메뉴 건너뛰기




Volumn 41, Issue 14, 2013, Pages 7144-7152

DNA G-quadruplex formation in response to remote downstream transcription activity: Long-range sensing and signal transducing in DNA double helix

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; GENOMIC DNA; GUANINE QUADRUPLEX;

EID: 84881504588     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt443     Document Type: Article
Times cited : (57)

References (40)
  • 2
    • 80052751115 scopus 로고    scopus 로고
    • Gene-specific transcription activation via long-range allosteric shape-shifting
    • Tsai C.J. and Nussinov R. (2011) Gene-specific transcription activation via long-range allosteric shape-shifting. Biochem. J., 439, 15-25
    • (2011) Biochem. J. , vol.439 , pp. 15-25
    • Tsai, C.J.1    Nussinov, R.2
  • 3
    • 0344897665 scopus 로고    scopus 로고
    • Nongenic transcription, gene regulation and action at a distance
    • Cook P.R. (2003) Nongenic transcription, gene regulation and action at a distance. J. Cell Sci., 116, 4483-4491
    • (2003) J. Cell Sci , vol.116 , pp. 4483-4491
    • Cook, P.R.1
  • 4
    • 70349542588 scopus 로고    scopus 로고
    • Close encounters of the 3C kind: Long-range chromatin interactions and transcriptional regulation
    • Palstra R.J. (2009) Close encounters of the 3C kind: Long-range chromatin interactions and transcriptional regulation. Brief. Funct. Genomic Proteomic, 8, 297-309
    • (2009) Brief. Funct. Genomic Proteomic , vol.8 , pp. 297-309
    • Palstra, R.J.1
  • 6
    • 0036923739 scopus 로고    scopus 로고
    • Dynamics of enhancer-promoter communication during differentiation- induced gene activation
    • Hatzis P. and Talianidis I. (2002) Dynamics of enhancer-promoter communication during differentiation-induced gene activation. Mol. Cell, 10, 1467-1477
    • (2002) Mol. Cell , vol.10 , pp. 1467-1477
    • Hatzis, P.1    Talianidis, I.2
  • 7
    • 24044540381 scopus 로고    scopus 로고
    • Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking
    • Wang Q., Carroll J.S. and Brown M. (2005) Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking. Mol. Cell, 19, 631-642
    • (2005) Mol. Cell , vol.19 , pp. 631-642
    • Wang, Q.1    Carroll, J.S.2    Brown, M.3
  • 8
    • 0023433855 scopus 로고
    • Supercoiling of the DNA template during transcription
    • Liu L.F. and Wang J.C. (1987) Supercoiling of the DNA template during transcription. Proc. Natl Acad. Sci. USA, 84, 7024-7027
    • (1987) Proc. Natl Acad. Sci. USA , vol.84 , pp. 7024-7027
    • Liu, L.F.1    Wang, J.C.2
  • 9
    • 0024279845 scopus 로고
    • Transcription generates positively and negatively supercoiled domains in the template
    • Wu H.Y., Shyy S.H., Wang J.C. and Liu L.F. (1988) Transcription generates positively and negatively supercoiled domains in the template. Cell, 53, 433-440
    • (1988) Cell , vol.53 , pp. 433-440
    • Wu, H.Y.1    Shyy, S.H.2    Wang, J.C.3    Liu, L.F.4
  • 10
    • 0024968110 scopus 로고
    • Transcription-driven supercoiling of DNA: Direct biochemical evidence from in vitro studies
    • Tsao Y.P., Wu H.Y. and Liu L.F. (1989) Transcription-driven supercoiling of DNA: Direct biochemical evidence from in vitro studies. Cell, 56, 111-118
    • (1989) Cell , vol.56 , pp. 111-118
    • Tsao, Y.P.1    Wu, H.Y.2    Liu, L.F.3
  • 11
    • 7544242666 scopus 로고    scopus 로고
    • The dynamic response of upstream DNA to transcriptiongenerated torsional stress
    • Kouzine F., Liu J., Sanford S., Chung H.J. and Levens D. (2004) The dynamic response of upstream DNA to transcriptiongenerated torsional stress. Nat. Struct. Mol. Biol., 11, 1092-1100
    • (2004) Nat. Struct. Mol. Biol , vol.11 , pp. 1092-1100
    • Kouzine, F.1    Liu, J.2    Sanford, S.3    Chung, H.J.4    Levens, D.5
  • 12
    • 38849132828 scopus 로고    scopus 로고
    • The functional response of upstream DNA to dynamic supercoiling in vivo
    • Kouzine F., Sanford S., Elisha-Feil Z. and Levens D. (2008) The functional response of upstream DNA to dynamic supercoiling in vivo. Nat. Struct. Mol. Biol., 15, 146-154
    • (2008) Nat. Struct. Mol. Biol , vol.15 , pp. 146-154
    • Kouzine, F.1    Sanford, S.2    Elisha-Feil, Z.3    Levens, D.4
  • 13
    • 79953313413 scopus 로고    scopus 로고
    • Targeting G-quadruplexes in gene promoters: A novel anticancer strategy?
    • 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
    • (2011) Nat. Rev. Drug. Discov , vol.10 , pp. 261-275
    • Balasubramanian, S.1    Hurley, L.H.2    Neidle, S.3
  • 14
    • 67249138595 scopus 로고    scopus 로고
    • Evidence of genome-wide G4 DNAmediated gene expression in human cancer cells
    • Verma A., Yadav V.K., Basundra R., Kumar A. and Chowdhury S. (2009) Evidence of genome-wide G4 DNAmediated gene expression in human cancer cells. Nucleic Acids Res., 37, 4194-4204
    • (2009) Nucleic Acids Res , vol.37 , pp. 4194-4204
    • Verma, A.1    Yadav, V.K.2    Basundra, R.3    Kumar, A.4    Chowdhury, S.5
  • 15
    • 0035075342 scopus 로고    scopus 로고
    • Functional and dysfunctional roles of quadruplex DNA in cells
    • Arthanari H. and Bolton P.H. (2001) Functional and dysfunctional roles of quadruplex DNA in cells. Chem. Biol., 8, 221-230
    • (2001) Chem. Biol , vol.8 , pp. 221-230
    • Arthanari, H.1    Bolton, P.H.2
  • 16
    • 37549000254 scopus 로고    scopus 로고
    • Neidle S. and Balasubramanian S. (eds. The Royal Society of Chemistry, London
    • Dexheimer T.S., Fry M. and Hurley L.H. (2006) In: Neidle S. and Balasubramanian S. (eds), Quadruplex Nucleic Acids. The Royal Society of Chemistry, London, pp. 180-207
    • (2006) Quadruplex Nucleic Acids , pp. 180-207
    • Dexheimer, T.S.1    Fry, M.2    Hurley, L.H.3
  • 18
    • 79957556530 scopus 로고    scopus 로고
    • DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase
    • 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
    • (2011) Cell , vol.145 , pp. 678-691
    • Paeschke, K.1    Capra, J.A.2    Zakian, V.A.3
  • 19
    • 84870883495 scopus 로고    scopus 로고
    • Telomere-And telomerase-interacting protein that unfolds telomere G-quadruplex and promotes telomere extension in mammalian cells
    • Wang F., Tang M.L., Zeng Z.X., Wu R.Y., Xue Y., Hao Y.H., Pang D.W., Zhao Y. and Tan Z. (2012) Telomere-And telomerase-interacting protein that unfolds telomere G-quadruplex and promotes telomere extension in mammalian cells. Proc. Natl Acad. Sci. USA, 109, 20413-20418
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 20413-20418
    • Wang, F.1    Tang, M.L.2    Zeng, Z.X.3    Wu, R.Y.4    Xue, Y.5    Hao, Y.H.6    Pang, D.W.7    Zhao, Y.8    Tan, Z.9
  • 20
    • 84875464903 scopus 로고    scopus 로고
    • Quantitative visualization of DNA G-quadruplex structures in human cells
    • Biffi G., Tannahill D., McCafferty J. and Balasubramanian S. (2013) Quantitative visualization of DNA G-quadruplex structures in human cells. Nat. Chem., 5, 182-186
    • (2013) Nat. Chem , vol.5 , pp. 182-186
    • Biffi, G.1    Tannahill, D.2    McCafferty, J.3    Balasubramanian, S.4
  • 21
    • 75649089282 scopus 로고    scopus 로고
    • Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA
    • 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
    • (2010) Nucleic Acids Res , vol.38 , pp. 327-338
    • Zheng, K.W.1    Chen, Z.2    Hao, Y.H.3    Tan, Z.4
  • 22
    • 84878526299 scopus 로고    scopus 로고
    • Co-Transcriptional formation of DNA:RNA hybrid G-quadruplex and potential function as constitutional cis element for transcription control
    • Zheng K.W., Xiao S., Liu J.Q., Zhang J.Y., Hao Y.H. and Tan Z. (2013) Co-Transcriptional formation of DNA:RNA hybrid G-quadruplex and potential function as constitutional cis element for transcription control. Nucleic Acids Res., 41, 5533-5541
    • (2013) Nucleic Acids Res , vol.41 , pp. 5533-5541
    • Zheng, K.W.1    Xiao, S.2    Liu, J.Q.3    Zhang, J.Y.4    Hao, Y.H.5    Tan, Z.6
  • 23
    • 0023790970 scopus 로고
    • Supercoiling of intracellular DNA can occur in eukaryotic cells
    • Giaever G.N. and Wang J.C. (1988) Supercoiling of intracellular DNA can occur in eukaryotic cells. Cell, 55, 849-856
    • (1988) Cell , vol.55 , pp. 849-856
    • Giaever, G.N.1    Wang, J.C.2
  • 24
    • 65649089445 scopus 로고    scopus 로고
    • 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
    • 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
    • (2009) J. Med. Chem , vol.52 , pp. 2863-2874
    • Sun, D.1    Hurley, L.H.2
  • 25
    • 0001505226 scopus 로고    scopus 로고
    • Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids
    • 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
    • (2000) Biopolymers , vol.56 , pp. 147-194
    • Hardin, C.C.1    Perry, A.G.2    White, K.3
  • 26
    • 77449111348 scopus 로고    scopus 로고
    • Biochemical techniques for the characterization of G-quadruplex structures: EMSA, DMS footprinting, and DNA polymerase stop assay
    • 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
    • (2010) Methods Mol. Biol , vol.608 , pp. 65-79
    • Sun, D.1    Hurley, L.H.2
  • 27
    • 34547138714 scopus 로고    scopus 로고
    • Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules
    • Kim J.H. and Larson R.G. (2007) Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules. Nucleic Acids Res., 35, 3848-3858
    • (2007) Nucleic Acids Res , vol.35 , pp. 3848-3858
    • Kim, J.H.1    Larson, R.G.2
  • 28
    • 0037015022 scopus 로고    scopus 로고
    • Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase
    • Forde N.R., Izhaky D., Woodcock G.R., Wuite G.J. and Bustamante C. (2002) Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase. Proc. Natl Acad. Sci. USA, 99, 11682-11687
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 11682-11687
    • Forde, N.R.1    Izhaky, D.2    Woodcock, G.R.3    Wuite, G.J.4    Bustamante, C.5
  • 29
    • 38849152177 scopus 로고    scopus 로고
    • DNA torsional stress propagates through chromatin fiber and participates in transcriptional regulation
    • Lavelle C. (2008) DNA torsional stress propagates through chromatin fiber and participates in transcriptional regulation. Nat. Struct. Mol. Biol., 15, 123-125
    • (2008) Nat. Struct. Mol. Biol , vol.15 , pp. 123-125
    • Lavelle, C.1
  • 30
    • 0035804245 scopus 로고    scopus 로고
    • Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase
    • Harada Y., Ohara O., Takatsuki A., Itoh H., Shimamoto N. and Kinosita K. Jr (2001) Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase. Nature, 409, 113-115
    • (2001) Nature , vol.409 , pp. 113-115
    • Harada, Y.1    Ohara, O.2    Takatsuki, A.3    Itoh, H.4    Shimamoto, N.5    Kinosita Jr., K.6
  • 32
    • 33846928449 scopus 로고    scopus 로고
    • G-quadruplexes in promoters throughout the human genome
    • Huppert J.L. and Balasubramanian S. (2007) G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res., 35, 406-413
    • (2007) Nucleic Acids Res , vol.35 , pp. 406-413
    • Huppert, J.L.1    Balasubramanian, S.2
  • 33
    • 34247645020 scopus 로고    scopus 로고
    • Extensive selection for the enrichment of G4 DNA motifs in transcriptional regulatory regions of warm blooded animals
    • 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
    • (2007) FEBS Lett , vol.581 , pp. 1951-1956
    • Zhao, Y.1    Du, Z.2    Li, N.3
  • 34
    • 39049170386 scopus 로고    scopus 로고
    • Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription
    • Du Z., Zhao Y. and Li N. (2008) Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription. Genome Res., 18, 233-241
    • (2008) Genome Res , vol.18 , pp. 233-241
    • Du, Z.1    Zhao, Y.2    Li, N.3
  • 35
    • 52449093394 scopus 로고    scopus 로고
    • Genome-wide computational and expression analyses reveal G-quadruplex DNA motifs as conserved cis-regulatory elements in human and related species
    • Verma A., Halder K., Halder R., Yadav V.K., Rawal P., Thakur R.K., Mohd F., Sharma A. and Chowdhury S. (2008) Genome-wide computational and expression analyses reveal G-quadruplex DNA motifs as conserved cis-regulatory elements in human and related species. J. Med. Chem., 51, 5641-5649
    • (2008) J. Med. Chem , vol.51 , pp. 5641-5649
    • Verma, A.1    Halder, K.2    Halder, R.3    Yadav, V.K.4    Rawal, P.5    Thakur, R.K.6    Mohd, F.7    Sharma, A.8    Chowdhury, S.9
  • 37
    • 0037015078 scopus 로고    scopus 로고
    • Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription
    • 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. USA, 99, 11593-11598
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 11593-11598
    • Siddiqui-Jain, A.1    Grand, C.L.2    Bearss, D.J.3    Hurley, L.H.4
  • 38
    • 79955632672 scopus 로고    scopus 로고
    • Heterogeneous nuclear ribonucleoprotein K and nucleolin as transcriptional activators of the vascular endothelial growth factor promoter through interaction with secondary DNA structures
    • Uribe D.J., Guo K., Shin Y.J. and Sun D. (2011) Heterogeneous nuclear ribonucleoprotein K and nucleolin as transcriptional activators of the vascular endothelial growth factor promoter through interaction with secondary DNA structures. Biochemistry, 50, 3796-3806
    • (2011) Biochemistry , vol.50 , pp. 3796-3806
    • Uribe, D.J.1    Guo, K.2    Shin, Y.J.3    Sun, D.4
  • 39
    • 77955040901 scopus 로고    scopus 로고
    • G-Quadruplex Hinders Translocation of BLM Helicase on DNA: A real-Time fluorescence spectroscopic unwinding study and comparison with duplex substrates
    • 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
    • (2010) J. Am. Chem. Soc , vol.132 , pp. 10521-10527
    • Liu, J.Q.1    Chen, C.Y.2    Xue, Y.3    Hao, Y.H.4    Tan, Z.5
  • 40
    • 79955864551 scopus 로고    scopus 로고
    • Transcription arrest by a G quadruplex forming-Trinucleotide repeat sequence from the human c-myb gene
    • 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
    • (2011) Biochemistry , vol.50 , pp. 4162-4172
    • Broxson, C.1    Beckett, J.2    Tornaletti, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.