TY - JOUR AU - Mirkin, E. V. AU - Mirkin, S. M. TI - Replication fork stalling at natural impediments JA - Microbiol. Mol. Biol. Rev. PY - 2007/// VL - 71 SP - 13 EP - 35 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1128/MMBR.00030-06 N1 - 10.1128/MMBR.00030-06 UR - http://dx.doi.org/10.1128/MMBR.00030-06 ER - TY - JOUR AU - Rudolph, C. J. AU - Dhillon, P. AU - Moore, T. AU - Lloyd, R. G. TI - Avoiding and resolving conflicts between DNA replication and transcription JA - DNA Repair (Amst.) PY - 2007/// VL - 6 SP - 981 EP - 993 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1016/j.dnarep.2007.02.017 N1 - 10.1016/j.dnarep.2007.02.017 UR - http://dx.doi.org/10.1016/j.dnarep.2007.02.017 ER - TY - JOUR AU - Cox, M. M. TI - The importance of repairing stalled replication forks JA - Nature PY - 2000/// VL - 404 SP - 37 EP - 41 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1038/35003501 N1 - 10.1038/35003501 UR - http://dx.doi.org/10.1038/35003501 ER - TY - JOUR AU - Cox, M. M. TI - Recombinational DNA repair of damaged replication forks in Escherichia coli: questions JA - Annu. Rev. Genet. PY - 2001/// VL - 35 SP - 53 EP - 82 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1146/annurev.genet.35.102401.090016 N1 - 10.1146/annurev.genet.35.102401.090016 UR - http://dx.doi.org/10.1146/annurev.genet.35.102401.090016 ER - TY - JOUR AU - Brewer, B. J. TI - When polymerases collide: replication and the transcriptional organization of the E. coli chromosome JA - Cell PY - 1988/// VL - 53 SP - 679 EP - 686 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1016/0092-8674(88)90086-4 N1 - 10.1016/0092-8674(88)90086-4 UR - http://dx.doi.org/10.1016/0092-8674(88)90086-4 ER - TY - JOUR AU - Jarosz, D. F. AU - Beuning, P. J. AU - Cohen, S. E. AU - Walker, G. C. TI - Y-family DNA polymerases in Escherichia coli JA - Trends Microbiol. PY - 2007/// VL - 15 SP - 70 EP - 77 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1016/j.tim.2006.12.004 N1 - 10.1016/j.tim.2006.12.004 UR - http://dx.doi.org/10.1016/j.tim.2006.12.004 ER - TY - JOUR AU - Goodman, M. F. TI - Error-prone repair DNA polymerases in prokaryotes and eukaryotes JA - Annu. Rev. Biochem. PY - 2002/// VL - 71 SP - 17 EP - 50 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1146/annurev.biochem.71.083101.124707 N1 - 10.1146/annurev.biochem.71.083101.124707 UR - http://dx.doi.org/10.1146/annurev.biochem.71.083101.124707 ER - TY - JOUR AU - Tippin, B. AU - Pham, P. AU - Goodman, M. F. TI - Error-prone replication for better or worse JA - Trends Microbiol. PY - 2004/// VL - 12 SP - 288 EP - 295 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1016/j.tim.2004.04.004 N1 - 10.1016/j.tim.2004.04.004 UR - http://dx.doi.org/10.1016/j.tim.2004.04.004 ER - TY - JOUR AU - Lusetti, S. L. AU - Cox, M. M. TI - The bacterial RecA protein and the recombinational DNA repair of stalled replication forks JA - Annu. Rev. Biochem. PY - 2002/// VL - 71 SP - 71 EP - 100 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1146/annurev.biochem.71.083101.133940 N1 - 10.1146/annurev.biochem.71.083101.133940 UR - http://dx.doi.org/10.1146/annurev.biochem.71.083101.133940 ER - TY - GEN AU - Kornberg, A. AU - Baker, T. A. TI - DNA Replication PY - 1992/// SP - 246 PB - Macmillan Publishers Limited. All rights reserved ER - TY - JOUR AU - Breier, A. M. AU - Weier, H. U. AU - Cozzarelli, N. R. TI - Independence of replisomes in Escherichia coli chromosomal replication JA - Proc. Natl Acad. Sci. USA PY - 2005/// VL - 102 SP - 3942 EP - 3947 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1073/pnas.0500812102 N1 - 10.1073/pnas.0500812102 UR - http://dx.doi.org/10.1073/pnas.0500812102 ER - TY - JOUR AU - Blattner, F. R. TI - The complete genome sequence of Escherichia coli K-12 JA - Science PY - 1997/// VL - 277 SP - 1453 EP - 1474 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1126/science.277.5331.1453 N1 - 10.1126/science.277.5331.1453 UR - http://dx.doi.org/10.1126/science.277.5331.1453 ER - TY - JOUR AU - Rocha, E. P. AU - Danchin, A. TI - Essentiality, not expressiveness, drives gene-strand bias in bacteria JA - Nature Genet. PY - 2003/// VL - 34 SP - 377 EP - 378 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1038/ng1209 N1 - 10.1038/ng1209 UR - http://dx.doi.org/10.1038/ng1209 ER - TY - JOUR AU - Rocha, E. P. AU - Danchin, A. TI - Gene essentiality determines chromosome organisation in bacteria JA - Nucleic Acids Res. PY - 2003/// VL - 31 SP - 6570 EP - 6577 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1093/nar/gkg859 N1 - 10.1093/nar/gkg859 UR - http://dx.doi.org/10.1093/nar/gkg859 ER - TY - JOUR AU - Mirkin, E. V. AU - Mirkin, S. M. TI - Mechanisms of transcription-replication collisions in bacteria JA - Mol. Cell. Biol. PY - 2005/// VL - 25 SP - 888 EP - 895 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1128/MCB.25.3.888-895.2005 N1 - 10.1128/MCB.25.3.888-895.2005 UR - http://dx.doi.org/10.1128/MCB.25.3.888-895.2005 ER - TY - JOUR AU - Wang, J. D. AU - Berkmen, M. B. AU - Grossman, A. D. TI - Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis JA - Proc. Natl Acad. Sci. USA PY - 2007/// VL - 104 SP - 5608 EP - 5613 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1073/pnas.0608999104 N1 - 10.1073/pnas.0608999104 UR - http://dx.doi.org/10.1073/pnas.0608999104 ER - TY - JOUR AU - Prado, F. AU - Aguilera, A. TI - Impairment of replication fork progression mediates RNA polII transcription-associated recombination JA - EMBO J. PY - 2005/// VL - 24 SP - 1267 EP - 1276 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1038/sj.emboj.7600602 N1 - 10.1038/sj.emboj.7600602 UR - http://dx.doi.org/10.1038/sj.emboj.7600602 ER - TY - JOUR AU - Kobayashi, T. TI - The replication fork barrier site forms a unique structure with Fob1p and inhibits the replication fork JA - Mol. Cell. Biol. PY - 2003/// VL - 23 SP - 9178 EP - 9188 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1128/MCB.23.24.9178-9188.2003 N1 - 10.1128/MCB.23.24.9178-9188.2003 UR - http://dx.doi.org/10.1128/MCB.23.24.9178-9188.2003 ER - TY - JOUR AU - Deshpande, A. M. AU - Newlon, C. S. TI - DNA replication fork pause sites dependent on transcription JA - Science PY - 1996/// VL - 272 SP - 1030 EP - 1033 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1126/science.272.5264.1030 N1 - 10.1126/science.272.5264.1030 UR - http://dx.doi.org/10.1126/science.272.5264.1030 ER - TY - JOUR AU - French, S. TI - Consequences of replication fork movement through transcription units in vivo. JA - Science PY - 1992/// VL - 258 SP - 1362 EP - 1365 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1126/science.1455232 N1 - 10.1126/science.1455232 UR - http://dx.doi.org/10.1126/science.1455232 ER - TY - JOUR AU - Vilette, D. AU - Ehrlich, S. D. AU - Michel, B. TI - Transcription-induced deletions in plasmid vectors: M13 DNA replication as a source of instability JA - Mol. Gen. Genet. PY - 1996/// VL - 252 SP - 398 EP - 403 PB - Macmillan Publishers Limited. All rights reserved ER - TY - JOUR AU - Huvet, M. TI - Human gene organization driven by the coordination of replication and transcription JA - Genome Res. PY - 2007/// VL - 17 SP - 1278 EP - 1285 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1101/gr.6533407 N1 - 10.1101/gr.6533407 UR - http://dx.doi.org/10.1101/gr.6533407 ER - TY - JOUR AU - Liu, B. AU - Alberts, B. M. TI - Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex JA - Science PY - 1995/// VL - 267 SP - 1131 EP - 1137 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1126/science.7855590 N1 - 10.1126/science.7855590 UR - http://dx.doi.org/10.1126/science.7855590 ER - TY - JOUR AU - Liu, B. TI - The DNA replication fork can pass RNA polymerase without displacing the nascent transcript JA - Nature PY - 1993/// VL - 366 SP - 33 EP - 39 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1038/366033a0 N1 - 10.1038/366033a0 UR - http://dx.doi.org/10.1038/366033a0 ER - TY - JOUR AU - Liu, B. AU - Wong, M. L. AU - Alberts, B. TI - A transcribing RNA polymerase molecule survives DNA replication without aborting its growing RNA chain JA - Proc. Natl Acad. Sci. USA PY - 1994/// VL - 91 SP - 10660 EP - 10664 PB - Macmillan Publishers Limited. All rights reserved ER - TY - JOUR AU - Ogawa, T. AU - Okazaki, T. TI - Discontinuous DNA replication JA - Annu. Rev. Biochem. PY - 1980/// VL - 49 SP - 421 EP - 457 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1146/annurev.bi.49.070180.002225 N1 - 10.1146/annurev.bi.49.070180.002225 UR - http://dx.doi.org/10.1146/annurev.bi.49.070180.002225 ER - TY - JOUR AU - Wang, T. C. TI - Discontinuous or semi-discontinuous DNA replication in Escherichia coli? JA - Bioessays PY - 2005/// VL - 27 SP - 633 EP - 636 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1002/bies.20233 N1 - 10.1002/bies.20233 UR - http://dx.doi.org/10.1002/bies.20233 ER - TY - JOUR AU - Johnson, A. AU - O/'Donnell, M. TI - Cellular DNA replicases: components and dynamics at the replication fork JA - Annu. Rev. Biochem. PY - 2005/// VL - 74 SP - 283 EP - 315 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1146/annurev.biochem.73.011303.073859 N1 - 10.1146/annurev.biochem.73.011303.073859 UR - http://dx.doi.org/10.1146/annurev.biochem.73.011303.073859 ER - TY - JOUR AU - Pomerantz, R. T. AU - O/'Donnell, M. TI - Replisome mechanics: insights into a twin DNA polymerase machine JA - Trends Microbiol. PY - 2007/// VL - 15 SP - 156 EP - 164 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1016/j.tim.2007.02.007 N1 - 10.1016/j.tim.2007.02.007 UR - http://dx.doi.org/10.1016/j.tim.2007.02.007 ER - TY - JOUR AU - Steitz, T. A. TI - The structural basis of the transition from initiation to elongation phases of transcription, as well as translocation and strand separation, by T7 RNA polymerase JA - Curr. Opin. Struct. Biol. PY - 2004/// VL - 14 SP - 4 EP - 9 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1016/j.sbi.2004.01.006 N1 - 10.1016/j.sbi.2004.01.006 UR - http://dx.doi.org/10.1016/j.sbi.2004.01.006 ER - TY - JOUR AU - Mentesana, P. E. AU - Chin-Bow, S. T. AU - Sousa, R. AU - McAllister, W. T. TI - Characterization of halted T7 RNA polymerase elongation complexes reveals multiple factors that contribute to stability JA - J. Mol. Biol. PY - 2000/// VL - 302 SP - 1049 EP - 1062 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1006/jmbi.2000.4114 N1 - 10.1006/jmbi.2000.4114 UR - http://dx.doi.org/10.1006/jmbi.2000.4114 ER - TY - JOUR AU - Jiang, M. AU - Rong, M. AU - Martin, C. AU - McAllister, W. T. TI - Interrupting the template strand of the T7 promoter facilitates translocation of the DNA during initiation, reducing transcript slippage and the release of abortive products JA - J. Mol. Biol. PY - 2001/// VL - 310 SP - 509 EP - 522 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1006/jmbi.2001.4793 N1 - 10.1006/jmbi.2001.4793 UR - http://dx.doi.org/10.1006/jmbi.2001.4793 ER - TY - JOUR AU - Uptain, S. M. AU - Kane, C. M. AU - Chamberlin, M. J. TI - Basic mechanisms of transcript elongation and its regulation JA - Annu. Rev. Biochem. PY - 1997/// VL - 66 SP - 117 EP - 172 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1146/annurev.biochem.66.1.117 N1 - 10.1146/annurev.biochem.66.1.117 UR - http://dx.doi.org/10.1146/annurev.biochem.66.1.117 ER - TY - JOUR AU - Trautinger, B. W. AU - Jaktaji, R. P. AU - Rusakova, E. AU - Lloyd, R. G. TI - RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription JA - Mol. Cell PY - 2005/// VL - 19 SP - 247 EP - 258 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1016/j.molcel.2005.06.004 N1 - 10.1016/j.molcel.2005.06.004 UR - http://dx.doi.org/10.1016/j.molcel.2005.06.004 ER - TY - JOUR AU - Stukenberg, P. T. AU - Turner, J. AU - O'Donnell, M. TI - An explanation for lagging strand replication: polymerase hopping among DNA sliding clamps JA - Cell PY - 1994/// VL - 78 SP - 877 EP - 887 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1016/S0092-8674(94)90662-9 N1 - 10.1016/S0092-8674(94)90662-9 UR - http://dx.doi.org/10.1016/S0092-8674(94)90662-9 ER - TY - JOUR AU - Keiler, K. C. TI - Biology of trans-translation JA - Annu. Rev. Microbiol. PY - 2008/// VL - 62 SP - 133 EP - 151 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1146/annurev.micro.62.081307.162948 N1 - 10.1146/annurev.micro.62.081307.162948 UR - http://dx.doi.org/10.1146/annurev.micro.62.081307.162948 ER - TY - JOUR AU - Okazaki, R. TI - Mechanism of DNA chain growth. I. Possible discontinuity and unusual secondary structure of newly synthesized chains JA - Proc. Natl Acad. Sci. USA PY - 1968/// VL - 59 SP - 598 EP - 605 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1073/pnas.59.2.598 N1 - 10.1073/pnas.59.2.598 UR - http://dx.doi.org/10.1073/pnas.59.2.598 ER - TY - JOUR AU - Sternglanz, R. AU - Wang, H. F. AU - Donegan, J. J. TI - Evidence that both growing DNA chains at a replication fork are synthesized discontinuously JA - Biochemistry PY - 1976/// VL - 15 SP - 1838 EP - 1843 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1021/bi00654a008 N1 - 10.1021/bi00654a008 UR - http://dx.doi.org/10.1021/bi00654a008 ER - TY - JOUR AU - Pauling, C. AU - Hamm, L. TI - Properties of a temperature-sensitive, radiation-sensitive mutant of Escherichia coli. II. DNA replication JA - Proc. Natl Acad. Sci. USA PY - 1969/// VL - 64 SP - 1195 EP - 1202 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1073/pnas.64.4.1195 N1 - 10.1073/pnas.64.4.1195 UR - http://dx.doi.org/10.1073/pnas.64.4.1195 ER - TY - JOUR AU - Gottesman, M. M. AU - Hicks, M. L. AU - Gellert, M. TI - Genetics and function of DNA ligase in Escherichia coli JA - J. Mol. Biol. PY - 1973/// VL - 77 SP - 531 EP - 547 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1016/0022-2836(73)90221-0 N1 - 10.1016/0022-2836(73)90221-0 UR - http://dx.doi.org/10.1016/0022-2836(73)90221-0 ER - TY - JOUR AU - Konrad, E. B. AU - Modrich, P. AU - Lehman, I. R. TI - Genetic and enzymatic characterization of a conditional lethal mutant of Escherichia coli K12 with a temperature-sensitive DNA ligase JA - J. Mol. Biol. PY - 1973/// VL - 77 SP - 519 EP - 529 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1016/0022-2836(73)90220-9 N1 - 10.1016/0022-2836(73)90220-9 UR - http://dx.doi.org/10.1016/0022-2836(73)90220-9 ER - TY - JOUR AU - Okazaki, R. AU - Arisawa, M. AU - Sugino, A. TI - Slow joining of newly replicated DNA chains in DNA polymerase I-deficient Escherichia coli mutants JA - Proc. Natl Acad. Sci. USA PY - 1971/// VL - 68 SP - 2954 EP - 2957 PB - Macmillan Publishers Limited. All rights reserved ER - TY - JOUR AU - Olivera, R. M. AU - Bonhoeffer, E. TI - Replication of Escherichia coli requires DNA polymerase I JA - Nature PY - 1974/// VL - 250 SP - 513 EP - 514 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1038/250513a0 N1 - 10.1038/250513a0 UR - http://dx.doi.org/10.1038/250513a0 ER - TY - JOUR AU - Wang, T. C. AU - Smith, K. C. TI - Discontinuous DNA replication in a lig-7 strain of Escherichia coli is not the result of mismatch repair, nucleotide-excision repair, or the base-excision repair of DNA uracil JA - Biochem. Biophys. Res. Commun. PY - 1989/// VL - 165 SP - 685 EP - 688 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1016/S0006-291X(89)80020-8 N1 - 10.1016/S0006-291X(89)80020-8 UR - http://dx.doi.org/10.1016/S0006-291X(89)80020-8 ER - TY - JOUR AU - Wang, T. C. AU - Chen, S. H. TI - Okazaki DNA fragments contain equal amounts of lagging-strand and leading-strand sequences JA - Biochem. Biophys. Res. Commun. PY - 1994/// VL - 198 SP - 844 EP - 849 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1006/bbrc.1994.1120 N1 - 10.1006/bbrc.1994.1120 UR - http://dx.doi.org/10.1006/bbrc.1994.1120 ER - TY - JOUR AU - Heller, R. C. AU - Marians, K. J. TI - Replication fork reactivation downstream of a blocked nascent leading strand JA - Nature PY - 2006/// VL - 439 SP - 557 EP - 562 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1038/nature04329 N1 - 10.1038/nature04329 UR - http://dx.doi.org/10.1038/nature04329 ER - TY - JOUR AU - Heller, R. C. AU - Marians, K. J. TI - Replisome assembly and the direct restart of stalled replication forks JA - Nature Rev. Mol. Cell Biol. PY - 2006/// VL - 7 SP - 932 EP - 943 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1038/nrm2058 N1 - 10.1038/nrm2058 UR - http://dx.doi.org/10.1038/nrm2058 ER - TY - JOUR AU - Heller, R. C. AU - Marians, K. J. TI - The disposition of nascent strands at stalled replication forks dictates the pathway of replisome loading during restart JA - Mol. Cell PY - 2005/// VL - 17 SP - 733 EP - 743 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1016/j.molcel.2005.01.019 N1 - 10.1016/j.molcel.2005.01.019 UR - http://dx.doi.org/10.1016/j.molcel.2005.01.019 ER - TY - JOUR AU - McInerney, P. AU - O/'Donnell, M. TI - Functional uncoupling of twin polymerases: mechanism of polymerase dissociation from a lagging-strand block JA - J. Biol. Chem. PY - 2004/// VL - 279 SP - 21543 EP - 21551 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1074/jbc.M401649200 N1 - 10.1074/jbc.M401649200 UR - http://dx.doi.org/10.1074/jbc.M401649200 ER - TY - JOUR AU - Severinov, K. AU - Mooney, R. AU - Darst, S. A. AU - Landick, R. TI - Tethering of the large subunits of Escherichia coli RNA polymerase JA - J. Biol. Chem. PY - 1997/// VL - 272 SP - 24137 EP - 24140 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1074/jbc.272.39.24137 N1 - 10.1074/jbc.272.39.24137 UR - http://dx.doi.org/10.1074/jbc.272.39.24137 ER - TY - JOUR AU - Severinov, K. AU - Mooney, R. AU - Darst, S. A. AU - Landick, R. TI - Tethering of the large subunits of Escherichia coli RNA polymerase JA - J. Biol. Chem. PY - 1997/// VL - 272 SP - 24137 EP - 24140 PB - Macmillan Publishers Limited. All rights reserved M3 - 10.1074/jbc.272.39.24137 N1 - 10.1074/jbc.272.39.24137 UR - http://dx.doi.org/10.1074/jbc.272.39.24137 ER -