Common fragile sites are characterized by histone hypoacetylation

Human Molecular Genetics

Volumn 18, Issue 23, 2009, Pages 4501-4512

  Jiang, Yanwen ^a   Lucas, Isabelle ^a   Young, David J ^a   Davis, Elizabeth M ^a   Karrison, Theodore ^a   Rest, Joshua S ^b   Le Beau, Michelle M ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b STONY BROOK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5 AZA 2' DEOXYCYTIDINE; CAFFEINE; HISTONE; NUCLEASE; TRICHOSTATIN A;

ACETYLATION; ARTICLE; CHROMATIN; CHROMOSOME BREAKAGE; CHROMOSOME FRAGILE SITE; CHROMOSOME REPLICATION; CONFORMATION; CONTROLLED STUDY; EPIGENETICS; GENETIC STABILITY; HUMAN; HUMAN CELL; HYPOTHESIS; PRIORITY JOURNAL; PROTEIN METHYLATION;

ACETYLATION; CELL LINE; CHROMATIN; CHROMOSOME FRAGILE SITES; EPIGENESIS, GENETIC; FEMALE; GENOME, HUMAN; GENOMIC INSTABILITY; HISTONES; HUMANS;

EID: 70449388892     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddp410     Document Type: Article

References (39)

1. Glover, T.W. (2006) Common fragile sites. Cancer Lett., 232, 4-12.
2. Gorgoulis, V.G., Vassiliou, L.V., Karakaidos, P., Zacharatos, P., Kotsinas, A., Liloglou, T., Venere, M., Ditullio, R.A. Jr, Kastrinakis, N.G., Levy, B. et al. (2005) Activation of the DNA damage checkpoint and genomic instability in human precancerous lesions. Nature, 434, 907-913 (see comment).
3. Lucas, I., Palakodeti, A. and Le Beau, M.M. (2007) The implications of replication in common fragile site induction. In Arrieta, I., Penagarikano, O. and Télez, M. (eds), Fragile Site. Nova Science Publishers Inc, Hauppauge, USA, pp. 67-98.
4. 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.
5. Le Beau, M.M., Rassool, F.V., Neilly, M.E., Espinosa, R. 3rd, 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.
6. El Achkar, E., Gerbault-Seureau, M., Muleris, M., Dutrillaux, B. and Debatisse, M. (2005) Premature condensation induces breaks at the interface of early and late replicating chromosome bands bearing common fragile sites. Proc. Natl. Acad. Sci. USA, 102, 18069-18074.
7. Harvey, K.J. and Newport, J. (2003) CpG methylation of DNA restricts prereplication complex assembly in Xenopus egg extracts. Mol. Cell. Biol., 23, 6769-6779.
8. Vogelauer, M., Rubbi, L., Lucas, I., Brewer, B.J. and Grunstein, M. (2002) Histone acetylation regulates the time of replication origin firing. Mol. Cell, 10, 1223-1233.
9. Kemp, M.G., Ghosh, M., Liu, G. and Leffak, M. (2005) The histone deacetylase inhibitor trichostatin A alters the pattern of DNA replication origin activity in human cells. Nucleic Acids Res., 33, 325-336 [erratum appears in Nucleic Acids Res. 2005;33(2):805].
10. Dazy, S., Gandrillon, O., Hyrien, O. and Prioleau, M.N. (2006) Broadening of DNA replication origin usage during metazoan cell differentiation. EMBO Rep., 7, 806-811 (see comment).
11. Lucas, I., Palakodeti, A., Jiang, Y., Young, D.J., Jiang, N., Fernald, A.A. and Le Beau, M.M. (2007) High-throughput mapping of origins of replication in human cells. EMBO Rep., 8, 770-777.
12. Wilke, C.M., Hall, B.K., Hoge, A., Paradee, W., Smith, D.I. and Glover, T.W. (1996) FRA3B extends over a broad region and contains a spontaneous HPV16 integration site: Direct evidence for the coincidence of viral integration sites and fragile sites. Hum. Mol. Genet., 5, 187-195.
13. Rassool, F.V., Le Beau, M.M., Shen, M.L., Neilly, M.E., Espinosa, R. 3rd, Ong, S.T., Boldog, F., Drabkin, H., McCarroll, R. and McKeithan, T.W. (1996) Direct cloning of DNA sequences from the common fragile site region at chromosome band 3p14.2. Genomics, 35, 109-117.
14. Arlt, M.F., Miller, D.E., Beer, D.G. and Glover, T.W. (2002) Molecular characterization of FRAXB and comparative common fragile site instability in cancer cells. Genes Chromosomes Cancer, 33, 82-92.
15. Krummel, K.A., Roberts, L.R., Kawakami, M., Glover, T.W. and Smith, D.I. (2000) The characterization of the common fragile site FRA16D and its involvement in multiple myeloma translocations. Genomics, 69 37-46.
16. Mishmar, D., Rahat, 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. USA, 95, 8141-8146.
17. Huang, H., Qian, C., Jenkins, R.B. and Smith, D.I. (1998) Fish mapping of YAC clones at human chromosomal band 7q31.2: Identification of YACS spanning FRA7G within the common region of LOH in breast and prostate cancer. Genes Chromosomes Cancer, 21, 152-159.
18. Limongi, M.Z., Pelliccia, F. and Rocchi, A. (2003) Characterization of the human common fragile site FRA2G. Genomics, 81, 93-97.
19. Yunis, J.J., Soreng, A.L. and Bowe, A.E. (1987) Fragile sites are targets of diverse mutagens and carcinogens. Oncogene, 1, 59-69.
20. Glover, T.W., Berger, C., Coyle, J. and Echo, B. (1984) DNA polymerase alpha inhibition by aphidicolin induces gaps and breaks at common fragile sites in human chromosomes. Hum. Genet., 67, 136-142.
21. Johnson, D.S., Li, W., Gordon, D.B., Bhattacharjee, A., Curry, B., Ghosh, J., Brizuela, L., Carroll, J.S., Brown, M., Flicek, P. et al. (2008) Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res., 18, 393-403.
22. Koch, C.M., Andrews, R.M., Flicek, P., Dillon, S.C., Karaoz, U., Clelland, G.K., Wilcox, S., Beare, D.M., Fowler, J.C., Couttet, P. et al. (2007) The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res., 17, 691-707.
23. Bieda, M., Xu, X., Singer, M.A., Green, R. and Farnham, P.J. (2006) Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res., 16, 595-605.
24. Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I. and Zhao, K. (2007) High-resolution profiling of histone methylations in the human genome. Cell, 129, 823-837.
25. Zheng, S., Ma, X., Zhang, L., Gunn, L., Smith, M.T., Wiemels, J.L., Leung, K., Buffler, P.A. and Wiencke, J.K. (2004) Hypermethylation of the 5′ CpG island of the FHIT gene is associated with hyperdiploid and translocation-negative subtypes of pediatric leukemia. Cancer Res. 64, 2000-2006.
26. Toledo, F., Coquelle, A., Svetlova, E. and Debatisse, M. (2000) Enhanced flexibility and aphidicolin-induced DNA breaks near mammalian replication origins: Implications for replicon mapping and chromosome fragility. Nucleic Acids Res., 28, 4805-4813.
27. Zlotorynski, E., Rahat, A., Skaug, J., Ben-Porat, N., Ozeri, E., Hershberg, R., Levi, A., Scherer, S.W., Margalit, H. and Kerem, B. (2003) Molecular basis for expression of common and rare fragile sites. Mol. Cell. Biol., 23, 7143-7151.
28. Smith, D.I., McAvoy, S., Zhu, Y. and Perez, D.S. (2007) Large common fragile site genes and cancer. Seminars Cancer Biol., 17, 31-41.
29. Zhang, H. and Freudenreich, C.H. (2007) An AT-rich sequence in human common fragile site FRA16D causes fork stalling and chromosome breakage in S. cerevisiae. Mol. Cell, 27, 367-379.
30. Tabancay, A.P. Jr and Forsburg, S.L. (2006) Eukaryotic DNA replication in a chromatin context. Curr. Top. Dev. Biol., 76, 129-184.
31. Iizuka, M., Matsui, T., Takisawa, H. and Smith, M.M. (2006) Regulation of replication licensing by acetyltransferase Hbo1. Mol. Cell. Biol. 26, 1098-1108.
32. Calvi, B.R., Byrnes, B.A. and Kolpakas, A.J. (2007) Conservation of epigenetic regulation, ORC binding and developmental timing of DNA replication origins in the genus Drosophila. Genetics, 177, 1291-1301.
33. Pandita, T.K. and Richardson, C. (2009) Chromatin remodeling finds its place in the DNA double-strand break response. Nucleic Acids Res., 37, 1363-1377.
34. Klose, R.J. and Bird, A.P. (2006) Genomic DNA methylation: The mark and its mediators. Trends Biochem. Sci., 31, 89-97.
35. Roulston, D. and Le Beau, M. (1997). Cytogenetic analysis of hematologic malignant diseases. In Barch, M.J., Knutsen, T. and Spurbeck, J.L. (eds), The AGT Cytogenetics Laboratory Manual, Lippincott-Raven, Philadelphia, PA.
36. Gilbert, N., Boyle, S., Sutherland, H., de Las Heras, J., Allan, J., Jenuwein, T. and Bickmore, W.A. (2003) Formation of facultative heterochromatin in the absence of HP1. EMBO J., 22, 5540-5550.
37. Becker, N.A., Thorland, E.C., Denison, S.R., Phillips, L.A. and Smith, D.I. (2002) Evidence that instability within the FRA3B region extends four megabases. Oncogene, 21, 8713-8722.
38. Hellman, A., Zlotorynski, E., Scherer, S.W., Cheung, J., Vincent, J.B., Smith, D.I., Trakhtenbrot, L. and Kerem, B. (2002) A role for common fragile site induction in amplification of human oncogenes. Cancer Cell, 1, 89-97.
39. Selzer, R.R., Richmond, T.A., Pofahl, N.J., Green, R.D., Eis, P.S., Nair, P., Brothman, A.R. and Stallings, R.L. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using finetiling oligonucleotide array CGH. Genes Chromosomes Cancer, 44, 305-319.