DNA secondary structures and epigenetic determinants of cancer genome evolution

Nature Structural and Molecular Biology

Volumn 18, Issue 8, 2011, Pages 950-955

  De, Subhajyoti ^a,b   Michor, Franziska ^a,b  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GUANINE QUADRUPLEX;

ARTICLE; CANCER CLASSIFICATION; COPY NUMBER VARIATION; DNA METHYLATION; DNA STRAND BREAKAGE; DNA STRUCTURE; EPIGENETICS; GENE SEQUENCE; GENETIC CONSERVATION; GENOME ANALYSIS; HUMAN; HUMAN CELL; PRIORITY JOURNAL; TUMOR GENE;

DNA BREAKS; DNA COPY NUMBER VARIATIONS; DNA METHYLATION; DNA, NEOPLASM; EPIGENESIS, GENETIC; GENOMIC INSTABILITY; HUMANS; MODELS, MOLECULAR; NEOPLASMS; NUCLEIC ACID CONFORMATION;

EID: 79961029908     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.2089     Document Type: Article

References (50)

1. Hanahan, D. & Weinberg, R.A. The hallmarks of cancer. Cell 100, 57-70 (2000). (Pubitemid 30046295)
2. Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899-905 (2010).
3. Leary, R.J. et al. Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc. Natl. Acad. Sci. USA 105, 16224-16229 (2008).
4. Parsons, D.W. et al. An integrated genomic analysis of human glioblastoma multiforme. Science 321, 1807-1812 (2008).
5. Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-1068 (2008).
6. Kim, J.I. et al. A highly annotated whole-genome sequence of a Korean individual. Nature 460, 1011-1015 (2009).
7. Stephens, P.J. et al. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 462, 1005-1010 (2009).
8. Feinberg, A.P., Ohlsson, R. & Henikoff, S. The epigenetic progenitor origin of human cancer. Nat. Rev. Genet. 7, 21-33 (2006). (Pubitemid 41828945)
9. Hastings, P.J., Lupski, J.R., Rosenberg, S.M. & Ira, G. Mechanisms of change in gene copy number. Nat. Rev. Genet. 10, 551-564 (2009).
10. Stratton, M.R., Campbell, P.J. & Futreal, P.A. The cancer genome. Nature 458, 719-724 (2009).
11. Wang, G., Christensen, L.A. & Vasquez, K.M. Z-DNA-forming sequences generate large-scale deletions in mammalian cells. Proc. Natl. Acad. Sci. USA 103, 2677-2682 (2006).
12. Wang, G. & Vasquez, K.M. Naturally occurring H-DNA-forming sequences are mutagenic in mammalian cells. Proc. Natl. Acad. Sci. USA 101, 13448-13453 (2004). (Pubitemid 39238423)
13. Zhao, J., Bacolla, A., Wang, G. & Vasquez, K.M. Non-B DNA structure-induced genetic instability and evolution. Cell. Mol. Life Sci. 67, 43-62 (2010).
14. Huppert, J.L. Structure, location and interactions of G-quadruplexes. FEBS J. 277, 3452-3458 (2010).
15. Lipps, H.J. & Rhodes, D. G-quadruplex structures: in vivo evidence and function. Trends Cell Biol. 19, 414-422 (2009).
16. Maizels, N. Dynamic roles for G4 DNA in the biology of eukaryotic cells. Nat. Struct. Mol. Biol. 13, 1055-1059 (2006). (Pubitemid 44885914)
17. Sun, D. & Hurley, L.H. Biochemical techniques for the characterization of G-quadruplex structures: EMSA, DMS footprinting, and DNA polymerase stop assay. Methods Mol. Biol. 608, 65-79 (2010).
18. Kruisselbrink, E. et al. Mutagenic capacity of endogenous G4 DNA underlies genome instability in FANCJ-defective C. elegans. Curr. Biol. 18, 900-905 (2008).
19. Pontier, D.B., Kruisselbrink, E., Guryev, V. & Tijsterman, M. Isolation of deletion alleles by G4 DNA-induced mutagenesis. Nat. Methods 6, 655-657 (2009).
20. Boán, F. & Gomez-Marquez, J. In vitro recombination mediated by G-quadruplexes. ChemBioChem 11, 331-334 (2010).
21. Eden, A., Gaudet, F., Waghmare, A. & Jaenisch, R. Chromosomal instability and tumors promoted by DNA hypomethylation. Science 300, 455 (2003). (Pubitemid 36444319)
22. Kanai, Y. Genome-wide DNA methylation profiles in precancerous conditions and cancers. Cancer Sci. 101, 36-45 (2010).
23. Carbone, L. et al. Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution. PLoS Genet. 5, e1000538 (2009).
24. Halder, K., Halder, R. & Chowdhury, S. Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals. Mol. Biosyst. 5, 1703-1712 (2009).
25. Huppert, J.L. & Balasubramanian, S. G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res. 35, 406-413 (2007). (Pubitemid 46232058)
26. Wong, H.M. & Huppert, J.L. Stable G-quadruplexes are found outside nucleosome-bound regions. Mol. Biosyst. 5, 1713-1719 (2009).
27. Behe, M. & Felsenfeld, G. Effects of methylation on a synthetic polynucleotide: the B-Z transition in poly(dG-m5dC)•poly(dG-m5dC). Proc. Natl. Acad. Sci. USA 78, 1619-1623 (1981).
28. Vargason, J.M. & Ho, P.S. The effect of cytosine methylation on the structure and geometry of the Holliday junction: the structure of d(CCGGTACm5CGG) at 1.5 A resolution. J. Biol. Chem. 277, 21041-21049 (2002). (Pubitemid 34967415)
29. Tsumagari, K. et al. Epigenetics of a tandem DNA repeat: chromatin DNaseI sensitivity and opposite methylation changes in cancers. Nucleic Acids Res. 36, 2196-2207 (2008). (Pubitemid 351566994)
30. Halder, R. et al. Guanine quadruplex DNA structure restricts methylation of CpG dinucleotides genome-wide. Mol. Biosyst. 6, 2439-2447 (2010).
31. O'Neil, J. & Look, A.T. Mechanisms of transcription factor deregulation in lymphoid cell transformation. Oncogene 26, 6838-6849 (2007). (Pubitemid 47585107)
32. Sen, D. & Gilbert, W. Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature 334, 364-366 (1988).
33. Sundquist, W.I. & Klug, A. Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops. Nature 342, 825-829 (1989). (Pubitemid 20023821)
34. Williamson, J.R., Raghuraman, M.K. & Cech, T.R. Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell 59, 871-880 (1989). (Pubitemid 20022377)
35. Rhead, B. et al. The UCSC Genome Browser database: update 2010. Nucleic Acids Res. 38, D613-D619 (2010).
36. Durkin, S.G. & Glover, T.W. Chromosome fragile sites. Annu. Rev. Genet. 41, 169-192 (2007).
37. Mani, P., Yadav, V.K., Das, S.K. & Chowdhury, S. Genome-wide analyses of recombination prone regions predict role of DNA structural motif in recombination. PLoS ONE 4, e4399 (2009).
38. Huppert, J.L. & Balasubramanian, S. Prevalence of quadruplexes in the human genome. Nucleic Acids Res. 33, 2908-2916 (2005). (Pubitemid 41511230)
39. Gehring, K., Leroy, J.L. & Gueron, M. A tetrameric DNA structure with protonated cytosine•cytosine base pairs. Nature 363, 561-565 (1993). (Pubitemid 23186646)
40. Sun, D. & Hurley, L.H. The importance of negative superhelicity in inducing the formation of G-quadruplex and i-motif structures in the c-Myc promoter: implications for drug targeting and control of gene expression. J. Med. Chem. 52, 2863-2874 (2009).
41. Crabbe, L., Verdun, R.E., Haggblom, C.I. & Karlseder, J. Defective telomere lagging strand synthesis in cells lacking WRN helicase activity. Science 306, 1951-1953 (2004). (Pubitemid 39627862)
42. Sarkies, P., Reams, C., Simpson, L.J. & Sale, J.E. Epigenetic instability due to defective replication of structured DNA. Mol. Cell 40, 703-713 (2010).
43. Basundra, R. et al. A novel G-quadruplex motif modulates promoter activity of human thymidine kinase 1. FEBS J. 277, 4254-4264 (2010).
44. Irizarry, R.A. et al. The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet. 41, 178-186 (2009).
45. Mekmaysy, C.S. et al. Effect of O6-methylguanine on the stability of G-quadruplex DNA. J. Am. Chem. Soc. 130, 6710-6711 (2008). (Pubitemid 351748399)
46. Shann, Y.J. et al. Genome-wide mapping and characterization of hypomethylated sites in human tissues and breast cancer cell lines. Genome Res. 18, 791-801 (2008).
47. Sadikovic, B. et al. In vitro analysis of integrated global high-resolution DNA methylation profiling with genomic imbalance and gene expression in osteosarcoma. PLoS ONE 3, e2834 (2008).
48. Chodavarapu, R.K. et al. Relationship between nucleosome positioning and DNA methylation. Nature 466, 388-392 (2010).
49. Maegawa, S. et al. Widespread and tissue specific age-related DNA methylation changes in mice. Genome Res. 20, 332-340 (2010).
50. Futreal, P.A. et al. A census of human cancer genes. Nat. Rev. Cancer 4, 177-183 (2004). (Pubitemid 38337497)