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Volumn 42, Issue 1, 2013, Pages 241-263

Molecular traffic jams on DNA

Author keywords

DNA curtains; FRET; helicase; optical tweezers; replisome; RNAP; roadblock

Indexed keywords

DNA BINDING MOTOR PROTEIN; DNA BINDING PROTEIN; DOUBLE STRANDED DNA; EXODEOXYRIBONUCLEASE V; HELICASE; PCRA PROTEIN; RECA PROTEIN; REPLICATION FACTOR A; SINGLE STRANDED DNA; UNCLASSIFIED DRUG;

EID: 84877784393     PISSN: 1936122X     EISSN: 19361238     Source Type: Book Series    
DOI: 10.1146/annurev-biophys-083012-130304     Document Type: Article
Times cited : (28)

References (107)
  • 1
    • 84860338675 scopus 로고    scopus 로고
    • R Loops: From transcription byproducts to threats to genome stability
    • Aguilera A, Garćia-Muse T. 2012. R Loops: From transcription byproducts to threats to genome stability. Mol. Cell 46:115-244
    • (2012) Mol. Cell , vol.46 , pp. 115-244
    • Aguilera, A.1    Garćia-Muse, T.2
  • 2
    • 67649637509 scopus 로고    scopus 로고
    • Srs2 disassembles Rad511 filaments by a protein-protein interaction triggeringATPturnover and dissociation ofRad51 from DNA
    • rfsti Antony E, Tomko EJ, Xiao Q, Krejci L, Lohman TM, Ellenberger T. 2009. Srs2 disassembles Rad511 filaments by a protein-protein interaction triggeringATPturnover and dissociation ofRad51 from DNA. Mol. Cell 35:105-155
    • (2009) Mol. Cell , vol.35 , pp. 105-155
    • Antony, E.1    Tomko, E.J.2    Xiao, Q.3    Krejci, L.4    Lohman, T.M.5    Ellenberger, T.6
  • 3
    • 84857748099 scopus 로고    scopus 로고
    • Recognition of SUMO-modified PCNA requires tandem receptor motifs in Srs2
    • Armstrong AA, Mohideen F, Lima CD. 2012. Recognition of SUMO-modified PCNA requires tandem receptor motifs in Srs2. Nature 483:59-633
    • (2012) Nature , vol.483 , pp. 59-633
    • Armstrong, A.A.1    Mohideen, F.2    Lima, C.D.3
  • 5
    • 33751237066 scopus 로고    scopus 로고
    • The S. cerevisiae Rrm3pDNAhelicase moves with the replication fork and affects replication of all yeast chromosomes
    • Azvolinsky A,Dunaway S, Torres JZ, Bessler JB, Zakian VA. 2006. The S. cerevisiae Rrm3pDNAhelicase moves with the replication fork and affects replication of all yeast chromosomes. Genes Dev. 20:3104-166
    • (2006) Genes Dev , vol.20 , pp. 3104-3166
    • Azvolinsky, A.1    Dunaway, S.2    Torres, J.Z.3    Bessler, J.B.4    Zakian, V.A.5
  • 6
    • 67449113551 scopus 로고    scopus 로고
    • Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae
    • Azvolinsky A, Giresi PG, Lieb JD, Zakian VA. 2009. Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae. Mol. Cell 34:722-344
    • (2009) Mol. Cell , vol.34 , pp. 722-344
    • Azvolinsky, A.1    Giresi, P.G.2    Lieb, J.D.3    Zakian, V.A.4
  • 7
    • 0035905687 scopus 로고    scopus 로고
    • Processive translocation and DNA unwinding by individual RecBCD enzyme molecules
    • Bianco PR, Brewer LR, Corzett M, Balhorn R, Yeh Y, et al. 2001. Processive translocation and DNA unwinding by individual RecBCD enzyme molecules. Nature 409:374-788
    • (2001) Nature , vol.409 , pp. 374-788
    • Bianco, P.R.1    Brewer, L.R.2    Corzett, M.3    Balhorn, R.4    Yeh, Y.5
  • 8
    • 84869009900 scopus 로고    scopus 로고
    • Nucleosomal elements that control the topography of the barrier to transcription
    • Bintu L, Ishibashi T, Dangkulwanich M, Wu Y-Y, Lubkowska L, et al. 2012. Nucleosomal elements that control the topography of the barrier to transcription. Cell 151:738-499
    • (2012) Cell , vol.151 , pp. 738-499
    • Bintu, L.1    Ishibashi, T.2    Dangkulwanich, M.3    Wu, Y.-Y.4    Lubkowska, L.5
  • 10
    • 76749129611 scopus 로고    scopus 로고
    • Unwinding the functions of the Pif1 family helicases
    • BochmanML, Sabouri N, Zakian VA. 2010. Unwinding the functions of the Pif1 family helicases. DNA Repair 9:237-499
    • (2010) DNA Repair , vol.9 , pp. 237-499
    • Bochman, M.L.1    Sabouri, N.2    Zakian, V.A.3
  • 11
    • 33750442129 scopus 로고    scopus 로고
    • Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II
    • Bondarenko VA, Steele LM, Ujv́ari A, Gaykalova DA, Kulaeva OI, et al. 2006. Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II. Mol. Cell 24:469-799
    • (2006) Mol. Cell , vol.24 , pp. 469-799
    • Bondarenko, V.A.1    Steele, L.M.2    Ujv́ari, A.3    Gaykalova, D.A.4    Kulaeva, O.I.5
  • 12
    • 0025098652 scopus 로고
    • In vitro replication through nucleosomes without histone displacement
    • Bonne-Andrea C, Wong ML, Alberts BM. 1990. In vitro replication through nucleosomes without histone displacement. Nature 343:719-266
    • (1990) Nature , vol.343 , pp. 719-266
    • Bonne-Andrea, C.1    Wong, M.L.2    Alberts, B.M.3
  • 13
    • 14844329013 scopus 로고    scopus 로고
    • Bacterial transcription elongation factors: New insights into molecular mechanism of action
    • Borukhov S, Lee J, Laptenko O. 2005. Bacterial transcription elongation factors: New insights into molecular mechanism of action. Mol. Microbiol. 55:1315-244
    • (2005) Mol. Microbiol , vol.55 , pp. 1315-1254
    • Borukhov, S.1    Lee, J.2    Laptenko, O.3
  • 14
    • 84862979650 scopus 로고    scopus 로고
    • A map of nucleosome positions in yeast at base-pair resolution
    • Brogaard K, Xi L, Wang J-P, Widom J. 2012. A map of nucleosome positions in yeast at base-pair resolution. Nature 486:496-5011
    • (2012) Nature , vol.486 , pp. 496-5011
    • Brogaard, K.1    Xi, L.2    Wang, J.-P.3    Widom, J.4
  • 15
    • 2542432027 scopus 로고    scopus 로고
    • Protein displacement by an assembly of helicase molecules aligned along single-stranded DNA
    • Byrd AK, Raney KD. 2004. Protein displacement by an assembly of helicase molecules aligned along single-stranded DNA. Nat. Struct. Mol. Biol. 11:531-388
    • (2004) Nat. Struct. Mol. Biol , vol.11 , pp. 531-388
    • Byrd, A.K.1    Raney, K.D.2
  • 16
    • 84860578766 scopus 로고    scopus 로고
    • Replication fork reversal after replication- transcription collision
    • De Septenville AL, Duigou S, Boubakri H, Michel B. 2012. Replication fork reversal after replication- transcription collision. PLoS Genet. 8:e10026222
    • (2012) PLoS Genet , Issue.8
    • De Septenville, A.L.1    Duigou, S.2    Boubakri, H.3    Michel, B.4
  • 17
    • 79953187302 scopus 로고    scopus 로고
    • Superfamily i helicases as modular components of DNA-processing machines
    • Dillingham MS. 2011. Superfamily I helicases as modular components of DNA-processing machines. Biochem. Soc. Trans. 39:413-233
    • (2011) Biochem. Soc. Trans , Issue.39 , pp. 413-233
    • Dillingham, M.S.1
  • 19
    • 80052008241 scopus 로고    scopus 로고
    • Linking RNA polymerase backtracking to genome instability in e coli
    • Dutta D, Shatalin K, Epshtein V, Gottesman ME, Nudler E. 2011. Linking RNA polymerase backtracking to genome instability in E. coli. Cell 146:533-433
    • (2011) Cell , vol.146 , pp. 533-433
    • Dutta, D.1    Shatalin, K.2    Epshtein, V.3    Gottesman, M.E.4    Nudler, E.5
  • 21
    • 34249932435 scopus 로고    scopus 로고
    • Probing transcription factor dynamics at the single-molecule level in a living cell
    • Elf J, LiGW, Xie XS. 2007. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316:1191-944
    • (2007) Science , vol.316 , pp. 1191-1944
    • Elf, J.1    Li, G.W.2    Xie, X.S.3
  • 22
    • 0033570150 scopus 로고    scopus 로고
    • Resolution of head-on collisions between the transcription machinery and bacteriophage ∂29 DNA polymerase is dependent on RNA polymerase translocation
    • Elias-ArnanzM. 1999. Resolution of head-on collisions between the transcription machinery and bacteriophage ∂29 DNA polymerase is dependent on RNA polymerase translocation. EMBO J. 18:5675-822
    • (1999) EMBO J. , vol.18 , pp. 5675-5822
    • Elias-Arnanz, M.1
  • 23
    • 1842377482 scopus 로고    scopus 로고
    • Bacteriophage ∂29 DNA replication arrest caused by codirectional collisions with the transcription machinery
    • Elias-Arnanz M, Salas M. 1997. Bacteriophage ∂29 DNA replication arrest caused by codirectional collisions with the transcription machinery. EMBO J. 16:5775-833
    • (1997) EMBO J. , vol.16 , pp. 5775-5833
    • Elias-Arnanz, M.1    Salas, M.2
  • 24
    • 0141625269 scopus 로고    scopus 로고
    • Transcription through the roadblocks: The role of RNA polymerase cooperation
    • Epshtein V. 2003. Transcription through the roadblocks: The role of RNA polymerase cooperation. EMBO J. 22:4719-277
    • (2003) EMBO J. , Issue.22 , pp. 4719-4287
    • Epshtein, V.1
  • 25
    • 74549191169 scopus 로고    scopus 로고
    • An allosteric mechanism of Rho-dependent transcription termination
    • Epshtein V,Dutta D, Wade J, Nudler E. 2010. An allosteric mechanism of Rho-dependent transcription termination. Nature 463:245-499
    • (2010) Nature , vol.463 , pp. 245-499
    • Epshtein, V.1    Dutta, D.2    Wade, J.3    Nudler, E.4
  • 26
    • 52649162907 scopus 로고    scopus 로고
    • DNA curtains and nanoscale curtain rods: Highthroughput tools for single molecule imaging
    • Fazio T, Visnapuu M-L, Wind S, Greene EC. 2008. DNA curtains and nanoscale curtain rods: Highthroughput tools for single molecule imaging. Langmuir 24:10524-311
    • (2008) Langmuir , vol.24 , pp. 10524-10321
    • Fazio, T.1    Visnapuu, M.-L.2    Wind, S.3    Greene, E.C.4
  • 27
    • 80053324949 scopus 로고    scopus 로고
    • Supported lipid bilayers andDNAcurtains for high-throughput singlemolecule studies
    • Finkelstein IJ, Greene EC. 2011. Supported lipid bilayers andDNAcurtains for high-throughput singlemolecule studies. Methods Mol. Biol. 745:447-611
    • (2011) Methods Mol. Biol , Issue.745 , pp. 447-611
    • Finkelstein, I.J.1    Greene, E.C.2
  • 28
    • 78650307167 scopus 로고    scopus 로고
    • Single-molecule imaging reveals mechanisms of protein disruption by a DNA translocase
    • Finkelstein IJ, Visnapuu M-L, GreeneEC. 2010. Single-molecule imaging reveals mechanisms of protein disruption by a DNA translocase. Nature 468:983-877
    • (2010) Nature , vol.468 , pp. 983-877
    • Finkelstein, I.J.1    Visnapuu, M.-L.2    Greene, E.C.3
  • 29
    • 63049138876 scopus 로고    scopus 로고
    • Polycomb proteins remain bound to chromatin and DNA during DNA replication in vitro
    • Francis NJ, Follmer NE, Simon MD, Aghia G, Butler JD. 2009. Polycomb proteins remain bound to chromatin and DNA during DNA replication in vitro. Cell 137:110-222
    • (2009) Cell , vol.137 , pp. 110-222
    • Francis, N.J.1    Follmer, N.E.2    Simon, M.D.3    Aghia, G.4    Butler, J.D.5
  • 30
    • 0029971350 scopus 로고    scopus 로고
    • The stability of nucleosomes at the replication fork
    • Gasser R, Koller T, Sogo JM. 1996. The stability of nucleosomes at the replication fork. J. Mol. Biol. 258:224-399
    • (1996) J. Mol. Biol , vol.258 , pp. 224-399
    • Gasser, R.1    Koller, T.2    Sogo, J.M.3
  • 31
    • 84855453503 scopus 로고    scopus 로고
    • Single-molecule studies reveal the function of a third polymerase in the replisome
    • Georgescu RE, Kurth I, O'Donnell ME. 2012. Single-molecule studies reveal the function of a third polymerase in the replisome. Nat. Struct. Mol. Biol. 19:113-166
    • (2012) Nat. Struct. Mol. Biol , Issue.19 , pp. 113-166
    • Georgescu, R.E.1    Kurth, I.2    O'Donnell, M.E.3
  • 32
    • 74249105084 scopus 로고    scopus 로고
    • Nanofabricated racks of aligned and anchored DNA substrates for single-molecule imaging
    • Gorman J, Fazio T, Wang F, Wind S, Greene EC. 2010. Nanofabricated racks of aligned and anchored DNA substrates for single-molecule imaging. Langmuir 26:1372-799
    • (2010) Langmuir , vol.26 , pp. 1372-1799
    • Gorman, J.1    Fazio, T.2    Wang, F.3    Wind, S.4    Greene, E.C.5
  • 33
    • 0027507943 scopus 로고
    • Disruption of the nucleosomes at the replication fork
    • Gruss C,Wu J, Koller T, Sogo JM. 1993. Disruption of the nucleosomes at the replication fork. EMBO J. 12:4533-455
    • (1993) EMBO J. , vol.12 , pp. 4533-4465
    • Gruss, C.1    Wu, J.2    Koller, T.3    Sogo, J.M.4
  • 34
    • 21244491441 scopus 로고    scopus 로고
    • Regulation of histone synthesis and nucleosome assembly
    • Gunjan A, Paik J, Verreault A. 2005. Regulation of histone synthesis and nucleosome assembly. Biochimie 87:625-355
    • (2005) Biochimie , vol.87 , pp. 625-355
    • Gunjan, A.1    Paik, J.2    Verreault, A.3
  • 35
    • 0031570793 scopus 로고    scopus 로고
    • Direct visualization of individualDNAmolecules by fluorescencemicroscopy: Characterization of the factors affecting signal/background and optimization of imaging conditions using YOYO
    • Gurrieri S,Wells KS, Johnson ID, Bustamante C. 1997. Direct visualization of individualDNAmolecules by fluorescencemicroscopy: Characterization of the factors affecting signal/background and optimization of imaging conditions using YOYO. Anal. Biochem. 249:44-533
    • (1997) Anal. Biochem , vol.249 , pp. 44-533
    • Gurrieri, S.1    Wells, K.S.2    Johnson, I.D.3    Bustamante, C.4
  • 36
    • 70449633073 scopus 로고    scopus 로고
    • Rep provides a second motor at the replisome to promote duplication of protein-bound DNA
    • Guy CP, Atkinson J, GuptaMK, Mahdi AA, Gwynn EJ, et al. 2009. Rep provides a second motor at the replisome to promote duplication of protein-bound DNA. Mol. Cell 36:654-666
    • (2009) Mol. Cell , vol.36 , pp. 654-666
    • Guy, C.P.1    Atkinson, J.2    Gupta, M.K.3    Mahdi, A.A.4    Gwynn, E.J.5
  • 37
    • 5444276316 scopus 로고    scopus 로고
    • Genometric analyses of the organization of circular chromosomes: A universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication
    • Guy L, Roten C-AH. 2004. Genometric analyses of the organization of circular chromosomes: A universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication. Gene 340:45-522
    • (2004) Gene , vol.340 , pp. 45-522
    • Guy, L.1    Roten, C.-A.H.2
  • 38
    • 84861374075 scopus 로고    scopus 로고
    • Single-molecule views of protein movement on single-stranded DNA
    • Ha T, Kozlov AG, Lohman TM. 2012. Single-molecule views of protein movement on single-stranded DNA. Annu. Rev. Biophys. 41:295-3199
    • (2012) Annu. Rev. Biophys , Issue.41 , pp. 295-3199
    • Ha, T.1    Kozlov, A.G.2    Lohman, T.M.3
  • 40
    • 84255198334 scopus 로고    scopus 로고
    • Collisions between replication and transcription complexes cause common fragile site instability at the longest human genes
    • Helmrich A, Ballarino M, Tora L. 2011. Collisions between replication and transcription complexes cause common fragile site instability at the longest human genes. Mol. Cell 44:966-777
    • (2011) Mol. Cell , vol.44 , pp. 966-777
    • Helmrich, A.1    Ballarino, M.2    Tora, L.3
  • 41
    • 50149109300 scopus 로고    scopus 로고
    • Single-molecule studies of RNA polymerase: Motoring along
    • Herbert KM, Greenleaf WJ, Block SM. 2008. Single-molecule studies of RNA polymerase: Motoring along. Annu. Rev. Biochem. 77:149-766
    • (2008) Annu. Rev. Biochem , vol.77 , pp. 149-766
    • Herbert, K.M.1    Greenleaf, W.J.2    Block, S.M.3
  • 42
    • 68149120313 scopus 로고    scopus 로고
    • Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II
    • Hodges C, Bintu L, Lubkowska L, Kashlev M, Bustamante C. 2009. Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science 325:626-288
    • (2009) Science , vol.325 , pp. 626-288
    • Hodges, C.1    Bintu, L.2    Lubkowska, L.3    Kashlev, M.4    Bustamante, C.5
  • 43
    • 69749086880 scopus 로고    scopus 로고
    • Single-molecule analysis reveals differential effect of ssDNA-binding proteins on DNA translocation by XPD helicase
    • Honda M, Park J, Pugh RA, Ha T, Spies M. 2009. Single-molecule analysis reveals differential effect of ssDNA-binding proteins on DNA translocation by XPD helicase. Mol. Cell 35:694-7033
    • (2009) Mol. Cell , vol.35 , pp. 694-7033
    • Honda, M.1    Park, J.2    Pugh, R.A.3    Ha, T.4    Spies, M.5
  • 44
    • 77956231587 scopus 로고    scopus 로고
    • Histone Sin mutations promote nucleosome traversal and histone displacement by RNA polymerase II
    • Hsieh F-K, Fisher M, Ujv́ari A, Studitsky VM, Luse DS. 2010. Histone Sin mutations promote nucleosome traversal and histone displacement by RNA polymerase II. EMBO Rep. 11:705-100
    • (2010) EMBO Rep , Issue.11 , pp. 705-100
    • Hsieh, F.-K.1    Fisher, M.2    Ujv́ari, A.3    Studitsky, V.M.4    Luse, D.S.5
  • 45
    • 0025993781 scopus 로고
    • Replication of the simian virus 40 chromosome with purified proteins
    • Ishimi Y, Sugasawa K, Hanaoka F, Kikuchi A. 1991. Replication of the simian virus 40 chromosome with purified proteins. J. Biol. Chem. 266:16141-488
    • (1991) J. Biol. Chem , vol.266 , pp. 16141-16488
    • Ishimi, Y.1    Sugasawa, K.2    Hanaoka, F.3    Kikuchi, A.4
  • 46
    • 0027078134 scopus 로고
    • Bound Lac repressor protein differentially inhibits the unwinding reactions catalyzed by DNA helicases
    • Yancey-Wrona JE,Matson SW. 1992. Bound Lac repressor protein differentially inhibits the unwinding reactions catalyzed by DNA helicases. Nucleic Acids Res. 20:6713-211
    • (1992) Nucleic Acids Res , vol.20 , pp. 6713-6221
    • Yancey-Wrona, J.E.1    Matson, S.W.2
  • 48
    • 33746713745 scopus 로고    scopus 로고
    • Real-time observation of RecA filament dynamics with single monomer resolution
    • Joo C, McKinney SA, Nakamura M, Rasnik I, Myong S, Ha T. 2006. Real-time observation of RecA filament dynamics with single monomer resolution. Cell 126:515-277
    • (2006) Cell , vol.126 , pp. 515-277
    • Joo, C.1    McKinney, S.A.2    Nakamura, M.3    Rasnik, I.4    Myong, S.5    Ha, T.6
  • 49
    • 0024379261 scopus 로고
    • Glu-111 is required for activation of the DNA cleavage center of EcoRI endonuclease
    • King K, Benkovic SJ, Modrich P. 1989. Glu-111 is required for activation of the DNA cleavage center of EcoRI endonuclease. J. Biol. Chem. 264:11807-155
    • (1989) J. Biol. Chem , vol.264 , pp. 11807-11165
    • King, K.1    Benkovic, S.J.2    Modrich, P.3
  • 52
    • 0037673941 scopus 로고    scopus 로고
    • DNA helicase Srs2 disrupts the Rad51 presynaptic filament
    • Krejci L, Van Komen S, Li Y, Villemain J, Reddy MS, et al. 2003. DNA helicase Srs2 disrupts the Rad51 presynaptic filament. Nature 423:305-99
    • (2003) Nature , vol.423 , pp. 305-399
    • Krejci, L.1    Van Komen, S.2    Li, Y.3    Villemain, J.4    Reddy, M.S.5
  • 53
    • 78649531872 scopus 로고    scopus 로고
    • Initiation of bacteriophage T4 DNA replication and replication fork dynamics a review in the Virology Journal series on bacteriophage T4 and its relatives
    • Kreuzer KN, Brister Jr. 2010. Initiation of bacteriophage T4 DNA replication and replication fork dynamics: A review in the Virology Journal series on bacteriophage T4 and its relatives. Virol. J. 7:3588
    • (2010) Virol. J. , vol.7 , pp. 3588
    • Kreuzer, K.N.1    Brister, J.R.2
  • 54
    • 0028801404 scopus 로고
    • Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription
    • KrugerW,PetersonCL, SilA,CoburnC,ArentsG, et al. 1995. Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription. Genes Dev. 9:2770-799
    • (1995) Genes Dev , vol.9 , pp. 2770-2799
    • Kruger, W.1    Peterson, C.L.2    Sil, A.3    Coburn, C.4    Arents, G.5
  • 56
    • 34147168036 scopus 로고    scopus 로고
    • Transcription through chromatin by RNA polymerase II: Histone displacement and exchange
    • Kulaeva OI, Gaykalova DA, Studitsky VM. 2007. Transcription through chromatin by RNA polymerase II: Histone displacement and exchange. Mutat. Res. 618:116-299
    • (2007) Mutat. Res , vol.618 , pp. 116-299
    • Kulaeva, O.I.1    Gaykalova, D.A.2    Studitsky, V.M.3
  • 57
    • 77954934291 scopus 로고    scopus 로고
    • RNA polymerase complexes cooperate to relieve the nucleosomal barrier and evict histones
    • Kulaeva OI, Hsieh F-K, Studitsky VM. 2010. RNA polymerase complexes cooperate to relieve the nucleosomal barrier and evict histones. Proc. Natl. Acad. Sci. USA 107:11325-300
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 11325-11310
    • Kulaeva, O.I.1    Hsieh, F.-K.2    Studitsky, V.M.3
  • 58
    • 79952263239 scopus 로고    scopus 로고
    • Mechanism of histone survival during transcription byRNApolymerase II
    • Kulaeva OI, StuditskyVM.2010. Mechanism of histone survival during transcription byRNApolymerase II. Transcription 1:85-888
    • (2010) Transcription , vol.1 , pp. 85-888
    • Kulaeva, O.I.1    Studitsky, V.M.2
  • 59
    • 33846914726 scopus 로고    scopus 로고
    • The regulatory roles and mechanism of transcriptional pausing
    • Landick R. 2006. The regulatory roles and mechanism of transcriptional pausing. Biochem. Soc. Trans. 34:1062-666
    • (2006) Biochem. Soc. Trans , vol.34 , pp. 1062-1666
    • Landick, R.1
  • 60
    • 34548061530 scopus 로고    scopus 로고
    • UvrD controls the access of recombination proteins to blocked replication forks
    • Lestini R, Michel B. 2007. UvrD controls the access of recombination proteins to blocked replication forks. EMBO J. 26:3804-144
    • (2007) EMBO J. , vol.26 , pp. 3804-3154
    • Lestini, R.1    Michel, B.2
  • 61
    • 63849284078 scopus 로고    scopus 로고
    • Effects ofmacromolecular crowding andDNAlooping on gene regulation kinetics
    • Li G-W, Berg OG, Elf J. 2009. Effects ofmacromolecular crowding andDNAlooping on gene regulation kinetics. Nat. Struct. Mol. Biol. 5:294-977
    • (2009) Nat. Struct. Mol. Biol , vol.5 , pp. 294-977
    • Li, G.-W.1    Berg, O.G.2    Elf, J.3
  • 62
    • 0028908039 scopus 로고
    • Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex
    • Liu B, Alberts BM. 1995. Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex. Science 267:1131-377
    • (1995) Science , vol.267 , pp. 1131-1377
    • Liu, B.1    Alberts, B.M.2
  • 63
    • 79953228899 scopus 로고    scopus 로고
    • Efficient and rapid nucleosome traversal by RNA polymerase II depends on a combination of transcript elongation factors
    • Luse DS, Spangler LC, Ujv́ari A. 2011. Efficient and rapid nucleosome traversal by RNA polymerase II depends on a combination of transcript elongation factors. J. Biol. Chem. 286:6040-488
    • (2011) J. Biol. Chem , Issue.286 , pp. 6040-6488
    • Luse, D.S.1    Spangler, L.C.2    Ujv́ari, A.3
  • 64
    • 76749147879 scopus 로고    scopus 로고
    • Srs2: The odd-job man in DNA repair
    • Marini V, Krejci L. 2010. Srs2: The "odd-job man" in DNA repair. Cell 9:268-755
    • (2010) Cell , vol.9 , pp. 268-755
    • Marini, V.1    Krejci, L.2
  • 65
    • 79953194151 scopus 로고    scopus 로고
    • Helicases that underpin replication of protein-boundDNAin Escherichia coli
    • McGlynn P. 2011. Helicases that underpin replication of protein-boundDNAin Escherichia coli. Biochem. Soc. Trans. 39:606-100
    • (2011) Biochem. Soc. Trans , Issue.39 , pp. 606-100
    • McGlynn, P.1
  • 66
    • 47049124441 scopus 로고    scopus 로고
    • Replication forks blocked by protein-DNA complexes have limited stability in vitro
    • McGlynn P, Guy CP. 2008. Replication forks blocked by protein-DNA complexes have limited stability in vitro. J. Mol. Biol. 381:249-555
    • (2008) J. Mol. Biol , vol.381 , pp. 249-555
    • McGlynn, P.1    Guy, C.P.2
  • 67
    • 84862763199 scopus 로고    scopus 로고
    • The conflict betweenDNAreplication and transcription
    • McGlynn P, SaveryNJ, Dillingham MS. 2012. The conflict betweenDNAreplication and transcription. Mol. Microbiol. 85:12-200
    • (2012) Mol. Microbiol , Issue.85 , pp. 12-200
    • McGlynn, P.1    Savery, N.J.2    Dillingham, M.S.3
  • 68
    • 79952126098 scopus 로고    scopus 로고
    • Co-directional replication-transcription conflicts lead to replication restart
    • Merrikh H, Machón C, Grainger WH, Grossman AD, Soultanas P. 2011. Co-directional replication-transcription conflicts lead to replication restart. Nature 470:554-577
    • (2011) Nature , vol.470 , pp. 554-577
    • Merrikh, H.1    MacHón, C.2    Grainger, W.H.3    Grossman, A.D.4    Soultanas, P.5
  • 70
    • 33947432388 scopus 로고    scopus 로고
    • Replication fork stalling at natural impediments
    • Mirkin EV,Mirkin SM. 2007. Replication fork stalling at natural impediments. Microbiol. Mol. Biol. Rev. 71:13-355
    • (2007) Microbiol. Mol. Biol. Rev , vol.71 , pp. 13-355
    • Mirkin, E.V.1    Mirkin, S.M.2
  • 72
    • 0033586732 scopus 로고    scopus 로고
    • DNA helicases displace streptavidin from biotin-labeled oligonucleotides
    • Morris PD, Raney KD. 1999. DNA helicases displace streptavidin from biotin-labeled oligonucleotides. Biochemistry 38:5164-711
    • (1999) Biochemistry , vol.38 , pp. 5164-5711
    • Morris, P.D.1    Raney, K.D.2
  • 73
    • 1542320757 scopus 로고    scopus 로고
    • Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions
    • Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, et al. 2004. Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions. EMBO J. 23:260-711
    • (2004) EMBO J. , vol.23 , pp. 260-711
    • Muthurajan, U.M.1    Bao, Y.2    Forsberg, L.J.3    Edayathumangalam, R.S.4    Dyer, P.N.5
  • 74
    • 4043135220 scopus 로고    scopus 로고
    • Regulation of RNA polymerase through the secondary channel
    • Nickels BE, Hochschild A. 2004. Regulation of RNA polymerase through the secondary channel. Cell 118:281-844
    • (2004) Cell , vol.118 , pp. 281-844
    • Nickels, B.E.1    Hochschild, A.2
  • 75
    • 84862673628 scopus 로고    scopus 로고
    • RNApolymerase backtracking in gene regulation and genome instability
    • Nudler E. 2012.RNApolymerase backtracking in gene regulation and genome instability. Cell 149:1438- 455
    • (2012) Cell , vol.149 , pp. 1438-1455
    • Nudler, E.1
  • 76
    • 77955605175 scopus 로고    scopus 로고
    • PcrA helicase dismantles RecA filaments by reeling in DNA in uniform steps
    • Park J, Myong S, Niedziela-Majka A, Lee KS, Yu J, et al. 2010. PcrA helicase dismantles RecA filaments by reeling in DNA in uniform steps. Cell 142:544-555
    • (2010) Cell , vol.142 , pp. 544-555
    • Park, J.1    Myong, S.2    Niedziela-Majka, A.3    Lee, K.S.4    Yu, J.5
  • 80
    • 84877790684 scopus 로고    scopus 로고
    • To prevent recombination during S phase
    • to prevent recombination during S phase. Nature 436:428-333
    • Nature , vol.436 , pp. 428-333
  • 81
    • 57649129186 scopus 로고    scopus 로고
    • The replisome uses mRNA as a primer after colliding with RNA polymerase
    • Pomerantz RT, O'Donnell M. 2008. The replisome uses mRNA as a primer after colliding with RNA polymerase. Nature 456:762-666
    • (2008) Nature , vol.456 , pp. 762-666
    • Pomerantz, R.T.1    O'Donnell, M.2
  • 82
    • 75749150810 scopus 로고    scopus 로고
    • Direct restart of a replication fork stalled by a head-on RNA polymerase
    • Pomerantz RT, O'Donnell M. 2010. Direct restart of a replication fork stalled by a head-on RNA polymerase. Science 327:590-922
    • (2010) Science , vol.327 , pp. 590-922
    • Pomerantz, R.T.1    O'Donnell, M.2
  • 83
    • 34248512303 scopus 로고    scopus 로고
    • A DNA-translocating Snf2 molecular motor: Saccharomyces cerevisiae Rdh54 displays processive translocation and extrudes DNA loops
    • Prasad TK, Robertson RB, Visnapuu M-L, Chi P, Sung P, Greene EC. 2007. A DNA-translocating Snf2 molecular motor: Saccharomyces cerevisiae Rdh54 displays processive translocation and extrudes DNA loops. J. Mol. Biol. 369:940-533
    • (2007) J. Mol. Biol , vol.369 , pp. 940-533
    • Prasad, T.K.1    Robertson, R.B.2    Visnapuu, M.-L.3    Chi, P.4    Sung, P.5    Greene, E.C.6
  • 84
    • 77951589688 scopus 로고    scopus 로고
    • Cooperation between translating ribosomes and RNA polymerase in transcription elongation
    • Proshkin S, Rahmouni AR, Mironov A, Nudler E. 2010. Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science 328:504-88
    • (2010) Science , vol.328 , pp. 504-588
    • Proshkin, S.1    Rahmouni, A.R.2    Mironov, A.3    Nudler, E.4
  • 85
    • 38349091095 scopus 로고    scopus 로고
    • The iron-containing domain is essential in Rad3 helicases for coupling of ATP hydrolysis to DNA translocation and for targeting the helicase to the single-stranded DNA-double-stranded DNA junction
    • Pugh RA, Honda M, Leesley H, Thomas A, Lin Y, et al. 2007. The iron-containing domain is essential in Rad3 helicases for coupling of ATP hydrolysis to DNA translocation and for targeting the helicase to the single-stranded DNA-double-stranded DNA junction. J. Biol. Chem. 283:1732-433
    • (2007) J. Biol. Chem , vol.283 , pp. 1732-1443
    • Pugh, R.A.1    Honda, M.2    Leesley, H.3    Thomas, A.4    Lin, Y.5
  • 86
    • 53549120600 scopus 로고    scopus 로고
    • Ferroplasma acidarmanus RPA2 facilitates efficient unwinding of forked DNA substrates by monomers of FacXPD helicase
    • Pugh RA, Lin Y, EllerC, LeesleyH, Cann IKO, Spies M. 2008. Ferroplasma acidarmanus RPA2 facilitates efficient unwinding of forked DNA substrates by monomers of FacXPD helicase. Cell 383:982-988
    • (2008) Cell , vol.383 , pp. 982-988
    • Pugh, R.A.1    Lin, Y.2    Ellerc, LeesleyH.3    Cann, I.K.O.4    Spies, M.5
  • 87
    • 84857194573 scopus 로고    scopus 로고
    • Regulation of translocation polarity by helicase domain 1 in SF2B helicases
    • Pugh RA, Wu CG, Spies M. 2011. Regulation of translocation polarity by helicase domain 1 in SF2B helicases. Nat. Struct. Mol. Biol. 31:503-144
    • (2011) Nat. Struct. Mol. Biol , Issue.31 , pp. 503-144
    • Pugh, R.A.1    Wu, C.G.2    Spies, M.3
  • 88
    • 48249113056 scopus 로고    scopus 로고
    • Translocation and unwinding mechanisms of RNA and DNA helicases
    • Pyle AM. 2008. Translocation and unwinding mechanisms of RNA and DNA helicases. Annu. Rev. Biophys. 37:317-366
    • (2008) Annu. Rev. Biophys , vol.37 , pp. 317-366
    • Pyle, A.M.1
  • 89
    • 84859397679 scopus 로고    scopus 로고
    • Translocation of e coli RecQ helicase on single-stranded DNA
    • Rad B, Kowalczykowski SC. 2012. Translocation of E. coli RecQ helicase on single-stranded DNA. Biochemistry 51:2921-299
    • (2012) Biochemistry , vol.51 , pp. 2921-2299
    • Rad, B.1    Kowalczykowski, S.C.2
  • 90
    • 0029022696 scopus 로고
    • Unwinding of chromatin by the SV40 large T antigen DNA helicase
    • Ramsperger U, Stahl H. 1995. Unwinding of chromatin by the SV40 large T antigen DNA helicase. EMBO J. 14:3215-255
    • (1995) EMBO J. , vol.14 , pp. 3215-3255
    • Ramsperger, U.1    Stahl, H.2
  • 91
    • 84862996270 scopus 로고    scopus 로고
    • RecQ helicases: At the crossroad of genome replication, repair, and recombination
    • Rezazadeh S. 2011. RecQ helicases: At the crossroad of genome replication, repair, and recombination. Mol. Biol. Rep. 39:4527-433
    • (2011) Mol. Biol. Rep , Issue.39 , pp. 4527-4443
    • Rezazadeh, S.1
  • 92
    • 1842610540 scopus 로고    scopus 로고
    • Mfd, the bacterial transcription repair coupling factor: Translocation, repair and termination
    • Roberts J, Park J-S. 2004. Mfd, the bacterial transcription repair coupling factor: Translocation, repair and termination. Cell 7:120-255
    • (2004) Cell , vol.7 , pp. 120-255
    • Roberts, J.1    Park, J.-S.2
  • 93
    • 0037160099 scopus 로고    scopus 로고
    • Saccharomyces cerevisiae RRM3, a 5- to 3- DNA helicase, physically interacts with proliferating cell nuclear antigen
    • Schmidt KH. 2002. Saccharomyces cerevisiae RRM3, a 5- to 3- DNA helicase, physically interacts with proliferating cell nuclear antigen. J. Biol. Chem. 277:45331-377
    • (2002) J. Biol. Chem , vol.277 , pp. 45331-45377
    • Schmidt, K.H.1
  • 94
    • 34548638261 scopus 로고    scopus 로고
    • Structure and mechanism of helicases and nucleic acid translocases
    • Singleton MR, Dillingham MS, Wigley DB. 2007. Structure and mechanism of helicases and nucleic acid translocases. Annu. Rev. Biochem. 76:23-500
    • (2007) Annu. Rev. Biochem , vol.76 , pp. 23-500
    • Singleton, M.R.1    Dillingham, M.S.2    Wigley, D.B.3
  • 95
    • 76749094639 scopus 로고    scopus 로고
    • Co-orientation of replication and transcription preserves genome integrity
    • Srivatsan A, Tehranchi A, MacAlpine DM, Wang JD. 2010. Co-orientation of replication and transcription preserves genome integrity. PLoS Genet. 6:e10008100
    • (2010) PLoS Genet , Issue.6
    • Srivatsan, A.1    Tehranchi, A.2    MacAlpine, D.M.3    Wang, J.D.4
  • 96
    • 0028125847 scopus 로고
    • A histone octamer can step around a transcribing polymerase without leaving the template
    • Studitsky VM, Clark DJ, Felsenfeld G. 1994. A histone octamer can step around a transcribing polymerase without leaving the template. Cell 76:371-822
    • (1994) Cell , vol.76 , pp. 371-822
    • Studitsky, V.M.1    Clark, D.J.2    Felsenfeld, G.3
  • 97
    • 0031451329 scopus 로고    scopus 로고
    • Mechanism of transcription through the nucleosome by eukaryotic RNA polymerase
    • Studitsky VM, Kassavetis GA, Geiduschek EP, Felsenfeld G. 1997. Mechanism of transcription through the nucleosome by eukaryotic RNA polymerase. Science 278:1960-633
    • (1997) Science , vol.278 , pp. 1960-1643
    • Studitsky, V.M.1    Kassavetis, G.A.2    Geiduschek, E.P.3    Felsenfeld, G.4
  • 98
    • 0026516913 scopus 로고
    • Nonconservative segregation of parental nucleosomes during simian virus 40 chromosome replication in vitro
    • Sugasawa K, Ishimi Y, Eki T, Hurwitz J, Kikuchi A, Hanaoka F. 1992. Nonconservative segregation of parental nucleosomes during simian virus 40 chromosome replication in vitro. Proc. Natl. Acad. Sci. USA 89:1055-599
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 1055-1599
    • Sugasawa, K.1    Ishimi, Y.2    Eki, T.3    Hurwitz, J.4    Kikuchi, A.5    Hanaoka, F.6
  • 99
    • 65649153311 scopus 로고    scopus 로고
    • FACT and Asf1 regulate nucleosome dynamics and coactivator binding at the HO promoter
    • Takahata S, Yu Y, Stillman DJ. 2009. FACT and Asf1 regulate nucleosome dynamics and coactivator binding at the HO promoter. Cell 34:405-155
    • (2009) Cell , vol.34 , pp. 405-155
    • Takahata, S.1    Yu, Y.2    Stillman, D.J.3
  • 101
    • 79959264470 scopus 로고    scopus 로고
    • Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters
    • Tolkunov D, Zawadzki KA, Singer C, Elfving N, Morozov AV, Broach Jr. 2011. Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters. Mol. Biol. Cell 22:2106-188
    • (2011) Mol. Biol. Cell , vol.22 , pp. 2106-2188
    • Tolkunov, D.1    Zawadzki, K.A.2    Singer, C.3    Elfving, N.4    Morozov, A.V.5    Broach, J.R.6
  • 102
    • 77952934028 scopus 로고    scopus 로고
    • Single-molecule studies of the replisome
    • van Oijen AM, Loparo JJ. 2010. Single-molecule studies of the replisome. Annu. Rev. Biophys. 39:429-488
    • (2010) Annu. Rev. Biophys , Issue.39 , pp. 429-488
    • Van Oijen, A.M.1    Loparo, J.J.2
  • 103
    • 13244252309 scopus 로고    scopus 로고
    • UvrD helicase, unlike Rep helicase, dismantles RecA nucleoprotein filaments in Escherichia coli
    • Veaute X, Delmas S, Selva M, Jeusset J, Le Cam E, et al. 2005. UvrD helicase, unlike Rep helicase, dismantles RecA nucleoprotein filaments in Escherichia coli. EMBO J. 24:180-899
    • (2005) EMBO J. , vol.24 , pp. 180-899
    • Veaute, X.1    Delmas, S.2    Selva, M.3    Jeusset, J.4    Le Cam, E.5
  • 104
  • 105
    • 0034677955 scopus 로고    scopus 로고
    • Histone octamer dissociation is not required for in vitro replication of simian virus 40 minichromosomes
    • Vestner B, Waldmann T, Gruss C. 2000. Histone octamer dissociation is not required for in vitro replication of simian virus 40 minichromosomes. J. Biol. Chem. 275:8190-955
    • (2000) J. Biol. Chem , vol.275 , pp. 8190-8955
    • Vestner, B.1    Waldmann, T.2    Gruss, C.3
  • 106
    • 80052643394 scopus 로고    scopus 로고
    • Chromosome organization by a nucleoid-associated protein in live bacteria
    • WangW,LiGW,ChenC,Xie XS, Zhuang X. 2011. Chromosome organization by a nucleoid-associated protein in live bacteria. Science 333:1445-499
    • (2011) Science , vol.333 , pp. 1445-1499
    • Wang, W.1    Li, G.W.2    Chen, C.3    Xie, X.S.4    Zhuang, X.5
  • 107
    • 0024359479 scopus 로고
    • The negative charge ofGlu-111 is required to activate the cleavage center of EcoRI endonuclease
    • Wright DJ, King K, Modrich P. 1989. The negative charge ofGlu-111 is required to activate the cleavage center of EcoRI endonuclease. J. Biol. Chem. 264:11816-21
    • (1989) J. Biol. Chem , vol.264 , pp. 11816-21
    • Wright, D.J.1    King, K.2    Modrich, P.3


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