Transcriptional Processing of G4 DNA

Molecular Carcinogenesis

Volumn 48, Issue 4, 2009, Pages 326-335

  Tornaletti, Silvia ^a,b  

^a UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

^b NONE   (United States)

Author keywords

G4 DNA; Mutagenesis; Transcription coupled repair

Indexed keywords

GUANINE QUADRUPLEX; RNA POLYMERASE; DNA;

CANCER GROWTH; DNA DAMAGE; DNA REPAIR; DNA REPLICATION; DNA SEQUENCE; DNA STRUCTURE; EXCISION REPAIR; GENE EXPRESSION REGULATION; GENETIC PREDISPOSITION; GENETIC TRANSCRIPTION; GENOMIC INSTABILITY; HUMAN; IN VITRO STUDY; MUTAGENESIS; PRIORITY JOURNAL; REVIEW; TRANSCRIPTION REGULATION; ANIMAL; CHEMISTRY; GENETICS;

ANIMALS; DNA; G-QUADRUPLEXES; HUMANS; TRANSCRIPTION, GENETIC;

EID: 65249109998     PISSN: 08991987     EISSN: 10982744     Source Type: Journal    
DOI: 10.1002/mc.20513     Document Type: Review

References (89)

1. Sinden RR. DNA structure and function. San Diego: Academic Press; 1994.
2. Phan AT, Kuryavyi V, Patel DJ. DNA architecture: From G to Z. Curr Opin Struc Biol 2006;16: 288-298.
3. Maizels N. Dynamic roles for G4 DNA in the biology of eukaryotic cells. Nat Struct Mol Biol 2006;13: 1055-1059.
4. Fry M.TetraplexDNAand its interacting proteins. Front Biosci 2007;12: 4336-4351.
5. Wang G, Vasquez KM. Z-DNA, an active element in the genome. Front Biosci 2007;12: 4424-4438.
6. Kouzine F, Levens D. Supercoil-driven DNA structures regulate genetic transactions. Front Biosci 2007;12: 4409-4423.
7. Bacolla A, Wells RD. Non-B DNA conformations, genomic rearrangements, and human disease. J Biol Chem 2004;279: 47411-47414.
8. Bacolla A, Wojciechowska M, Kosmider B, Larson JE, Wells RD. The involvement of non-B DNA structures in gross chromosomal rearrangements. DNA Repair 2006;5: 1161-1170.
9. Wang G, Vasquez KM. Non-B DNA structure-induced genetic instability. Mut Res 2006;598: 103-119.
10. Raghavan SC, Lieber MR. DNA structures at chromosomal translocation sites. BioEssays 2006;28: 480-494.
11. Maizels N. Genomic stability: FANCJ-dependent G4 DNA repair. Curr Biol 2008;18: R613-R614.
12. Mirkin SM. Expandable DNA repeats and human disease. Nature 2007;447: 932-940.
13. Duquette ML, Handa P, Vincent JA, Taylor AF, Maizels N. Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA. Genes Dev 2004;18: 1618-1629.
14. Wang G, Vasquez KM. Naturally occurring H-DNA-forming sequences are mutagenic in mammalian cells. Proc Natl Acad Sci USA 2004;101: 13448-13453.
15. Duquette ML, Pham P, Goodman MF, Maizels N. AID binds to transcription-induced structures in c-MYC that map to regions associated with translocation and hypermutation. Oncogene 2005;24: 5791-5798.
16. Duquette ML, Huber MD, Maizels N. G-rich proto-oncogenes are targeted for genomic instability in B-cell lymphomas. Cancer Res 2007;67: 2586-2594.
17. Wang G, Christensen LA, Vasquez KM. Z-DNA-forming sequences generate large-scale deletions in mammalian cells. Proc Natl Acad Sci USA 2006;103: 2677-2682.
18. Kruisselbrink E, Guryev V, Brouwer K, Pontier DB, Cuppen E, Tijsterman M. Mutagenic capacity of endogenous G4 DNA underlies genome instability in FANCJ-defective C. Elegans. Curr Biol 2008;18: 900-905.
19. Li X, Manley JL. Cotranscriptional processes and their influence on genome stability. Genes Dev 2006; 20:1838-1847.
20. Hanawalt PC. Transcription-coupled repair and human disease. Science 1994; 266:1957-1958.
21. Sen D, Gilbert W. Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications formeiosis. Nature 1988;334: 364-366.
22. SundquistWI,KlugA.TelomericDNAdimerizesbyformation of guanine tetrads between harpin loops. Nature 1989;342: 825-829.
23. Williamson JR, Raghuraman MK, Cech TR. Monovalent cation-induced structure of telomeric DNA: The G quartet model. Cell 1989;59: 871-880.
24. Huppert JL. Four-stranded nucleic acids: Structure, function and targeting of G-quadruplexes. Chem Soc Rev 2008;37: 1375-1384.
25. Todd AK, Johnston M, Neidle S. Higly prevalent putative quadruplex sequence motifs in human DNA. Nucleic Acids Res 2005;33: 2901-2907.
26. Huppert JL, Balasubramanian S. Prevalence of quadruplexes in the human genome. Nucleic Acids Res 2005;33: 2908-2916.
27. Eddy J, Maizels N. Gene function correlates with potential for G4 DNA formation in the human genome. Nucleic Acids Res 2006;34: 3887-3896.
28. Huppert JL. Hunting G-quadruplexes. Biochimie 2008;90: 1140-1148.
29. Paeschke K, Simonsson T, Postberg J, Rhodes D, Lipps HJ. Telomere end-binding proteins control the formation of G- quadruplex DNA structures in vivo. Nat Struct Mol Biol 2005; 12: 847-854.
30. Huber MD, Duquette ML, Shiels JC, Maizels N. A conserved G4 DNA binding domain in RecQ family helicases. J Mol Biol 2006;358: 1071-1080.
31. Wu Y, Shin-ya K, Brosh RM, Jr. FANCJ helicase defective in Fanconi anemia and breast cancer unwind G-quadruplex DNA to defend genomic stability. Mol Cell Biol 2008;28: 4116-4128.
32. Sun H, Yabuki A, Maizels N. A human nuclease specific for G4 DNA. Proc Natl Acad Sci USA 2001;98: 12444-12449.
33. Hsu CL, Stevens A. Yeast cells lacking 5'-3' exoribonu- clease 1 contain mRNA species that are poly(A) deficient and partially lack the 5' cap structure. Mol Cell Biol 1993;13: 4826-4835.
34. Huertas P, Aguilera A. Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. Mol Cell 2003;12: 711-721.
35. Li X, Manley JL. Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability. Cell 2005;122: 365-378.
36. Li X, Manley JL. New talents for an old acquaintance: The SR protein splicing factor ASF/SF2 functions in the maintenance of genome stability. Cell Cycle 2005;2: 1706-1708.
37. Youds JL, Barber LJ, Ward JD, et al. DOG-1 is the Caenorhabditis elegans BRIP1/FANCJ homologue and functions in interstrand cross-link repair. Mol Cell Biol 2008;28: 1470-1479.
38. Taniguchi T, D'Andrea AD. Molecular pathogenesis of Fanconi anemia: Recent progress. Blood 2006;107: 4223-4233.
39. Nouspikel T. Nucleotide excision repair and neurological diseases. DNA Repair 2008;7: 1 155-1 167.
40. Sugasawa K, Ng JM, Masutani C, et al. Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair. Mol Cell 1998;2: 223-232.
41. Tornaletti S, Hanawalt PC. Effect of DNA lesions on transcription elongation. Biochimie 1999;81: 139-146.
42. Tornaletti S. Transcription arrest at DNA damage sites. Mutat Res 2005;577: 131-145.
43. Scicchitano D. Transcription past DNAadducts derived from polyciclic aromatic hydrocarbons. Mutat Res 2005;577: 146-154.
44. Savery N. The molecular mechanism of transcription-coupled repair. Trends Microbiol 2007;15: 326-333.
45. Sarasin A, Stary A. New insights for understanding the transcription-coupled repair pathway. DNA Repair 2007;6: 265-269.
46. Svejstrup JQ. Contending with transcriptional arrest during RNAPII transcript elongation. Trends Biochem Sci 2007;32: 165-171.
47. Fousteri M, Mullenders LHF. Transcription-coupled nucleotide excision repair in mammalian cells: Molecular mechanisms and biological effects. Cell Res 2008;18: 73-84.
48. Branum ME, Reardon JT, Sancar A. DNA repair excision nuclease attacks undamaged DNA. A potential source of spontaneous mutations. J Biol Chem 2001;276: 25421-25426.
49. Datta A, Jinks-Robertson S. Association of increased spontaneous mutation rates with high levels of transcription in yeast. Science 1995;268: 1616-1619.
50. Aguilera A, Gaomez-Gonzaalez B. Genome instability: A mechanistic view of its causes and consequences. Nat Rev Gen 2008;9: 204-217.
51. Wang G, Levy DD, Seidman MM, Glazer PM. Targeted mutagenesis in mammalian cells mediated by intracellular triple helix formation. Mol Cell Biol 1995;15: 1759-1768.
52. Oussatcheva EA, Hashem VI, Zou Y, Sinden RR, Potaman VN. Involvement of the nucleotide excision repair protein UvrA in instability of CAG*CTG repeat sequences in Escherichia coli. J Biol Chem 2001;276: 30878-30884.
53. Bacolla A, Jaworski A, Connors TD, Wells RD. Pkd1 unusual DNA conformations are recognized by nucleotide excision repair. J Biol Chem 2001;276: 18597-18604.
54. Lin Y, Dion V, Wilson JH. Transcription promotes contraction of CAG repeat tracts in human cells. Nat Struct Mol Biol 2006;13: 179-180.
55. Jung J, Bonini N. CREB-binding protein modulates repeat instability in a Drosophila model for PolyQ disease. Science 2007; 315:1857-1859.
56. Tian M, Alt FW. Transcription-induced cleavage of immuno- globulin switch regions by nucleotide excision repair nucleases in vitro. J Biol Chem 2000;275: 24163-24172.
57. Peters A, Storb U. Somatic hypermutation of immunoglo- bulin genes is linked to transcription initiation. Immunity 1996;4: 57-65.
58. Schrader CE, Vardo J, Linehan E, et al. Deletion of the nucleotide excision repair gene Ercc1 reduces immunoglo- bulin class switching and alters mutations near switch recombination junctions. J Exp Med 2004;200: 321-330.
59. Liu L, Wang J. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci USA 1987;84: 7024-7027.
60. Wu HY, Shyy SH, Wang JC, Liu LF. Transcription generates positively and negatively supercoiled domains in the template. Cell 1988;53: 433-440.
61. ConawayJW, Bond MW, Conaway RC. An RNA polymerase II transcription system from rat liver. J Biol Chem 1987;262: 8293-8297.
62. Conaway RC, Reines D, Garrett KP, Powell W, Conaway JW. Purification of RNA polymerase II general transcription factors from rat liver. Methods Enzymol 1996;273: 194-207.
63. Donahue BA, Yin S, Taylor J-S, Reines D, Hanawalt P. Transcript cleavage by RNA polymerase II arrested by a cyclobutane pyrimidine dimer in the DNA template. Proc Natl Acad Sci USA 1994;91: 8502-8506.
64. Samkurashvili I, Luse DS. Structural changes in the RNA polymerase II transcription complex during transition from initiation to elongation. Mol Cell Biol 1998;18: 5343-5354.
65. Viswanathan A, Doetsch PW. Effects of non-bulky DNA base damages on Escherichia coli RNA polymerase-mediated elongation and promoter clearance. J Biol Chem 1998;273: 21276-21281.
66. Kathe SD, Shen GP, Wallace SS. Single-stranded breaks in DNA but not oxidative DNA base damages block transcrip- tional elongation by RNA polymerase II in HeLa cell nuclear extracts [erratum appears in J Biol Chem. 2004 Jun 25;279(26):27830]. J Biol Chem 2004; 279: 18511-18520.
67. Larsen E, Kwon K, Coin F, Egly JM, Klungland A. Transcription activities at 8-oxoG lesions in DNA. DNA Repair 2004;3: 1457-1468.
68. Charlet-Berguerand N, Feuerhahn S, Kong SE, et al. RNA polymerase II bypass of oxidative DNA damage is regulated by transcription elongation factors. EMBO J 2006;25: 5481-5491.
69. Edwards AM, Kane CM. Identifying regulators of transcript elongation in eukaryotes. San Diego: Academic Press; 1996.
70. Reines D, Dvir A, Conaway JM, Conaway RC. Assays for investigating transcription by RNA polymerase II in vitro. Methods 1997;12: 192-202.
71. Kalogeraki VS, Tornaletti S, Cooper PK, Hanawalt PC. Comparative TFIIS-mediated transcript cleavage by mammalian RNA polymerase II arrested at a lesion in different transcription systems. DNA Repair 2005;4: 1075-1087.
72. Kuraoka I, Endou M, Yamaguchi Y, Wada T, Handa H, Tanaka K. Effects of endogenous DNA base lesions on transcription elongation by mammalian RNA polymerase II. Implications for transcription-coupled DNA repair and transcriptional mutagenesis. J Biol Chem 2003;278: 7294-7299.
73. Tornaletti S, Maeda LS, Kolodner RD, Hanawalt PC. Effect of 8-oxoguanine on transcription elongation by T7 RNA polymerase and mammalian RNA polymerase II. DNA Repair 2004;3: 483-494.
74. Peck LJ, Wang JC. Transcriptional block caused bya negative supercoiling induced structural change in an alternating CG sequence. Cell 1985;40: 129-137.
75. Droge P, Pohl FM. The influence of an alternate template conformation on elongating phage T7 RNA polymerase. Nucleic Acids Res 1991;19: 5301-53066.
76. Ditlevson JV, Tornaletti S, Belotserkovskii BP, et al. Inhibitory effect of a short Z-DNA forming sequence on transcription elongation by T7 RNA polymerase. Nucleic Acids Res 2008; 36: 3163-3170.
77. Durand R, Job C, Zarling DA, Teissaere M, Jovin TM, Job D. Comparative transcription of right- and left-handed poly[d(G-C)] by wheat germ RNA polymerase II. EMBO J 1983; 2: 1707-1714.
78. Wells RD. DNA triplexes and Friedreich ataxia. FASEBJ 2008; 22: 1625-1634.
79. Grabczyk E, Fishman MC. A long purine-pyrimidine homo- polymer acts as a transcriptional diode. J Biol Chem 1995;270: 1791-1797.
80. GrabczykE, Usdin K. The GAA. TTC tripletrepeatexpanded in Friedreich's ataxia impedes transcription elongation by T7 RNA polymerase in a length and supercoil dependent manner. Nucleic Acids Res 2000;28: 2815-2822.
81. Grabczyk E, Mancuso M, Sammarco MC. A persistent RNA.DNA hybrid formed by transcription of the Friedreich ataxia triplet repeat in live bacteria, and byT7 RNAP in vitro. Nucleic Acids Res 2007;35: 5351-5359.
82. Belotserkovskii BP, De Silva E, Tonaletti S, Wang G, Vasquez KM. A triplex-forming sequence from the human c-MYC promoter interferes with DNA transcription. J Biol Chem 2007;282: 32433-32441.
83. Maizels N. Immunoglobulin gene diversification. Annu Rev Genet 2005;39: 23-46.
84. Tornaletti S, Park-Snyder S, Hanawalt PC. G4-forming sequences in the non-transcribed DNA strand pose blocks to T7 RNA polymerase and mammalian RNA polymerase II. J Biol Chem 2008;283: 12756-12762.
85. Gu W, Powell W, Mote J, Jr., Reines D. Nascent RNAcleavage by RNA polymerase II does not require upstream translocation of the elongation complex on DNA. J Biol Chem 1993;268: 25604-25616.
86. Tornaletti S, Reines D, Hanawalt PC. Structural characterization of RNA polymerase II complexes arrested by a cyclobutane pyrimidine dimer in the transcribed strand of template DNA. J Biol Chem 1999;274: 24124-24130.
87. Uptain SM, Kane CM, Chamberlin MJ. Basic mechanisms of transcript elongation and its regulation. Annu Rev Biochem 1997;66: 117-172.
88. Daniels GA, Lieber MR. RNA:DNA complex formation upon transcription of immunoglobulin switch regions: Implications for the mechanism and regulation of class switch recombination. Nucleic Acids Res 1995;23: 5006-5011.
89. Wright BE, Schmidt KH, Minnick MF. Mechanisms by which transcription can regulate somatic hypermutation. Genes Immun 2004;5: 176-182.