Co-transcriptional formation of DNA: RNA hybrid G-quadruplex and potential function as constitutional cis element for transcription control

Nucleic Acids Research

Volumn 41, Issue 10, 2013, Pages 5533-5541

  Zheng, Ke Wei ^a   Xiao, Shan ^a   Liu, Jia Quan ^a   Zhang, Jia Yu ^a   Hao, Yu Hua ^a   Tan, Zheng ^a  

^a INSTITUTE OF ZOOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DOUBLE STRANDED DNA; GUANINE QUADRUPLEX; RIBONUCLEASE A; RNA;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; DNA CROSS LINKING; DNA RNA HYBRIDIZATION; DNA STRAND; DNA TEMPLATE; DNA TRANSCRIPTION; GENE; GENE EXPRESSION; GENE FUNCTION; GENE NUMBER; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENETIC TRANSFECTION; HUMAN; HUMAN TISSUE; IN VITRO STUDY; IN VIVO STUDY; NUCLEIC ACID STRUCTURE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA TRANSCRIPTION; STRUCTURE ANALYSIS; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS;

DNA; G-QUADRUPLEXES; GENOME, HUMAN; HEK293 CELLS; HUMANS; PLASMIDS; REGULATORY ELEMENTS, TRANSCRIPTIONAL; RNA; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 84878526299     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt264     Document Type: Article

References (35)

1. 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.
2. Neidle, S. and Parkinson, G. (2002) Telomere maintenance as a target for anticancer drug discovery. Nat. Rev. Drug Discov., 1, 383-393.
3. Collie, G.W. and Parkinson, G.N. (2011) The application of DNA and RNA G-quadruplexes to therapeutic medicines. Chem. Soc. Rev., 40, 5867-5892.
4. Balasubramanian, S., Hurley, L.H. and Neidle, S. (2011) Targeting G-quadruplexes in gene promoters: A novel anticancer strategy? Nat. Rev. Drug Discov., 10, 261-275.
5. Todd, A.K. (2007) Bioinformatics approaches to quadruplex sequence location. Methods, 43, 246-251.
6. Huppert, J.L. (2010) Structure, location and interactions of G-quadruplexes. FEBS J., 277, 3452-3458.
7. Huppert, J.L. and Balasubramanian, S. (2007) G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res., 35, 406-413.
8. Biffi, G., Tannahill, D., McCafferty, J. and Balasubramanian, S. (2013) Quantitative visualization of DNA G-quadruplex structures in human cells. Nat. Chem., 5, 182-185.
9. Xu, Y., Kimura, T. and Komiyama, M. (2008) Human telomere RNA and DNA form an intermolecular G-quadruplex. Nucleic Acids Symp. Ser., 169-170.
10. Wanrooij, P.H., Uhler, J.P., Shi, Y., Westerlund, F., Falkenberg, M. and Gustafsson, C.M. (2012) A hybrid G-quadruplex structure formed between RNA and DNA explains the extraordinary stability of the mitochondrial R-loop. Nucleic Acids Res., 40, 10334-10344.
11. Zheng, K.W., Chen, Z., Hao, Y.H. and Tan, Z. (2010) Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA. Nucleic Acids Res., 38, 327-338.
12. Harris, M.E. and Christian, E.L. (2009) RNA crosslinking methods. Methods Enzymol., 468, 127-146.
13. Zheng, K.W., Zhang, D., Zhang, L.X., Hao, Y.H., Zhou, X. and Tan, Z. (2011) Dissecting the strand folding orientation and formation of G-quadruplexes in single- and double-stranded nucleic acids by ligand-induced photocleavage footprinting. J. Am. Chem. Soc., 133, 1475-1483.
14. 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. USA, 101, 6062-6067.
15. Castle, J.C., Armour, C.D., Lower, M., Haynor, D., Biery, M., Bouzek, H., Chen, R., Jackson, S., Johnson, J.M., Rohl, C.A. et al. (2010) Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification. PLoS One, 5, e11779.
16. Sun, D. and Hurley, L.H. (2010) Biochemical techniques for the characterization of G-quadruplex structures: EMSA, DMS footprinting, and DNA polymerase stop assay. Methods Mol. Biol., 608, 65-79.
17. Hardin, C.C., Perry, A.G. and White, K. (2000) Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids. Biopolymers, 56, 147-194.
18. Fletcher, T.M., Sun, D., Salazar, M. and Hurley, L.H. (1998) Effect of DNA secondary structure on human telomerase activity. Biochemistry, 37, 5536-5541.
19. Ren, L., Zhang, A., Huang, J., Wang, P., Weng, X., Zhang, L., Liang, F., Tan, Z. and Zhou, X. (2007) Quaternary ammonium zinc phthalocyanine: Inhibiting telomerase by stabilizing G quadruplexes and inducing G-quadruplex structure transition and formation. Chembiochem, 8, 775-780.
20. Zhang, L., Huang, J., Ren, L., Bai, M., Wu, L., Zhai, B. and Zhou, X. (2008) Synthesis and evaluation of cationic phthalocyanine derivatives as potential inhibitors of telomerase. Bioorg. Med. Chem., 16, 303-312.
21. Yaku, H., Murashima, T., Miyoshi, D. and Sugimoto, N. (2012) Specific binding of anionic porphyrin and phthalocyanine to the G-quadruplex with a variety of in vitro and in vivo applications. Molecules, 17, 10586-10613.
22. Yaku, H., Fujimoto, T., Murashima, T., Miyoshi, D. and Sugimoto, N. (2012) Phthalocyanines: A new class of G-quadruplex-ligands with many potential applications. Chem. Commun., 48, 6203-6216.
23. Yaku, H., Murashima, T., Miyoshi, D. and Sugimoto, N. (2010) Anionic phthalocyanines targeting G-quadruplexes and inhibiting telomerase activity in the presence of excessive DNA duplexes. Chem. Commun., 46, 5740-5742.
24. Alzeer, J. and Luedtke, N.W. (2010) pH-mediated fluorescence and G-quadruplex binding of amido phthalocyanines. Biochemistry, 49, 4339-4348.
25. Alzeer, J., Vummidi, B.R., Roth, P.J. and Luedtke, N.W. (2009) Guanidinium-modified phthalocyanines as high-affinity G-quadruplex fluorescent probes and transcriptional regulators. Angew. Chem. Int. Ed. Engl., 48, 9362-9365.
26. Sun, D. and Hurley, L.H. (2009) 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.
27. McLuckie, K.I., Waller, Z.A., Sanders, D.A., Alves, D., Rodriguez, R., Dash, J., McKenzie, G.J., Venkitaraman, A.R. and Balasubramanian, S. (2011) G-quadruplex-binding benzo[a]phenoxazines down-regulate c-KIT expression in human gastric carcinoma cells. J. Am. Chem. Soc., 133, 2658-2663.
28. Wang, X.D., Ou, T.M., Lu, Y.J., Li, Z., Xu, Z., Xi, C., Tan, J.H., Huang, S.L., An, L.K., Li, D. et al. (2010) Turning off transcription of the bcl-2 gene by stabilizing the bcl-2 promoter quadruplex with quindoline derivatives. J. Med. Chem., 53, 4390-4398.
29. Tian, M., Zhang, X., Li, Y., Ju, Y., Xiang, J., Zhao, C. and Tang, Y. (2010) Inducement of G-quadruplex DNA forming and downregulation of oncogene c-myc by bile acid-amino acid conjugate-BAA. Nucleosides Nucleotides Nucleic Acids, 29, 190-199.
30. 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.
31. Liu, J.Q., Chen, C.Y., Xue, Y., Hao, Y.H. and Tan, Z. (2010) G-quadruplex hinders translocation of BLM helicase on DNA: A real-time fluorescence spectroscopic unwinding study and comparison with duplex substrates. J. Am. Chem. Soc., 132, 10521-10527.
32. Broxson, C., Beckett, J. and Tornaletti, S. (2011) Transcription arrest by a G quadruplex forming-trinucleotide repeat sequence from the human c-myb gene. Biochemistry, 50, 4162-4172.
33. Huppert, J.L. (2008) Four-stranded nucleic acids: Structure, function and targeting of G-quadruplexes. Chem. Soc. Rev., 37, 1375-1384.
34. Paeschke, K., Capra, J.A. and Zakian, V.A. (2011) DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase. Cell, 145, 678-691.
35. Xu, Y., Ishizuka, T., Yang, J., Ito, K., Katada, H., Komiyama, M. and Hayashi, T. (2012) Oligonucleotide models of telomeric DNA and RNA form a Hybrid G-quadruplex structure as a potential component of telomeres. J. Biol. Chem., 287, 41787-41796.