Blow JJ. Cell type-specific responses of human cells to inhibition of replication licensing. Oncogene 2002;21:6624–6632.PubMedCrossRefGoogle Scholar
  57. 57.
    Wohlschlegel JA, Kutok JL, Weng AP, Dutta A. Expression of geminin as a marker of cell proliferation in normal tissues and malignancies. Am J Pathol 2002;161:267–273.PubMedGoogle Scholar
  58. 58.
    Li X, Zhao Q, Liao R, et al. The SCF(Skp2) ubiquitin ligase complex interacts with the human replication licensing factor Cdt1 and regulates Cdt1 degradation. J Biol Chem 2003;278:30854–30858.PubMedCrossRefGoogle Scholar
  59. 59.
    Vaziri C, Saxena S, Jeon Y, et al. A p53-dependent checkpoint pathway pre prevents rereplication. Mol Cell 2003;11:997–1008.PubMedCrossRefGoogle Scholar
  60. 60.
    Yoshida K, Inoue I. Regulation of geminin and Cdt1 expression by E2F transcription factors. Oncogene 2004;23:3802–3812.PubMedCrossRefGoogle Scholar
  61. 61.
    Krieg PA, Melton DA. In vitro RNA synthesis with SP6 RNA polymerase. Methods Enzymol 1987;155:397–415.PubMedCrossRefGoogle Scholar
  62. 62.
    Lawyer FC, Stoffel S, Saiki RK, et al. Isolation, characterization, and expression in Escherichia coli of the DNA polymerase gene from Thermus aquaticus. J Biol Chem 1989;264:6427–6437.PubMedGoogle Scholar
  63. 63.
    Studier FW, Rosenberg AH, Dunn JJ, Dubendorff JW. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol 1990;185:60–89.PubMedCrossRefGoogle Scholar
  64. 64.
    Kollmar R, Farnham PJ. Site-specific initiation of transcription by RNA polymerase II. Proc Soc Exp Biol Med 1993;203:127–139.PubMedGoogle Scholar
  65. 65.
    Chou KC, Kezdy FJ, Reusser F. Kinetics of processive nucleic acid polymerases and nucleases. Anal Biochem 1994;221:217–230.PubMedCrossRefGoogle Scholar
  66. 66.
    Tabor S, Richardson CC. A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy-and dideoxyribonucleotides. Proc Natl Acad Sci USA 1995;92:6339–6343.PubMedCrossRefGoogle Scholar
  67. 67.
    Goldberg S, Schwartz H, Darnell JE Jr. Evidence from UV transcription mapping in HeLa cells that heterogeneous nuclear RNA is the messenger RNA precursor. Proc Natl Acad Sci USA 1977;74:4520–4523.PubMedCrossRefGoogle Scholar
  68. 68.
    Hoffmann-Berling H. DNA unwinding enzymes. Prog Clin Biol Res 1982;102 Pt C:89–98.PubMedGoogle Scholar
  69. 69.
    Wang JC. DNA topoisomerases: why so many? J Biol Chem 1991;266:6659–6662.PubMedGoogle Scholar
  70. 70.
    Anderson HJ, Roberge M. DNA topoisomerase II: a review of its involvement in chromosome structure, DNA replication, transcription and mitosis. Cell Biol Int Rep 1992;16:717–724.PubMedCrossRefGoogle Scholar
  71. 71.
    Gasser SM, Walter R, Dang Q, Cardenas ME. Topoisomerase II: its functions and phosphorylation. Antonie Van Leeuwenhoek 1992;62:15–24.PubMedCrossRefGoogle Scholar
  72. 72.
    D’Incalci M. DNA-topoisomerase inhibitors. Curr Opin Oncol 1 1993;5:1023–1028.CrossRefGoogle Scholar
  73. 73.
    Ferguson LR, Baguley BC. Topoisomerase II enzymes and mutagenicity. Environ Mol Mutagen 1994;24:245–261.PubMedCrossRefGoogle Scholar
  74. 74.
    Larsen AK, Skladanowski A, Bojanowski K. The roles of DNA topoisomerase II during the cell cycle. Prog Cell Cycle Res 1996;2:229–239.PubMedGoogle Scholar
  75. 75.
    Kato S, Kikuchi A. DNA topoisomerase: the key enzyme that regulates DNA super structure. Nagoya J Med Sci 1998;61:11–26.PubMedGoogle Scholar
  76. 76.
    Wang JC. Cellular roles of DNA topoisomerases: a molecular perspective. Nat Rev Mol Cell Biol 2002;3:430–440.PubMedCrossRefGoogle Scholar
  77. 77.
    Gimenez-Abian JF, Clarke DJ. Replication-coupled topoisomerase II templates the mitotic chromosome scaffold? Cell Cycle 2003;2:230–232.PubMedGoogle Scholar
  78. 78.
    Leppard JB, Champoux JJ. Human DNA topoisomerase I: relaxation, roles, and damage control. Chromosoma 2005;114:75–85.PubMedCrossRefGoogle Scholar
  79. 79.
    Sharp SJ, Schaack J, Cooley L, et al. Structure and transcription of eukaryotic tRNA genes. CRC Crit Rev Biochem 1985;19:107–144.PubMedCrossRefGoogle Scholar
  80. 80.
    Persson BC. Modification of tRNA as a regulatory device. Mol Microbiol 1993;8:1011–1016.PubMedCrossRefGoogle Scholar
  81. 81.
    Green R, Noller HF. Ribosomes and translation. Annu Rev Biochem 1997;66:679–716.PubMedCrossRefGoogle Scholar
  82. 82.
    Sutherland GR, Richards RI. Simple tandem DNA repeats and human genetic disease. Proc Natl Acad Sci USA 1995;92:3636–3641.PubMedCrossRefGoogle Scholar
  83. 83.
    Horii A, Han HJ, Shimada M, et al. Frequent replication errors at microsatellite loci in tumors of patients with multiple primary cancers. Cancer Res 1994;54:3373–3375.PubMedGoogle Scholar
  84. 84.
    Loeb LA. Microsatellite instability: marker of a mutator phenotype in cancer. Cancer Res 1994;54:5059–5063.PubMedGoogle Scholar
  85. 85.
    Mao L, Lee DJ, Tockman MS, et al. Microsatellite alterations as clonal markers for the detection of human cancer. Proc Natl Acad Sci USA 1994;91:9871–9875.PubMedCrossRefGoogle Scholar
  86. 86.
    Merlo A, Mabry M, Gabrielson E, et al. Frequent microsatellite instability in primary small cell lung cancer. Cancer Res 1994;54:2098–2101.PubMedGoogle Scholar
  87. 87.
    Wooster R, Cleton-Jansen AM, Collins N, et al. Instability of short tandem repeats (microsatellites) in human cancers. Nat Genet 1994;6:152–156.PubMedCrossRefGoogle Scholar
  88. 88.
    Fong KM, Zimmerman PV, Smith PJ. Microsatellite instability and other molecular abnormalities in non-small cell lung cancer. Cancer Res 1995;55:28–30.PubMedGoogle Scholar
  89. 89.
    Miozzo M, Sozzi G, Musso K, et al. Microsatellite alterations in bronchial and sputum specimens of lung cancer patients. Cancer Res 1996;56:2285–2288.PubMedGoogle Scholar
  90. 90.
    Bocker T, Diermann J, Friedl W, et al. Microsatellite instability analysis: a multicenter study for reliability and quality control. Cancer Res 1997;57:4739–4743.PubMedGoogle Scholar
  91. 91.
    Dietmaier W, Wallinger S, Bocker T, et al. Diagnostic microsatellite instability: definition and correlation with mismatch repair protein expression. Cancer Res 1997;57:4749–56.PubMedGoogle Scholar
  92. 92.
    Lothe RA. Microsatellite instability in human solid tumors. Mol Med Today 1997;3:61–68.PubMedCrossRefGoogle Scholar
  93. 93.
    Arzimanoglou II, Gilbert F, Barber HR. Microsatellite instability in human solid tumors. Cancer 1998;82:1808–1820.PubMedCrossRefGoogle Scholar
  94. 94.
    Boland CR, Thibodeau SN, Hamilton SR, et al. A National Cancer Institute Workshop on Microsatellite Instability for cancer detection and familial predisposition: development of international criteria for the determination of microsatellite instability in colorectal cancer. Cancer Res 1998;58:5248–5257.PubMedGoogle Scholar
  95. 95.
    Boyer JC, Farber RA. Mutation rate of a microsatellite sequence in normal human fibroblasts. Cancer Res 1998;58:3946–3949.PubMedGoogle Scholar
  96. 96.
    Hanford MG, Rushton BC, Gowen LC, Farber RA. Microsatellite mutation rates in cancer cell lines deficient or proficient in mismatch repair. Oncogene 1998;16:2389–2393.PubMedCrossRefGoogle Scholar
  97. 97.
    Jackson AL, Chen R, Loeb LA. Induction of microsatellite instability by oxidative DNA damage. Proc Natl Acad Sci USA 1998;95:12468–12473.PubMedCrossRefGoogle Scholar
  98. 98.
    Johannsdottir JT, Jonasson JG, Bergthorsson JT, et al. The effect of mismatch repair deficiency on tumourigenesis; microsatellite instability affecting genes containing short repeated sequences. Int J Oncol 2000;16:133–139.PubMedGoogle Scholar
  99. 99.
    Kim WS, Park C, Hong SK, et al. Microsatellite instability(MSI) in non-small cell lung cancer (NSCLC) is highly associated with transforming growth factor-beta type II receptor(TGF-beta RII) frameshift mutation. Anticancer Res 2000;20:1499–1502.PubMedGoogle Scholar
  100. 100.
    Biessmann H, Mason JM. Telomeric repeat sequences. Chromosoma 1994;103:154–161.PubMedCrossRefGoogle Scholar
  101. 101.
    Feng J, Funk WD, Wang SS, et al. The RNA component of human telomerase. Science 1995;269:1236–1241.PubMedCrossRefGoogle Scholar
  102. 102.
    Counter CM. The roles of telomeres and telomerase in cell life span. Mutat Res 1996;366:45–63.PubMedGoogle Scholar
  103. 103.
    Wellinger RJ, Sen D. The DNA structures at the ends of eukaryotic chromosomes. Eur J Cancer 1997;33:735–749.PubMedCrossRefGoogle Scholar
  104. 104.
    Chakhparonian M, Wellinger RJ. Telomere maintenance and DNA replication: how closely are these two connected? Trends Genet 2003;19:439–446.PubMedCrossRefGoogle Scholar
  105. 105.
    Bayne S, Liu JP. Hormones and growth factors regulate telomerase activity in ageing and cancer. Mol Cell Endocrinol 2005;240:11–22.PubMedCrossRefGoogle Scholar
  106. 106.
    Blackburn EH. Telomeres and telomerase: their mechanisms of action and the effects of altering their functions. FEBS Lett 2005;579:859–862.PubMedCrossRefGoogle Scholar
  107. 107.
    Blasco MA. Telomeres and human disease: ageing, cancer and beyond. Nat Rev Genet 2005;6:611–622.PubMedCrossRefGoogle Scholar
  108. 108.
    Boukamp P, Popp S, Krunic D. Telomere-dependent chromosomal instability. J Invest Dermatol Symp Proc 2005;10:89–94.CrossRefGoogle Scholar
  109. 109.
    Brunori M, Luciano P, Gilson E, Geli V. The telomerase cycle: normal and pathological aspects. J Mol Med 2005;83:244–257.PubMedCrossRefGoogle Scholar
  110. 110.
    Dong CK, Masutomi K, Hahn WC. Telomerase: regulation, function and transformation. Crit Rev Oncol Hematol 2005;54:85–93.PubMedCrossRefGoogle Scholar
  111. 111.
    Jacobs JJ, de Lange T. p16INK4a as a second effector of the telomere damage pathway. Cell Cycle 2005;4:1364–1368.PubMedGoogle Scholar
  112. 112.
    Opitz OG. Telomeres, telomerase and malignant transformation. Curr Mol Med 2005;5:219–226.PubMedCrossRefGoogle Scholar
  113. 113.
    Viscardi V, Clerici M, Cartagena-Lirola H, Longhese MP. Telomeres and DNA damage checkpoints. Biochimie 2005;87:613–624.PubMedCrossRefGoogle Scholar
  114. 114.
    Autexier C, Lue NF. The structure and function of telomerase reverse transcriptase. Annu Rev Biochem 2006;75:493–517.PubMedCrossRefGoogle Scholar
  115. 115.
    Bhattacharyya MK, Lustig AJ. Telomere dynamics in genome stability. Trends Biochem Sci 2006;31:114–122.PubMedCrossRefGoogle Scholar
  116. 116.
    Pallen CJ, Tan YH, Guy GR. Protein phosphatases in cell signaling. Curr Opin Cell Biol 1992;4:1000–1007.PubMedCrossRefGoogle Scholar
  117. 117.
    Boulikas T. Control of DNA replication by protein phosphorylation. Anticancer Res 1994;14:2465–2472.PubMedGoogle Scholar
  118. 118.
    Berndt N. Protein dephosphorylation and the intracellular control of the cell number. Front Biosci 1999;4:D22–D42.PubMedCrossRefGoogle Scholar
  119. 119.
    Appella E, Anderson CW. Post-translational modifications and activation of p53 by genotoxic stresses. Eur J Biochem 2001;268:2764–2772.PubMedCrossRefGoogle Scholar
  120. 120.
    Obaya AJ, Sedivy JM. Regulation of cyclin-Cdk activity in mammalian cells. Cell Mol Life Sci 2002;59:126–142.PubMedCrossRefGoogle Scholar
  121. 121.
    Fu M, Wang C, Wang J, et al. Acetylation in hormone signaling and the cell cycle. Cytokine Growth Factor Rev 2002;13:259–276.PubMedCrossRefGoogle Scholar
  122. 122.
    Haglund K, Dikic I. Ubiquitylation and cell signaling. EMBO J 2005;24:3353–3359.PubMedCrossRefGoogle Scholar
  123. 123.
    Legube G, Trouche D. Regulating histone acetyltransferases and deacetylases. EMBO Rep 2003;4:944–947.PubMedCrossRefGoogle Scholar
  124. 124.
    Marmorstein R. Structural and chemical basis of histone acetylation. Novartis Found Symp 2004;259:78–98.PubMedCrossRefGoogle Scholar
  125. 125.
    Moore JD, Krebs JE. Histone modifications and DNA double-strand break repair. Biochem Cell Biol 2004;82:446–452.PubMedCrossRefGoogle Scholar
  126. 126.
    Peterson CL, Laniel MA. Histones and histone modifications. Curr Biol 2004;14:R546–R551.PubMedCrossRefGoogle Scholar
  127. 127.
    Quivy V, Calomme C, Dekoninck A, et al. Gene activation and gene silencing: a subtle equilibrium. Cloning Stem Cells 2004;6:140–149.PubMedCrossRefGoogle Scholar
  128. 128.
    Wang Y, Fischle W, Cheung W, et al. Beyond the double helix: writing and reading the histone code. Novartis Found Symp 2004;259:3–17.PubMedCrossRefGoogle Scholar
  129. 129.
    Fraga MF, Esteller M. Towards the human cancer epigenome: a first draft of histone modifications. Cell Cycle 2005;4:1377–1381.PubMedGoogle Scholar
  130. 130.
    Khan AU, Krishnamurthy S. Histone modifications as key regulators of transcription. Front Biosci 2005;10:866–872.PubMedCrossRefGoogle Scholar
  131. 131.
    Verdone L, Caserta M, Di Mauro E. Role of histone acetylation in the control of gene expression. Biochem Cell Biol 2005;83:344–353.PubMedCrossRefGoogle Scholar
  132. 132.
    Yu Y, Waters R. Histone acetylation, chromatin remodelling and nucleotide excision repair: hint from the study on MFA2 in Saccharomyces cerevisiae. Cell Cycle 2005;4:1043–1045.PubMedGoogle Scholar
  133. 133.
    Verdone L, Agricola E, Caserta M, Di Mauro E. Histone acetylation in gene regulation. Brief Funct Genomic Proteomic 2006;5:209–221.PubMedCrossRefGoogle Scholar
  134. 134.
    Haura EB, Turkson J, Jove R. Mechanisms of disease: insights into the emerging role of signal transducers and activators of transcription in cancer. Nat Clin Pract Oncol 2005;2:315–324.PubMedCrossRefGoogle Scholar
  135. 135.
    Wang JC. Finding primary targets of transcriptional regulators. Cell Cycle 2005;4:356–358.PubMedGoogle Scholar
  136. 136.
    Wittenberg C, Reed SI. Cell cycle-dependent transcription in yeast: promoters, transcription factors, and transcriptomes. Oncogene 2005;24:2746–2755.PubMedCrossRefGoogle Scholar
  137. 137.
    Zaidi SK, Young DW, Choi JY, et al. The dynamic organization of gene-regulatory machinery in nuclear microenvironments. EMBO Rep 2005;6:128–133.PubMedCrossRefGoogle Scholar
  138. 138.
    Barrera LO, Ren B. The transcriptional regulatory code of eukaryotic cells—insights from genome-wide analysis of chromatin organization and transcription factor binding. Curr Opin Cell Biol 2006;18:291–298.PubMedCrossRefGoogle Scholar
  139. 139.
    Dillon N. Gene regulation and large-scale chromatin organization in the nucleus. Chromosome Res 2006;14:117–126.PubMedCrossRefGoogle Scholar
  140. 140.
    Maston GA, Evans SK, Green MR. Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet 2006;7:29–59.PubMedCrossRefGoogle Scholar
  141. 141.
    Thomas MC, Chiang CM. The general transcription machinery and general cofactors. Crit Rev Biochem Mol Biol 2006;41:105–178.PubMedCrossRefGoogle Scholar
  142. 142.
    Engelkamp D, van Heyningen V. Transcription factors in disease. Curr Opin Genet Dev 1996;6:334–342.PubMedCrossRefGoogle Scholar
  143. 143.
    Tamura T, Konishi Y, Makino Y, Mikoshiba K. Mechanisms of transcriptional regulation and neural gene expression. Neurochem Int 1996;29:573–581.PubMedCrossRefGoogle Scholar
  144. 144.
    Bieker JJ, Ouyang L, Chen X. Transcriptional factors for specific globin genes. Ann NY Acad Sci 1998;850:64–69.PubMedCrossRefGoogle Scholar
  145. 143.
    Hertel KJ, Lynch KW, Maniatis T. Common themes in the function of transcription and splicing enhancers. Curr Opin Cell Biol 1997;9:350–357.PubMedCrossRefGoogle Scholar
  146. 146.
    Arnosti DN. Analysis and function of transcriptional regulatory elements: insights from Drosophila. Annu Rev Entomol 2003;48:579–602.PubMedCrossRefGoogle Scholar
  147. 147.
    Scannell DR, Wolfe K. Rewiring the transcriptional regulatory circuits of cells. Genome Biol 2004;5:206.PubMedCrossRefGoogle Scholar
  148. 148.
    Villard J. Transcription regulation and human diseases. Swiss Med Wkly 2004;134:571–579.PubMedGoogle Scholar
  149. 149.
    Hampsey M. Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol Mol Biol Rev 1998;62:465–503.PubMedGoogle Scholar
  150. 150.
    Berk AJ. Activation of RNA polymerase II transcription. Curr Opin Cell Biol 1999;11:330–335.PubMedCrossRefGoogle Scholar
  151. 151.
    Berk AJ. TBP-like factors come into focus. Cell 2000;103:5–8.PubMedCrossRefGoogle Scholar
  152. 152.
    Green MR. TBP-associated factors (TAFIIs): multiple, selective transcriptional mediators in common complexes. Trends Biochem Sci 2000;25:59–63.PubMedCrossRefGoogle Scholar
  153. 153.
    Pugh BF. Control of gene expression through regulation of the TATA-binding protein. Gene 2000;255:1–14.PubMedCrossRefGoogle Scholar
  154. 154.
    Burley SK, Kamada K. Transcription factor complexes. Curr Opin Struct Biol 2002;12:225–230.PubMedCrossRefGoogle Scholar
  155. 155.
    Featherstone M. Coactivators in transcription initiation: here are your orders. Curr Opin Genet Dev 2002;12:149–155.PubMedCrossRefGoogle Scholar
  156. 156.
    Davidson I. The genetics of TBP and TBP-related factors. Trends Biochem Sci 2003;28:391–398.PubMedCrossRefGoogle Scholar
  157. 157.
    Hochheimer A, Tjian R. Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression. Genes Dev 2003;17:1309–1320.PubMedCrossRefGoogle Scholar
  158. 158.
    Asturias FJ. RNA polymerase II structure and organization of the preinitiation complex. Curr Opin Struct Biol 2004;14:121–129.PubMedCrossRefGoogle Scholar
  159. 159.
    Matangkasombut O, Auty R, Buratowski S. Structure and function of the TFIID complex. Adv Protein Chem 2004;67:67–92.PubMedCrossRefGoogle Scholar
  160. 160.
    Brady J, Kashanchi F. Tat gets the “green“ light on transcription initiation. Retrovirology 2005;2:69.PubMedCrossRefGoogle Scholar
  161. 161.
    Thomas MC, Chiang CM. The general transcription machinery and general cofactors. Crit Rev Biochem Mol Biol 2006;41:105–178.PubMedCrossRefGoogle Scholar
  162. 162.
    Dang CV, Resar LM, Emison E, et al. Function of the c-Myc oncogenic transcription factor. Exp Cell Res 1999;253:63–77.PubMedCrossRefGoogle Scholar
  163. 163.
    Kuramoto N, Ogita K, Yoneda Y. Gene transcription through Myc family members in eukaryotic cells. Jpn J Pharmacol 1999;80:103–109.PubMedCrossRefGoogle Scholar
  164. 164.
    Grandori C, Cowley SM, James LP, Eisenman RN. The Myc/Max/Mad network and the transcriptional control of cell behavior. Annu Rev Cell Dev Biol 2000;16:653–699.PubMedCrossRefGoogle Scholar
  165. 165.
    Baudino TA, Cleveland JL. The Max network gone mad. Mol Cell Biol 2001;21:691–702.PubMedCrossRefGoogle Scholar
  166. 166.
    Eisenman RN. The Max network: coordinated transcriptional regulation of cell growth and proliferation. Harvey Lect 2000–2001;96:1–32.PubMedGoogle Scholar
  167. 167.
    Luscher B. Function and regulation of the transcription factors of the Myc/Max/Mad network. Gene 2001;277:1–14.PubMedCrossRefGoogle Scholar
  168. 168.
    Zhou ZQ, Hurlin PJ. The interplay between Mad and Myc in proliferation and differentiation. Trends Cell Biol 2001;11:S10–S14.PubMedGoogle Scholar
  169. 169.
    Lee LA, Dang CV. Myc target transcriptomes. Curr Top Microbiol Immunol 2006;302:145–167.PubMedCrossRefGoogle Scholar
  170. 170.
    Nair SK, Burley SK. Structural aspects of interactions within the Myc/Max/Mad network. Curr Top Microbiol Immunol 2006;302:123–143.PubMedCrossRefGoogle Scholar
  171. 171.
    Pirity M, Blanck JK, Schreiber-Agus N. Lessons learned from Myc/Max/Mad knockout mice. Curr Top Microbiol Immunol 2006;302:205–234.PubMedCrossRefGoogle Scholar
  172. 172.
    Rottmann S, Luscher B. The Mad side of the Max network: antagonizing the function of Myc and more. Curr Top Microbiol Immunol. 2006;302:63–122.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC. 2008

Authors and Affiliations

  • Philip T. Cagle
    • 1
    • 2
  1. 1.Pathology and Laboratory MedicineWeill Medical College of Cornell UniversityNew York
  2. 2.The Methodist HospitalHoustonUSA

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