Avoiding and resolving conflicts between DNA replication and transcription

DNA Repair

Volumn 6, Issue 7, 2007, Pages 981-993

  Rudolph, Christian J ^a   Dhillon, Paraminder ^a   Moore, Timothy ^a   Lloyd, Robert G ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

CSA; CSB; DksA; DNA polymerase; GreA; GreB; Induced recombination; Mfd; RNA polymerase; Stalled replication forks; TFIIS

Indexed keywords

DNA POLYMERASE; RNA POLYMERASE;

ARTICLE; CELL GROWTH; CELL VIABILITY; CHROMOSOME DUPLICATION; COMPLEX FORMATION; DNA DAMAGE; DNA REPAIR; DNA REPLICATION; DNA TEMPLATE; DNA TRANSCRIPTION; GENE EXPRESSION; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; RNA TRANSLATION;

ANIMALS; DNA REPAIR; DNA REPLICATION; DNA-DIRECTED RNA POLYMERASES; HUMANS; TRANSCRIPTION, GENETIC;

EID: 34249941504     PISSN: 15687864     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dnarep.2007.02.017     Document Type: Article

References (150)

1. Cooper S. Checkpoints and restriction points in bacteria and eukaryotic cells. Bioessays 28 (2006) 1035-1039
2. Margolin W., and Bernander R. How do prokaryotic cells cycle?. Curr. Biol. 14 (2004) R768-R770
3. Kearsey S.E., and Cotterill S. Enigmatic variations: divergent modes of regulating eukaryotic DNA replication. Mol. Cell 12 (2003) 1067-1075
4. Stillman B. DNA replication. Genomic views of genome duplication. Science 294 (2001) 2301-2304
5. Tanaka T., Knapp D., and Nasmyth K. Loading of an Mcm protein onto DNA replication origins is regulated by Cdc6p and CDKs. Cell 90 (1997) 649-660
6. Diffley J. Regulation of early events in chromosome replication. Curr. Biol. 14 (2004) R778-R786
7. Johnson A., and O'Donnell M. Cellular DNA replicases: components and dynamics at the replication fork. Annu. Rev. Biochem. 74 (2005) 283-315
8. Lopes M., Cotta-Ramusino C., Pellicioli A., Liberi G., Plevani P., Muzi-Falconi M., Newlon C.S., and Foiani M. The DNA replication checkpoint response stabilizes stalled replication forks. Nature 412 (2001) 557-561
9. Cooper S. Regulation of DNA synthesis in bacteria: analysis of the Bates/Kleckner licensing/initiation-mass model for cell cycle control. Mol. Microbiol. 62 (2006) 303-307
10. Sherratt D.J. Bacterial chromosome dynamics. Science 301 (2003) 780-785
11. Wang X., Liu X., Possoz C., and Sherratt D.J. The two Escherichia coli chromosome arms locate to separate cell halves. Genes Dev. 20 (2006) 1727-1731
12. Boye E., Stokke T., Kleckner N., and Skarstad K. Coordinating DNA replication initiation with cell growth: differential roles for DnaA and SeqA proteins. Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 12206-12211
13. Slater S., Wold S., Lu M., Boye E., Skarstad K., and Kleckner N. E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration. Cell 82 (1995) 927-936
14. Kaguni J. DnaA: controlling the initiation of bacterial DNA replication and more. Annu. Rev. Microbiol. 60 (2006) 351-371
15. Nielsen H.J., Ottesen J.R., Youngren B., Austin S.J., and Hansen F.G. The Escherichia coli chromosome is organized with the left and right chromosome arms in separate cell halves. Mol. Microbiol. 62 (2006) 331-338
16. Boye E., Lobner-Olesen A., and Skarstad K. Limiting DNA replication to once and only once. EMBO Rep. 1 (2000) 479-483
17. Messer W. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol. Rev. 26 (2002) 355-374
18. Marians K.J. Prokaryotic DNA replication. Annu. Rev. Biochem. 61 (1992) 673-719
19. Baker T.A., and Bell S.P. Polymerases and the replisome: machines within machines. Cell 92 (1998) 295-305
20. Fang L., Davey M.J., and O'Donnell M. Replisome assembly at oriC, the replication origin of E. coli, reveals an explanation for initiation sites outside an origin. Mol. Cell 4 (1999) 541-553
21. den Blaauwen T., Aarsman M.E., Wheeler L.J., and Nanninga N. Pre-replication assembly of E. coli replisome components. Mol. Microbiol. 62 (2006) 695-708
22. Friedberg E.C., Walker G.C., Siede W., Wood R., Schultz R., and Ellenberger T. DNA Repair and Mutagenesis (2006), ASM Press, Washington, DC
23. Lindahl T. The Croonian Lecture, 1996: endogenous damage to DNA. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 351 (1996) 1529-1538
24. Marians K.J. Replication and recombination intersect. Curr. Opin. Genet. Dev. 10 (2000) 151-156
25. Liu J., and Marians K.J. PriA-directed assembly of a primosome on D loop DNA. J. Biol. Chem. 274 (1999) 25033-25041
26. McGlynn P., and Lloyd R.G. Recombinational repair and restart of damaged replication forks. Nat. Rev. Mol. Cell Biol. 3 (2002) 859-870
27. Ivessa A.S., Lenzmeier B.A., Bessler J.B., Goudsouzian L.K., Schnakenberg S.L., and Zakian V.A. The Saccharomyces cerevisiae helicase Rrm3p facilitates replication past nonhistone protein-DNA complexes. Mol. Cell 12 (2003) 1525-1536
28. Michel B. Replication fork arrest and DNA recombination. Trends Biochem. Sci. 25 (2000) 173-178
29. Marians K.J. Mechanisms of replication fork restart in Escherichia coli. Philos. Trans. R. Soc. Lond B: Biol. Sci. 359 (2004) 71-77
30. Michel B., Grompone G., Flores M.J., and Bidnenko V. Multiple pathways process stalled replication forks. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 12783-12788
31. Heller R.C., and Marians K.J. Replication fork reactivation downstream of a blocked nascent leading strand. Nature 439 (2006) 557-562
32. Friedberg E.C., Lehmann A.R., and Fuchs R.P. Trading places: how do DNA polymerases switch during translesion DNA synthesis?. Mol. Cell 18 (2005) 499-505
33. A.N. Other, Other articles in this issue of DNA repair, DNA Rep., this issue (see other articles).
34. Sandler S.J. Multiple genetic pathways for restarting DNA replication forks in Escherichia coli K-12. Genetics 155 (2000) 487-497
35. Heller R.C., and Marians K.J. Unwinding of the nascent lagging strand by Rep and PriA enables the direct restart of stalled replication forks. J. Biol. Chem. 280 (2005) 34143-34151
36. Heller R.C., and Marians K.J. The disposition of nascent strands at stalled replication forks dictates the pathway of replisome loading during restart. Mol. Cell 17 (2005) 733-743
37. Prado F., and Aguilera A. Partial depletion of histone H4 increases homologous recombination-mediated genetic instability. Mol. Cell. Biol. 25 (2005) 1526-1536
38. Tornaletti S. Transcription arrest at DNA damage sites. Mutat. Res. 577 (2005) 131-145
39. Uptain S.M., Kane C.M., and Chamberlin M.J. Basic mechanisms of transcript elongation and its regulation. Annu. Rev. Biochem. 66 (1997) 117-172
40. Selby C.P., Drapkin R., Reinberg D., and Sancar A. RNA polymerase II stalled at a thymine dimer: footprint and effect on excision repair. Nucleic Acids Res. 25 (1997) 787-793
41. Tornaletti S., and Hanawalt P.C. Effect of DNA lesions on transcription elongation. Biochimie 81 (1999) 139-146
42. Viswanathan A., and Doetsch P.W. Effects of nonbulky DNA base damages on Escherichia coli RNA polymerase-mediated elongation and promoter clearance. J. Biol. Chem. 273 (1998) 21276-21281
43. Donahue B.A., Fuchs R.P., Reines D., and Hanawalt P.C. Effects of aminofluorene and acetylaminofluorene DNA adducts on transcriptional elongation by RNA polymerase II. J. Biol. Chem. 271 (1996) 10588-10594
44. Donahue B.A., Yin S., Taylor J.S., Reines D., and Hanawalt P.C. Transcript cleavage by RNA polymerase II arrested by a cyclobutane pyrimidine dimer in the DNA template. Proc. Natl. Acad. Sci. U.S.A. 91 (1994) 8502-8506
45. Trautinger B.W., Jaktaji R.P., Rusakova E., and Lloyd R.G. RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription. Mol. Cell 19 (2005) 247-258
46. McClure W.R. Mechanism and control of transcription initiation in prokaryotes. Annu. Rev. Biochem. 54 (1985) 171-204
47. Mooney R.A., Artsimovitch I., and Landick R. Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. J. Bacteriol. 180 (1998) 3265-3275
48. Vassylyev D.G., Sekine S., Laptenko O., Lee J., Vassylyeva M.N., Borukhov S., and Yokoyama S. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature 417 (2002) 712-719
49. Erie D.A. The many conformational states of RNA polymerase elongation complexes and their roles in the regulation of transcription. Biochem. Biophys. Acta 1577 (2002) 224-239
50. Chamberlin M.J. New models for the mechanism of transcription elongation and its regulation. Harvey Lect. 88 (1992) 1-21
51. Krummel B., and Chamberlin M.J. Structural analysis of ternary complexes of Escherichia coli RNA polymerase. Deoxyribonuclease I footprinting of defined complexes. J. Mol. Biol. 225 (1992) 239-250
52. Komissarova N., and Kashlev M. Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3′ end of the RNA intact and extruded. Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 1755-1760
53. Samkurashvili I., and Luse D.S. Translocation and transcriptional arrest during transcript elongation by RNA polymerase II. J. Biol. Chem. 271 (1996) 23495-23505
54. Park J.S., Marr M.T., and Roberts J.W. E. coli transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation. Cell 109 (2002) 757-767
55. Borukhov S., Lee J., and Laptenko O. Bacterial transcription elongation factors: new insights into molecular mechanism of action. Mol. Microbiol. 55 (2005) 1315-1324
56. Opalka N., Chlenov M., Chacon P., Rice W.J., Wriggers W., and Darst S.A. Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase. Cell 114 (2003) 335-345
57. Conaway R.C., Kong S.E., and Conaway J.W. TFIIS and GreB: two like-minded transcription elongation factors with sticky fingers. Cell 114 (2003) 224-272
58. Toulme F., Mosrin-Huaman C., Sparkowski J., Das A., Leng M., and Rachid Rahmouni A. GreA and GreB proteins revive backtracked RNA polymerase in vivo by promoting transcript trimming. EMBO J. 19 (2000) 6853-6859
59. Marr M.T., and Roberts J.W. Function of transcription cleavage factors GreA and GreB at a regulatory pause site. Mol. Cell 6 (2000) 1275-1285
60. Kettenberger H., Armache K.J., and Cramer P. Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell 114 (2003) 347-357
61. Reines D., Conaway J.W., and Conaway R.C. The RNA polymerase II general elongation factors. Trends Biochem. Sci. 21 (1996) 351-355
62. Cashel M., Gentry D.R., Hernandez V.J., and Vinella D. The stringent response. In: Neidhardt F.C., Curtiss III R., Ingraham J.L., Lin E.C.C., Low K.B., Magasanik B., Reznikoff W.S., Riley M., Schaechter M., and Umbarger H.E. (Eds). Escherichia coli and Salmonella Cellular and Molecular Biology. 2nd ed. (1996), ASM Press, Washington, DC 1458-1496
63. Magnusson L.U., Farewell A., and Nystrom T. ppGpp: a global regulator in Escherichia coli. Trends Microbiol. 13 (2005) 236-242
64. Perederina A., Svetlov V., Vassylyeva M.N., Tahirov T.H., Yokoyama S., Artsimovitch I., and Vassylyev D.G. Regulation through the secondary channel-structural framework for ppGpp-DksA synergism during transcription. Cell 118 (2004) 297-309
65. Paul B.J., Barker M.M., Ross W., Schneider D.A., Webb C., Foster J.W., and Gourse R.L. DksA; a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell 118 (2004) 311-322
66. Selby C.P., and Sancar A. Molecular mechanism of transcription-repair coupling. Science 260 (1993) 53-58
67. Deaconescu A.M., Chambers A.L., Smith A.J., Nickels B.E., Hochschild A., Savery N.J., and Darst S.A. Structural basis for bacterial transcription-coupled DNA repair. Cell 124 (2006) 507-520
68. Smith A.J., and Savery N.J. RNA polymerase mutants defective in the initiation of transcription-coupled DNA repair. Nucleic Acids Res. 33 (2005) 755-764
69. Chambers A.L., Smith A.J., and Savery N.J. A DNA translocation motif in the bacterial transcription-repair coupling factor, Mfd. Nucleic Acids Res. 31 (2003) 6409-6418
70. Svejstrup J.Q. Transcription repair coupling factor: a very pushy enzyme. Mol. Cell 9 (2002) 1151-1152
71. Woudstra E.C., Gilbert C., Fellows J., Jansen L., Brouwer J., Erdjument-Bromage H., Tempst P., and Svejstrup J.Q. A Rad26-Def1 complex coordinates repair and RNA pol II proteolysis in response to DNA damage. Nature 415 (2002) 929-933
72. Svejstrup J.Q. Rescue of arrested RNA polymerase II complexes. J. Cell Sci. 116 (2003) 447-451
73. Shuin T., Yamazaki I., Tamura K., Kamada M., and Ashida S. Recent advances in ideas on the molecular pathology and clinical aspects of Von Hippel-Lindau disease. Int. J. Clin. Oncol. 9 (2004) 283-287
74. Kuznetsova A.V., Meller J., Schnell P.O., Nash J.A., Ignacak M.L., Sanchez Y., Conaway J.W., Conaway R.C., and Czyzyk-Krzeska M.F. von Hippel-Lindau protein binds hyperphosphorylated large subunit of RNA polymerase II through a proline hydroxylation motif and targets it for ubiquitination. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 2706-2711
75. Gillette T.G., Gonzalez F., Delahodde A., Johnston S.A., and Kodadek T. Physical and functional association of RNA polymerase II and the proteasome. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 5904-5909
76. Ljungman M., and Lane D.P. Transcription-guarding the genome by sensing DNA damage. Nat. Rev. Cancer 4 (2004) 727-737
77. Laine J.P., and Egly J.M. When transcription and repair meet: a complex system. Trends Genet. 22 (2006) 430-436
78. Selby C.P., Witkin E.M., and Sancar A. Escherichia coli mfd mutant deficient in "mutation frequency decline" lacks strand-specific repair: in vitro complementation with purified coupling factor. Proc. Natl. Acad. Sci. U.S.A. 88 (1991) 11574-11578
79. Tantin D. RNA polymerase II elongation complexes containing the Cockayne syndrome group B protein interact with a molecular complex containing the transcription factor IIH components xeroderma pigmentosum B and p62. J. Biol. Chem. 273 (1998) 27794-27799
80. Trautinger B.W., and Lloyd R.G. Modulation of DNA repair by mutations flanking the DNA channel through RNA polymerase. EMBO J. 21 (2002) 6944-6953
81. Mahdi A.A., Buckman C., Harris L., and Lloyd R.G. Rep and PriA helicase activities prevent RecA from provoking unnecessary recombination during replication fork repair. Genes Dev. 20 (2006) 2135-2147
82. McGlynn P., and Lloyd R.G. Modulation of RNA polymerase by (p)ppGpp reveals a RecG-dependent mechanism for replication fork progression. Cell 101 (2000) 35-45
83. Wong J.M., and Ingles C.J. A compromised yeast RNA polymerase II enhances UV sensitivity in the absence of global genome nucleotide excision repair. Mol. Gen. Genet. 264 (2001) 842-851
84. Brewer B.J. When polymerases collide: replication and the transcriptional organization of the E. coli chromosome. Cell 53 (1988) 679-686
85. French S. Consequences of replication fork movement through transcription units in vivo. Science 258 (1992) 1362-1365
86. Mirkin E.V., and Mirkin S.M. Mechanisms of transcription-replication collisions in bacteria. Mol. Cell. Biol. 25 (2005) 888-895
87. Blattner F.R., Plunkett III G., Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., and Shao Y. The complete genome sequence of Escherichia coli K-12. Science 277 (1997) 1453-1474
88. McLean M.J., Wolfe K.H., and Devine K.M. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J. Mol. Evol. 47 (1998) 691-696
89. Rebollo J.E., Francois V., and Louarn J.M. Detection and possible role of two large nondivisible zones on the Escherichia coli chromosome. Proc. Natl. Acad. Sci. U.S.A. 85 (1988) 9391-9395
90. de Massy B., Bejar S., Louarn J., Louarn J.M., and Bouche J.P. Inhibition of replication forks exiting the terminus region of the Escherichia coli chromosome occurs at two loci separated by 5 min. Proc. Natl. Acad. Sci. U.S.A. 84 (1987) 1759-1763
91. Hyrien O. Mechanisms and consequences of replication fork arrest. Biochimie 82 (2000) 5-17
92. Campbell J.L. Eukaryotic DNA replication. Annu. Rev. Biochem. 55 (1986) 733-771
93. Linskens M.H., and Huberman J.A. Organization of replication of ribosomal DNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 8 (1988) 4927-4935
94. Ivessa A.S., and Zakian V.A. To fire or not to fire: origin activation in Saccharomyces cerevisiae ribosomal DNA. Genes Dev. 16 (2002) 2459-2464
95. Brewer B.J., and Fangman W.L. A replication fork barrier at the 3′ end of yeast ribosomal RNA genes. Cell 55 (1988) 637-643
96. Deshpande A.M., and Newlon C.S. DNA replication fork pause sites dependent on transcription. Science 272 (1996) 1030-1033
97. Brewer B.J., Lockshon D., and Fangman W.L. The arrest of replication forks in the rDNA of yeast occurs independently of transcription. Cell 71 (1992) 267-276
98. Liu B., Wong M.L., Tinker R.L., Geiduschek E.P., and Alberts B.M. The DNA replication fork can pass RNA polymerase without displacing the nascent transcript. Nature 366 (1993) 33-39
99. Elias-Arnanz M., and Salas M. Bacteriophage phi29 DNA replication arrest caused by codirectional collisions with the transcription machinery. EMBO J. 16 (1997) 5775-5783
100. Mirkin E.V., Castro Roa D., Nudler E., and Mirkin S.M. Transcription regulatory elements are punctuation marks for DNA replication. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 7276-7281
101. Liu B., and Alberts B.M. Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex. Science 267 (1995) 1131-1137
102. Liu L.F., and Wang J.C. Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. U.S.A. 84 (1987) 7024-7027
103. Takeuchi Y., Horiuchi T., and Kobayashi T. Transcription-dependent recombination and the role of fork collision in yeast rDNA. Genes Dev. 17 (2003) 1497-1506
104. Dammann R., Lucchini R., Koller T., and Sogo J.M. Chromatin structures and transcription of rDNA in yeast Saccharomyces cerevisiae. Nucleic Acids Res. 21 (1993) 2331-2338
105. Pasero P., Bensimon A., and Schwob E. Single-molecule analysis reveals clustering and epigenetic regulation of replication origins at the yeast rDNA locus. Genes Dev. 16 (2002) 2479-2484
106. Sogo J.M., Lopes M., and Foiani M. Fork reversal and ssDNA accumulation at stalled replication forks owing to checkpoint defects. Science 297 (2002) 599-602
107. Grompone G., Ehrlich S.D., and Michel B. Replication restart in gyrB Escherichia coli mutants. Mol. Microbiol. 48 (2003) 845-854
108. Bidnenko V., Ehrlich S.D., and Michel B. Replication fork collapse at replication terminator sequences. EMBO J. 21 (2002) 3898-3907
109. Bidnenko V., Lestini R., and Michel B. The Escherichia coli UvrD helicase is essential for Tus removal during recombination-dependent replication restart from Ter sites. Mol. Microbiol. 62 (2006) 382-396
110. Neylon C., Kralicek A.V., Hill T.M., and Dixon N.E. Replication termination in Escherichia coli: structure and antihelicase activity of the Tus-Ter complex. Microbiol. Mol. Biol. Rev. 69 (2005) 501-526
111. Mulcair M., Schaeffer P., Oakley A., Cross H., Neylon C., Hill T., and Dixon N. A molecular mousetrap determines polarity of termination of DNA replication in E. coli. Cell 125 (2006) 1309-1319
112. Hiasa H., and Marians K.J. Differential inhibition of the DNA translocation and DNA unwinding activities of DNA helicases by the Escherichia coli Tus protein. J. Biol. Chem. 267 (1992) 11379-11385
113. Kobayashi T. The replication fork barrier site forms a unique structure with Fob1 p and inhibits the replication fork. Mol. Cell. Biol. 23 (2003) 9178-9188
114. Kobayashi T., and Horiuchi T. A yeast gene product, Fob1 protein, required for both replication fork blocking and recombinational hotspot activities. Genes Cells 1 (1996) 465-474
115. Gruber M., Wellinger R.E., and Sogo J.M. Architecture of the replication fork stalled at the 3′ end of yeast ribosomal genes. Mol. Cell. Biol. 20 (2000) 5777-5787
116. Calzada A., Hodgson B., Kanemaki M., Bueno A., and Labib K. Molecular anatomy and regulation of a stable replisome at a paused eukaryotic DNA replication fork. Genes Dev. 19 (2005) 1905-1919
117. Hill T.M., and Marians K.J. Escherichia coli Tus protein acts to arrest the progression of DNA replication forks in vitro. Proc. Natl. Acad. Sci. U.S.A. 87 (1990) 2481-2485
118. Torres J.Z., Schnakenberg S.L., and Zakian V.A. Saccharomyces cerevisiae Rrm3p DNA helicase promotes genome integrity by preventing replication fork stalling: viability of rrm3 cells requires the intra-S-phase checkpoint and fork restart activities. Mol. Cell. Biol. 24 (2004) 3198-3212
119. Ivessa A.S., Zhou J.Q., and Zakian V.A. The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosomal DNA. Cell 100 (2000) 479-489
120. Possoz C., Filipe S.R., Grainge I., and Sherratt D.J. Tracking of controlled Escherichia coli replication fork stalling and restart at repressor-bound DNA in vivo. EMBO J. 25 (2006) 2596-2604
121. Payne B.T., van Knippenberg I.C., Bell H., Filipe S.R., Sherratt D.J., and McGlynn P. Replication fork blockage by transcription factor-DNA complexes in Escherichia coli. Nucleic Acids Res. 34 (2006) 5194-5202
122. Rothstein R., Michel B., and Gangloff S. Replication fork pausing and recombination, or "gimme a break". Genes Dev. 14 (2000) 1-10
123. Michel B., Flores M.J., Viguera E., Grompone G., Seigneur M., and Bidnenko V. Rescue of arrested replication forks by homologous recombination. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 8181-8188
124. Horiuchi T., Fujimura Y., Nishitani H., Kobayashi T., and Hidaka M. The DNA replication fork blocked at the Ter site may be an entrance for the RecBCD enzyme into duplex DNA. J. Bacteriol. 176 (1994) 4656-4663
125. Fujiwara Y., and Tatsumi M. Replicative bypass repair of ultraviolet damage to DNA of mammalian cells: caffeine sensitive and caffeine resistant mechanisms. Mutat. Res. 37 (1976) 91-110
126. Higgins N.P., Kato K., and Strauss B. A model for replication repair in mammalian cells. J. Mol. Biol. 101 (1976) 417-425
127. Seigneur M., Bidnenko V., Ehrlich S.D., and Michel B. RuvAB acts at arrested replication forks. Cell 95 (1998) 419-430
128. McGlynn P., and Lloyd R.G. Rescue of stalled replication forks by RecG: simultaneous translocation on the leading and lagging strand templates supports an active DNA unwinding model of fork reversal and Holliday junction formation. Proc. Nat. Acad. Sci. U.S.A. 98 (2001) 8227-8234
129. Kodama K., Kobayashi T., Niki H., Hiraga S., Oshima T., Mori H., and Horiuchi T. Amplification of Hot DNA segments in Escherichia coli. Mol. Microbiol. 45 (2002) 1575-1588
130. Keil R.L., and Roeder G.S. Cis-acting, recombination-stimulating activity in a fragment of the ribosomal DNA of S. cerevisiae. Cell 39 (1984) 377-386
131. Prado F., Piruat J.I., and Aguilera A. Recombination between DNA repeats in yeast hpr1Δ cells is linked to transcription elongation. EMBO J. 16 (1997) 2826-2835
132. Huang G.S., and Keil R.L. Requirements for activity of the yeast mitotic recombination hotspot HOT1: RNA polymerase I and multiple cis-acting sequences. Genetics 141 (1995) 845-855
133. Kobayashi T., Heck D.J., Nomura M., and Horiuchi T. Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I. Genes Dev. 12 (1998) 3821-3830
134. Serizawa N., Horiuchi T., and Kobayashi T. Transcription-mediated hyper-recombination in HOT1. Genes Cells 9 (2004) 305-315
135. Ward T.R., Hoang M.L., Prusty R., Lau C.K., Keil R.L., Fangman W.L., and Brewer B.J. Ribosomal DNA replication fork barrier and HOT1 recombination hot spot: shared sequences but independent activities. Mol. Cell. Biol. 20 (2000) 4948-4957
136. Aguilera A. The connection between transcription and genomic instability. EMBO J. 21 (2002) 195-201
137. Wai H., Johzuka K., Vu L., Eliason K., Kobayashi T., Horiuchi T., and Nomura M. Yeast RNA polymerase I enhancer is dispensable for transcription of the chromosomal rRNA gene and cell growth, and its apparent transcription enhancement from ectopic promoters requires Fob1 protein. Mol. Cell. Biol. 21 (2001) 5541-5553
138. Morey N.J., Greene C.N., and Jinks-Robertson S. Genetic analysis of transcription-associated mutation in Saccharomyces cerevisiae. Genetics 154 (2000) 109-120
139. Freedman J.A., and Jinks-Robertson S. Effects of mismatch repair and Hpr1 on transcription-stimulated mitotic recombination in the yeast Saccharomyces cerevisiae. DNA Rep. (Amst.) 3 (2004) 1437-1446
140. Freedman J.A., and Jinks-Robertson S. Genetic requirements for spontaneous and transcription-stimulated mitotic recombination in Saccharomyces cerevisiae. Genetics 162 (2002) 15-27
141. Prado F., and Aguilera A. Impairment of replication fork progression mediates RNApol II transcription-associated recombination. EMBO J. 24 (2005) 1267-1276
142. Chavez S., Beilharz T., Rondon A.G., Erdjument-Bromage H., Tempst P., Svejstrup J.Q., Lithgow T., and Aguilera A. A protein complex containing Tho2, Hpr1, Mft1 and a novel protein, Thp2, connects transcription elongation with mitotic recombination in Saccharomyces cerevisiae. EMBO J. 19 (2000) 5824-5834
143. Piruat J.I., and Aguilera A. A novel yeast gene, THO2, is involved in RNA pol II transcription and provides new evidence for transcriptional elongation-associated recombination. EMBO J. 17 (1998) 4859-4872
144. Strasser K., Masuda S., Mason P., Pfannstiel J., Oppizzi M., Rodriguez-Navarro S., Rondon A.G., Aguilera A., Struhl K., Reed R., and Hurt E. TREX is a conserved complex coupling transcription with messenger RNA export. Nature 417 (2002) 304-308
145. Luna R., Jimeno S., Marin M., Huertas P., Garcia-Rubio M., and Aguilera A. Interdependence between transcription and mRNP processing and export, and its impact on genetic stability. Mol. Cell 18 (2005) 711-722
146. Chavez S., and Aguilera A. The yeast HPR1 gene has a functional role in transcriptional elongation that uncovers a novel source of genome instability. Genes Dev. 11 (1997) 3459-3470
147. Wellinger R.E., Prado F., and Aguilera A. Replication fork progression is impaired by transcription in hyperrecombinant yeast cells lacking a functional THO complex. Mol. Cell. Biol. 26 (2006) 3327-3334
148. Courcelle J., and Hanawalt P.C. RecA-dependent recovery of arrested DNA replication forks. Annu. Rev. Genet. 37 (2003) 611-646
149. McGlynn P. Links between DNA replication and recombination in prokaryotes. Curr. Opin. Genet. Dev. 14 (2004) 107-112
150. Bernhardt T.G., and de Boer P.A. Screening for synthetic lethal mutants in Escherichia coli and identification of EnvC (YibP) as a periplasmic septal ring factor with murein hydrolase activity. Mol. Microbiol. 52 (2004) 1255-1269