Imaging genome abnormalities in cancer research

Cell and Chromosome

Volumn 3, Issue , 2004, Pages

  Heng, Henry H Q ^a   Stevens, Joshua B ^a   Liu, Guo ^a   Bremer, Steven W ^a   Ye, Christine J ^a,b  

^a WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b SeeDNA Biotech Inc   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ANTINEOPLASTIC AGENT;

APOPTOSIS; CANCER CELL; CANCER GROWTH; CANCER RESEARCH; CARCINOGENESIS; CHROMATIN STRUCTURE; CHROMOSOME ABERRATION; CHROMOSOME CONDENSATION; CHROMOSOME STRUCTURE; DRUG RESPONSE; GENE ACTIVITY; GENE FUNCTION; GENE STRUCTURE; GENETIC STABILITY; HUMAN; MEIOSIS; MITOSIS; NONHUMAN; REVIEW;

EID: 2942518251     PISSN: 14759268     EISSN: None     Source Type: Journal    
DOI: 10.1186/1475-9268-3-1     Document Type: Review

References (80)

1. Rowley JD: The critical role of chromosome translocations in human leukemias. Annu Rev Genet 1998, 32:495-519.
2. Mitelman F: Recurrent chromosome aberrations in cancer. Mutation Research 2000, 462:247-253.
3. Heng HHQ, Spyropoulos B, Moens P: FISH technology in chromosome and genome research. BioEssays 1997, 19:75-84.
4. Heng HH, Krawetz SA, Lu W, Bremer S, Liu G, Ye CJ: Re-defining the chromatin loop domain. Cytogent Cell Genet 2001, 93:155-161.
5. Ibora F, Cook PR, Jackson DA: Applying microscopy to the analysis of nuclear structure and function. Methods 2003,29:131-141.
6. Zink D, Sadoni N, Stelzer E: Visualizing chromatin and chromosomes in living cells. Methods 2003, 29:42-50.
7. Weber B: Cancer genomics. Cancer Cell 2002, 1:37-47.
8. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D: Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 1992, 258:818-821.
9. Sharp PA: RNA Interference-2001. Genes Dev 2001, 15:485-490.
10. Baylin SB, Herman JG: DNA hypermethylation in tumorigenesis: epigenetics joins genetics. Trends Genet 2000, 16:168-174.
11. Lengauer C, Kinzler KW, Vogelstein B: Genetic instabilities in human cancers. Nature 1998, 396:643-649.
12. Baynton K, Otterlei M, Bjoras M, von Kobbe C, Bohr VA, Seeberg E: WRN interacts physically and functionally with the recombination mediator protein RAD52. J Biol Chem 2003, 278:36476-36486.
13. Okorokov AL, Rubbi CP, Metcalfe S, Milner J: The interaction of p53 with the nuclear matrix is mediated by F-actin and modulated by DNA damage. Oncogene 2002, 21:356-367.
14. Cairns BR: Emerging roles for chromatin remodeling in cancer biology. Trends Cell Biol 2001, 11:S15-21.
15. Heng HHQ, Squire J, Tsui LC: High resolution mapping of mammalian genes by in situ hybridization to free chromatin. Proc Natl Acad Sci USA 1992, 89:9509-9513.
16. Heng HH, Tsui LC: High-resolution free chromatin/DNA fiber FISH. J Chromatography 1998, 806:219-229.
17. Raderschall E, Golub EI, Haaf T: Nuclear foci of mammalian recombination proteins are located at single-stranded DNA regions formed after DNA damage. Proc Natl Acad Sci U S A 1999, 96:1921-1926.
18. Gerdes MG, Carter KC, Moen PT, Lawrence JB: Dynamic changes in the higher-level chromatin organization of specific sequences revealed by in situ hybridization to nuclear halos. J Cell Biol 1994, 126:289-304.
19. Craig JM, Boyle S, Perry P, Bickmore WA: Scaffold attachments within the human genome. J Cell Sci 1997, 110:2673-2682.
20. de Belle I, Cai S, Kohwi-Shigematsu T: The genomic sequences bound to special AT-rich sequence-binding protein 1 (SATB1) in vivo in Jurkat T cells are tightly associated with the nuclear matrix at the bases of the chromatin loops. J Cell Biol 1998, 141:335-348.
21. Sumer H, Craig JM, Sibson M, Choo KH: A rapid method of genomic array analysis of scaffold/matrix attachment regions (S/MARs) identifies a 2.5-Mb region of enhanced scaffold/matrix attachment at a human neocentromere. Genome Res 2003, 13:1737-1743.
22. Bode J, Goetze S, Heng HH, Krawetz SA, Benham C: From DNA structure to gene expression: Mediators of nuclear compartmentalization and dynamics. Chromosome Res 2003, 11:435-445.
23. Heng HHQ, Goetze S, Ye CJ, Liu G, Stevens JB, Bremer SW, Bode J, Wykes SM, Krawetz SA: Chromatin loops are selectively anchored using Scaffold/matrix attachment regions. J Cell Sci in press.
24. Gerasimova IT, Byre K, Corces VG: A chromatin insulator determines the nuclear location of DNA. Mol Cell 2000, 6:1025-1035.
25. Volpi EV, Chevret E, Jones T, Vatcheva R, Williamson J, Beck S, Campbell RD, Goldsworthy M, Powis SH, Ragoussis J, Trowsdale J, Sheer D: Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. J Cell Sci 2000, 113:1565-1576.
26. Heng HH, Tsui LC, Moens PB: Organization of heterologous DNA inserts on the mouse meiotic chromosome core. Chromosoma 1994, 103:401-407.
27. Heng HH, Chamberlain JW, Shi XM, Spyropoulos B, Tsui LC, Moens PB: Regulation of meiotic chromatin loop size by chromosomal position. Proc Natl Acad Sci U S A 1996, 93:2795-2800.
28. Kotin RM, Menninger JC, Ward DC, Berns KI: Mapping and direct visualization of a region-specific viral DNA integration site on human chromosome 19q13-qter. Genomics 1991, 10:831-834.
29. Omori F, Messner HA, Ye J, Nell J, Gronda M, Heng HHQ: Non-targeted integration of recombinant adeno-associated virus in human cells detected by fluorescence in situ hybridization. Human Gene Therapy 1999, 10:537-543.
30. Kitsberg D, Selig S, Brandeis M, Simon I, Keshet I, Driscoll DJ, Nicholls RD, Cedar H: Allele-specific replication timing of imprinted gene regions. Nature 1993, 364:459-463.
31. Zijlmans JM, Martens UM, Poon SS, Raap AK, Tanke HJ, Ward RK, Lansdorp PM: Telomeres in the mouse have large inter-chromosomal variations in the number of T2AG3 repeats. Proc Natl Acad Sci U S A 1997, 94:7423-7428.
32. Caburet S, Conti C, Bensimon A: Combing the genome for genomic instability. Trends Biotechnol 2002, 20:344-50.
33. Haaf T, Ward DC: Structural analysis of alpha-satellite DNA and centromere proteins using extended chromatin and chromosomes. Hum Mol Genet 1994, 3:697-709.
34. Heng HHQ, Spyropoulos B, Moens PB: DNA-protein in situ codetection. In situ hybridization protocols. Methods in Molecular Biology Volume 123. Clifton, New Jersey, Humana Press; 2000:15-27.
35. Christian AT, Pattee MS, Attix CM, Reed BE, Sorensen KJ, Tucker JD: Detection of DNA point mutations and mRNA expression levels by rolling circle amplification in individual cells. Proc Natl Acad Sci U S A 2001, 98:14238-14243.
36. Belmont AS: Visualizing chromosome dynamics with GFP. Trends Cell Biol 2001, 11:250-257.
37. Richardson C, Moynahan ME, Jasin M: Double-strand break repair by interchromosomal recombination: suppression of chromosomal translocations. Genes Dev 1998, 12:3831-3842.
38. Pihan GA, Doxsey SJ: The mitotic machinery as a source of genetic instability in cancer. Semin Cancer Biol 1999, 9:289-302.
39. Hirano T: The ABCs of SMC proteins: two-armed ATPases for chromosome condensation, cohesion, and repair. Genes Dev 2002, 16:399-414.
40. Heng HQ, Chen YW: Studies on the structure of the chromosome and its formation, I. A new method. The nucleus 1986, 29:5-8.
41. Heng HQ, Chen WY, Wang YC: Effects of pingyanymycin on chromosomes: A possible structural basis for chromosome aberration. Mutation Research 1988, 199:199-205.
42. Heng HHQ, Shi XM: From free chromatin analysis to high-resolution fiber FISH. Cell Res 1997, 7:119-124.
43. Smith L, Plug A, Thayer M: Delayed replication timing leads to delayed mitotic chromosome condensation and chromosomal instability of chromosome translocations. Proc Natl Acad Sci USA 2001, 98:13300-13305.
44. Gisselsson D, Pettersson L, Hoglund M, Heidenblad M, Gorunova L, Wiegant J, Mertens F, Dal Chi P, Mitelman F, Mandahl N: Chromosomal breakage-fusion-bridge events cause genetic intratumor heterogeneity. Proc Natl Acad Sci USA 2000, 97:5357-5362.
45. Speicher MR, Gwyn Ballard S, Ward DC: Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat Genet 1996, 12:368-75.
46. Schrock E, du Manoir S, Veldman T, Schoell B, Wienberg J, Ferguson-Smith MA, Ning Y, Ledbetter DH, Bar-Am I, Soenksen D, Garini Y, Ried T: Multicolor spectral karyotyping of human chromosomes. Science 1996, 273:494-497.
47. Schmidt-Kittler O, Ragg T, Daskalakis A, Granzow M, Ahr A, Blankenstein TJ, Kaufmann M, Diebold J, Arnholdt H, Muller P, Bischoff J, Harich D, Schlimok G, Riethmuller G, Eils R, Klein CA: From latent disseminated cells to overt metastasis: genetic analysis of systemic breast cancer progression. Proc Natl Acad Sci USA 2003, 100:7737-7742.
48. Ye J, Lu W, Moens P, Liu G, Bremer S, Wang Y, Hughes M, Krawetz SA, Heng HHQ: The combination of SKY and specific loci detection with FISH or Immunostaining. Cytogenet Cell Genet 2001, 93:195-202.
49. Beheshti B, Karaskova J, Park PC, Squire JA, Beatty BG: Identification of a high frequency of chromosomal rearrangements in the centromeric regions of prostate cancer cell lines by sequential giemsa banding and spectral karyotyping. Mol Diagn 2000, 5:23-32.
50. Heng HHQ, Ye CJ, Yang FT, Ebrahim S, Liu G, Bremer S, Thomas MC, Ye J, Chen TJ, Tuck-Muller C, Yu JW, Krawetz SA, Johnson A: Analysis of marker or complex chromosomal rearrangements present in pre-and postnatal karyotypes utilizing a combination of G-banding, SKY and FISH. Clinical Genetics 2003, 63:358-367.
51. Heng HHQ, Liu G, Lu W, Bremer S, Ye CJ, Hughes M, Moens P: Multicolor SKY painting of mouse meiotic chromosomes. Genome 2001, 44:293-298.
52. Vig BK, Athwal RS: Sequence of centromere separation: separation in a quasistable mouse-human somatic cell hybrid. Chromosoma 1989, 98:167-173.
53. Rodriguez MJ, Lopez MA, Garcia-Orad A, Vig BK: Sequence of centromere separation: effect of 5-azacytidine-induced epigenetic alteration. Mutagenesis 2001, 16:109-14.
54. Nasmyth K: Segregating sister genomes: the molecular biology of chromosome separation. Science 2002, 297:559-65.
55. Lemieux N, Drouin R, Richer CL: High-resolution dynamic and morphological G-bands (GBG and GTG): A comparative study. Hum Genet 1990, 85:261-266.
56. Holmquist GP: Chromosome bands, their chromatin flavors, and their functional features. Am J Hum Genet 1992, 51:17-37.
57. Jeppesen P, Turner BM: The inactive X chromosome in female mammals is distinguished by a lack of histone H4 acetylation, a cytogenetic marker for gene expression. Cell 1993, 74:281-9.
58. Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, Wang H, de la Cruz CC, Otte AP, Panning B, Zhang Y: Role of histone H3 lysine 27 methylation in X inactivation. Science 2003, 300:131-135.
59. Barton SC, Arney KL, Shi W, Niveleau A, Fundele R, Surani MA, Haaf T: Genome-wide methylation patterns in normal and uniparental early mouse embryos. Hum Mol Genet 2001, 10:2983-2987.
60. Hendzel MJ, Wei Y, Mancini MA, Van Hooser A, Ranalli T, Brinkley BR, Bazett-Jones DP, Allis CD: Mitosis-specific phosphorylation of histone H3 initiates primarily within pericentromeric heterochromatin during G2 and spreads in an ordered fashion coincident with mitotic chromosome condensation. Chromosoma 1997, 106:348-360.
61. Flagiello D, Bernardino-Sgherri J, Dutrillaux B: Complex relationships between 5-aza-dC induced DNA demethylation and chromosome compaction at mitosis. Chromosoma 2002, 111:37-44.
62. Hagstrom KA, Meyer JB: Condensin and cohesin: more than chromosome compactor and glue. Nat Rev Genet 2003, 4:520-534.
63. Cremer T, Cremer C: Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2001, 2:292-301.
64. Parada L, Misteli T: Chromosome positioning in the interphase nucleus. Trends Cell Biol 2002, 12:425-32.
65. O'Brien TP, Bult CJ, Cremer C, Grunze M, Knowles BB, Langowski J, McNally J, Pederson T, Politz JC, Pombo A, Schmahl G, Spatz JP, van Driel R: Genome function and nuclear architecture: from gene expression to nanoscience. Genome Res 2003, 13:1029-41.
66. Boyle S, Gilchrist S, Bridger JM, Mahy NL, Ellis JA, Bickmore WA: The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum Mol Genet 2001, 10:211-9.
67. Parada LA, McQueen PG, Munson PJ, Misteli T: Conservation of relative chromosome positioning in normal and cancer cells. Current Biology 2002, 12:1692-1697.
68. Roix JJ, McQueen PG, Munson PJ, Parada LA, Misteli T: Spatial proximity of translocation-prone gene loci in human lymphomas. Nat Genet 2003, 34:287-291.
69. Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, van Sluis P, Hermus MC, van Asperen R, Boon K, Voute PA, Heisterkamp S, van Kampen A, Versteeg R: The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 2001, 291:1289-1292.
70. Cooke MS, Evans MD, Dizdaroglu M, Lunec J: Oxidative DNA damage: mechanisms, mutation, and disease. FASEB J 2003, 17:1195-1214.
71. Hussain SP, Hofseth LJ, Harris CC: Radical causes of cancer. Nat Rev Cancer 2003, 3:276-285.
72. Tchirkov A, Lansdorp PM: Role of oxidative stress in telomere shortening in cultured fibroblasts from normal individuals and patients with ataxia-telangiectasia. Hum Mol Genet 2003, 12:227-32.
73. Thompson HL, Schild D: Recombinational DNA repair and human disease. Mutat Res 2002, 509:49-78.
74. German J: Bloom syndrome: a Mendelian prototype of somatic mutational disease. Medicine 1993, 72:393-406.
75. Van Brabant AJ, Stan R, Ellis NA: DNA helicases, genomic instability, and human genetic disease. Annu Rev Genomics Hum Genet 2000, 1:409-459.
76. Haaf T, Schmid M: Experimental condensation inhibition in constitutive and facultative heterochromatin of mammalian chromosomes. Cytogenet Cell Genet 2000, 91:113-23.
77. Tuck-Muller CM, Narayan A, Tsien F, Smeets DF, Sawyer J, Fiala ES, Sohn OS, Ehrlich M: DNA hypomethylation and unusual chromosome instability in cell lines from ICF syndrome patients. Cytogenet Cell Genet 2000, 89:121-8.
78. Baylin SB, Esteller M, Rountree MR, Bachman KE, Schuebel K, Herman JG: Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer. Hum Mol Genet 2001, 10:687-692.
79. Rieder CL, Khodjakov A: Mitosis through the microscope: advances in seeing inside live dividing cells. Science 2003, 300:91-96.
80. Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG: High-resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998, 20:207-211.