Over half of breakpoints in gene pairs involved in cancer-specific recurrent translocations are mapped to human chromosomal fragile sites

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Burrow, Allison A ^a   Williams, Laura E ^a   Pierce, Levi C T ^b   Wang, Yuh Hwa ^a  

^a WAKE FOREST SCHOOL OF MEDICINE   (United States)

^b University of Kansas   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HIGH MOBILITY GROUP A PROTEIN; LAMININ ALPHA4; MIXED LINEAGE LEUKEMIA PROTEIN; PROTEIN AFF4; PROTEIN CBFB; PROTEIN MYH11; TUMOR PROTEIN; UNCLASSIFIED DRUG; DNA;

ARTICLE; AT RICH SEQUENCE; CANCER GROWTH; CHROMOSOME BREAKAGE; CHROMOSOME FRAGILE SITE; CHROMOSOME PAIRING; CHROMOSOME TRANSLOCATION; CONTROLLED STUDY; DNA FLANKING REGION; DNA SEQUENCE; GENE MAPPING; GENE REARRANGEMENT; GENE STRUCTURE; HUMAN; HUMAN CHROMOSOME; MALIGNANT NEOPLASTIC DISEASE; NUCLEOTIDE SEQUENCE; STRUCTURAL CHROMOSOME ABERRATION; TUMOR CELL; BIOLOGY; CONFORMATION; GENE TRANSLOCATION; GENETIC DATABASE; GENETICS; HUMAN GENOME; NEOPLASM;

CHROMOSOME BREAKAGE; CHROMOSOME FRAGILE SITES; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA; GENOME, HUMAN; HUMANS; NEOPLASMS; NUCLEIC ACID CONFORMATION; SEQUENCE ANALYSIS, DNA; TRANSLOCATION, GENETIC;

EID: 60549094865     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-59     Document Type: Article

References (48)

1. Gasparini P Sozzi G Pierotti MA The role of chromosomal alterations in human cancer development J Cell Biochem 2007, 102(2):320-331. 10.1002/ jcb.21481 17722107
2. Keen-Kim D Nooraie F Rao PN Cytogenetic biomarkers for human cancer Front Biosci 2008, 13:5928-5949. 10.2741/3127 18508633
3. Weterings E Chen DJ The endless tale of non-homologous end-joining Cell Res 2008, 18(1):114-124. 10.1038/cr.2008.3 18166980
4. Mitelman F Mertens F Johansson B A breakpoint map of recurrent chromosomal rearrangements in human neoplasia Nat Genet 1997, 15(Spec No):417-474. 10.1038/ng0497supp-417 9140409
5. O'Keefe LV Richards RI Common chromosomal fragile sites and cancer: focus on FRA16D Cancer Lett 2006, 232(1):37-47. 10.1016/ j.canlet.2005.07.041 16242840
6. Richards RI Fragile and unstable chromosomes in cancer: Causes and consequences TRENDS in Genetics 2001, 17:339-345. 10.1016/ S0168-9525(01)02303-4 11377796
7. Glover TW Common fragile sites Cancer Lett 2006, 232(1):4-12. 10.1016/ j.canlet.2005.08.032 16229941
8. Kremer EJ Pritchard M Lynch M Yu S Holman K Baker E Warren ST Schlessinger D Sutherland GR Richards RI Mapping of DNA instability at the fragile X to a trinucleotide repeat sequence p(CCG)n Science 1991, 252(5013):1711-1714. 10.1126/science.1675488 1675488
9. Sutherland GR Baker E Richards RI Fragile sites still breaking Trends Genet 1998, 14(12):501-506. 10.1016/S0168-9525(98)01628-X 9865156
10. Craig-Holmes AP Strong LC Goodacre A Pathak S Variation in the expression of aphidicolin-induced fragile sites in human lymphocyte cultures Hum Genet 1987, 76(2):134-137. 10.1007/BF00284909 3111974
11. Tunca B Egeli U Zorluoglu A Yilmazlar T Yerci O Kizil A The expression of fragile sites in lymphocytes of patients with rectum cancer and their first-degree relatives Cancer Lett 2000, 152(2):201-209. 10.1016/ S0304-3835(00)00334-7 10773413
12. Popescu NC Genetic alterations in cancer as a result of breakage at fragile sites Cancer Lett 2003, 192:1-17. 10.1016/S0304-3835(02)00596-7 12637148
13. Yunis JJ Soreng AL Constitutive fragile sites and cancer Science 1984, 226(4679):1199-1204. 10.1126/science.6239375 6239375
14. Durkin SG Glover TW Chromosome fragile sites Annu Rev Genet 2007, 41:169-192. 10.1146/annurev.genet.41.042007.165900 17608616
15. Re A Cora D Puliti AM Caselle M Sbrana I Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis BMC Bioinformatics 2006, 7:413. 1601973 16981993 10.1186/1471-2105-7-413
16. Durkin SG Ragland RL Arlt MF Mulle JG Warren ST Glover TW Replication stress induces tumor-like microdeletions in FHIT/FRA3B Proc Natl Acad Sci USA 2008. 105(1):246-251. 2224195 18162546 10.1073/pnas.0708097105
17. Mishmar D Rahat A Scherer SW Nyakatura G Hinzmann B Kohwi Y Mandel-Gutfroind Y Lee JR Drescher B Sas DE Margalit H Platzer M Weiss A Tsui LC Rosenthal A Kerem B Molecular characterization of a common fragile site (FRA7H) on human chromosome 7 by the cloning of a simian virus 40 integration site Proc Natl Acad Sci USA 1998. 95(14):8141-8146. 20943 9653154 10.1073/pnas.95.14.8141
18. Zlotorynski E Rahat A Skaug J Ben-Porat N Ozeri E Hershberg R Levi A Scherer SW Margalit H Kerem B Molecular basis for expression of common and rare fragile sites Mol Cell Biol 2003, 23(20):7143-7151. 230307 14517285 10.1128/MCB.23.20.7143-7151.2003
19. Hansen RS Canfield TK Fjeld AD Mumm S Laird CD Gartler SM A variable domain of delayed replication in FRAXA fragile X chromosomes: X inactivation-like spread of late replication Proc Natl Acad Sci USA 1997, 94(9):4587-4592. 20767 9114034 10.1073/pnas.94.9.4587
20. Hellman A Rahat A Scherer SW Darvasi A Tsui LC Kerem B Replication delay along FRA7H, a common fragile site on human chromosome 7, leads to chromosomal instability Mol Cell Biol 2000, 20(12):4420-4427. 85809 10825205 10.1128/MCB.20.12.4420-4427.2000
21. Le Beau MM Rassool FV Neilly ME Espinosa R 3rd Glover TW Smith DI McKeithan TW Replication of a common fragile site, FRA3B, occurs late in S phase and is delayed further upon induction: Implications for the mechanism of fragile site induction Hum Mol Genet 1998, 7(4):755-761. 10.1093/hmg/7.4.755 9499431
22. Handt O Baker E Dayan S Gartler SM Woollatt E Richards RI Hansen RS Analysis of replication timing at the FRA10B and FRA16B fragile site loci Chromosome Res 2000, 8(8):677-688. 10.1023/A:1026737203447 11196131
23. Freudenreich CH Molecular mechanisms of chromosome fragility Chemtracts - Biochemistry and Molecular Biology 2005, 18:141-152.
24. Zhang H Freudenreich CH An AT-rich sequence in human common fragile site FRA16D causes fork stalling and chromosome breakage in S. cerevisiae Molecular Cell 2007, 27:367-379. 2144737 17679088 10.1016/ j.molcel.2007.06.012
25. Casper AM Nghiem P Arlt MF Glover TW ATR regulates fragile site stability Cell 2002, 111:779-789. 10.1016/S0092-8674(02)01113-3 12526805
26. Novo FJ de Mendibil IO Vizmanos JL TICdb: A collection of gene-mapped translocation breakpoints in cancer BMC Genomics 2007, 8:33. 1794234 17257420 10.1186/1471-2164-8-33
27. Mitelman F Johansson B Mertens F Mitelman Database of Chromosome Aberrations in Cancer 2008 http://cgap.nci.nih.gov/Chromosomes/Mitelman
28. Smith DI McAvoy S Zhu Y Perez DS Large common fragile site genes and cancer Semin Cancer Biol 2007. 17(1):31-41. 10.1016/ j.semcancer.2006.10.003 17140807
29. Arlt MF Durkin SG Ragland RL Glover TW Common fragile sites as targets for chromosome rearrangements DNA Repair 2006, 5:1126-1135. 10.1016/ j.dnarep.2006.05.010 16807141
30. Fechter A Buettel I Kuehnel E Schwab M Savelyeva L Cloning of genetically tagged chromosome break sequences reveals new fragile sites at 6p21 and 13q22 Int J Cancer 2007, 120(11):2359-2367. 10.1002/ ijc.22564 17290399
31. Arlt MF Xu B Durkin SG Casper AM Kastan MB Glover TW BRCA1 is required for common-fragile-site stability via its G 2/M checkpoint function Mol Cell Biol 2004, 24(15):6701-6709. 10.1128/MCB.24.15.6701-6709.2004 15254237 444841
32. Howlett NG Taniguchi T Durkin SG D'Andrea AD Glover TW The Fanconi anemia pathway is required for the DNA replication stress response and for the regulation of common fragile site stability Hum Mol Genet 2005, 14:693-701. 10.1093/hmg/ddi065 15661754
33. Durkin SG Arlt MF Howlett NG Glover TW Depletion of CHK1, but not CHK2, induces chromosomal instability and breaks at common fragile sites Oncogene 2006, 25(32):4381-4388. 10.1038/sj.onc.1209466 16732333
34. Lopes M Cotta-Ramusino C Pellicioli A Liberi G Plevani P Muzi-Falconi M Newlon CS Foiani M The DNA replication checkpoint response stabilizes stalled replication forks Nature 2001. 412(6846):557-561. 10.1038/ 35087613 11484058
35. Tercero JA Diffley JF Regulation of DNA replication fork progression through damaged DNA by the Mec1/Rad53 checkpoint Nature 2001, 412(6846):553-557. 10.1038/35087607 11484057
36. Ozeri-Galai E Schwartz M Rahat A Kerem B Interplay between ATM and ATR in the regulation of common fragile site stability Oncogene 2008, 27:2109-2117. 10.1038/sj.onc.1210849 17934520
37. Kanaar R Hoeijmakers JH van Gent DC Molecular mechanisms of DNA double strand break repair Trends Cell Biol 1998, 8(12):483-489. 10.1016/ S0962-8924(98)01383-X 9861670
38. Pfeiffer P Goedecke W Obe G Mechanisms of DNA double-strand break repair and their potential to induce chromosomal aberrations Mutagenesis 2000, 15(4):289-302. 10.1093/mutage/15.4.289 10887207
39. Gottlich B Reichenberger S Feldmann E Pfeiffer P Rejoining of DNA double-strand breaks in vitro by single-strand annealing Eur J Biochem 1998, 258(2):387-395. 10.1046/j.1432-1327.1998.2580387.x 9874203
40. Lieber MR Raghavan SC Yu K Mechanistic aspects of lymphoid chromosomal translocations J Natl Cancer Inst Monogr 2008, 39:8-11. 10.1093/ jncimonographs/lgn012 18647994
41. Schwartz M Zlotorynski E Goldberg M Ozeri E Rahat A le Sage C Chen BP Chen DJ Agami R Kerem B Homologous recombination and nonhomologous end-joining repair pathways regulate fragile site stability Genes Dev 2005, 19(22):2715-2726. 1283964 16291645 10.1101/gad.340905
42. Klugbauer S Pfeiffer P Gassenhuber H Beimfohr C Rabes HM RET rearrangements in radiation-induced papillary thyroid carcinomas: High prevalence of topoisomerase I sites at breakpoints and microhomology-mediated end joining in ELE1 and RET chimeric genes Genomics 2001, 73(2):149-160. 10.1006/geno.2000.6434 11318605
43. Sutherland GRBE Richards RI Fragile Sites Encyclopedia of Molecular Biology and Molecular Medicine 1996, 2:313-318.
44. Rozier L El-Achkar E Apiou F Debatisse M Characterization of a conserved aphidicolin-sensitive common fragile site at human 4q22 and mouse 6C1: possible association with an inherited disease and cancer Oncogene 2004, 23(41):6872-6880. 10.1038/sj.onc.1207809 15286716
45. Karadeniz NN Tunca Y Imirzalioglu N New heritable fragile site at 15q13 in both members of a nonconsanguineous couple Am J Med Genet A 2003, 118A(3):290-292. 10.1002/ajmg.a.10196 12673662
46. Zuker M Mfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res 2003, 31(13):3406-3415. 169194 12824337 10.1093/nar/gkg595
47. Anderson S DePamphilis ML Metabolism of Okazaki fragments during simian virus 40 DNA replication The Journal of biological chemistry 1979, 254(22):11495-11504. 227871
48. Hay RT DePamphilis ML Initiation of SV40 DNA replication in vivo: location and structure of 5' ends of DNA synthesized in the ori region Cell 1982, 28(4):767-779. 10.1016/0092-8674(82)90056-3 6178514