Two breakpoint clusters at fragile site FRA3B form phased nucleosomes

Genome Research

Volumn 14, Issue 7, 2004, Pages 1350-1357

  Mulvihill, David J ^a   Wang, Yuh Hwa ^a  

^a RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APHIDICOLIN; ENDONUCLEASE; FRAGILE HISTIDINE TRIAD PROTEIN; GENOMIC DNA;

ARTICLE; CHROMATIN STRUCTURE; CHROMOSOME BREAKAGE; CHROMOSOME DELETION; CHROMOSOME FRAGILE SITE; CHROMOSOME TRANSLOCATION; CONTROLLED STUDY; DNA SEQUENCE; DOWNSTREAM PROCESSING; GENE CLUSTER; GENE EXPRESSION; HUMAN; HUMAN CELL; INTRON; METAPHASE CHROMOSOME; NUCLEOSOME; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION;

ACID ANHYDRIDE HYDROLASES; BINDING SITES; BIOLOGICAL FACTORS; CELL LINE, TRANSFORMED; CELL LINE, TUMOR; CHROMATIN; CHROMOSOME BREAKAGE; CHROMOSOME MAPPING; DEOXYRIBONUCLEASE I; DNA, NEOPLASM; HELA CELLS; HERPESVIRUS 4, HUMAN; HETEROCHROMATIN; HUMANS; LYMPHOCYTES; METAPHASE; NEOPLASM PROTEINS; NUCLEIC ACID CONFORMATION; NUCLEOSOMES;

EID: 3543139536     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.2304404     Document Type: Article

References (32)

1. Boldog, F., Gemmill, R.M., West, J., Robinson, M., Robinson, L., Li, E., Roche, J., Todd, S., Waggoner, B., Lundstrom, R., et al. 1997. Chromosome 3p14 homozygous deletions and sequence analysis of FRA3B. Hum. Mol. Genet. 6: 193-203.
2. Casper, A.M., Nghiem, P., Arlt, M.F., and Glover, T.W. 2002. ATR regulates fragile site stability. Cell 111: 779-789.
3. Coffee, B., Zhang, F., Ceman, S., Warren, S.T., and Reines, D. 2002. Histone modifications depict an aberrantly heterochromatinized FMR1 gene in fragile x syndrome. Am. J. Hum. Genet. 71: 923-932.
4. Corbin, S., Neilly, M.E., Espinosa III, R., Davis, E.M., McKeithan, T.W., and Le Beau, M.M. 2002. Identification of unstable sequences within the common fragile site at 3p14.2: Implications for the mechanism of deletions within fragile histidine triad gene/common fragile site at 3p14.2 in tumors. Cancer Res. 62: 3477-3484.
5. Eberhart, D.E. and Warren, S.T. 1996. Nuclease sensitivity of permeabilized cells confirms altered chromatin formation at the fragile X locus. Somat. Cell Mol. Genet. 22: 435-441.
6. Englander, E.W. and Howard, B.H. 1995. Nucleosome positioning by human Alu elements in chromatin. J. Biol. Chem. 270: 10091-10096.
7. Englander, E.W., Wolffe, A.P., and Howard, B.H. 1993. Nucleosome interactions with a human Alu element. Transcriptional repression and effects of template methylation. J. Biol. Chem. 268: 19565-19573.
8. Godde, J.S., Kass, S.U., Hirst, M.C., and Wolffe, A.P. 1996. Nucleosome assembly on methylated CGG triplet repeats in fragile X mental retardation gene 1 promoter. J. Biol. Chem. 271: 24325-24328.
9. Hansen, R.S., Canfield, T.K., Field, A.D., Mumm, S., Laird, C.D., and Gartler, S.M. 1997. A variable domain of delayed replication in FRAXA fragile X chromosomes: X inactivation-like spread of late replication. Proc. Natl. Acad. Sci. 94: 4587-4592.
10. Hellman, A., Rahat, A., Scherer, S.W., Darvasi, A., Tsui, L.C., and Kerem, B. 2000. Replication delay along FRA7H, a common fragile site on human chromosome 7, leads to chromosomal instability. Mol. Cell. Biol. 20: 4420-4427.
11. Hellman, A., Zlotorynski, E., Scherer, S.W., Cheung, J., Vincent, J.B., Smith, D., Trakhtenbrot, L., and Kerem, B. 2002. A role for common fragile site induction in amplification of human oncogenes. Cancer Cell 1: 89-97.
12. Hsu, Y.-Y. and Wang, Y.-H. 2002. Human fragile site FRA16B DNA excludes nucleosomes in the presence of distamycin. J. Biol. Chem. 277: 17315-17319.
13. Huebner, K. and Croce, C.M. 2001. FRA3B and other common fragile sites: The weakest links. Nat. Rev. Cancer 1: 214-221.
14. Le Beau, M.M., Rassool, F.V., Neilly, M.E., Espinosa III, R., Glover, T.W., Smith, D.I., and McKeithan, T.W. 1998. 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. 7: 755-761.
15. Loyola, A., LeRoy, G., Wang, Y.-H., and Remberg, D. 2001. Reconstitution of recombination chromatin establishes a requirement for histone-tail modifications during chromatin assembly and transcription. Genes & Dev. 15: 2837-2851.
16. Michael, D. and Rajewsky, M.F. 2001. Induction of the common fragile site FRA3B does not affect FHIT expression. Oncogene. 20: 1798-1801.
17. Miller, S.A., Dykes, D.D., and Polesky, H.F. 1988. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16: 1215.
18. Mimori, K., Druck, T., Inoue, H., Alder, H., Berk, L., Mori, M., Huebner, K., and Croce, C.M. 1999. Cancer-specific chromosome alterations in the constitutive fragile region FRA3B. Proc. Natl. Acad. Sci. 96: 7456-7461.
19. Mishmar, D., Rabat, A., Scherer, S.W., Nyakatura, G., Hinzmann, B., Kohwi, Y., Mandel-Gutfroind, Y., Lee, J.R., Drescher, B., Sas, D.E., et al. 1998. 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. 95: 8141-8146.
20. Ohta, M., Inoue, H., Cotticelli, M.G., Kastury, K., Baffa, R., Palazzo, J., Siprashvili, Z., Mori, M., McCue, P., Druck, T., et al. 1996. The FHIT gene, spanning the chromosome 3p14.2 fragile site and renal carcinoma-associated t(3;8) breakpoint, is abnormal in digestive tract cancers. Cell 84: 587-597.
21. Pieretti, M., Zhang, F., Fu, Y.H., Warren, S.T., Oostra, B.A., Caskey, C.T., and Nelson, D.L. 1991. Absence of expression of the FMR1 gene in fragile X syndrome. Cell 66: 817-822.
22. Richards, R.I. 2001. Fragile and unstable chromosomes in cancer: Causes and consequences. Trends Genet. 17: 339-345.
23. Sarai, A., Mazur, J., Nussinov, R., and Jernigan, R.L. 1989. Sequence dependence of DNA conformational flexibility. Biochemistry 28: 7842-7849.
24. Shimada, T., Inokuchi, K., and Nienhuis, A.W. 1986. Chromatin structure of the human dihydrofolate reductase gene promoter. Multiple protein-binding sites. J. Biol. Chem. 261: 1445-1452.
25. Subramanian, P.S., Nelson, D.L., and Chinault, A.C. 1996. Large domains of apparent delayed replication timing associated with triplet repeat expansion at FRAXA and FRAXE. Am. J. Hum. Genet. 59: 407-416.
26. Sutherland, G.R. 1991. Chromosomal fragile sites. Genet. Anal. Tech. Appl. 8: 161-166.
27. Travers, A. and Drew, H. 1997. DNA recognition and nucleosome organization. Biopolymers 44: 423-433.
28. Usdin, K. and Woodford, K.J. 1995. CGG repeats associated with DNA instability and chromosome fragility form structures that block DNA synthesis in vitro. Nucleic Acids Res. 23: 4202-4209.
29. Wang, L., Paradee, W., Mullins, C., Shridhar, R., Rosati, R., Wilke, C.M., Glover, T.W., and Smith, D.I. 1997. Aphidicolin-induced FRA3B breakpoints cluster in two distinct regions. Genomics 41: 485-488.
30. Wang, L., Darling, J., Zhang, J.S., Huang, H., Liu, W., and Smith, D.I. 1999. Allele-specific late replication and fragility of the most active common fragile site, FRA3B. Hum. Mol. Genet. 8: 431-437.
31. Wang, Y.-H. and Griffith, J.D. 1996. Methylation of expanded CCG triplet repeat DNA from fragile X syndrome patients enhances nucleosome exclusion J. Biol. Chem. 271: 22937-22940.
32. Wang, Y.-H., Gellibolian, R., Shimizu, M., Wells, R.D. and Griffith, J.D. 1996. Long CCG triplet repeat blocks exclude nucleosomes: A possible mechanism for the nature of fragile sites in chromosomes. J. Mol. Biol. 263: 511-516.