Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription

Genome Research

Volumn 18, Issue 2, 2008, Pages 233-241

  Du, Zhuo ^a   Zhao, Yiqiang ^a   Li, Ning ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA;

ARTICLE; CONTROLLED STUDY; GENE CONTROL; GENE EXPRESSION; GENE SEQUENCE; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HUMAN; MULTIGENE FAMILY; PRIORITY JOURNAL;

COMPUTATIONAL BIOLOGY; G-QUADRUPLEXES; GENE EXPRESSION REGULATION; GENOME, HUMAN; HUMANS; MODELS, GENETIC; REGULATORY ELEMENTS, TRANSCRIPTIONAL; RNA POLYMERASE II; TRANSCRIPTION, GENETIC;

EID: 39049170386     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.6905408     Document Type: Article

References (60)

1. Ambrus, A., Chen, D., Dai, J., Jones, R.A., and Yang, D. 2005. Solution structure of the biologically relevant G-quadruplex element in the human c-MYC promoter. Implications for G-quadruplex stabilization. Biochemistry 44: 2048-2058.
2. 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.
3. Brodsky, A.S., Meyer, C.A., Swinburne, I.A., Hall, G., Keenan, B.J., Liu, X.S., Fox, E.A., and Silver, P.A. 2005. Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. Genome Biol. 6: R64. doi: 10.1186/gb-2005-6-8-r64.
4. Burge, S., Parkinson, G.N., Hazel, P., Todd, A.K., and Neidle, S. 2006. Quadruplex DNA: Sequence, topology and structure. Nucleic Acids Res. 34: 5402-5415. doi: 10.1093/nar/gkl655.
5. Catasti, P., Chen, X., Moyzis, R.K., Bradbury, E.M., and Gupta, G. 1996. Structure-function correlations of the insulin-linked polymorphic region. J. Mol. Biol. 264: 534-545.
6. Chaudhuri, J. and Alt, F.W. 2004. Class-switch recombination: Interplay of transcription, DNA deamination and DNA repair. Nat. Rev. Immunol. 4: 541-552.
7. Clark, S.P., Lewis, C.D., and Felsenfeld, G. 1990. Properties of BGP1, a poly(dG)-binding protein from chicken erythrocytes. Nucleic Acids Res. 18: 5119-5126. doi: 10.1093/nar/18.17.5119.
8. Cogoi, S. and Xodo, L.E. 2006. G-quadruplex formation within the promoter of the KRAS proto-oncogene and its effect on transcription. Nucleic Acids Res. 34: 2536-2549. doi: 10.1093/nar/gkl286.
9. Dai, J., Chen, D., Jones, R.A., Hurley, L.H., and Yang, D. 2006. NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region. Nucleic Acids Res. 34: 5133-5144. doi: 10.1093/nar/gkl610.
10. Dayn, A., Malkhosyan, S., and Mirkin, S.M. 1992. Transcriptionally driven cruciform formation in vivo. Nucleic Acids Res. 20: 5991-5997. doi: 10.1093/nar/20.22.5991.
11. De Armond, R., Wood, S., Sun, D., Hurley, L.H., and Ebbinghaus, S.W. 2005. Evidence for the presence of a guanine quadruplex forming region within a polypurine tract of the hypoxia inducible factor 1alpha promoter. Biochemistry 44: 16341-16350.
12. Dexheimer, T.S., Fry, M., and Hurley, L.H. 2006. DNA quadruplexes and gene regulation. In Quadruplex nucleic acids (eds. S. Neidle and S. Balasubramanian), pp. 180-207. RSC Publishing, Cambridge, UK
13. Drolet, M. 2006. Growth inhibition mediated by excess negative supercoiling: The interplay between transcription elongation, R-loop formation and DNA topology. Mol. Microbiol. 59: 723-730.
14. Du, Z., Kong, P., Gao, Y., and Li, N. 2007. Enrichment of G4 DNA motif in transcriptional regulatory region of chicken genome. Biochem. Biophys. Res. Commun. 354: 1067-1070.
15. Duquette, M.L., Handa, P., Vincent, J.A., Taylor, A.F., and Maizels, N. 2004. Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA. Genes & Dev. 18: 1618-1629.
16. The ENCODE Project Consortium. 2004. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636-640.
17. The ENCODE Project Consortium. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
18. Eyre, T.A., Ducluzeau, F., Sneddon, T.P., Povey, S., Bruford, E.A., and Lush, M.J. 2006. The HUGO Gene Nomenclature Database, 2006 updates. Nucleic Acids Res. 34: D319-D321. doi: 10.1093/nar/gkj147.
19. Fanger, N.A., Borges, L., and Cosman, D. 1999. The leukocyte immunoglobulin-like receptors (LIRs): A new family of immune regulators. J. Leukoc. Biol. 66: 231-236.
20. Fernando, H., Reszka, A.P., Huppert, J., Ladame, S., Rankin, S., Venkitaraman, A.R., Neidle, S., and Balasubramanian, S. 2006. A conserved quadruplex motif located in a transcription activation site of the human c-kit oncogene. Biochemistry 45: 7854-7860.
21. Fry, M. 2007. Tetraplex DNA and its interacting proteins. Front. Biosci. 12: 4336-4351.
22. Fu, P.K., Bradley, P.M., and Turro, C. 2003. Stabilization of duplex DNA structure and suppression of transcription in vitro by bis(quinone diimine) complexes of rhodium(III) and ruthenium(II). Inorg. Chem. 42: 878-884.
23. Gellert, M., Lipsett, M.N., and Davies, D.R. 1962. Helix formation by guanylic acid. Proc. Natl. Acad. Sci. 48: 2013-2018.
24. Grand, C.L., Han, H., Munoz, R.M., Weitman, S., Von Hoff, D.D., Hurley, L.H., and Bearss, D.J. 2002. The cationic porphyrin TMPyP4 down-regulates c-MYC and human telomerase reverse transcriptase expression and inhibits tumor growth in vivo. Mol. Cancer Ther. 1: 565-573.
25. Greive, S.J. and von Hippel, P.H. 2005. Thinking quantitatively about transcriptional regulation. Nat. Rev. Mol. Cell Biol. 6: 221-232.
26. Guschlbauer, W., Chantot, J.F., and Thiele, D. 1990. Four-stranded nucleic acid structures 25 years later: From guanosine gels to telomer DNA. J. Biomol. Struct. Dyn. 8: 491-511.
27. Han, H. and Hurley, L.H. 2000. G-quadruplex DNA: A potential target for anti-cancer drug design. Trends Pharmacol. Sci. 21: 136-142.
28. Hanakahi, L.A., Sun, H., and Maizels, N. 1999. High affinity interactions of nucleolin with G-G-paired rDNA. J. Biol. Chem. 274: 15908-15912.
29. Huppert, J.L. and Balasubramanian, S. 2005. Prevalence of quadruplexes in the human genome. Nucleic Acids Res. 33: 2908-2916. doi: 10.1093/nar/gki609.
30. Huppert, J.L. and Balasubramanian, S. 2007. G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res. 35: 406-413. doi: 10.1093/nar/gkl1057.
31. Karolchik, D., Hinrichs, A.S., Furey, T.S., Roskin, K.M., Sugnet, C.W., Haussler, D., and Kent, W.J. 2004. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 32: D493-D496. doi: 10.1093/nar/gkh103.
32. Kasprzyk, A., Keefe, D., Smedley, D., London, D., Spooner, W., Melsopp, C., Hammond, M., Rocca-Serra, P., Cox, T., and Birney, E. 2004. EnsMart: A generic system for fast and flexible access to biological data. Genome Res. 14: 160-169.
33. Keniry, M.A. 2000. Quadruplex structures in nucleic acids. Biopolymers 56: 123-146.
34. Kennedy, G.C. and Rutter, W.J. 1992. Pur-1, a zinc-finger protein that binds to purine-rich sequences, transactivates an insulin promoter in heterologous cells. Proc. Natl. Acad. Sci. 89: 11498-11502.
35. Korzheva, N., Mustaev, A., Kozlov, M., Malhotra, A., Nikiforov, V., Goldfarb, A., and Darst, S.A. 2000. A structural model of transcription elongation. Science 289: 619-625.
36. Lew, A., Rutter, W.J., and Kennedy, G.C. 2000. Unusual DNA structure of the diabetes susceptibility locus IDDM2 and its effect on transcription by the insulin promoter factor Pur-1/MAZ. Proc. Natl. Acad. Sci. 97: 12508-12512.
37. Lewis, C.D., Clark, S.P., Felsenfeld, G., and Gould, H. 1988. An erythrocyte-specific protein that binds to the poly(dG) region of the chicken beta-globin gene promoter. Genes & Dev. 2: 863-873.
38. Liu, L.F. and Wang, J.C. 1987. Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. 84: 7024-7027.
39. Maizels, N. 2006. Dynamic roles for G4 DNA in the biology of eukaryotic cells. Nat. Struct. Mol. Biol. 13: 1055-1059.
40. Mergny, J.L., De Cian, A., Ghelab, A., Sacca, B., and Lacroix, L. 2005. Kinetics of tetramolecular quadruplexes. Nucleic Acids Res. 33: 81-94. doi: 10.1093/nar/gki148.
41. Rankin, S., Reszka, A.P., Huppert, J., Zloh, M., Parkinson, G.N., Todd, A.K., Ladame, S., Balasubramanian, S., and Neidle, S. 2005. Putative DNA quadruplex formation within the human c-kit oncogene. J. Am. Chem. Soc. 127: 10584-10589.
42. Rawal, P., Kummarasetti, V.B., Ravindran, J., Kumar, N., Halder, K., Sharma, R., Mukerji, M., Das, S.K., and Chowdhury, S. 2006. Genome-wide prediction of G4 DNA as regulatory motifs: Role in Escherichia coli global regulation. Genome Res. 16: 644-655.
43. Roberts, S.G., Choy, B., Walker, S.S., Lin, Y.S., and Green, M.R. 1995. A role for activator-mediated TFIIB recruitment in diverse aspects of transcriptional regulation. Curr. Biol. 5: 508-516.
44. Seenisamy, J., Rezler, E.M., Powell, T.J., Tye, D., Gokhale, V., Joshi, C.S., Siddiqui-Jain, A., and Hurley, L.H. 2004. The dynamic character of the G-quadruplex element in the c-MYC promoter and modification by TMPyP4. J. Am. Chem. Soc. 126: 8702-8709.
45. Sen, D. and Gilbert, W. 1990. A sodium-potassium switch in the formation of four-stranded G4-DNA. Nature 344: 410-414.
46. Shafer, R.H. and Smirnov, I. 2000. Biological aspects of DNA/RNA quadruplexes. Biopolymers 56: 209-227.
47. Siddiqui-Jain, A., Grand, C.L., Bearss, D.J., and Hurley, L.H. 2002. Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc. Natl. Acad. Sci. 99: 11593-11598.
48. Simonsson, T. 2001. G-quadruplex DNA structures-variations on a theme. Biol. Chem. 382: 621-628.
49. Su, A.I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K.A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., et al. 2004. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. 101: 6062-6067.
50. Sun, D., Guo, K., Rusche, J.J., and Hurley, L.H. 2005. Facilitation of a structural transition in the polypurine/polypyrimidine tract within the proximal promoter region of the human VEGF gene by the presence of potassium and G-quadruplex-interactive agents. Nucleic Acids Res. 33: 6070-6080. doi: 10.1093/nar/gki917.
51. Thomas, P.D., Campbell, M.J., Kejariwal, A., Mi, H., Karlak, B., Daverman, R., Diemer, K., Muruganujan, A., and Narechania, A. 2003. PANTHER: A library of protein families and subfamilies indexed by function. Genome Res. 13: 2129-2141.
52. Todd, A.K., Johnston, M., and Neidle, S. 2005. Highly prevalent putative quadruplex sequence motifs in human DNA. Nucleic Acids Res. 33: 2901-2907. doi: 10.1093/nar/gki553.
53. Wright, B.E. 2004. Stress-directed adaptive mutations and evolution. Mol. Microbiol. 52: 643-650.
54. Xu, Y. and Sugiyama, H. 2006. Formation of the G-quadruplex and i-motif structures in retinoblastoma susceptibility genes (Rb). Nucleic Acids Res. 34: 949-954. doi: 10.1093/nar/gkj485.
55. Yafe, A., Etzioni, S., Weisman-Shomer, P., and Fry, M. 2005. Formation and properties of hairpin and tetraplex structures of guanine-rich regulatory sequences of muscle-specific genes. Nucleic Acids Res. 33: 2887-2900. doi: 10.1093/nar/gki606.
56. Yu, K., Chedin, F., Hsieh, C.L., Wilson, T.E., and Lieber, M.R. 2003. R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells. Nat. Immunol. 4: 442-451.
57. Yudkovsky, N., Ranish, J.A., and Hahn, S. 2000. A transcription reinitiation intermediate that is stabilized by activator. Nature 408: 225-229.
58. Zawel, L., Kumar, K.P., and Reinberg, D. 1995. Recycling of the general transcription factors during RNA polymerase II transcription. Genes & Dev. 9: 1479-1490.
59. Zaychikov, E., Denissova, L., and Heumann, H. 1995. Translocation of the Escherichia coli transcription complex observed in the registers 11 to 20: "Jumping" of RNA polymerase and asymmetric expansion and contraction of the "transcription bubble". Proc. Natl. Acad. Sci. 92: 1739-1743.
60. Zhao, Y., Du, Z., and Li, N. 2007. Extensive selection for the enrichment of G4 DNA motifs in transcriptional regulatory regions of warm blooded animals. FEBS Lett. 581: 1951-1956.