-
1
-
-
84875229761
-
Early replication fragile sites: Where rep-lication-transcription collisions cause genetic instability
-
Mortusewicz O, Herr P, Helleday T (2013) Early replication fragile sites: Where rep-lication-transcription collisions cause genetic instability. EMBO J 32(4):493-495.
-
(2013)
EMBO J
, vol.32
, Issue.4
, pp. 493-495
-
-
Mortusewicz, O.1
Herr, P.2
Helleday, T.3
-
2
-
-
84862490443
-
Replication-transcription conflicts in bacteria
-
Merrikh H, Zhang Y, Grossman AD, Wang JD (2012) Replication-transcription conflicts in bacteria. Nat Rev Microbiol 10(7):449-458.
-
(2012)
Nat Rev Microbiol
, vol.10
, Issue.7
, pp. 449-458
-
-
Merrikh, H.1
Zhang, Y.2
Grossman, A.D.3
Wang, J.D.4
-
3
-
-
84876188716
-
Transcription-replication encounters, consequences and genomic instability
-
Helmrich A, Ballarino M, Nudler E, Tora L (2013) Transcription-replication encounters, consequences and genomic instability. Nat Struct Mol Biol 20(4):412-418.
-
(2013)
Nat Struct Mol Biol
, vol.20
, Issue.4
, pp. 412-418
-
-
Helmrich, A.1
Ballarino, M.2
Nudler, E.3
Tora, L.4
-
4
-
-
77953634888
-
Does interference between replication and transcription contribute to genomic instability in cancer cells?
-
Tuduri S, Crabbe L, Tourrière H, Coquelle A, Pasero P (2010) Does interference between replication and transcription contribute to genomic instability in cancer cells? Cell Cycle 9(10):1886-1892.
-
(2010)
Cell Cycle
, vol.9
, Issue.10
, pp. 1886-1892
-
-
Tuduri, S.1
Crabbe, L.2
Tourrière, H.3
Coquelle, A.4
Pasero, P.5
-
5
-
-
84860338675
-
R loops: From transcription byproducts to threats to genome stability
-
Aguilera A, García-Muse T (2012) R loops: From transcription byproducts to threats to genome stability. Mol Cell 46(2):115-124.
-
(2012)
Mol Cell
, vol.46
, Issue.2
, pp. 115-124
-
-
Aguilera, A.1
García-Muse, T.2
-
6
-
-
84857191660
-
Transcription as a source of genome instability
-
Kim N, Jinks-Robertson S (2012) Transcription as a source of genome instability. Nat Rev Genet 13(3):204-214.
-
(2012)
Nat Rev Genet
, vol.13
, Issue.3
, pp. 204-214
-
-
Kim, N.1
Jinks-Robertson, S.2
-
7
-
-
0026733965
-
Consequences of replication fork movement through transcription units in vivo
-
French S (1992) Consequences of replication fork movement through transcription units in vivo. Science 258(5086):1362-1365.
-
(1992)
Science
, vol.258
, Issue.5086
, pp. 1362-1365
-
-
French, S.1
-
8
-
-
79952126098
-
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(7335): 554-557.
-
(2011)
Nature
, vol.470
, Issue.7335
, pp. 554-557
-
-
Merrikh, H.1
Machón, C.2
Grainger, W.H.3
Grossman, A.D.4
Soultanas, P.5
-
9
-
-
84863023752
-
Interference between DNA replication and transcription as a cause of genomic instability
-
Lin YL, Pasero P (2012) Interference between DNA replication and transcription as a cause of genomic instability. Curr Genomics 13(1):65-73.
-
(2012)
Curr Genomics
, vol.13
, Issue.1
, pp. 65-73
-
-
Lin, Y.L.1
Pasero, P.2
-
10
-
-
34249941504
-
Avoiding and resolving conflicts between DNA replication and transcription
-
Rudolph CJ, Dhillon P, Moore T, Lloyd RG (2007) Avoiding and resolving conflicts between DNA replication and transcription. DNA Repair (Amst) 6(7):981-993.
-
(2007)
DNA Repair (Amst)
, vol.6
, Issue.7
, pp. 981-993
-
-
Rudolph, C.J.1
Dhillon, P.2
Moore, T.3
Lloyd, R.G.4
-
11
-
-
76749094639
-
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(1):e1000810.
-
(2010)
PLoS Genet
, vol.6
, Issue.1
, pp. e1000810
-
-
Srivatsan, A.1
Tehranchi, A.2
MacAlpine, D.M.3
Wang, J.D.4
-
12
-
-
84875609978
-
Accelerated gene evolution through replication-transcription conflicts
-
Paul S, Million-Weaver S, Chattopadhyay S, Sokurenko E, Merrikh H (2013) Accelerated gene evolution through replication-transcription conflicts. Nature 495(7442): 512-515.
-
(2013)
Nature
, vol.495
, Issue.7442
, pp. 512-515
-
-
Paul, S.1
Million-Weaver, S.2
Chattopadhyay, S.3
Sokurenko, E.4
Merrikh, H.5
-
13
-
-
14044272631
-
Localisation of human Y-family DNA polymerase kappa: Relationship to PCNA foci
-
Ogi T, Kannouche P, Lehmann AR (2005) Localisation of human Y-family DNA polymerase kappa: Relationship to PCNA foci. J Cell Sci 118(Pt 1):129-136.
-
(2005)
J Cell Sci
, vol.118
, Issue.1
, pp. 129-136
-
-
Ogi, T.1
Kannouche, P.2
Lehmann, A.R.3
-
14
-
-
84864003585
-
Escherichia coli DNA polymerase IV (Pol IV), but not Pol II, dynamically switches with a stalled Pol III replicase
-
Heltzel JM, Maul RW, Wolff DW, Sutton MD (2012) Escherichia coli DNA polymerase IV (Pol IV), but not Pol II, dynamically switches with a stalled Pol III replicase. J Bacteriol 194(14):3589-3600.
-
(2012)
J Bacteriol
, vol.194
, Issue.14
, pp. 3589-3600
-
-
Heltzel, J.M.1
Maul, R.W.2
Wolff, D.W.3
Sutton, M.D.4
-
15
-
-
0035862988
-
Domain structure, localization, and function of DNA polymerase eta, defective in xeroderma pigmentosum variant cells
-
Kannouche P, et al. (2001) Domain structure, localization, and function of DNA polymerase eta, defective in xeroderma pigmentosum variant cells. Genes Dev 15(2): 158-172.
-
(2001)
Genes Dev
, vol.15
, Issue.2
, pp. 158-172
-
-
Kannouche, P.1
-
16
-
-
84887143167
-
Translesion DNA synthesis and mutagenesis in prokaryotes
-
Fuchs RP, Fujii S (2013) Translesion DNA synthesis and mutagenesis in prokaryotes. Cold Spring Harb Perspect Biol 5(12):a012682.
-
(2013)
Cold Spring Harb Perspect Biol
, vol.5
, Issue.12
, pp. a012682
-
-
Fuchs, R.P.1
Fujii, S.2
-
17
-
-
84857411787
-
Y-family DNA polymerases and their role in tolerance of cellular DNA damage
-
Sale JE, Lehmann AR, Woodgate R (2012) Y-family DNA polymerases and their role in tolerance of cellular DNA damage. Nat Rev Mol Cell Biol 13(3):141-152.
-
(2012)
Nat Rev Mol Cell Biol
, vol.13
, Issue.3
, pp. 141-152
-
-
Sale, J.E.1
Lehmann, A.R.2
Woodgate, R.3
-
18
-
-
33745021288
-
Characterization of Escherichia coli translesion synthesis polymerases and their accessory factors
-
Beuning PJ, Simon SM, Godoy VG, Jarosz DF, Walker GC (2006) Characterization of Escherichia coli translesion synthesis polymerases and their accessory factors. Methods Enzymol 408:318-340.
-
(2006)
Methods Enzymol
, vol.408
, pp. 318-340
-
-
Beuning, P.J.1
Simon, S.M.2
Godoy, V.G.3
Jarosz, D.F.4
Walker, G.C.5
-
19
-
-
10044234196
-
Properties and functions of Escherichia coli: Pol IV and Pol V
-
Fuchs RP, Fujii S, Wagner J (2004) Properties and functions of Escherichia coli: Pol IV and Pol V. Adv Protein Chem 69:229-264.
-
(2004)
Adv Protein Chem
, vol.69
, pp. 229-264
-
-
Fuchs, R.P.1
Fujii, S.2
Wagner, J.3
-
20
-
-
33846695786
-
Y-family DNA polymerases in Escherichia coli
-
Jarosz DF, Beuning PJ, Cohen SE, Walker GC (2007) Y-family DNA polymerases in Escherichia coli. Trends Microbiol 15(2):70-77.
-
(2007)
Trends Microbiol
, vol.15
, Issue.2
, pp. 70-77
-
-
Jarosz, D.F.1
Beuning, P.J.2
Cohen, S.E.3
Walker, G.C.4
-
21
-
-
0037205001
-
Specialized DNA polymerases, cellular survival, and the genesis of mutations
-
Friedberg EC, Wagner R, Radman M (2002) Specialized DNA polymerases, cellular survival, and the genesis of mutations. Science 296(5573):1627-1630.
-
(2002)
Science
, vol.296
, Issue.5573
, pp. 1627-1630
-
-
Friedberg, E.C.1
Wagner, R.2
Radman, M.3
-
22
-
-
0035997344
-
Error-prone repair DNA polymerases in prokaryotes and eukaryotes
-
Goodman MF (2002) Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu Rev Biochem 71:17-50.
-
(2002)
Annu Rev Biochem
, vol.71
, pp. 17-50
-
-
Goodman, M.F.1
-
23
-
-
33744546833
-
Translesion synthesis DNA polymerases and control of genome stability
-
Shcherbakova PV, Fijalkowska IJ (2006) Translesion synthesis DNA polymerases and control of genome stability. Front Biosci 11:2496-2517.
-
(2006)
Front Biosci
, vol.11
, pp. 2496-2517
-
-
Shcherbakova, P.V.1
Fijalkowska, I.J.2
-
24
-
-
0037205402
-
Low fidelity DNA synthesis by a y family DNA polymerase due to misalignment in the active site
-
Kokoska RJ, Bebenek K, Boudsocq F, Woodgate R, Kunkel TA (2002) Low fidelity DNA synthesis by a y family DNA polymerase due to misalignment in the active site. J Biol Chem 277(22):19633-19638.
-
(2002)
J Biol Chem
, vol.277
, Issue.22
, pp. 19633-19638
-
-
Kokoska, R.J.1
Bebenek, K.2
Boudsocq, F.3
Woodgate, R.4
Kunkel, T.A.5
-
25
-
-
77949570579
-
Structural diversity of the Y-family DNA polymerases
-
Pata JD (2010) Structural diversity of the Y-family DNA polymerases. Biochim Biophys Acta 1804(5):1124-1135.
-
(2010)
Biochim Biophys Acta
, vol.1804
, Issue.5
, pp. 1124-1135
-
-
Pata, J.D.1
-
26
-
-
0037072865
-
Fidelity of Escherichia coli DNA polymerase IV. Preferential generation of small deletion mutations by dNTP-stabilized misalignment
-
Kobayashi S, Valentine MR, Pham P, O' Donnell M, Goodman MF (2002) Fidelity of Escherichia coli DNA polymerase IV. Preferential generation of small deletion mutations by dNTP-stabilized misalignment. J Biol Chem 277(37):34198-34207.
-
(2002)
J Biol Chem
, vol.277
, Issue.37
, pp. 34198-34207
-
-
Kobayashi, S.1
Valentine, M.R.2
Pham, P.3
O'Donnell, M.4
Goodman, M.F.5
-
28
-
-
35148899681
-
Stress-induced mutagenesis in bacteria
-
Foster PL (2007) Stress-induced mutagenesis in bacteria. Crit Rev Biochem Mol Biol 42(5):373-397.
-
(2007)
Crit Rev Biochem Mol Biol
, vol.42
, Issue.5
, pp. 373-397
-
-
Foster, P.L.1
-
29
-
-
0035404535
-
Evolving responsively: Adaptive mutation
-
Rosenberg SM (2001) Evolving responsively: Adaptive mutation. Nat Rev Genet 2(7): 504-515.
-
(2001)
Nat Rev Genet
, vol.2
, Issue.7
, pp. 504-515
-
-
Rosenberg, S.M.1
-
30
-
-
77957275003
-
Roles for the transcription elongation factor NusA in both DNA repair and damage tolerance pathways in Escherichia coli
-
Cohen SE, et al. (2010) Roles for the transcription elongation factor NusA in both DNA repair and damage tolerance pathways in Escherichia coli. Proc Natl Acad Sci USA 107(35):15517-15522.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, Issue.35
, pp. 15517-15522
-
-
Cohen, S.E.1
-
31
-
-
84868159034
-
Two mechanisms produce mutation hotspots at DNA breaks in Escherichia coli
-
Shee C, Gibson JL, Rosenberg SM (2012) Two mechanisms produce mutation hotspots at DNA breaks in Escherichia coli. Cell Rep 2(4):714-721.
-
(2012)
Cell Rep
, vol.2
, Issue.4
, pp. 714-721
-
-
Shee, C.1
Gibson, J.L.2
Rosenberg, S.M.3
-
32
-
-
2942674474
-
Adaptive mutation and amplification in Escherichia coli: Two pathways of genome adaptation under stress
-
Hersh MN, Ponder RG, Hastings PJ, Rosenberg SM (2004) Adaptive mutation and amplification in Escherichia coli: Two pathways of genome adaptation under stress. Res Microbiol 155(5):352-359.
-
(2004)
Res Microbiol
, vol.155
, Issue.5
, pp. 352-359
-
-
Hersh, M.N.1
Ponder, R.G.2
Hastings, P.J.3
Rosenberg, S.M.4
-
33
-
-
84878568164
-
Competitive fitness during feast and famine: How SOS DNA polymerases influence physiology and evolution in Escherichia coli
-
Corzett CH, Goodman MF, Finkel SE (2013) Competitive fitness during feast and famine: How SOS DNA polymerases influence physiology and evolution in Escherichia coli. Genetics 194(2):409-420.
-
(2013)
Genetics
, vol.194
, Issue.2
, pp. 409-420
-
-
Corzett, C.H.1
Goodman, M.F.2
Finkel, S.E.3
-
34
-
-
6344273134
-
Distinctive genetic features exhibited by the Y-family DNA polymerases in Bacillus subtilis
-
Duigou S, Ehrlich SD, Noirot P, Noirot-Gros MF (2004) Distinctive genetic features exhibited by the Y-family DNA polymerases in Bacillus subtilis. Mol Microbiol 54(2): 439-451.
-
(2004)
Mol Microbiol
, vol.54
, Issue.2
, pp. 439-451
-
-
Duigou, S.1
Ehrlich, S.D.2
Noirot, P.3
Noirot-Gros, M.F.4
-
35
-
-
0037377855
-
Roles of YqjH and YqjW, homologs of the Escherichia coli UmuC/DinB or Y superfamily of DNA polymerases, in stationary-phase mutagenesis and UV-inducedmutagenesis of Bacillus subtilis
-
Sung HM, Yeamans G, Ross CA, Yasbin RE (2003) Roles of YqjH and YqjW, homologs of the Escherichia coli UmuC/DinB or Y superfamily of DNA polymerases, in stationary-phase mutagenesis and UV-inducedmutagenesis of Bacillus subtilis. J Bacteriol 185(7):2153-2160.
-
(2003)
J Bacteriol
, vol.185
, Issue.7
, pp. 2153-2160
-
-
Sung, H.M.1
Yeamans, G.2
Ross, C.A.3
Yasbin, R.E.4
-
36
-
-
84892528066
-
Role of the Y-family DNA polymerases YqjH and YqjW in protecting sporulating Bacillus subtilis cells from DNA damage
-
Rivas-Castillo AM, Yasbin RE, Robleto E, Nicholson WL, Pedraza-Reyes M (2010) Role of the Y-family DNA polymerases YqjH and YqjW in protecting sporulating Bacillus subtilis cells from DNA damage. Curr Microbiol 60(4):263-267.
-
(2010)
Curr Microbiol
, vol.60
, Issue.4
, pp. 263-267
-
-
Rivas-Castillo, A.M.1
Yasbin, R.E.2
Robleto, E.3
Nicholson, W.L.4
Pedraza-Reyes, M.5
-
37
-
-
22644446002
-
DNA polymerase I acts in translesion synthesis mediated by the Y-polymerases in Bacillus subtilis
-
Duigou S, Ehrlich SD, Noirot P, Noirot-Gros MF (2005) DNA polymerase I acts in translesion synthesis mediated by the Y-polymerases in Bacillus subtilis. Mol Microbiol 57(3):678-690.
-
(2005)
Mol Microbiol
, vol.57
, Issue.3
, pp. 678-690
-
-
Duigou, S.1
Ehrlich, S.D.2
Noirot, P.3
Noirot-Gros, M.F.4
-
38
-
-
2342419732
-
DNA replication fidelity
-
Kunkel TA (2004) DNA replication fidelity. J Biol Chem 279(17):16895-16898.
-
(2004)
J Biol Chem
, vol.279
, Issue.17
, pp. 16895-16898
-
-
Kunkel, T.A.1
-
39
-
-
84864326787
-
DNA damage by reactive species: Mechanisms, mutation and repair
-
Jena NR (2012) DNA damage by reactive species: Mechanisms, mutation and repair. J Biosci 37(3):503-517.
-
(2012)
J Biosci
, vol.37
, Issue.3
, pp. 503-517
-
-
Jena, N.R.1
-
40
-
-
0021320685
-
Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli
-
Walker GC (1984) Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli. Microbiol Rev 48(1):60-93.
-
(1984)
Microbiol Rev
, vol.48
, Issue.1
, pp. 60-93
-
-
Walker, G.C.1
-
41
-
-
0037202616
-
Replication of damaged DNA in mammalian cells: New solutions to an old problem
-
Lehmann AR (2002) Replication of damaged DNA in mammalian cells: New solutions to an old problem. Mutat Res 509(1-2):23-34.
-
(2002)
Mutat Res
, vol.509
, Issue.1-2
, pp. 23-34
-
-
Lehmann, A.R.1
-
42
-
-
78650147137
-
Regulation of horizontal gene transfer in Bacillus subtilis by activation of a conserved site-specific protease
-
Bose B, Grossman AD (2011) Regulation of horizontal gene transfer in Bacillus subtilis by activation of a conserved site-specific protease. J Bacteriol 193(1):22-29.
-
(2011)
J Bacteriol
, vol.193
, Issue.1
, pp. 22-29
-
-
Bose, B.1
Grossman, A.D.2
-
43
-
-
0014010834
-
Inhibition of the synthesis of deoxyribonucleic acid in bacteria by 6-(p-hydroxyphenylazo)-2,4-dihydroxypyrimidine. I. Metabolic studies in Streptococcus fecalis
-
Brown NC, Handschumacher RE (1966) Inhibition of the synthesis of deoxyribonucleic acid in bacteria by 6-(p-hydroxyphenylazo)-2,4-dihydroxypyrimidine. I. Metabolic studies in Streptococcus fecalis. J Biol Chem 241(13):3083-3089.
-
(1966)
J Biol Chem
, vol.241
, Issue.13
, pp. 3083-3089
-
-
Brown, N.C.1
Handschumacher, R.E.2
-
44
-
-
33846586523
-
Replication is required for the RecA localization response to DNA damage in Bacillus subtilis
-
Simmons LA, Grossman AD, Walker GC (2007) Replication is required for the RecA localization response to DNA damage in Bacillus subtilis. Proc Natl Acad Sci USA 104(4):1360-1365.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, Issue.4
, pp. 1360-1365
-
-
Simmons, L.A.1
Grossman, A.D.2
Walker, G.C.3
-
45
-
-
23744466646
-
Localization of RecA in Escherichia coli K-12 using RecA-GFP
-
Renzette N, et al. (2005) Localization of RecA in Escherichia coli K-12 using RecA-GFP. Mol Microbiol 57(4):1074-1085.
-
(2005)
Mol Microbiol
, vol.57
, Issue.4
, pp. 1074-1085
-
-
Renzette, N.1
-
46
-
-
34247644455
-
Analysis of temporal gene expression during Bacillus subtilis spore germination and outgrowth
-
Keijser BJ, et al. (2007) Analysis of temporal gene expression during Bacillus subtilis spore germination and outgrowth. J Bacteriol 189(9):3624-3634.
-
(2007)
J Bacteriol
, vol.189
, Issue.9
, pp. 3624-3634
-
-
Keijser, B.J.1
-
47
-
-
33750946025
-
Replication arrest-stimulated recombination: Dependence on the RecA paralog, RadA/Sms and translesion polymerase
-
Lovett ST (2006) Replication arrest-stimulated recombination: Dependence on the RecA paralog, RadA/Sms and translesion polymerase, DinB. DNA Repair (Amst) 5(12): 1421-1427.
-
(2006)
DinB. DNA Repair (Amst)
, vol.5
, Issue.12
, pp. 1421-1427
-
-
Lovett, S.T.1
-
48
-
-
84878932551
-
Preferential D-loop extension by a translesion DNA polymerase underlies error-prone recombination
-
Pomerantz RT, Kurth I, Goodman MF, O'Donnell ME (2013) Preferential D-loop extension by a translesion DNA polymerase underlies error-prone recombination. Nat Struct Mol Biol 20(6):748-755.
-
(2013)
Nat Struct Mol Biol
, vol.20
, Issue.6
, pp. 748-755
-
-
Pomerantz, R.T.1
Kurth, I.2
Goodman, M.F.3
O'Donnell, M.E.4
-
49
-
-
84865717172
-
DNA repair and genome maintenance in Bacillus subtilis
-
Lenhart JS, Schroeder JW, Walsh BW, Simmons LA (2012) DNA repair and genome maintenance in Bacillus subtilis. Microbiol Mol Biol Rev 76(3):530-564.
-
(2012)
Microbiol Mol Biol Rev
, vol.76
, Issue.3
, pp. 530-564
-
-
Lenhart, J.S.1
Schroeder, J.W.2
Walsh, B.W.3
Simmons, L.A.4
-
50
-
-
84871340015
-
Bacterial DNA repair: Recent insights into the mechanism of RecBCD, AddAB and AdnAB
-
Wigley DB (2013) Bacterial DNA repair: Recent insights into the mechanism of RecBCD, AddAB and AdnAB. Nat Rev Microbiol 11(1):9-13.
-
(2013)
Nat Rev Microbiol
, vol.11
, Issue.1
, pp. 9-13
-
-
Wigley, D.B.1
-
51
-
-
0028792495
-
SOS-regulated proteins in translesion DNA synthesis and mutagenesis
-
Walker GC (1995) SOS-regulated proteins in translesion DNA synthesis and mutagenesis. Trends Biochem Sci 20(10):416-420.
-
(1995)
Trends Biochem Sci
, vol.20
, Issue.10
, pp. 416-420
-
-
Walker, G.C.1
-
53
-
-
79952271901
-
New discoveries linking transcription to DNA repair and damage tolerance pathways
-
Cohen SE, Walker GC (2011) New discoveries linking transcription to DNA repair and damage tolerance pathways. Transcription 2(1):37-40.
-
(2011)
Transcription
, vol.2
, Issue.1
, pp. 37-40
-
-
Cohen, S.E.1
Walker, G.C.2
-
54
-
-
34547789312
-
Transcriptionassociated mutagenesis in yeast is directly proportional to the level of gene expression and influenced by the direction of DNA replication
-
Kim N, Abdulovic AL, Gealy R, Lippert MJ, Jinks-Robertson S (2007) Transcriptionassociated mutagenesis in yeast is directly proportional to the level of gene expression and influenced by the direction of DNA replication. DNA Repair (Amst) 6(9): 1285-1296.
-
(2007)
DNA Repair (Amst)
, vol.6
, Issue.9
, pp. 1285-1296
-
-
Kim, N.1
Abdulovic, A.L.2
Gealy, R.3
Lippert, M.J.4
Jinks-Robertson, S.5
-
56
-
-
56749157389
-
Transcription-coupled DNA repair: Two decades of progress and surprises
-
Hanawalt PC, Spivak G (2008) Transcription-coupled DNA repair: Two decades of progress and surprises. Nat Rev Mol Cell Biol 9(12):958-970.
-
(2008)
Nat Rev Mol Cell Biol
, vol.9
, Issue.12
, pp. 958-970
-
-
Hanawalt, P.C.1
Spivak, G.2
-
57
-
-
84892610198
-
UvrD facilitates DNA repair by pulling RNA polymerase backwards
-
Epshtein V, et al. (2014) UvrD facilitates DNA repair by pulling RNA polymerase backwards. Nature 505(7483):372-377.
-
(2014)
Nature
, vol.505
, Issue.7483
, pp. 372-377
-
-
Epshtein, V.1
-
58
-
-
0033880695
-
Escherichia coli DNA polymerase IV mutator activity: Genetic requirements and mutational specificity
-
Wagner J, Nohmi T (2000) Escherichia coli DNA polymerase IV mutator activity: Genetic requirements and mutational specificity. J Bacteriol 182(16):4587-4595.
-
(2000)
J Bacteriol
, vol.182
, Issue.16
, pp. 4587-4595
-
-
Wagner, J.1
Nohmi, T.2
-
59
-
-
1642267937
-
Polymerases leave fingerprints: Analysis of the mutational spectrum in Escherichia coli rpoB to assess the role of polymerase IV in spontaneous mutation
-
Wolff E, Kim M, Hu K, Yang H, Miller JH (2004) Polymerases leave fingerprints: Analysis of the mutational spectrum in Escherichia coli rpoB to assess the role of polymerase IV in spontaneous mutation. J Bacteriol 186(9):2900-2905.
-
(2004)
J Bacteriol
, vol.186
, Issue.9
, pp. 2900-2905
-
-
Wolff, E.1
Kim, M.2
Hu, K.3
Yang, H.4
Miller, J.H.5
-
60
-
-
84895808218
-
Nucleotide selection by the Y-family DNA polymerase Dpo4 involves template translocation and misalignment
-
Brenlla A, Markiewicz RP, Rueda D, Romano LJ (2014) Nucleotide selection by the Y-family DNA polymerase Dpo4 involves template translocation and misalignment. Nucleic Acids Res 42(4):2555-2563.
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.4
, pp. 2555-2563
-
-
Brenlla, A.1
Markiewicz, R.P.2
Rueda, D.3
Romano, L.J.4
-
61
-
-
0037008746
-
The mutational specificity of the Dbh lesion bypass polymerase and its implications
-
Potapova O, Grindley ND, Joyce CM (2002) The mutational specificity of the Dbh lesion bypass polymerase and its implications. J Biol Chem 277(31):28157-28166.
-
(2002)
J Biol Chem
, vol.277
, Issue.31
, pp. 28157-28166
-
-
Potapova, O.1
Grindley, N.D.2
Joyce, C.M.3
-
62
-
-
0034671730
-
Fidelity and processivity of DNA synthesis by DNA polymerase kappa, the product of the human DINB1 gene
-
Ohashi E, et al. (2000) Fidelity and processivity of DNA synthesis by DNA polymerase kappa, the product of the human DINB1 gene. J Biol Chem 275(50):39678-39684.
-
(2000)
J Biol Chem
, vol.275
, Issue.50
, pp. 39678-39684
-
-
Ohashi, E.1
-
63
-
-
84877247843
-
Human polymerase kappa uses a templateslippage deletion mechanism, but can realign the slipped strands to favour base substitution mutations over deletions
-
Mukherjee P, Lahiri I, Pata JD (2013) Human polymerase kappa uses a templateslippage deletion mechanism, but can realign the slipped strands to favour base substitution mutations over deletions. Nucleic Acids Res 41(9):5024-5035.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.9
, pp. 5024-5035
-
-
Mukherjee, P.1
Lahiri, I.2
Pata, J.D.3
-
64
-
-
0034214838
-
Poliota, a remarkably errorprone human DNA polymerase
-
Tissier A, McDonald JP, Frank EG, Woodgate R (2000) poliota, a remarkably errorprone human DNA polymerase. Genes Dev 14(13):1642-1650.
-
(2000)
Genes Dev
, vol.14
, Issue.13
, pp. 1642-1650
-
-
Tissier, A.1
McDonald, J.P.2
Frank, E.G.3
Woodgate, R.4
-
65
-
-
0034327552
-
Human DNA polymerase kappa synthesizes DNA with extraordinarily low fidelity
-
Zhang Y, et al. (2000) Human DNA polymerase kappa synthesizes DNA with extraordinarily low fidelity. Nucleic Acids Res 28(21):4147-4156.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.21
, pp. 4147-4156
-
-
Zhang, Y.1
-
66
-
-
84255198334
-
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(6):966-977.
-
(2011)
Mol Cell
, vol.44
, Issue.6
, pp. 966-977
-
-
Helmrich, A.1
Ballarino, M.2
Tora, L.3
-
67
-
-
84867339877
-
Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing
-
Lee H, Popodi E, Tang H, Foster PL (2012) Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. Proc Natl Acad Sci USA 109(41):E2774-E2783.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.41
, pp. E2774-E2783
-
-
Lee, H.1
Popodi, E.2
Tang, H.3
Foster, P.L.4
-
68
-
-
84884686924
-
Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage
-
Kennedy SR, Salk JJ, Schmitt MW, Loeb LA (2013) Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage. PLoS Genet 9(9):e1003794.
-
(2013)
PLoS Genet
, vol.9
, Issue.9
, pp. e1003794
-
-
Kennedy, S.R.1
Salk, J.J.2
Schmitt, M.W.3
Loeb, L.A.4
-
69
-
-
78049445172
-
Evidence that mutation is universally biased towards AT in bacteria
-
Hershberg R, Petrov DA (2010) Evidence that mutation is universally biased towards AT in bacteria. PLoS Genet 6(9):e1001115.
-
(2010)
PLoS Genet
, vol.6
, Issue.9
, pp. e1001115
-
-
Hershberg, R.1
Petrov, D.A.2
-
70
-
-
84865973296
-
A selective force favoring increased G+C content in bacterial genes
-
Raghavan R, Kelkar YD, Ochman H (2012) A selective force favoring increased G+C content in bacterial genes. Proc Natl Acad Sci USA 109(36):14504-14507.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.36
, pp. 14504-14507
-
-
Raghavan, R.1
Kelkar, Y.D.2
Ochman, H.3
-
71
-
-
75649142564
-
The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo
-
Boubakri H, de Septenville AL, Viguera E, Michel B (2010) The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo. EMBO J 29(1):145-157.
-
(2010)
EMBO J
, vol.29
, Issue.1
, pp. 145-157
-
-
Boubakri, H.1
De Septenville, A.L.2
Viguera, E.3
Michel, B.4
-
72
-
-
22544464455
-
RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription
-
Trautinger BW, Jaktaji RP, Rusakova E, Lloyd RG (2005) RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription. Mol Cell 19(2):247-258.
-
(2005)
Mol Cell
, vol.19
, Issue.2
, pp. 247-258
-
-
Trautinger, B.W.1
Jaktaji, R.P.2
Rusakova, E.3
Lloyd, R.G.4
-
73
-
-
77952527102
-
The transcription factor DksA prevents conflicts between DNA replication and transcription machinery
-
Tehranchi AK, et al. (2010) The transcription factor DksA prevents conflicts between DNA replication and transcription machinery. Cell 141(4):595-605.
-
(2010)
Cell
, vol.141
, Issue.4
, pp. 595-605
-
-
Tehranchi, A.K.1
-
74
-
-
80052008241
-
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(4):533-543.
-
(2011)
Cell
, vol.146
, Issue.4
, pp. 533-543
-
-
Dutta, D.1
Shatalin, K.2
Epshtein, V.3
Gottesman, M.E.4
Nudler, E.5
-
75
-
-
17144426028
-
Impairment of replication fork progression mediates RNA polII transcription-associated recombination
-
Prado F, Aguilera A (2005) Impairment of replication fork progression mediates RNA polII transcription-associated recombination. EMBO J 24(6):1267-1276.
-
(2005)
EMBO J
, vol.24
, Issue.6
, pp. 1267-1276
-
-
Prado, F.1
Aguilera, A.2
-
76
-
-
63549139991
-
Stimulation of direct-repeat recombination by RNA polymerase III transcription
-
de la Loza MC, Wellinger RE, Aguilera A (2009) Stimulation of direct-repeat recombination by RNA polymerase III transcription. DNA Repair (Amst) 8(5):620-626.
-
(2009)
DNA Repair (Amst)
, vol.8
, Issue.5
, pp. 620-626
-
-
De La Loza, M.C.1
Wellinger, R.E.2
Aguilera, A.3
-
77
-
-
0038046165
-
Transcription-dependent recombination and the role of fork collision in yeast rDNA
-
Takeuchi Y, Horiuchi T, Kobayashi T (2003) Transcription-dependent recombination and the role of fork collision in yeast rDNA. Genes Dev 17(12):1497-1506.
-
(2003)
Genes Dev
, vol.17
, Issue.12
, pp. 1497-1506
-
-
Takeuchi, Y.1
Horiuchi, T.2
Kobayashi, T.3
-
78
-
-
0024277974
-
Mitotic recombination in the rDNA of S. Cerevisiae is suppressed by the combined action of DNA topoisomerases I and II
-
Christman MF, Dietrich FS, Fink GR (1988) Mitotic recombination in the rDNA of S. cerevisiae is suppressed by the combined action of DNA topoisomerases I and II. Cell 55(3):413-425.
-
(1988)
Cell
, vol.55
, Issue.3
, pp. 413-425
-
-
Christman, M.F.1
Dietrich, F.S.2
Fink, G.R.3
-
79
-
-
0025225502
-
Induction of RNA-stabilized DNA conformers by transcription of an immunoglobulin switch region
-
Reaban ME, Griffin JA (1990) Induction of RNA-stabilized DNA conformers by transcription of an immunoglobulin switch region. Nature 348(6299):342-344.
-
(1990)
Nature
, vol.348
, Issue.6299
, pp. 342-344
-
-
Reaban, M.E.1
Griffin, J.A.2
-
80
-
-
67649559461
-
DUTP incorporation into genomic DNA is linked to transcription in yeast
-
Kim N, Jinks-Robertson S (2009) dUTP incorporation into genomic DNA is linked to transcription in yeast. Nature 459(7250):1150-1153.
-
(2009)
Nature
, vol.459
, Issue.7250
, pp. 1150-1153
-
-
Kim, N.1
Jinks-Robertson, S.2
-
81
-
-
84887589423
-
Transcription-associated genome instability
-
Gaillard H, Herrera-Moyano E, Aguilera A (2013) Transcription-associated genome instability. Chem Rev 113(11):8638-8661.
-
(2013)
Chem Rev
, vol.113
, Issue.11
, pp. 8638-8661
-
-
Gaillard, H.1
Herrera-Moyano, E.2
Aguilera, A.3
-
82
-
-
84872422245
-
Transcription coupled repair at the interface between transcription elongation and mRNP biogenesis
-
Gaillard H, Aguilera A (2013) Transcription coupled repair at the interface between transcription elongation and mRNP biogenesis. Biochim Biophys Acta 1829(1): 141-150.
-
(2013)
Biochim Biophys Acta
, vol.1829
, Issue.1
, pp. 141-150
-
-
Gaillard, H.1
Aguilera, A.2
-
83
-
-
84860845976
-
Mfd and transcriptional derepression cause genetic diversity in Bacillus subtilis
-
Robleto EA, Martin HA, Pedraza-Reyes M (2012) Mfd and transcriptional derepression cause genetic diversity in Bacillus subtilis. Front Biosci (Elite Ed) 4:1246-1254.
-
(2012)
Front Biosci(Elite Ed)
, vol.4
, pp. 1246-1254
-
-
Robleto, E.A.1
Martin, H.A.2
Pedraza-Reyes, M.3
-
84
-
-
0016703286
-
Turnover in bacterial DNA containing thymine or 5-bromouracil
-
Grivell AR, Grivell MB, Hanawalt PC (1975) Turnover in bacterial DNA containing thymine or 5-bromouracil. J Mol Biol 98(1):219-233.
-
(1975)
J Mol Biol
, vol.98
, Issue.1
, pp. 219-233
-
-
Grivell, A.R.1
Grivell, M.B.2
Hanawalt, P.C.3
-
85
-
-
0034713911
-
The role of nucleotide excision repair of Escherichia coli in repair of spontaneous and gamma-radiation-induced DNA damage in the lacZalpha gene
-
Kuipers GK, et al. (2000) The role of nucleotide excision repair of Escherichia coli in repair of spontaneous and gamma-radiation-induced DNA damage in the lacZalpha gene. Mutat Res 460(2):117-125.
-
(2000)
Mutat Res
, vol.460
, Issue.2
, pp. 117-125
-
-
Kuipers, G.K.1
-
86
-
-
84888247843
-
Removal of misincorporated ribonucleotides from prokaryotic genomes: An unexpected role for nucleotide excision repair
-
Vaisman A, et al. (2013) Removal of misincorporated ribonucleotides from prokaryotic genomes: An unexpected role for nucleotide excision repair. PLoS Genet 9(11):e1003878.
-
(2013)
PLoS Genet
, vol.9
, Issue.11
, pp. e1003878
-
-
Vaisman, A.1
-
87
-
-
84888130075
-
Removal of N-6-methyladenine by the nucleotide excision repair pathway triggers the repair of mismatches in yeast gap-repair intermediates
-
Guo X, Jinks-Robertson S (2013) Removal of N-6-methyladenine by the nucleotide excision repair pathway triggers the repair of mismatches in yeast gap-repair intermediates. DNA Repair (Amst) 12(12):1053-1061.
-
(2013)
DNA Repair (Amst)
, vol.12
, Issue.12
, pp. 1053-1061
-
-
Guo, X.1
Jinks-Robertson, S.2
-
88
-
-
0022798707
-
Excision repair functions in Saccharomyces cerevisiae recognize and repair methylation of adenine by the Escherichia coli dam gene
-
Hoekstra MF, Malone RE (1986) Excision repair functions in Saccharomyces cerevisiae recognize and repair methylation of adenine by the Escherichia coli dam gene. Mol Cell Biol 6(10):3555-3558.
-
(1986)
Mol Cell Biol
, vol.6
, Issue.10
, pp. 3555-3558
-
-
Hoekstra, M.F.1
Malone, R.E.2
-
89
-
-
77953377798
-
Abasic sites in the transcribed strand of yeast DNA are removed by transcription-coupled nucleotide excision repair
-
Kim N, Jinks-Robertson S (2010) Abasic sites in the transcribed strand of yeast DNA are removed by transcription-coupled nucleotide excision repair. Mol Cell Biol 30(13):3206-3215.
-
(2010)
Mol Cell Biol
, vol.30
, Issue.13
, pp. 3206-3215
-
-
Kim, N.1
Jinks-Robertson, S.2
-
90
-
-
84878537085
-
Oxidative DNA damage and nucleotide excision repair
-
Melis JP, van Steeg H, Luijten M (2013) Oxidative DNA damage and nucleotide excision repair. Antioxid Redox Signal 18(18):2409-2419.
-
(2013)
Antioxid Redox Signal
, vol.18
, Issue.18
, pp. 2409-2419
-
-
Melis, J.P.1
Van Steeg, H.2
Luijten, M.3
-
91
-
-
0024468299
-
A new mechanism for repairing oxidative damage to DNA: (A)BC excinuclease removes AP sites and thymine glycols from DNA
-
Lin JJ, Sancar A (1989) A new mechanism for repairing oxidative damage to DNA: (A)BC excinuclease removes AP sites and thymine glycols from DNA. Biochemistry 28(20):7979-7984.
-
(1989)
Biochemistry
, vol.28
, Issue.20
, pp. 7979-7984
-
-
Lin, J.J.1
Sancar, A.2
-
92
-
-
0025017257
-
UvrABC nuclease complex repairs thymine glycol, an oxidative DNA base damage
-
Kow YW, Wallace SS, Van Houten B (1990) UvrABC nuclease complex repairs thymine glycol, an oxidative DNA base damage. Mutat Res 235(2):147-156.
-
(1990)
Mutat Res
, vol.235
, Issue.2
, pp. 147-156
-
-
Kow, Y.W.1
Wallace, S.S.2
Van Houten, B.3
-
93
-
-
0021348870
-
Repair of damage in double-stranded phi X174 (RF) DNA due to radiation-induced water radicals
-
Nabben FJ, et al. (1984) Repair of damage in double-stranded phi X174 (RF) DNA due to radiation-induced water radicals. Int J Radiat Biol Relat Stud Phys Chem Med 45(4):379-388.
-
(1984)
Int J Radiat Biol Relat Stud Phys Chem Med
, vol.45
, Issue.4
, pp. 379-388
-
-
Nabben, F.J.1
-
94
-
-
0035816649
-
DNA repair excision nuclease attacks undamaged DNA. A potential source of spontaneous mutations
-
Branum ME, Reardon JT, Sancar A (2001) DNA repair excision nuclease attacks undamaged DNA. A potential source of spontaneous mutations. J Biol Chem 276(27): 25421-25426.
-
(2001)
J Biol Chem
, vol.276
, Issue.27
, pp. 25421-25426
-
-
Branum, M.E.1
Reardon, J.T.2
Sancar, A.3
-
95
-
-
0023728921
-
Repair of DNA-containing pyrimidine dimers
-
Grossman L, Caron PR, Mazur SJ, Oh EY (1988) Repair of DNA-containing pyrimidine dimers. FASEB J 2(11):2696-2701.
-
(1988)
FASEB J
, vol.2
, Issue.11
, pp. 2696-2701
-
-
Grossman, L.1
Caron, P.R.2
Mazur, S.J.3
Oh, E.Y.4
-
96
-
-
0035265678
-
SOS mutator DNA polymerase IV functions in adaptive mutation and not adaptive amplification
-
McKenzie GJ, Lee PL, Lombardo MJ, Hastings PJ, Rosenberg SM (2001) SOS mutator DNA polymerase IV functions in adaptive mutation and not adaptive amplification. Mol Cell 7(3):571-579.
-
(2001)
Mol Cell
, vol.7
, Issue.3
, pp. 571-579
-
-
McKenzie, G.J.1
Lee, P.L.2
Lombardo, M.J.3
Hastings, P.J.4
Rosenberg, S.M.5
-
97
-
-
84881342072
-
R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli
-
Wimberly H, et al. (2013) R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli. Nat Commun 4:2115.
-
(2013)
Nat Commun
, vol.4
, pp. 2115
-
-
Wimberly, H.1
-
98
-
-
0029931416
-
Estimate of the genomic mutation rate deleterious to overall fitness in E. Coli
-
Kibota TT, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli. Nature 381(6584):694-696.
-
(1996)
Nature
, vol.381
, Issue.6584
, pp. 694-696
-
-
Kibota, T.T.1
Lynch, M.2
-
101
-
-
33745211644
-
Methods for determining spontaneous mutation rates
-
Foster PL (2006) Methods for determining spontaneous mutation rates. Methods Enzymol 409:195-213.
-
(2006)
Methods Enzymol
, vol.409
, pp. 195-213
-
-
Foster, P.L.1
-
102
-
-
80051918561
-
PGAT: A multistrain analysis resource for microbial genomes
-
Brittnacher MJ, et al. (2011) PGAT: A multistrain analysis resource for microbial genomes. Bioinformatics 27(17):2429-2430.
-
(2011)
Bioinformatics
, vol.27
, Issue.17
, pp. 2429-2430
-
-
Brittnacher, M.J.1
-
103
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.5
, pp. 1792-1797
-
-
Edgar, R.C.1
|