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Volumn 2013, Issue 2, 2013, Pages

Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOSIDE TRIPHOSPHATE; RNA POLYMERASE II;

EID: 84884682805     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.00971     Document Type: Article
Times cited : (106)

References (73)
  • 1
    • 28544432440 scopus 로고    scopus 로고
    • Direct observation of base-pair stepping by RNA polymerase
    • doi: 10.1038/nature04268
    • Abbondanzieri EA, Greenleaf WJ, Shaevitz JW, Landick R, Block SM. 2005. Direct observation of base-pair stepping by RNA polymerase. Nature 438:460-5. doi: 10.1038/nature04268.
    • (2005) Nature , vol.438 , pp. 460-465
    • Abbondanzieri, E.A.1    Greenleaf, W.J.2    Shaevitz, J.W.3    Landick, R.4    Block, S.M.5
  • 2
    • 0034691146 scopus 로고    scopus 로고
    • Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals
    • doi: 10.1073/pnas.97.13.7090
    • Artsimovitch I, Landick R. 2000. Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Proc Natl Acad Sci USA 97:7090-5. doi: 10.1073/pnas.97.13.7090.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 7090-7095
    • Artsimovitch, I.1    Landick, R.2
  • 3
    • 33846958387 scopus 로고    scopus 로고
    • Mechanochemical kinetics of transcription elongation
    • doi: 10.1103/PhysRevLett.98.068103
    • Bai L, Fulbright RM, Wang MD. 2007. Mechanochemical kinetics of transcription elongation. Phys Rev Lett 98:068103. doi: 10.1103/PhysRevLett.98.068103.
    • (2007) Phys Rev Lett , vol.98 , pp. 068103
    • Bai, L.1    Fulbright, R.M.2    Wang, M.D.3
  • 4
    • 7444253928 scopus 로고    scopus 로고
    • Sequence-dependent kinetic model for transcription elongation by RNA polymerase
    • doi: 10.1016/j.jmb.2004.08.107
    • Bai L, Shundrovsky A, Wang MD. 2004. Sequence-dependent kinetic model for transcription elongation by RNA polymerase. J Mol Biol 344:335-49. doi: 10.1016/j.jmb.2004.08.107.
    • (2004) J Mol Biol , vol.344 , pp. 335-349
    • Bai, L.1    Shundrovsky, A.2    Wang, M.D.3
  • 5
    • 12944324227 scopus 로고    scopus 로고
    • A ratchet mechanism of transcription elongation and its control
    • doi: 10.1016/j.cell.2004.11.045
    • Bar-Nahum G, Epshtein V, Ruckenstein AE, Rafikov R, Mustaev A, Nudler E. 2005. A ratchet mechanism of transcription elongation and its control. Cell 120:183-93. doi: 10.1016/j.cell.2004.11.045.
    • (2005) Cell , vol.120 , pp. 183-193
    • Bar-Nahum, G.1    Epshtein, V.2    Ruckenstein, A.E.3    Rafikov, R.4    Mustaev, A.5    Nudler, E.6
  • 6
    • 84869009900 scopus 로고    scopus 로고
    • Nucleosomal elements that control the topography of the barrier to transcription
    • doi: 10.1016/j.cell.2012.10.009
    • Bintu L, Ishibashi T, Dangkulwanich M, Wu YY, Lubkowska L, Kashlev M, et al. 2012. Nucleosomal elements that control the topography of the barrier to transcription. Cell 151:738-49. doi: 10.1016/j.cell.2012.10.009.
    • (2012) Cell , vol.151 , pp. 738-749
    • Bintu, L.1    Ishibashi, T.2    Dangkulwanich, M.3    Wu, Y.Y.4    Lubkowska, L.5    Kashlev, M.6
  • 7
    • 82955167888 scopus 로고    scopus 로고
    • The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes
    • doi: 10.1038/nsmb.2164
    • Bintu L, Kopaczynska M, Hodges C, Lubkowska L, Kashlev M, Bustamante C. 2011. The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes. Nat Struct Mol Biol 18:1394-9. doi: 10.1038/nsmb.2164.
    • (2011) Nat Struct Mol Biol , vol.18 , pp. 1394-1399
    • Bintu, L.1    Kopaczynska, M.2    Hodges, C.3    Lubkowska, L.4    Kashlev, M.5    Bustamante, C.6
  • 8
    • 33750442129 scopus 로고    scopus 로고
    • Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II
    • doi: 10.1016/j.molcel.2006.09.009
    • Bondarenko VA, Steele LM, Ujari A, Gaykalova DA, Kulaeva OI, Polikanov YS, et al. 2006. Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II. Mol Cell 24:469-79. doi: 10.1016/j.molcel.2006.09.009.
    • (2006) Mol Cell , vol.24 , pp. 469-479
    • Bondarenko, V.A.1    Steele, L.M.2    Ujari, A.3    Gaykalova, D.A.4    Kulaeva, O.I.5    Polikanov, Y.S.6
  • 9
    • 49449102926 scopus 로고    scopus 로고
    • Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation
    • doi: 10.1038/nsmb.1458
    • Brueckner F, Cramer P. 2008. Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation. Nat Struct Mol Biol 15:811-8. doi: 10.1038/nsmb.1458.
    • (2008) Nat Struct Mol Biol , vol.15 , pp. 811-818
    • Brueckner, F.1    Cramer, P.2
  • 10
    • 0028071373 scopus 로고
    • Entropic elasticity of lambda-phage DNA
    • doi: 10.1126/science.8079175
    • Bustamante C, Marko JF, Siggia ED, Smith S. 1994. Entropic elasticity of lambda-phage DNA. Science 265:1599-600. doi: 10.1126/science.8079175.
    • (1994) Science , vol.265 , pp. 1599-1600
    • Bustamante, C.1    Marko, J.F.2    Siggia, E.D.3    Smith, S.4
  • 11
    • 79952440464 scopus 로고    scopus 로고
    • Structural basis of RNA polymerase II backtracking, arrest and reactivation
    • doi: 10.1038/nature09785
    • Cheung AC, Cramer P. 2011. Structural basis of RNA polymerase II backtracking, arrest and reactivation. Nature 471:249-53. doi: 10.1038/nature09785.
    • (2011) Nature , vol.471 , pp. 249-253
    • Cheung, A.C.1    Cramer, P.2
  • 12
    • 82455199223 scopus 로고    scopus 로고
    • Structural basis of initial RNA polymerase II transcription
    • doi: 10.1038/emboj.2011.396
    • Cheung AC, Sainsbury S, Cramer P. 2011. Structural basis of initial RNA polymerase II transcription. EMBO J 30:4755-63. doi: 10.1038/emboj.2011.396.
    • (2011) EMBO J , vol.30 , pp. 4755-4763
    • Cheung, A.C.1    Sainsbury, S.2    Cramer, P.3
  • 13
    • 0016734139 scopus 로고
    • Partition analysis and the concept of net rate constants as tools in enzyme kinetics
    • doi: 10.1021/bi00685a029
    • Cleland WW. 1975. Partition analysis and the concept of net rate constants as tools in enzyme kinetics. Biochemistry 14:3220-4. doi: 10.1021/bi00685a029.
    • (1975) Biochemistry , vol.14 , pp. 3220-3224
    • Cleland, W.W.1
  • 14
    • 84880920116 scopus 로고    scopus 로고
    • Eukaryotic transcriptional dynamics: From single molecules to cell populations
    • doi: 10.1038/nrg3484
    • Coulon A, Chow CC, Singer RH, Larson DR. 2013. Eukaryotic transcriptional dynamics: from single molecules to cell populations. Nat Rev Genet 14:572-84. doi: 10.1038/nrg3484.
    • (2013) Nat Rev Genet , vol.14 , pp. 572-584
    • Coulon, A.1    Chow, C.C.2    Singer, R.H.3    Larson, D.R.4
  • 15
    • 0034737593 scopus 로고    scopus 로고
    • Single-molecule study of transcriptional pausing and arrest by E coli RNA polymerase
    • doi: 10.1126/science.287.5462.2497
    • Davenport RJ, Wuite GJ, Landick R, Bustamante C. 2000. Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase. Science 287:2497-500. doi: 10.1126/science.287.5462.2497.
    • (2000) Science , vol.287 , pp. 2497-2500
    • Davenport, R.J.1    Wuite, G.J.2    Landick, R.3    Bustamante, C.4
  • 16
    • 66149143165 scopus 로고    scopus 로고
    • The origin of short transcriptional pauses
    • doi: 10.1016/j.bpj.2008.12.3918
    • Depken M, Galburt EA, Grill SW. 2009. The origin of short transcriptional pauses. Biophys J 96:2189-93. doi: 10.1016/j.bpj.2008.12.3918.
    • (2009) Biophys J , vol.96 , pp. 2189-2193
    • Depken, M.1    Galburt, E.A.2    Grill, S.W.3
  • 17
    • 0026728955 scopus 로고
    • The single-nucleotie addition cycle in transcription: A biophysical and biochemical perspective
    • doi: 10.1146/annurev.bb.21.060192.002115
    • Erie DA, Yager TD, von Hippel PH. 1992. The single-nucleotie addition cycle in transcription: a biophysical and biochemical perspective. Annu Rev Biophys Biomol Struct 21:379-415. doi: 10.1146/annurev.bb.21.060192.002115.
    • (1992) Annu Rev Biophys Biomol Struct , vol.21 , pp. 379-415
    • Erie, D.A.1    Yager, T.D.2    von Hippel, P.H.3
  • 18
    • 0037015022 scopus 로고    scopus 로고
    • Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase
    • doi: 10.1073/pnas.142417799
    • Forde NR, Izhaky D, Woodcock GR, Wuite GJ, 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 99:11682-7. doi: 10.1073/pnas.142417799.
    • (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
  • 19
    • 0035958552 scopus 로고    scopus 로고
    • Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation
    • doi: 10.1016/S0092-8674(01)00420-2
    • Foster JE, Holmes SF, Erie DA. 2001. Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation. Cell 106:243-52. doi: 10.1016/S0092-8674(01)00420-2.
    • (2001) Cell , vol.106 , pp. 243-252
    • Foster, J.E.1    Holmes, S.F.2    Erie, D.A.3
  • 20
    • 34147206187 scopus 로고    scopus 로고
    • Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner
    • doi: 10.1038/nature05701
    • Galburt EA, Grill SW, Wiedmann A, Lubkowska L, Choy J, Nogales E, et al. 2007. Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner. Nature 446:820-3. doi: 10.1038/nature05701.
    • (2007) Nature , vol.446 , pp. 820-823
    • Galburt, E.A.1    Grill, S.W.2    Wiedmann, A.3    Lubkowska, L.4    Choy, J.5    Nogales, E.6
  • 21
    • 18944368782 scopus 로고    scopus 로고
    • Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II
    • doi: 10.1016/j.molcel.2005.04.011
    • Gong XQ, Zhang C, Feig M, Burton ZF. 2005. Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II. Mol Cell 18:461-70. doi: 10.1016/j.molcel.2005.04.011.
    • (2005) Mol Cell , vol.18 , pp. 461-470
    • Gong, X.Q.1    Zhang, C.2    Feig, M.3    Burton, Z.F.4
  • 22
    • 14644407528 scopus 로고    scopus 로고
    • Thinking quantitatively about transcriptional regulation
    • doi: 10.1038/nrm1588
    • Greive SJ, von Hippel PH. 2005. Thinking quantitatively about transcriptional regulation. Nat Rev Mol Cell Biol 6:221-32. doi: 10.1038/nrm1588.
    • (2005) Nat Rev Mol Cell Biol , vol.6 , pp. 221-232
    • Greive, S.J.1    von Hippel, P.H.2
  • 23
    • 0031561795 scopus 로고    scopus 로고
    • A model for the mechanism of polymerase translocation
    • doi: 10.1006/jmbi.1996.0707
    • Guajardo R, Sousa R. 1997. A model for the mechanism of polymerase translocation. J Mol Biol 265:8-19. doi: 10.1006/jmbi.1996.0707.
    • (1997) J Mol Biol , vol.265 , pp. 8-19
    • Guajardo, R.1    Sousa, R.2
  • 24
    • 50149109300 scopus 로고    scopus 로고
    • Single-molecule studies of RNA polymerase: Motoring along
    • doi: 10.1146/annurev.biochem.77.073106.100741
    • Herbert KM, Greenleaf WJ, Block SM. 2008. Single-molecule studies of RNA polymerase: motoring along. Annu Rev Biochem 77:149-76. doi: 10.1146/annurev.biochem.77.073106.100741.
    • (2008) Annu Rev Biochem , vol.77 , pp. 149-176
    • Herbert, K.M.1    Greenleaf, W.J.2    Block, S.M.3
  • 25
    • 33744981369 scopus 로고    scopus 로고
    • Sequence-resolved detection of pausing by single RNA polymerase molecules
    • doi: 10.1016/j.cell.2006.04.032
    • Herbert KM, La Porta A, Wong BJ, Mooney RA, Neuman KC, Landick R, et al. 2006. Sequence-resolved detection of pausing by single RNA polymerase molecules. Cell 125:1083-94. doi: 10.1016/j.cell.2006.04.032.
    • (2006) Cell , vol.125 , pp. 1083-1094
    • Herbert, K.M.1    la Porta, A.2    Wong, B.J.3    Mooney, R.A.4    Neuman, K.C.5    Landick, R.6
  • 26
    • 68149120313 scopus 로고    scopus 로고
    • Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II
    • doi: 10.1126/science.1172926
    • Hodges C, Bintu L, Lubkowska L, Kashlev M, Bustamante C. 2009. Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science 325:626-8. doi: 10.1126/science.1172926.
    • (2009) Science , vol.325 , pp. 626-628
    • Hodges, C.1    Bintu, L.2    Lubkowska, L.3    Kashlev, M.4    Bustamante, C.5
  • 27
    • 0041315524 scopus 로고    scopus 로고
    • Downstream DNA sequence effects on transcription elongation Allosteric binding of nucleoside triphosphates facilitates translocation via a ratchet motion
    • doi: 10.1074/jbc.M304496200
    • Holmes SF, Erie DA. 2003. Downstream DNA sequence effects on transcription elongation. Allosteric binding of nucleoside triphosphates facilitates translocation via a ratchet motion. J Biol Chem 278:35597-608. doi: 10.1074/jbc.M304496200.
    • (2003) J Biol Chem , vol.278 , pp. 35597-35608
    • Holmes, S.F.1    Erie, D.A.2
  • 28
    • 84873408886 scopus 로고    scopus 로고
    • Intrinsic translocation barrier as an initial step in pausing by RNA polymerase II
    • doi: 10.1016/j.jmb.2012.12.002
    • Imashimizu M, Kireeva ML, Lubkowska L, Gotte D, Parks AR, Strathern JN, et al. 2013. Intrinsic translocation barrier as an initial step in pausing by RNA polymerase II. J Mol Biol 425:697-712. doi: 10.1016/j.jmb.2012.12.002.
    • (2013) J Mol Biol , vol.425 , pp. 697-712
    • Imashimizu, M.1    Kireeva, M.L.2    Lubkowska, L.3    Gotte, D.4    Parks, A.R.5    Strathern, J.N.6
  • 29
    • 0027220197 scopus 로고
    • Conformational coupling in DNA polymerase fidelity
    • doi: 10.1146/annurev.bi.62.070193.003345
    • Johnson KA. 1993. Conformational coupling in DNA polymerase fidelity. Annu Rev Biochem 62:685-713. doi: 10.1146/annurev.bi.62.070193.003345.
    • (1993) Annu Rev Biochem , vol.62 , pp. 685-713
    • Johnson, K.A.1
  • 30
    • 44449103640 scopus 로고    scopus 로고
    • The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin
    • doi: 10.1016/j.molcel.2008.04.023
    • Kaplan CD, Larsson KM, Kornberg RD. 2008. The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin. Mol Cell 30:547-56. doi: 10.1016/j.molcel.2008.04.023.
    • (2008) Mol Cell , vol.30 , pp. 547-556
    • Kaplan, C.D.1    Larsson, K.M.2    Kornberg, R.D.3
  • 31
    • 0043244876 scopus 로고    scopus 로고
    • Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage
    • doi: 10.1016/S0092-8674(03)00598-1
    • Kettenberger H, Armache KJ, Cramer P. 2003. Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell 114:347-57. doi: 10.1016/S0092-8674(03)00598-1.
    • (2003) Cell , vol.114 , pp. 347-357
    • Kettenberger, H.1    Armache, K.J.2    Cramer, P.3
  • 32
    • 77953711880 scopus 로고    scopus 로고
    • Translocation by multi-subunit RNA polymerases
    • doi: 10.1016/j.bbagrm.2010.01.007
    • Kireeva M, Kashlev M, Burton ZF. 2010. Translocation by multi-subunit RNA polymerases. Biochim Biophys Acta 1799:389-401. doi: 10.1016/j.bbagrm.2010.01.007.
    • (2010) Biochim Biophys Acta , vol.1799 , pp. 389-401
    • Kireeva, M.1    Kashlev, M.2    Burton, Z.F.3
  • 33
  • 34
    • 67049100283 scopus 로고    scopus 로고
    • Mechanism of sequence-specific pausing of bacterial RNA polymerase
    • doi: 10.1073/pnas.0900407106
    • Kireeva ML, Kashlev M. 2009. Mechanism of sequence-specific pausing of bacterial RNA polymerase. Proc Natl Acad Sci USA 106:8900-5. doi: 10.1073/pnas.0900407106.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 8900-8905
    • Kireeva, M.L.1    Kashlev, M.2
  • 35
    • 44449094019 scopus 로고    scopus 로고
    • Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation
    • doi: 10.1016/j.molcel.2008.04.017
    • Kireeva ML, Nedialkov YA, Cremona GH, Purtov YA, Lubkowska L, Malagon F, et al. 2008. Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation. Mol Cell 30:557-66. doi: 10.1016/j.molcel.2008.04.017.
    • (2008) Mol Cell , vol.30 , pp. 557-566
    • Kireeva, M.L.1    Nedialkov, Y.A.2    Cremona, G.H.3    Purtov, Y.A.4    Lubkowska, L.5    Malagon, F.6
  • 36
    • 0030950638 scopus 로고    scopus 로고
    • RNA polymerase switches between inactivated and activated states by translocating back and forth along the DNA and the RNA
    • doi: 10.1074/jbc.272.24.15329
    • Komissarova N, Kashlev M. 1997a. RNA polymerase switches between inactivated and activated states by translocating back and forth along the DNA and the RNA. J Biol Chem 272:15329-38. doi: 10.1074/jbc.272.24.15329.
    • (1997) J Biol Chem , vol.272 , pp. 15329-15338
    • Komissarova, N.1    Kashlev, M.2
  • 37
    • 0031059249 scopus 로고    scopus 로고
    • Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3' end of the RNA intact and extruded
    • doi: 10.1073/pnas.94.5.1755
    • Komissarova N, Kashlev M. 1997b. Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3' end of the RNA intact and extruded. Proc Natl Acad Sci USA 94:1755-60. doi: 10.1073/pnas.94.5.1755.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 1755-1760
    • Komissarova, N.1    Kashlev, M.2
  • 38
    • 54349103761 scopus 로고    scopus 로고
    • Nucleosome immobilization strategies for single-pair FRET microscopy
    • doi: 10.1002/cphc.200800370
    • Koopmans WJ, Schmidt T, van Noort J. 2008. Nucleosome immobilization strategies for single-pair FRET microscopy. Chemphyschem 9:2002-9. doi: 10.1002/cphc.200800370.
    • (2008) Chemphyschem , vol.9 , pp. 2002-2009
    • Koopmans, W.J.1    Schmidt, T.2    van Noort, J.3
  • 39
    • 33846914726 scopus 로고    scopus 로고
    • The regulatory roles and mechanism of transcriptional pausing
    • doi: 10.1042/BST0341062
    • Landick R. 2006. The regulatory roles and mechanism of transcriptional pausing. Biochem Soc Trans 34:1062-6. doi: 10.1042/BST0341062.
    • (2006) Biochem Soc Trans , vol.34 , pp. 1062-1066
    • Landick, R.1
  • 40
    • 84860211901 scopus 로고    scopus 로고
    • Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II
    • doi: 10.1073/pnas.1200939109
    • Larson MH, Zhou J, Kaplan CD, Palangat M, Kornberg RD, Landick R, et al. 2012. Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II. Proc Natl Acad Sci USA 109:6555-60. doi: 10.1073/pnas.1200939109.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 6555-6560
    • Larson, M.H.1    Zhou, J.2    Kaplan, C.D.3    Palangat, M.4    Kornberg, R.D.5    Landick, R.6
  • 41
    • 11444262202 scopus 로고    scopus 로고
    • Rapid spontaneous accessibility of nucleosomal DNA
    • doi: 10.1038/nsmb869
    • Li G, Levitus M, Bustamante C, Widom J. 2005. Rapid spontaneous accessibility of nucleosomal DNA. Nat Struct Mol Biol 12:46-53. doi: 10.1038/nsmb869.
    • (2005) Nat Struct Mol Biol , vol.12 , pp. 46-53
    • Li, G.1    Levitus, M.2    Bustamante, C.3    Widom, J.4
  • 42
    • 0032512794 scopus 로고    scopus 로고
    • New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning
    • doi: 10.1006/jmbi.1997.1494
    • Lowary PT, Widom J. 1998. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J Mol Biol 276:19-42. doi: 10.1006/jmbi.1997.1494.
    • (1998) J Mol Biol , vol.276 , pp. 19-42
    • Lowary, P.T.1    Widom, J.2
  • 43
    • 33646188087 scopus 로고    scopus 로고
    • Mutations in the Saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-azauracil
    • doi: 10.1534/genetics.105.052415
    • Malagon F, Kireeva ML, Shafer BK, Lubkowska L, Kashlev M, Strathern JN. 2006. Mutations in the Saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-azauracil. Genetics 172:2201-9. doi: 10.1534/genetics.105.052415.
    • (2006) Genetics , vol.172 , pp. 2201-2209
    • Malagon, F.1    Kireeva, M.L.2    Shafer, B.K.3    Lubkowska, L.4    Kashlev, M.5    Strathern, J.N.6
  • 44
    • 84867297989 scopus 로고    scopus 로고
    • Active site opening and closure control translocation of multisubunit RNA polymerase
    • doi: 10.1093/nar/gks383
    • Malinen AM, Turtola M, Parthiban M, Vainonen L, Johnson MS, Belogurov GA. 2012. Active site opening and closure control translocation of multisubunit RNA polymerase. Nucleic Acids Res 40:7442-51. doi: 10.1093/nar/gks383.
    • (2012) Nucleic Acids Res , vol.40 , pp. 7442-7451
    • Malinen, A.M.1    Turtola, M.2    Parthiban, M.3    Vainonen, L.4    Johnson, M.S.5    Belogurov, G.A.6
  • 45
    • 79953855317 scopus 로고    scopus 로고
    • A unified model of transcription elongation: What have we learned from single-molecule experiments?
    • doi: 10.1016/j.bpj.2010.12.3734
    • Maoiléidigh DÓ, Tadigotla VR, Nudler E, Ruckenstein AE. 2011. A unified model of transcription elongation: what have we learned from single-molecule experiments? Biophys J 100:1157-66. doi: 10.1016/j.bpj.2010.12.3734.
    • (2011) Biophys J , vol.100 , pp. 1157-1166
    • Maoiléidigh, D.O.1    Tadigotla, V.R.2    Nudler, E.3    Ruckenstein, A.E.4
  • 46
    • 50149118845 scopus 로고    scopus 로고
    • Thermal probing of E coli RNA polymerase off-pathway mechanisms
    • doi: 10.1016/j.jmb.2008.06.079
    • Mejia YX, Mao H, Forde NR, Bustamante C. 2008. Thermal probing of E. coli RNA polymerase off-pathway mechanisms. J Mol Biol 382:628-37. doi: 10.1016/j.jmb.2008.06.079.
    • (2008) J Mol Biol , vol.382 , pp. 628-637
    • Mejia, Y.X.1    Mao, H.2    Forde, N.R.3    Bustamante, C.4
  • 48
    • 84869783692 scopus 로고    scopus 로고
    • RNA polymerase stalls in a post-translocated register and can hyper-translocate
    • doi: 10.4161/trns.22307
    • Nedialkov YA, Nudler E, Burton ZF. 2012. RNA polymerase stalls in a post-translocated register and can hyper-translocate. Transcription 3:260-9. doi: 10.4161/trns.22307.
    • (2012) Transcription , vol.3 , pp. 260-269
    • Nedialkov, Y.A.1    Nudler, E.2    Burton, Z.F.3
  • 49
    • 84862673628 scopus 로고    scopus 로고
    • RNA polymerase backtracking in gene regulation and genome instability
    • doi: 10.1016/j.cell.2012.06.003
    • Nudler E. 2012. RNA polymerase backtracking in gene regulation and genome instability. Cell 149:1438-45. doi: 10.1016/j.cell.2012.06.003.
    • (2012) Cell , vol.149 , pp. 1438-1445
    • Nudler, E.1
  • 50
    • 0031552174 scopus 로고    scopus 로고
    • The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase
    • doi: 10.1016/S0092-8674(00)80180-4
    • Nudler E, Mustaev A, Lukhtanov E, Goldfarb A. 1997. The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell 89:33-41. doi: 10.1016/S0092-8674(00)80180-4.
    • (1997) Cell , vol.89 , pp. 33-41
    • Nudler, E.1    Mustaev, A.2    Lukhtanov, E.3    Goldfarb, A.4
  • 51
    • 0016273095 scopus 로고
    • Ribonucleic acid chain elongation by Escherichia coli ribonucleic acid polymerase I Isolation of ternary complexes and the kinetics of elongation
    • Rhodes G, Chamberlin MJ. 1974. Ribonucleic acid chain elongation by Escherichia coli ribonucleic acid polymerase. I. Isolation of ternary complexes and the kinetics of elongation. J Biol Chem 249:6675-83.
    • (1974) J Biol Chem , vol.249 , pp. 6675-6683
    • Rhodes, G.1    Chamberlin, M.J.2
  • 52
    • 0029859713 scopus 로고    scopus 로고
    • Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes
    • doi: 10.1093/nar/24.22.4501
    • Sugimoto N, Nakano S, Yoneyama M, Honda K. 1996. Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res 24:4501-5. doi: 10.1093/nar/24.22.4501.
    • (1996) Nucleic Acids Res , vol.24 , pp. 4501-4505
    • Sugimoto, N.1    Nakano, S.2    Yoneyama, M.3    Honda, K.4
  • 53
    • 67449116330 scopus 로고    scopus 로고
    • Structural basis of transcription: Mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA
    • doi: 10.1016/j.molcel.2009.06.002
    • Sydow JF, Brueckner F, Cheung AC, Damsma GE, Dengl S, Lehmann E, et al. 2009. Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. Mol Cell 34:710-21. doi: 10.1016/j.molcel.2009.06.002.
    • (2009) Mol Cell , vol.34 , pp. 710-721
    • Sydow, J.F.1    Brueckner, F.2    Cheung, A.C.3    Damsma, G.E.4    Dengl, S.5    Lehmann, E.6
  • 55
    • 57249108333 scopus 로고    scopus 로고
    • Bridge helix and trigger loop perturbations generate superactive RNA polymerases
    • doi: 10.1186/jbiol98
    • Tan L, Wiesler S, Trzaska D, Carney HC, Weinzierl RO. 2008. Bridge helix and trigger loop perturbations generate superactive RNA polymerases. J Biol 7:40. doi: 10.1186/jbiol98.
    • (2008) J Biol , vol.7 , pp. 40
    • Tan, L.1    Wiesler, S.2    Trzaska, D.3    Carney, H.C.4    Weinzierl, R.O.5
  • 56
    • 24044497229 scopus 로고    scopus 로고
    • Structural basis of transcription inhibition by antibiotic streptolydigin
    • doi: 10.1016/j.molcel.2005.07.020
    • Temiakov D, Zenkin N, Vassylyeva MN, Perederina A, Tahirov TH, Kashkina E, et al. 2005. Structural basis of transcription inhibition by antibiotic streptolydigin. Mol Cell 19:655-66. doi: 10.1016/j.molcel.2005.07.020.
    • (2005) Mol Cell , vol.19 , pp. 655-666
    • Temiakov, D.1    Zenkin, N.2    Vassylyeva, M.N.3    Perederina, A.4    Tahirov, T.H.5    Kashkina, E.6
  • 57
    • 1642290007 scopus 로고    scopus 로고
    • Measurement of histone-DNA interaction free energy in nucleosomes
    • doi: 10.1016/j.ymeth.2003.10.018
    • Thåström A, Lowary PT, Widom J. 2004. Measurement of histone-DNA interaction free energy in nucleosomes. Methods 33:33-44. doi: 10.1016/j.ymeth.2003.10.018.
    • (2004) Methods , vol.33 , pp. 33-44
    • Thåström, A.1    Lowary, P.T.2    Widom, J.3
  • 58
    • 34547204502 scopus 로고    scopus 로고
    • A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing
    • doi: 10.1016/j.molcel.2007.06.008
    • Toulokhonov I, Zhang J, Palangat M, Landick R. 2007. A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing. Mol Cell 27:406-19. doi: 10.1016/j.molcel.2007.06.008.
    • (2007) Mol Cell , vol.27 , pp. 406-419
    • Toulokhonov, I.1    Zhang, J.2    Palangat, M.3    Landick, R.4
  • 60
    • 84863142625 scopus 로고    scopus 로고
    • Unwrapping of nucleosomal DNA ends: A multiscale molecular dynamics study
    • doi: 10.1016/j.bpj.2011.11.4028
    • Voltz K, Trylska J, Calimet N, Smith JC, Langowski J. 2012. Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study. Biophys J 102:849-58. doi: 10.1016/j.bpj.2011.11.4028.
    • (2012) Biophys J , vol.102 , pp. 849-858
    • Voltz, K.1    Trylska, J.2    Calimet, N.3    Smith, J.C.4    Langowski, J.5
  • 61
    • 0037058904 scopus 로고    scopus 로고
    • Reaction pathways in transcript elongation
    • doi: 10.1016/S0301-4622(02)00160-6
    • von Hippel PH, Pasman Z. 2002. Reaction pathways in transcript elongation. Biophys Chem 101-102:401-23. doi: 10.1016/S0301-4622(02)00160-6.
    • (2002) Biophys Chem , vol.101-102 , pp. 401-423
    • von Hippel, P.H.1    Pasman, Z.2
  • 62
    • 84859710196 scopus 로고    scopus 로고
    • Mechanism of translesion transcription by RNA polymerase II and its role in cellular resistance to DNA damage
    • doi: 10.1016/j.molcel.2012.02.006
    • Walmacq C, Cheung AC, Kireeva ML, Lubkowska L, Ye C, Gotte D, et al. 2012. Mechanism of translesion transcription by RNA polymerase II and its role in cellular resistance to DNA damage. Mol Cell 46:18-29. doi: 10.1016/j.molcel.2012.02.006.
    • (2012) Mol Cell , vol.46 , pp. 18-29
    • Walmacq, C.1    Cheung, A.C.2    Kireeva, M.L.3    Lubkowska, L.4    Ye, C.5    Gotte, D.6
  • 63
    • 66349138227 scopus 로고    scopus 로고
    • Structural basis of transcription: Backtracked RNA polymerase II at 3.4 angstrom resolution
    • doi: 10.1126/science.1168729
    • Wang D, Bushnell DA, Huang X, Westover KD, Levitt M, Kornberg RD. 2009. Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. Science 324:1203-6. doi: 10.1126/science.1168729.
    • (2009) Science , vol.324 , pp. 1203-1206
    • Wang, D.1    Bushnell, D.A.2    Huang, X.3    Westover, K.D.4    Levitt, M.5    Kornberg, R.D.6
  • 64
    • 33751235874 scopus 로고    scopus 로고
    • Structural basis of transcription: Role of the trigger loop in substrate specificity and catalysis
    • doi: 10.1016/j.cell.2006.11.023
    • Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD. 2006. Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 127:941-54. doi: 10.1016/j.cell.2006.11.023.
    • (2006) Cell , vol.127 , pp. 941-954
    • Wang, D.1    Bushnell, D.A.2    Westover, K.D.3    Kaplan, C.D.4    Kornberg, R.D.5
  • 65
    • 84873323216 scopus 로고    scopus 로고
    • Structural basis of transcriptional pausing in bacteria
    • doi: 10.1016/j.cell.2012.12.020
    • Weixlbaumer A, Leon K, Landick R, Darst SA. 2013. Structural basis of transcriptional pausing in bacteria. Cell 152:431-41. doi: 10.1016/j.cell.2012.12.020.
    • (2013) Cell , vol.152 , pp. 431-441
    • Weixlbaumer, A.1    Leon, K.2    Landick, R.3    Darst, S.A.4
  • 66
    • 8344234112 scopus 로고    scopus 로고
    • Structural basis of transcription: Nucleotide selection by rotation in the RNA polymerase II active center
    • doi: 10.1016/j.cell.2004.10.016
    • Westover KD, Bushnell DA, Kornberg RD. 2004. Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center. Cell 119:481-9. doi: 10.1016/j.cell.2004.10.016.
    • (2004) Cell , vol.119 , pp. 481-489
    • Westover, K.D.1    Bushnell, D.A.2    Kornberg, R.D.3
  • 67
    • 0842347710 scopus 로고    scopus 로고
    • DNA translocation and nucleosome remodeling assays by the RSC chromatin remodeling complex
    • doi: 10.1016/S0076-6879(03)77020-7
    • Wittmeyer J, Saha A, Cairns B. 2004. DNA translocation and nucleosome remodeling assays by the RSC chromatin remodeling complex. Methods Enzymol 377:322-43. doi: 10.1016/S0076-6879(03)77020-7.
    • (2004) Methods Enzymol , vol.377 , pp. 322-343
    • Wittmeyer, J.1    Saha, A.2    Cairns, B.3
  • 68
    • 0036318088 scopus 로고    scopus 로고
    • Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation
    • doi: 10.1046/j.1432-1033.2002.02970.x
    • Wu P, Nakano S, Sugimoto N. 2002. Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation. Eur J Biochem 269:2821-30. doi: 10.1046/j.1432-1033.2002.02970.x.
    • (2002) Eur J Biochem , vol.269 , pp. 2821-2830
    • Wu, P.1    Nakano, S.2    Sugimoto, N.3
  • 69
    • 0026084789 scopus 로고
    • A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli
    • doi: 10.1021/bi00218a032
    • Yager TD, von Hippel PH. 1991. A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli. Biochemistry 30:1097-118. doi: 10.1021/bi00218a032.
    • (1991) Biochemistry , vol.30 , pp. 1097-1118
    • Yager, T.D.1    von Hippel, P.H.2
  • 70
    • 1342313235 scopus 로고    scopus 로고
    • The structural mechanism of translocation and helicase activity in T7 RNA polymerase
    • doi: 10.1016/S0092-8674(04)00120-5
    • Yin YW, Steitz TA. 2004. The structural mechanism of translocation and helicase activity in T7 RNA polymerase. Cell 116:393-404. doi: 10.1016/S0092-8674(04)00120-5.
    • (2004) Cell , vol.116 , pp. 393-404
    • Yin, Y.W.1    Steitz, T.A.2
  • 71
    • 84861846613 scopus 로고    scopus 로고
    • Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases
    • doi: 10.1073/pnas.1205063109
    • Zamft B, Bintu L, Ishibashi T, Bustamante C. 2012. Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases. Proc Natl Acad Sci USA 109:8948-53. doi: 10.1073/pnas.1205063109.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 8948-8953
    • Zamft, B.1    Bintu, L.2    Ishibashi, T.3    Bustamante, C.4
  • 72
    • 33947638345 scopus 로고    scopus 로고
    • DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC
    • doi: 10.1016/j.molcel.2006.10.025
    • Zhang Y, Smith CL, Saha A, Grill SW, Mihardja S, Smith SB, et al. 2006. DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol Cell 24:559-68. doi: 10.1016/j.molcel.2006.10.025.
    • (2006) Mol Cell , vol.24 , pp. 559-568
    • Zhang, Y.1    Smith, C.L.2    Saha, A.3    Grill, S.W.4    Mihardja, S.5    Smith, S.B.6
  • 73
    • 81355150826 scopus 로고    scopus 로고
    • Applied force provides insight into transcriptional pausing and its modulation by transcription factor NusA
    • doi: 10.1016/j.molcel.2011.09.018
    • Zhou J, Ha KS, La Porta A, Landick R, Block SM. 2011. Applied force provides insight into transcriptional pausing and its modulation by transcription factor NusA. Mol Cell 44:635-46. doi: 10.1016/j.molcel.2011.09.018.
    • (2011) Mol Cell , vol.44 , pp. 635-646
    • Zhou, J.1    Ha, K.S.2    la Porta, A.3    Landick, R.4    Block, S.M.5


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