메뉴 건너뛰기




Volumn 5, Issue 3, 2014, Pages 195-202

DNA topology and transcription

Author keywords

DNA topoisomerases; DNA topological domain; DNA topology; Torsional stress; Transcription

Indexed keywords

COHESIN; DNA; DNA TOPOISOMERASE; HISTONE H2A; RNA POLYMERASE II; TATA BINDING PROTEIN; TRANSCRIPTION FACTOR CTCF; TRANSCRIPTION FACTOR IIH;

EID: 84900873196     PISSN: 19491034     EISSN: 19491042     Source Type: Journal    
DOI: 10.4161/nucl.28909     Document Type: Article
Times cited : (43)

References (93)
  • 1
    • 0013924261 scopus 로고
    • Physical and topological properties of circular DNA
    • PMID:4290891
    • Vinograd J, Lebowitz J. Physical and topological properties of circular DNA. J Gen Physiol 1966; 49:103-25; PMID:4290891; http://dx.doi.org/10.1085/jgp.49.6.103
    • (1966) J Gen Physiol , vol.49 , pp. 103-125
    • Vinograd, J.1    Lebowitz, J.2
  • 2
    • 84876216563 scopus 로고    scopus 로고
    • Master transcription factors and mediator establish super-enhancers at key cell identity genes
    • PMID:23582322
    • Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, Rahl PB, Lee TI, Young RA. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 2013; 153:307-19; PMID:23582322; http://dx.doi.org/10.1016/j.cell.2013.03.035
    • (2013) Cell , vol.153 , pp. 307-319
    • Whyte, W.A.1    Orlando, D.A.2    Hnisz, D.3    Abraham, B.J.4    Lin, C.Y.5    Kagey, M.H.6    Rahl, P.B.7    Lee, T.I.8    Young, R.A.9
  • 3
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 A resolution
    • PMID:9305837
    • Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 1997; 389:251-60; PMID:9305837; http://dx.doi.org/10.1038/38444
    • (1997) Nature , vol.389 , pp. 251-260
    • Luger, K.1    Mäder, A.W.2    Richmond, R.K.3    Sargent, D.F.4    Richmond, T.J.5
  • 4
    • 29244467484 scopus 로고    scopus 로고
    • Role of linker histone in chromatin structure and function: H1 stoichiometry and nucleosome repeat length
    • PMID:16506093
    • Woodcock CL, Skoultchi AI, Fan Y. Role of linker histone in chromatin structure and function: H1 stoichiometry and nucleosome repeat length. Chromosome Res 2006; 14:17-25; PMID:16506093; http://dx.doi.org/10.1007/s10577-005-1024-3
    • (2006) Chromosome Res , vol.14 , pp. 17-25
    • Woodcock, C.L.1    Skoultchi, A.I.2    Fan, Y.3
  • 5
    • 0026455115 scopus 로고
    • Chromatin structure of Schizosaccharomyces pombe. A nucleosome repeat length that is shorter than the chromatosomal DNA length
    • PMID:1518041
    • Godde JS, Widom J. Chromatin structure of Schizosaccharomyces pombe. A nucleosome repeat length that is shorter than the chromatosomal DNA length. J Mol Biol 1992; 226:1009-25; PMID:1518041; http://dx.doi.org/10.1016/0022-2836(92)91049-U
    • (1992) J Mol Biol , vol.226 , pp. 1009-1025
    • Godde, J.S.1    Widom, J.2
  • 7
    • 0023433855 scopus 로고
    • Supercoiling of the DNA template during transcription
    • PMID:2823250
    • Liu LF, Wang JC. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A 1987; 84:7024-7; PMID:2823250; http://dx.doi.org/10.1073/pnas.84.20.7024
    • (1987) Proc Natl Acad Sci U S A , vol.84 , pp. 7024-7027
    • Liu, L.F.1    Wang, J.C.2
  • 8
    • 84863418617 scopus 로고    scopus 로고
    • The importance of being supercoiled: How DNA mechanics regulate dynamic processes
    • PMID:22233557
    • Baranello L, Levens D, Gupta A, Kouzine F. The importance of being supercoiled: how DNA mechanics regulate dynamic processes. Biochim Biophys Acta 2012; 1819:632-8; PMID:22233557; http://dx.doi.org/10.1016/j.bbagrm.2011.12.007
    • (2012) Biochim Biophys Acta , vol.1819 , pp. 632-638
    • Baranello, L.1    Levens, D.2    Gupta, A.3    Kouzine, F.4
  • 9
    • 84886853624 scopus 로고    scopus 로고
    • Topology of mammalian developmental enhancers and their regulatory landscapes
    • PMID:24153303
    • de Laat W, Duboule D. Topology of mammalian developmental enhancers and their regulatory landscapes. Nature 2013; 502:499-506; PMID:24153303; http://dx.doi.org/10.1038/nature12753
    • (2013) Nature , vol.502 , pp. 499-506
    • de Laat, W.1    Duboule, D.2
  • 10
    • 84861964135 scopus 로고    scopus 로고
    • Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor
    • PMID:22682246
    • Deng W, Lee J, Wang H, Miller J, Reik A, Gregory PD, Dean A, Blobel GA. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell 2012; 149:1233-44; PMID:22682246; http://dx.doi.org/10.1016/j.cell.2012.03.051
    • (2012) Cell , vol.149 , pp. 1233-1244
    • Deng, W.1    Lee, J.2    Wang, H.3    Miller, J.4    Reik, A.5    Gregory, P.D.6    Dean, A.7    Blobel, G.A.8
  • 11
    • 33749373092 scopus 로고    scopus 로고
    • Mapping chromatin interactions by chromosome conformation capture
    • Chapter 21: p. Unit 21 11
    • Miele A, et al. Mapping chromatin interactions by chromosome conformation capture. Curr Protoc Mol Biol, 2006. Chapter 21: p. Unit 21 11.
    • (2006) Curr Protoc Mol Biol
    • Miele, A.1
  • 12
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • PMID:22495300
    • Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 2012; 485:376-80; PMID:22495300; http://dx.doi.org/10.1038/nature11082
    • (2012) Nature , vol.485 , pp. 376-380
    • Dixon, J.R.1    Selvaraj, S.2    Yue, F.3    Kim, A.4    Li, Y.5    Shen, Y.6    Hu, M.7    Liu, J.S.8    Ren, B.9
  • 13
    • 50649101663 scopus 로고    scopus 로고
    • DNA topoisomerases: Harnessing and constraining energy to govern chromosome topology
    • PMID:18755053
    • Schoeffler AJ, Berger JM. DNA topoisomerases: harnessing and constraining energy to govern chromosome topology. Q Rev Biophys 2008; 41:41-101; PMID:18755053; http://dx.doi.org/10.1017/S003358350800468X
    • (2008) Q Rev Biophys , vol.41 , pp. 41-101
    • Schoeffler, A.J.1    Berger, J.M.2
  • 14
    • 63349102030 scopus 로고    scopus 로고
    • Phylogenomics of DNA topoisomerases: Their origin and putative roles in the emergence of modern organisms
    • PMID:19208647
    • Forterre P, Gadelle D. Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms. Nucleic Acids Res 2009; 37:679-92; PMID:19208647; http://dx.doi.org/10.1093/nar/gkp032
    • (2009) Nucleic Acids Res , vol.37 , pp. 679-692
    • Forterre, P.1    Gadelle, D.2
  • 15
    • 8444231721 scopus 로고    scopus 로고
    • Non-B DNA conformations, genomic rearrangements, and human disease
    • PMID:15326170
    • Bacolla A, Wells RD. Non-B DNA conformations, genomic rearrangements, and human disease. J Biol Chem 2004; 279:47411-4; PMID:15326170; http://dx.doi.org/10.1074/jbc.R400028200
    • (2004) J Biol Chem , vol.279 , pp. 47411-47414
    • Bacolla, A.1    Wells, R.D.2
  • 16
    • 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
    • PMID:19385599
    • Sun D, Hurley LH. 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 2009; 52:2863-74; PMID:19385599; http://dx.doi.org/10.1021/jm900055s
    • (2009) J Med Chem , vol.52 , pp. 2863-2874
    • Sun, D.1    Hurley, L.H.2
  • 17
    • 0037803571 scopus 로고    scopus 로고
    • Timeline: Z-DNA: The long road to biological function
    • PMID:12838348
    • Rich A, Zhang S. Timeline: Z-DNA: the long road to biological function. Nat Rev Genet 2003; 4:566-72; PMID:12838348; http://dx.doi.org/10.1038/nrg1115
    • (2003) Nat Rev Genet , vol.4 , pp. 566-572
    • Rich, A.1    Zhang, S.2
  • 18
    • 7544242666 scopus 로고    scopus 로고
    • The dynamic response of upstream DNA to transcription-generated torsional stress
    • PMID:15502847
    • Kouzine F, Liu J, Sanford S, Chung HJ, Levens D. The dynamic response of upstream DNA to transcription-generated torsional stress. Nat Struct Mol Biol 2004; 11:1092-100; PMID:15502847; http://dx.doi.org/10.1038/nsmb848
    • (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
  • 19
    • 84878317678 scopus 로고    scopus 로고
    • Transitions for regulating early transcription
    • PMID:23706732
    • Michel M, Cramer P. Transitions for regulating early transcription. Cell 2013; 153:943-4; PMID:23706732; http://dx.doi.org/10.1016/j.cell.2013.04.050
    • (2013) Cell , vol.153 , pp. 943-944
    • Michel, M.1    Cramer, P.2
  • 20
    • 84872398729 scopus 로고    scopus 로고
    • Transcription-associated histone modifications and cryptic transcription
    • PMID:22982198
    • Smolle M, Workman JL. Transcription-associated histone modifications and cryptic transcription. Biochim Biophys Acta 2013; 1829:84-97; PMID:22982198; http://dx.doi.org/10.1016/j.bbagrm.2012.08.008
    • (2013) Biochim Biophys Acta , vol.1829 , pp. 84-97
    • Smolle, M.1    Workman, J.L.2
  • 21
    • 37249012276 scopus 로고    scopus 로고
    • Nucleosome destabilization in the epigenetic regulation of gene expression
    • PMID:18059368
    • Henikoff S. Nucleosome destabilization in the epigenetic regulation of gene expression. Nat Rev Genet 2008; 9:15-26; PMID:18059368; http://dx.doi.org/10.1038/nrg2206
    • (2008) Nat Rev Genet , vol.9 , pp. 15-26
    • Henikoff, S.1
  • 22
    • 79959346319 scopus 로고    scopus 로고
    • Functional consequences of bidirectional promoters
    • PMID:21601935
    • Wei W, Pelechano V, Järvelin AI, Steinmetz LM. Functional consequences of bidirectional promoters. Trends Genet 2011; 27:267-76; PMID:21601935; http://dx.doi.org/10.1016/j.tig.2011.04.002
    • (2011) Trends Genet , vol.27 , pp. 267-276
    • Wei, W.1    Pelechano, V.2    Järvelin, A.I.3    Steinmetz, L.M.4
  • 23
    • 84887161037 scopus 로고    scopus 로고
    • Control of transcriptional elongation
    • PMID:24050178
    • Kwak H, Lis JT. Control of transcriptional elongation. Annu Rev Genet 2013; 47:483-508; PMID:24050178; http://dx.doi.org/10.1146/annurev-genet-110711-155440
    • (2013) Annu Rev Genet , vol.47 , pp. 483-508
    • Kwak, H.1    Lis, J.T.2
  • 24
    • 84889562158 scopus 로고    scopus 로고
    • Divergent transcription: A driving force for new gene origination?
    • PMID:24267885
    • Wu X, Sharp PA. Divergent transcription: a driving force for new gene origination? Cell 2013; 155:990-6; PMID:24267885; http://dx.doi.org/10.1016/j.cell.2013.10.048
    • (2013) Cell , vol.155 , pp. 990-996
    • Wu, X.1    Sharp, P.A.2
  • 25
    • 84887995915 scopus 로고    scopus 로고
    • Gene regulation by antisense transcription
    • PMID:24217315
    • Pelechano V, Steinmetz LM. Gene regulation by antisense transcription. Nat Rev Genet 2013; 14:880-93; PMID:24217315; http://dx.doi.org/10.1038/nrg3594
    • (2013) Nat Rev Genet , vol.14 , pp. 880-893
    • Pelechano, V.1    Steinmetz, L.M.2
  • 26
    • 33644855266 scopus 로고    scopus 로고
    • Regulation of higher-order chromatin structures by nucleosome-remodelling factors
    • PMID:16503135
    • Varga-Weisz PD, Becker PB. Regulation of higher-order chromatin structures by nucleosome-remodelling factors. Curr Opin Genet Dev 2006; 16:151-6; PMID:16503135; http://dx.doi.org/10.1016/j.gde.2006.02.006
    • (2006) Curr Opin Genet Dev , vol.16 , pp. 151-156
    • Varga-Weisz, P.D.1    Becker, P.B.2
  • 27
    • 0034704235 scopus 로고    scopus 로고
    • Generation of superhelical torsion by ATP-dependent chromatin remodeling activities
    • PMID:11163188
    • Havas K, Flaus A, Phelan M, Kingston R, Wade PA, Lilley DM, Owen-Hughes T. Generation of superhelical torsion by ATP-dependent chromatin remodeling activities. Cell 2000; 103:1133-42; PMID:11163188; http://dx.doi.org/10.1016/S0092-8674(00)00215-4
    • (2000) Cell , vol.103 , pp. 1133-1142
    • Havas, K.1    Flaus, A.2    Phelan, M.3    Kingston, R.4    Wade, P.A.5    Lilley, D.M.6    Owen-Hughes, T.7
  • 28
    • 84862834099 scopus 로고    scopus 로고
    • SWI/SNF-mediated chromatin remodeling induces Z-DNA formation on a nucleosome
    • PMID:22264354
    • Mulholland N, Xu Y, Sugiyama H, Zhao K. SWI/SNF-mediated chromatin remodeling induces Z-DNA formation on a nucleosome. Cell Biosci 2012; 2:3; PMID:22264354; http://dx.doi.org/10.1186/2045-3701-2-3
    • (2012) Cell Biosci , vol.2 , pp. 3
    • Mulholland, N.1    Xu, Y.2    Sugiyama, H.3    Zhao, K.4
  • 29
    • 33847787053 scopus 로고    scopus 로고
    • Characterization of Z-DNA as a nucleosome-boundary element in yeast Saccharomyces cerevisiae
    • PMID:17284586
    • Wong B, Chen S, Kwon JA, Rich A. Characterization of Z-DNA as a nucleosome-boundary element in yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2007; 104:2229-34; PMID:17284586; http://dx.doi.org/10.1073/pnas.0611447104
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 2229-2234
    • Wong, B.1    Chen, S.2    Kwon, J.A.3    Rich, A.4
  • 30
    • 33645228949 scopus 로고    scopus 로고
    • Cooperative activity of BRG1 and Z-DNA formation in chromatin remodeling
    • PMID:16537901
    • Liu H, Mulholland N, Fu H, Zhao K. Cooperative activity of BRG1 and Z-DNA formation in chromatin remodeling. Mol Cell Biol 2006; 26:2550-9; PMID:16537901; http://dx.doi.org/10.1128/MCB.26.7.2550-2559.2006
    • (2006) Mol Cell Biol , vol.26 , pp. 2550-2559
    • Liu, H.1    Mulholland, N.2    Fu, H.3    Zhao, K.4
  • 31
    • 0033826515 scopus 로고    scopus 로고
    • Role of histone N-terminal tails and their acetylation in nucleosome dynamics
    • PMID:10982840
    • Morales V, Richard-Foy H. Role of histone N-terminal tails and their acetylation in nucleosome dynamics. Mol Cell Biol 2000; 20:7230-7; PMID:10982840; http://dx.doi.org/10.1128/MCB.20.19.7230-7237.2000
    • (2000) Mol Cell Biol , vol.20 , pp. 7230-7237
    • Morales, V.1    Richard-Foy, H.2
  • 32
    • 0034603806 scopus 로고    scopus 로고
    • Topological effects of the TATA box binding protein on minicircle DNA and a possible thermodynamic linkage to chromatin remodeling
    • PMID:10736150
    • Kahn JD. Topological effects of the TATA box binding protein on minicircle DNA and a possible thermodynamic linkage to chromatin remodeling. Biochemistry 2000; 39:3520-4; PMID:10736150; http://dx.doi.org/10.1021/bi992263f
    • (2000) Biochemistry , vol.39 , pp. 3520-3524
    • Kahn, J.D.1
  • 33
    • 0027168221 scopus 로고
    • DNA topology and a minimal set of basal factors for transcription by RNA polymerase II
    • PMID:8490964
    • Parvin JD, Sharp PA. DNA topology and a minimal set of basal factors for transcription by RNA polymerase II. Cell 1993; 73:533-40; PMID:8490964; http://dx.doi.org/10.1016/0092-8674(93)90140-L
    • (1993) Cell , vol.73 , pp. 533-540
    • Parvin, J.D.1    Sharp, P.A.2
  • 34
    • 0025899335 scopus 로고
    • Inhibition of 5S RNA transcription in vitro by nucleosome cores with low or high levels of histone acetylation
    • PMID:1879554
    • Roberge M, O'Neill TE, Bradbury EM. Inhibition of 5S RNA transcription in vitro by nucleosome cores with low or high levels of histone acetylation. FEBS Lett 1991; 288:215-8; PMID:1879554; http://dx.doi.org/10.1016/0014-5793(91)81037-9
    • (1991) FEBS Lett , vol.288 , pp. 215-218
    • Roberge, M.1    O'Neill, T.E.2    Bradbury, E.M.3
  • 35
    • 78049246250 scopus 로고    scopus 로고
    • Fast signals and slow marks: The dynamics of histone modifications
    • PMID:20685123
    • Barth TK, Imhof A. Fast signals and slow marks: the dynamics of histone modifications. Trends Biochem Sci 2010; 35:618-26; PMID:20685123; http://dx.doi.org/10.1016/j.tibs.2010.05.006
    • (2010) Trends Biochem Sci , vol.35 , pp. 618-626
    • Barth, T.K.1    Imhof, A.2
  • 36
    • 77954957199 scopus 로고    scopus 로고
    • Topoisomerase I regulates open chromatin and controls gene expression in vivo
    • PMID:20526281
    • Durand-Dubief M, Persson J, Norman U, Hartsuiker E, Ekwall K. Topoisomerase I regulates open chromatin and controls gene expression in vivo. EMBO J 2010; 29:2126-34; PMID:20526281; http://dx.doi.org/10.1038/emboj.2010.109
    • (2010) EMBO J , vol.29 , pp. 2126-2134
    • Durand-Dubief, M.1    Persson, J.2    Norman, U.3    Hartsuiker, E.4    Ekwall, K.5
  • 37
    • 84864662191 scopus 로고    scopus 로고
    • Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening
    • PMID:22751016
    • Grünberg S, Warfield L, Hahn S. Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening. Nat Struct Mol Biol 2012; 19:788-96; PMID:22751016; http://dx.doi.org/10.1038/nsmb.2334
    • (2012) Nat Struct Mol Biol , vol.19 , pp. 788-796
    • Grünberg, S.1    Warfield, L.2    Hahn, S.3
  • 38
    • 33751218319 scopus 로고    scopus 로고
    • Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching
    • PMID:17110577
    • Revyakin A, Liu C, Ebright RH, Strick TR. Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science 2006; 314:1139-43; PMID:17110577; http://dx.doi.org/10.1126/science.1131398
    • (2006) Science , vol.314 , pp. 1139-1143
    • Revyakin, A.1    Liu, C.2    Ebright, R.H.3    Strick, T.R.4
  • 40
    • 84893755427 scopus 로고    scopus 로고
    • Transcription-generated torsional stress destabilizes nucleosomes
    • PMID:24317489
    • Teves SS, Henikoff S. Transcription-generated torsional stress destabilizes nucleosomes. Nat Struct Mol Biol 2014; 21:88-94; PMID:24317489; http://dx.doi.org/10.1038/nsmb.2723
    • (2014) Nat Struct Mol Biol , vol.21 , pp. 88-94
    • Teves, S.S.1    Henikoff, S.2
  • 41
    • 0028232284 scopus 로고
    • RAD25 is a DNA helicase required for DNA repair and RNA polymerase II transcription
    • PMID:8202161
    • Guzder SN, Sung P, Bailly V, Prakash L, Prakash S. RAD25 is a DNA helicase required for DNA repair and RNA polymerase II transcription. Nature 1994; 369:578-81; PMID:8202161; http://dx.doi.org/10.1038/369578a0
    • (1994) Nature , vol.369 , pp. 578-581
    • Guzder, S.N.1    Sung, P.2    Bailly, V.3    Prakash, L.4    Prakash, S.5
  • 42
    • 84875613843 scopus 로고    scopus 로고
    • Structural visualization of key steps in human transcription initiation
    • PMID:23446344
    • He Y, Fang J, Taatjes DJ, Nogales E. Structural visualization of key steps in human transcription initiation. Nature 2013; 495:481-6; PMID:23446344; http://dx.doi.org/10.1038/nature11991
    • (2013) Nature , vol.495 , pp. 481-486
    • He, Y.1    Fang, J.2    Taatjes, D.J.3    Nogales, E.4
  • 43
    • 0034717308 scopus 로고    scopus 로고
    • Mechanism of ATP-dependent promoter melting by transcription factor IIH
    • PMID:10827951
    • Kim TK, Ebright RH, Reinberg D. Mechanism of ATP-dependent promoter melting by transcription factor IIH. Science 2000; 288:1418-22; PMID:10827951; http://dx.doi.org/10.1126/science.288.5470.1418
    • (2000) Science , vol.288 , pp. 1418-1422
    • Kim, T.K.1    Ebright, R.H.2    Reinberg, D.3
  • 45
    • 79954562232 scopus 로고    scopus 로고
    • Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells
    • PMID:21460038
    • Min IM, Waterfall JJ, Core LJ, Munroe RJ, Schimenti J, Lis JT. Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells. Genes Dev 2011; 25:742-54; PMID:21460038; http://dx.doi.org/10.1101/gad.2005511
    • (2011) Genes Dev , vol.25 , pp. 742-754
    • Min, I.M.1    Waterfall, J.J.2    Core, L.J.3    Munroe, R.J.4    Schimenti, J.5    Lis, J.T.6
  • 46
    • 84874175008 scopus 로고    scopus 로고
    • Precise maps of RNA polymerase reveal how promoters direct initiation and pausing
    • PMID:23430654
    • Kwak H, Fuda NJ, Core LJ, Lis JT. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 2013; 339:950-3; PMID:23430654; http://dx.doi.org/10.1126/science.1229386
    • (2013) Science , vol.339 , pp. 950-953
    • Kwak, H.1    Fuda, N.J.2    Core, L.J.3    Lis, J.T.4
  • 47
    • 84871699564 scopus 로고    scopus 로고
    • Promoter-proximal pausing of RNA polymerase II: Emerging roles in metazoans
    • PMID:22986266
    • Adelman K, Lis JT. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat Rev Genet 2012; 13:720-31; PMID:22986266; http://dx.doi.org/10.1038/nrg3293
    • (2012) Nat Rev Genet , vol.13 , pp. 720-731
    • Adelman, K.1    Lis, J.T.2
  • 48
    • 79955795581 scopus 로고    scopus 로고
    • Paused RNA polymerase II as a developmental checkpoint
    • PMID:21565610
    • Levine M. Paused RNA polymerase II as a developmental checkpoint. Cell 2011; 145:502-11; PMID:21565610; http://dx.doi.org/10.1016/j.cell.2011.04.021
    • (2011) Cell , vol.145 , pp. 502-511
    • Levine, M.1
  • 50
    • 74949123158 scopus 로고    scopus 로고
    • DNA topoisomerase I inhibition by camptothecin induces escape of RNA polymerase II from promoter-proximal pause site, antisense transcription and histone acetylation at the human HIF-1alpha gene locus
    • PMID:19854946
    • Baranello L, Bertozzi D, Fogli MV, Pommier Y, Capranico G. DNA topoisomerase I inhibition by camptothecin induces escape of RNA polymerase II from promoter-proximal pause site, antisense transcription and histone acetylation at the human HIF-1alpha gene locus. Nucleic Acids Res 2010; 38:159-71; PMID:19854946; http://dx.doi.org/10.1093/nar/gkp817
    • (2010) Nucleic Acids Res , vol.38 , pp. 159-171
    • Baranello, L.1    Bertozzi, D.2    Fogli, M.V.3    Pommier, Y.4    Capranico, G.5
  • 51
    • 84879682825 scopus 로고    scopus 로고
    • Transcription under torsion
    • PMID:23812716
    • Ma J, Bai L, Wang MD. Transcription under torsion. Science 2013; 340:1580-3; PMID:23812716; http://dx.doi.org/10.1126/science.1235441
    • (2013) Science , vol.340 , pp. 1580-1583
    • Ma, J.1    Bai, L.2    Wang, M.D.3
  • 52
    • 0026578605 scopus 로고
    • DNA supercoiling in chromatin structure and gene expression
    • PMID:1581628
    • Freeman LA, Garrard WT. DNA supercoiling in chromatin structure and gene expression. Crit Rev Eukaryot Gene Expr 1992; 2:165-209; PMID:1581628
    • (1992) Crit Rev Eukaryot Gene Expr , vol.2 , pp. 165-209
    • Freeman, L.A.1    Garrard, W.T.2
  • 53
    • 38849132828 scopus 로고    scopus 로고
    • The functional response of upstream DNA to dynamic supercoiling in vivo
    • PMID:18193062
    • Kouzine F, Sanford S, Elisha-Feil Z, Levens D. The functional response of upstream DNA to dynamic supercoiling in vivo. Nat Struct Mol Biol 2008; 15:146-54; PMID:18193062; http://dx.doi.org/10.1038/nsmb.1372
    • (2008) Nat Struct Mol Biol , vol.15 , pp. 146-154
    • Kouzine, F.1    Sanford, S.2    Elisha-Feil, Z.3    Levens, D.4
  • 54
    • 0026629273 scopus 로고
    • Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates
    • PMID:1618865
    • Izban MG, Luse DS. Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates. J Biol Chem 1992; 267:13647-55; PMID:1618865
    • (1992) J Biol Chem , vol.267 , pp. 13647-13655
    • Izban, M.G.1    Luse, D.S.2
  • 55
    • 46149108345 scopus 로고    scopus 로고
    • Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci
    • PMID:18614012
    • Petesch SJ, Lis JT. Rapid, transcription-independent loss of nucleosomes over a large chromatin domain at Hsp70 loci. Cell 2008; 134:74-84; PMID:18614012; http://dx.doi.org/10.1016/j.cell.2008.05.029
    • (2008) Cell , vol.134 , pp. 74-84
    • Petesch, S.J.1    Lis, J.T.2
  • 56
    • 73449148377 scopus 로고    scopus 로고
    • Nucleosome assembly depends on the torsion in the DNA molecule: A magnetic tweezers study
    • PMID:20006952
    • Gupta P, Zlatanova J, Tomschik M. Nucleosome assembly depends on the torsion in the DNA molecule: a magnetic tweezers study. Biophys J 2009; 97:3150-7; PMID:20006952; http://dx.doi.org/10.1016/j.bpj.2009.09.032
    • (2009) Biophys J , vol.97 , pp. 3150-3157
    • Gupta, P.1    Zlatanova, J.2    Tomschik, M.3
  • 57
    • 10044236090 scopus 로고    scopus 로고
    • Femtonewton force spectroscopy of single extended DNA molecules
    • PMID:10990855
    • Meiners JC, Quake SR. Femtonewton force spectroscopy of single extended DNA molecules. Phys Rev Lett 2000; 84:5014-7; PMID:10990855; http://dx.doi.org/10.1103/PhysRevLett.84.5014
    • (2000) Phys Rev Lett , vol.84 , pp. 5014-5017
    • Meiners, J.C.1    Quake, S.R.2
  • 58
    • 33751212444 scopus 로고    scopus 로고
    • A breaking strategy for topoisomerase IIbeta/PARP-1-dependent regulated transcription
    • PMID:17106262
    • Ju BG, Rosenfeld MG. A breaking strategy for topoisomerase IIbeta/PARP-1-dependent regulated transcription. Cell Cycle 2006; 5:2557-60; PMID:17106262; http://dx.doi.org/10.4161/cc.5.22.3497
    • (2006) Cell Cycle , vol.5 , pp. 2557-2560
    • Ju, B.G.1    Rosenfeld, M.G.2
  • 59
    • 84896698176 scopus 로고    scopus 로고
    • Kinase-mediated changes in nucleosome conformation trigger chromatin decondensation via poly(ADP-ribosyl)ation
    • PMID:24508391
    • Thomas CJ, Kotova E, Andrake M, Adolf-Bryfogle J, Glaser R, Regnard C, Tulin AV. Kinase-mediated changes in nucleosome conformation trigger chromatin decondensation via poly(ADP-ribosyl)ation. Mol Cell 2014; 53:831-42; PMID:24508391; http://dx.doi.org/10.1016/j.molcel.2014.01.005
    • (2014) Mol Cell , vol.53 , pp. 831-842
    • Thomas, C.J.1    Kotova, E.2    Andrake, M.3    Adolf-Bryfogle, J.4    Glaser, R.5    Regnard, C.6    Tulin, A.V.7
  • 60
    • 84885660614 scopus 로고    scopus 로고
    • Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss
    • PMID:24113677
    • Sheinin MY, Li M, Soltani M, Luger K, Wang MD. Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss. Nat Commun 2013; 4:2579; PMID:24113677; http://dx.doi.org/10.1038/ncomms3579
    • (2013) Nat Commun , vol.4 , pp. 2579
    • Sheinin, M.Y.1    Li, M.2    Soltani, M.3    Luger, K.4    Wang, M.D.5
  • 61
    • 70350754211 scopus 로고    scopus 로고
    • Rates of in situ transcription and splicing in large human genes
    • PMID:19820712
    • Singh J, Padgett RA. Rates of in situ transcription and splicing in large human genes. Nat Struct Mol Biol 2009; 16:1128-33; PMID:19820712; http://dx.doi.org/10.1038/nsmb.1666
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 1128-1133
    • Singh, J.1    Padgett, R.A.2
  • 63
    • 65249169329 scopus 로고    scopus 로고
    • Forces and torques in the nucleus: Chromatin under mechanical constraints
    • PMID:19234543
    • Lavelle C. Forces and torques in the nucleus: chromatin under mechanical constraints. Biochem Cell Biol 2009; 87:307-22; PMID:19234543; http://dx.doi.org/10.1139/O08-123
    • (2009) Biochem Cell Biol , vol.87 , pp. 307-322
    • Lavelle, C.1
  • 64
    • 34347231949 scopus 로고    scopus 로고
    • Supercoil-driven DNA structures regulate genetic transactions
    • PMID:17485385
    • Kouzine F, Levens D. Supercoil-driven DNA structures regulate genetic transactions. Front Biosci 2007; 12:4409-23; PMID:17485385; http://dx.doi.org/10.2741/2398
    • (2007) Front Biosci , vol.12 , pp. 4409-4423
    • Kouzine, F.1    Levens, D.2
  • 65
    • 84889242115 scopus 로고    scopus 로고
    • Genetic determinants and cellular constraints in noisy gene expression
    • PMID:24311680
    • Sanchez A, Golding I. Genetic determinants and cellular constraints in noisy gene expression. Science 2013; 342:1188-93; PMID:24311680; http://dx.doi.org/10.1126/science.1242975
    • (2013) Science , vol.342 , pp. 1188-1193
    • Sanchez, A.1    Golding, I.2
  • 66
    • 33646779199 scopus 로고    scopus 로고
    • The FUSE/FBP/FIR/TFIIH system is a molecular machine programming a pulse of c-myc expression
    • PMID:16628215
    • Liu J, Kouzine F, Nie Z, Chung HJ, Elisha-Feil Z, Weber A, Zhao K, Levens D. The FUSE/FBP/FIR/TFIIH system is a molecular machine programming a pulse of c-myc expression. EMBO J 2006; 25:2119-30; PMID:16628215; http://dx.doi.org/10.1038/sj.emboj.7601101
    • (2006) EMBO J , vol.25 , pp. 2119-2130
    • Liu, J.1    Kouzine, F.2    Nie, Z.3    Chung, H.J.4    Elisha-Feil, Z.5    Weber, A.6    Zhao, K.7    Levens, D.8
  • 67
    • 11144274567 scopus 로고    scopus 로고
    • TFIIH operates through an expanded proximal promoter to fine-tune c-myc expression
    • PMID:15601838
    • Weber A, Liu J, Collins I, Levens D. TFIIH operates through an expanded proximal promoter to fine-tune c-myc expression. Mol Cell Biol 2005; 25:147-61; PMID:15601838; http://dx.doi.org/10.1128/MCB.25.1.147-161.2005
    • (2005) Mol Cell Biol , vol.25 , pp. 147-161
    • Weber, A.1    Liu, J.2    Collins, I.3    Levens, D.4
  • 68
    • 79952282523 scopus 로고    scopus 로고
    • JTV1 co-activates FBP to induce USP29 transcription and stabilize p53 in response to oxidative stress
    • PMID:21285945
    • Liu J, Chung HJ, Vogt M, Jin Y, Malide D, He L, Dundr M, Levens D. JTV1 co-activates FBP to induce USP29 transcription and stabilize p53 in response to oxidative stress. EMBO J 2011; 30:846-58; PMID:21285945; http://dx.doi.org/10.1038/emboj.2011.11
    • (2011) EMBO J , vol.30 , pp. 846-858
    • Liu, J.1    Chung, H.J.2    Vogt, M.3    Jin, Y.4    Malide, D.5    He, L.6    Dundr, M.7    Levens, D.8
  • 69
    • 79952284127 scopus 로고    scopus 로고
    • Hallmarks of cancer: The next generation
    • PMID:21376230
    • Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011; 144:646-74; PMID:21376230; http://dx.doi.org/10.1016/j.cell.2011.02.013
    • (2011) Cell , vol.144 , pp. 646-674
    • Hanahan, D.1    Weinberg, R.A.2
  • 72
    • 57849109058 scopus 로고    scopus 로고
    • Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    • PMID:19056941
    • Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 2008; 322:1845-8; PMID:19056941; http://dx.doi.org/10.1126/science.1162228
    • (2008) Science , vol.322 , pp. 1845-1848
    • Core, L.J.1    Waterfall, J.J.2    Lis, J.T.3
  • 75
    • 84865800494 scopus 로고    scopus 로고
    • The long-range interaction landscape of gene promoters
    • PMID:22955621
    • Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature 2012; 489:109-13; PMID:22955621; http://dx.doi.org/10.1038/nature11279
    • (2012) Nature , vol.489 , pp. 109-113
    • Sanyal, A.1    Lajoie, B.R.2    Jain, G.3    Dekker, J.4
  • 76
    • 84881171344 scopus 로고    scopus 로고
    • Enhancer transcripts mark active estrogen receptor binding sites
    • PMID:23636943
    • Hah N, Murakami S, Nagari A, Danko CG, Kraus WL. Enhancer transcripts mark active estrogen receptor binding sites. Genome Res 2013; 23:1210-23; PMID:23636943; http://dx.doi.org/10.1101/gr.152306.112
    • (2013) Genome Res , vol.23 , pp. 1210-1223
    • Hah, N.1    Murakami, S.2    Nagari, A.3    Danko, C.G.4    Kraus, W.L.5
  • 77
    • 84861531483 scopus 로고    scopus 로고
    • Overcoming the nucleosome barrier during transcript elongation
    • PMID:22465610
    • Petesch SJ, Lis JT. Overcoming the nucleosome barrier during transcript elongation. Trends Genet 2012; 28:285-94; PMID:22465610; http://dx.doi.org/10.1016/j.tig.2012.02.005
    • (2012) Trends Genet , vol.28 , pp. 285-294
    • Petesch, S.J.1    Lis, J.T.2
  • 78
    • 34147193819 scopus 로고    scopus 로고
    • Beta-globin intergenic transcription and histone acetylation dependent on an enhancer
    • PMID:17283048
    • Kim A, Zhao H, Ifrim I, Dean A. Beta-globin intergenic transcription and histone acetylation dependent on an enhancer. Mol Cell Biol 2007; 27:2980-6; PMID:17283048; http://dx.doi.org/10.1128/MCB.02337-06
    • (2007) Mol Cell Biol , vol.27 , pp. 2980-2986
    • Kim, A.1    Zhao, H.2    Ifrim, I.3    Dean, A.4
  • 79
    • 84878451215 scopus 로고    scopus 로고
    • Gene regulation by the act of long non-coding RNA transcription
    • PMID:23721193
    • Kornienko AE, Guenzl PM, Barlow DP, Pauler FM. Gene regulation by the act of long non-coding RNA transcription. BMC Biol 2013; 11:59; PMID:23721193; http://dx.doi.org/10.1186/1741-7007-11-59
    • (2013) BMC Biol , vol.11 , pp. 59
    • Kornienko, A.E.1    Guenzl, P.M.2    Barlow, D.P.3    Pauler, F.M.4
  • 80
    • 33847205083 scopus 로고    scopus 로고
    • What are the molecular ties that maintain genomic loops?
    • PMID:17280735
    • Marenduzzo D, Faro-Trindade I, Cook PR. What are the molecular ties that maintain genomic loops? Trends Genet 2007; 23:126-33; PMID:17280735; http://dx.doi.org/10.1016/j.tig.2007.01.007
    • (2007) Trends Genet , vol.23 , pp. 126-133
    • Marenduzzo, D.1    Faro-Trindade, I.2    Cook, P.R.3
  • 81
    • 34548708489 scopus 로고    scopus 로고
    • A facilitated tracking and transcription mechanism of long-range enhancer function
    • PMID:17704132
    • Zhu X, Ling J, Zhang L, Pi W, Wu M, Tuan D. A facilitated tracking and transcription mechanism of long-range enhancer function. Nucleic Acids Res 2007; 35:5532-44; PMID:17704132; http://dx.doi.org/10.1093/nar/gkm595
    • (2007) Nucleic Acids Res , vol.35 , pp. 5532-5544
    • Zhu, X.1    Ling, J.2    Zhang, L.3    Pi, W.4    Wu, M.5    Tuan, D.6
  • 82
    • 0022553738 scopus 로고
    • Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites
    • PMID:3002631
    • Cockerill PN, Garrard WT. Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell 1986; 44:273-82; PMID:3002631; http://dx.doi.org/10.1016/0092-8674(86)90761-0
    • (1986) Cell , vol.44 , pp. 273-282
    • Cockerill, P.N.1    Garrard, W.T.2
  • 83
    • 84881387394 scopus 로고    scopus 로고
    • Cell-cycle specific association of transcription factors and RNA polymerase ii with the human β-globin gene locus
    • PMID:23519692
    • Rosenberg M, Fan AX, Lin IJ, Liang SY, Bungert J. Cell-cycle specific association of transcription factors and RNA polymerase ii with the human β-globin gene locus. J Cell Biochem 2013; 114:1997-2006; PMID:23519692; http://dx.doi.org/10.1002/jcb.24542
    • (2013) J Cell Biochem , vol.114 , pp. 1997-2006
    • Rosenberg, M.1    Fan, A.X.2    Lin, I.J.3    Liang, S.Y.4    Bungert, J.5
  • 84
    • 84885218257 scopus 로고    scopus 로고
    • DNA Topoisomerases: Beyond the standard role
    • PMID:24135702
    • Baranello L, Kouzine F, Levens D. DNA Topoisomerases: Beyond the standard role. Transcription 2013; 4; PMID:24135702; http://dx.doi.org/10.4161/trns.26598
    • (2013) Transcription , pp. 4
    • Baranello, L.1    Kouzine, F.2    Levens, D.3
  • 85
    • 70549099970 scopus 로고    scopus 로고
    • The role of supercoiling in transcriptional control of MYC and its importance in molecular therapeutics
    • PMID:19907434
    • Brooks TA, Hurley LH. The role of supercoiling in transcriptional control of MYC and its importance in molecular therapeutics. Nat Rev Cancer 2009; 9:849-61; PMID:19907434; http://dx.doi.org/10.1038/nrc2733
    • (2009) Nat Rev Cancer , vol.9 , pp. 849-861
    • Brooks, T.A.1    Hurley, L.H.2
  • 86
    • 84872531927 scopus 로고    scopus 로고
    • Epigenetic regulation by Z-DNA silencer function controls cancer-associated ADAM-12 expression in breast cancer: Cross-talk between MeCP2 and NF1 transcription factor family
    • PMID:23135915
    • Ray BK, Dhar S, Henry C, Rich A, Ray A. Epigenetic regulation by Z-DNA silencer function controls cancer-associated ADAM-12 expression in breast cancer: cross-talk between MeCP2 and NF1 transcription factor family. Cancer Res 2013; 73:736-44; PMID:23135915; http://dx.doi.org/10.1158/0008-5472.CAN-12-2601
    • (2013) Cancer Res , vol.73 , pp. 736-744
    • Ray, B.K.1    Dhar, S.2    Henry, C.3    Rich, A.4    Ray, A.5
  • 87
    • 79551522264 scopus 로고    scopus 로고
    • Theoretical analysis of the stress induced B-Z transition in superhelical DNA
    • PMID:21283778
    • Zhabinskaya D, Benham CJ. Theoretical analysis of the stress induced B-Z transition in superhelical DNA. PLoS Comput Biol 2011; 7:e1001051; PMID:21283778; http://dx.doi.org/10.1371/journal.pcbi.1001051
    • (2011) PLoS Comput Biol , vol.7
    • Zhabinskaya, D.1    Benham, C.J.2
  • 88
    • 84873559405 scopus 로고    scopus 로고
    • Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements
    • PMID:23405090
    • Sawaya S, Bagshaw A, Buschiazzo E, Kumar P, Chowdhury S, Black MA, Gemmell N. Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements. PLoS One 2013; 8:e54710; PMID:23405090; http://dx.doi.org/10.1371/journal.pone.0054710
    • (2013) PLoS One , vol.8
    • Sawaya, S.1    Bagshaw, A.2    Buschiazzo, E.3    Kumar, P.4    Chowdhury, S.5    Black, M.A.6    Gemmell, N.7
  • 89
    • 33745255099 scopus 로고    scopus 로고
    • A topoisomerase IIbeta-mediated dsDNA break required for regulated transcription
    • PMID:16794079
    • Ju BG, Lunyak VV, Perissi V, Garcia-Bassets I, Rose DW, Glass CK, Rosenfeld MG. A topoisomerase IIbeta-mediated dsDNA break required for regulated transcription. Science 2006; 312:1798-802; PMID:16794079; http://dx.doi.org/10.1126/science.1127196
    • (2006) Science , vol.312 , pp. 1798-1802
    • Ju, B.G.1    Lunyak, V.V.2    Perissi, V.3    Garcia-Bassets, I.4    Rose, D.W.5    Glass, C.K.6    Rosenfeld, M.G.7
  • 90
    • 71249101060 scopus 로고    scopus 로고
    • Nuclear receptor-induced chromosomal proximity and DNA breaks underlie specific translocations in cancer
    • PMID:19962179
    • Lin C, Yang L, Tanasa B, Hutt K, Ju BG, Ohgi K, Zhang J, Rose DW, Fu XD, Glass CK, et al. Nuclear receptor-induced chromosomal proximity and DNA breaks underlie specific translocations in cancer. Cell 2009; 139:1069-83; PMID:19962179; http://dx.doi.org/10.1016/j.cell.2009.11.030
    • (2009) Cell , vol.139 , pp. 1069-1083
    • Lin, C.1    Yang, L.2    Tanasa, B.3    Hutt, K.4    Ju, B.G.5    Ohgi, K.6    Zhang, J.7    Rose, D.W.8    Fu, X.D.9    Glass, C.K.10
  • 93
    • 84898015781 scopus 로고    scopus 로고
    • Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes
    • PMID:24366878
    • Benedetti F, Dorier J, Burnier Y, Stasiak A. Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes. Nucleic Acids Res 2014; 42:2848-55; PMID:24366878; http://dx.doi.org/10.1093/nar/gkt1353
    • (2014) Nucleic Acids Res , vol.42 , pp. 2848-2855
    • Benedetti, F.1    Dorier, J.2    Burnier, Y.3    Stasiak, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.