1. O'DonnellM, LangstonL, StillmanB (2013) Principles and concepts of DNA replication in bacteria, archaea, and eukarya. Cold Spring Harb Perspect Biol 5: a010108.
2. GaoF, LuoH, ZhangCT (2013) DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes. Nucleic Acids Res 41: D90–93.
3. Kornberg A, Baker TA (2005) DNA Replication, 2nd Edition: University Science Books.
4. MottML, BergerJM (2007) DNA replication initiation: mechanisms and regulation in bacteria. Nat Rev Microbiol 5: 343–354.
5. Reyes-LamotheR, NicolasE, SherrattDJ (2012) Chromosome replication and segregation in bacteria. Annu Rev Genet 46: 121–143.
6. SkarstadK, KatayamaT (2013) Regulating DNA replication in bacteria. Cold Spring Harb Perspect Biol 5: a012922.
7. KuzminovA (1999) Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol Mol Biol Rev 63: 751–813.
8. CoxMM, GoodmanMF, KreuzerKN, SherrattDJ, SandlerSJ, et al. (2000) The importance of repairing stalled replication forks. Nature 404: 37–41.
9. HellerRC, MariansKJ (2006) Replisome assembly and the direct restart of stalled replication forks. Nat Rev Mol Cell Biol 7: 932–943.
10. YeelesJT, PoliJ, MariansKJ, PaseroP (2013) Rescuing stalled or damaged replication forks. Cold Spring Harb Perspect Biol 5: a012815.
11. MirkinEV, MirkinSM (2005) Mechanisms of transcription-replication collisions in bacteria. Mol Cell Biol 25: 888–895.
12. MirkinEV, MirkinSM (2007) Replication fork stalling at natural impediments. Microbiol Mol Biol Rev 71: 13–35.
13. RudolphCJ, DhillonP, MooreT, LloydRG (2007) Avoiding and resolving conflicts between DNA replication and transcription. DNA Repair 6: 981–993.
14. McGlynnP, SaveryNJ, DillinghamMS (2012) The conflict between DNA replication and transcription. Mol Microbiol 85: 12–20.
15. MerrikhH, ZhangY, GrossmanAD, WangJD (2012) Replication-transcription conflicts in bacteria. Nat Rev Microbiol 10: 449–458.
16. HelmrichA, BallarinoM, NudlerE, ToraL (2013) Transcription-replication encounters, consequences and genomic instability. Nat Struct Mol Biol 20: 412–418.
17. FrenchS (1992) Consequences of replication fork movement through transcription units in vivo. Science 258: 1362–1365.
18. BoubakriH, de SeptenvilleAL, VigueraE, MichelB (2010) The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo. EMBO J 29: 145–157.
19. De SeptenvilleAL, DuigouS, BoubakriH, MichelB (2012) Replication fork reversal after replication-transcription collision. PLoS Genet 8: e1002622.
20. BidnenkoV, LestiniR, MichelB (2006) The Escherichia coli UvrD helicase is essential for Tus removal during recombination-dependent replication restart from Ter sites. Mol Microbiol 62: 382–396.
21. BidnenkoV, EhrlichSD, MichelB (2002) Replication fork collapse at replication terminator sequences. EMBO J 21: 3898–3907.
22. SimmonsLA, BreierAM, CozzarelliNR, KaguniJM (2004) Hyperinitiation of DNA replication in Escherichia coli leads to replication fork collapse and inviability. Mol Microbiol 51: 349–358.
23. NeylonC, KralicekAV, HillTM, DixonNE (2005) Replication termination in Escherichia coli: structure and antihelicase activity of the Tus-Ter complex. Microbiol Mol Biol Rev 69: 501–526.
24. DugginIG, WakeRG, BellSD, HillTM (2008) The replication fork trap and termination of chromosome replication. Mol Microbiol 70: 1323–1333.
25. KaplanDL, BastiaD (2009) Mechanisms of polar arrest of a replication fork. Mol Microbiol 72: 279–285.
26. HillTM, HensonJM, KuempelPL (1987) The terminus region of the Escherichia coli chromosome contains two separate loci that exhibit polar inhibition of replication. Proc Natl Acad Sci U S A 84: 1754–1758.
27. de MassyB, BejarS, LouarnJ, LouarnJM, BoucheJP (1987) 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: 1759–1763.
28. EsnaultE, ValensM, EspeliO, BoccardF (2007) Chromosome structuring limits genome plasticity in Escherichia coli. PLoS Genet 3: e226.
29. YoshikawaH, SueokaN (1963) Sequential replication of Bacillus subtilis chromosome. I. Comparison of marker frequencies in exponential and stationary growth phases. Proc Natl Acad Sci U S A 49: 559–566.
30. SueokaN, YoshikawaH (1965) The chromosome of Bacillus subtilis. I. Theory of marker frequency analysis. Genetics 52: 747–757.
31. MastersM, BrodaP (1971) Evidence for the bidirectional replication of the Escherichia coli chromosome. Nat New Biol 232: 137–140.
32. BirdRE, LouarnJ, MartuscelliJ, CaroL (1972) Origin and sequence of chromosome replication in Escherichia coli. J Mol Biol 70: 549–566.
33. LouarnJ, PatteJ, LouarnJM (1977) Evidence for a fixed termination site of chromosome replication in Escherichia coli K12. J Mol Biol 115: 295–314.
34. ChandlerM, SilverL, CaroL (1977) Suppression of an Escherichia coli dnaA mutation by the integrated R factor R100.1: origin of chromosome replication during exponential growth. J Bacteriol 131: 421–430.
35. KuempelPL, DuerrSA, MaglothinPD (1978) Chromosome replication in an Escherichia coli dnaA mutant integratively suppressed by prophage P2. J Bacteriol 134: 902–912.
36. Maisnier-PatinS, DasguptaS, KrabbeM, NordstromK (1998) Conversion to bidirectional replication after unidirectional initiation from R1 plasmid origin integrated at oriC in Escherichia coli. Mol Microbiol 30: 1067–1079.
37. SkovgaardO, BakM, Lobner-OlesenA, TommerupN (2011) Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing. Genome Res 21: 1388–1393.
38. KodamaK, KobayashiT, NikiH, HiragaS, OshimaT, et al. (2002) Amplification of Hot DNA segments in Escherichia coli. Mol Microbiol 45: 1575–1588.
39. SangurdekarDP, HamannBL, SmirnovD, SriencF, HanawaltPC, et al. (2010) Thymineless death is associated with loss of essential genetic information from the replication origin. Mol Microbiol 75: 1455–1467.
40. KuongKJ, KuzminovA (2012) Disintegration of nascent replication bubbles during thymine starvation triggers RecA- and RecBCD-dependent replication origin destruction. J Biol Chem 287: 23958–23970.
41. RudolphCJ, UptonAL, StockumA, NieduszynskiCA, LloydRG (2013) Avoiding chromosome pathology when replication forks collide. Nature 500: 608–611.
42. SeigneurM, BidnenkoV, EhrlichSD, MichelB (1998) RuvAB acts at arrested replication forks. Cell 95: 419–430.
43. SeigneurM, EhrlichSD, MichelB (2000) RuvABC-dependent double-strand breaks in dnaBts mutants require RecA. Mol Microbiol 38: 565–574.
44. McGlynnP, LloydRG (2000) Modulation of RNA polymerase by (p)ppGpp reveals a RecG-dependent mechanism for replication fork progression. Cell 101: 35–45.
45. KhanSR, KuzminovA (2012) Replication forks stalled at ultraviolet lesions are rescued via RecA and RuvABC protein-catalyzed disintegration in Escherichia coli. J Biol Chem 287: 6250–6265.
46. MichelB, BoubakriH, BaharogluZ, LeMassonM, LestiniR (2007) Recombination proteins and rescue of arrested replication forks. DNA Repair 6: 967–980.
47. AlverRC, BielinskyAK (2010) Termination at sTop2. Mol Cell 39: 487–489.
48. FachinettiD, BermejoR, CocitoA, MinardiS, KatouY, et al. (2010) Replication termination at eukaryotic chromosomes is mediated by Top2 and occurs at genomic loci containing pausing elements. Mol Cell 39: 595–605.
49. SteinacherR, OsmanF, DalgaardJZ, LorenzA, WhitbyMC (2012) The DNA helicase Pfh1 promotes fork merging at replication termination sites to ensure genome stability. Genes Dev 26: 594–602.
50. NishimuraY, CaroL, BergCM, HirotaY (1971) Chromosome replication in Escherichia coli. IV. Control of chromosome replication and cell division by an integrated episome. J Mol Biol 55: 441–456.
51. LindahlG, HirotaY, JacobF (1971) On the process of cellular division in Escherichia coli: replication of the bacterial chromosome under control of prophage P2. Proc Natl Acad Sci U S A 68: 2407–2411.
52. LouarnJ, PatteJ, LouarnJM (1982) Suppression of Escherichia coli dnaA46 mutations by integration of plasmid R100.1. derivatives: constraints imposed by the replication terminus. J Bacteriol 151: 657–667.
53. Maisnier-PatinS, NordstromK, DasguptaS (2001) RecA-mediated rescue of Escherichia coli strains with replication forks arrested at the terminus. J Bacteriol 183: 6065–6073.
54. KouzminovaEA, KuzminovA (2008) Patterns of chromosomal fragmentation due to uracil-DNA incorporation reveal a novel mechanism of replication-dependent double-stranded breaks. Mol Microbiol 68: 202–215.
55. KogomaT (1997) Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription. Microbiol Mol Biol Rev 61: 212–238.
56. SandlerSJ (2005) Requirements for replication restart proteins during constitutive stable DNA replication in Escherichia coli K-12. Genetics 169: 1799–1806.
57. ItohT, TomizawaJ (1980) Formation of an RNA primer for initiation of replication of ColE1 DNA by ribonuclease H. Proc Natl Acad Sci U S A 77: 2450–2454.
58. KuesU, StahlU (1989) Replication of plasmids in Gram-negative bacteria. Microbiol Rev 53: 491–516.
59. WimberlyH, SheeC, ThorntonPC, SivaramakrishnanP, RosenbergSM, et al. (2013) R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli. Nat Commun 4: 2115.
60. MaduikeNZ, TehranchiAK, WangJD, KreuzerKN (2014) Replication of the Escherichia coli chromosome in RNase HI-deficient cells: multiple initiation regions and fork dynamics. Mol Microbiol 91: 39–56.
61. NishitaniH, HidakaM, HoriuchiT (1993) Specific chromosomal sites enhancing homologous recombination in Escherichia coli mutants defective in RNase H. Mol Gen Genet 240: 307–314.
62. InoueN, UchidaH (1991) Transcription and initiation of ColE1 DNA replication in Escherichia coli K-12. J Bacteriol 173: 1208–1214.
63. LeelaJK, SyedaAH, AnupamaK, GowrishankarJ (2013) Rho-dependent transcription termination is essential to prevent excessive genome-wide R-loops in Escherichia coli. Proc Natl Acad Sci U S A 110: 258–263.
64. HarinarayananR, GowrishankarJ (2003) Host factor titration by chromosomal R-loops as a mechanism for runaway plasmid replication in transcription termination-defective mutants of Escherichia coli. J Mol Biol 332: 31–46.
65. AnupamaK, LeelaJK, GowrishankarJ (2011) Two pathways for RNase E action in Escherichia coli in vivo and bypass of its essentiality in mutants defective for Rho-dependent transcription termination. Mol Microbiol 82: 1330–1348.
66. GowrishankarJ, HarinarayananR (2004) Why is transcription coupled to translation in bacteria? Mol Microbiol 54: 598–603.
67. GowrishankarJ, LeelaJK, AnupamaK (2013) R-loops in bacterial transcription: their causes and consequences. Transcription 4: 153–157.
68. DuttaD, ShatalinK, EpshteinV, GottesmanME, NudlerE (2011) Linking RNA polymerase backtracking to genome instability in E. coli. Cell 146: 533–543.
69. NudlerE (2012) RNA polymerase backtracking in gene regulation and genome instability. Cell 149: 1438–1445.
70. PetersJM, MooneyRA, GrassJA, JessenED, TranF, et al. (2012) Rho and NusG suppress pervasive antisense transcription in Escherichia coli. Genes Dev 26: 2621–2633.
71. WadeJT, GraingerDC (2014) Pervasive transcription: illuminating the dark matter of bacterial transcriptomes. Nat Rev Microbiol 12: 647–653.
72. RudolphCJ, UptonAL, BriggsGS, LloydRG (2010) Is RecG a general guardian of the bacterial genome? DNA Repair 9: 210–223.
73. RudolphCJ, MahdiAA, UptonAL, LloydRG (2010) RecG protein and single-strand DNA exonucleases avoid cell lethality associated with PriA helicase activity in Escherichia coli. Genetics 186: 473–492.
74. TrautingerBW, JaktajiRP, RusakovaE, LloydRG (2005) RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription. Mol Cell 19: 247–258.
75. BarryER, BellSD (2006) DNA replication in the archaea. Microbiol Mol Biol Rev 70: 876–887.
76. MakarovaKS, KooninEV (2013) Archaeology of eukaryotic DNA replication. Cold Spring Harb Perspect Biol 5: a012963.
77. LeonardAC, MechaliM (2013) DNA replication origins. Cold Spring Harb Perspect Biol 5: a010116.
78. HawkinsM, MallaS, BlytheMJ, NieduszynskiCA, AllersT (2013) Accelerated growth in the absence of DNA replication origins. Nature 503: 544–547.
79. MichelB, BernanderR (2014) Chromosome replication origins: do we really need them? BioEssays 36: 585–590.
80. HelmrichA, BallarinoM, ToraL (2011) Collisions between replication and transcription complexes cause common fragile site instability at the longest human genes. Mol Cell 44: 966–977.
81. WahbaL, AmonJD, KoshlandD, Vuica-RossM (2011) RNase H and multiple RNA biogenesis factors cooperate to prevent RNA: DNA hybrids from generating genome instability. Mol Cell 44: 978–988.
82. MischoHE, Gomez-GonzalezB, GrzechnikP, RondonAG, WeiW, et al. (2011) Yeast Sen1 helicase protects the genome from transcription-associated instability. Mol Cell 41: 21–32.
83. GinnoPA, LottPL, ChristensenHC, KorfI, ChedinF (2012) R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol Cell 45: 814–825.
84. BhatiaV, BarrosoSI, Garcia-RubioML, TuminiE, Herrera-MoyanoE, et al. (2014) BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2. Nature 511: 362–365.
85. TuduriS, CrabbeL, TourriereH, CoquelleA, PaseroP (2010) Does interference between replication and transcription contribute to genomic instability in cancer cells? Cell Cycle 9: 1886–1892.
86. BermejoR, LaiMS, FoianiM (2012) Preventing replication stress to maintain genome stability: resolving conflicts between replication and transcription. Mol Cell 45: 710–718.
87. AguileraA, Garcia-MuseT (2012) R loops: from transcription byproducts to threats to genome stability. Mol Cell 46: 115–124.
88. FongYW, CattoglioC, TjianR (2013) The intertwined roles of transcription and repair proteins. Mol Cell 52: 291–302.
89. MontecuccoA, BiamontiG (2013) Pre-mRNA processing factors meet the DNA damage response. Front Genet 4: 102.
90. ChanYA, HieterP, StirlingPC (2014) Mechanisms of genome instability induced by RNA-processing defects. Trends Genet 30: 245–253.
91. HamperlS, CimprichKA (2014) The contribution of co-transcriptional RNA: DNA hybrid structures to DNA damage and genome instability. DNA Repair 19: 84–94.
92. Skourti-StathakiK, ProudfootNJ (2014) A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression. Genes Dev 28: 1384–1396.
93. AguileraA, GaillardH (2014) Transcription and recombination: when RNA meets DNA. Cold Spring Harb Perspect Biol 6: a016543.
94. GrohM, GromakN (2014) Out of balance: R-loops in human disease. PLoS Genet 10: e1004630.
95. MechaliM (2010) Eukaryotic DNA replication origins: many choices for appropriate answers. Nat Rev Mol Cell Biol 11: 728–738.
96. MasaiH, MatsumotoS, YouZ, Yoshizawa-SugataN, OdaM (2010) Eukaryotic chromosome DNA replication: where, when, and how? Annu Rev Biochem 79: 89–130.
97. TuduriS, TourriereH, PaseroP (2010) Defining replication origin efficiency using DNA fiber assays. Chromosome Res 18: 91–102.
98. BlowJJ, GeXQ, JacksonDA (2011) How dormant origins promote complete genome replication. Trends Biochem Sci 36: 405–414.
99. KarnaniN, DuttaA (2011) The effect of the intra-S-phase checkpoint on origins of replication in human cells. Genes Dev 25: 621–633.
100. ImJS, KeatonM, LeeKY, KumarP, ParkJ, et al. (2014) ATR checkpoint kinase and CRL1βTRCP collaborate to degrade ASF1a and thus repress genes overlapping with clusters of stalled replication forks. Genes Dev 28: 875–887.
101. KimN, Jinks-RobertsonS (2012) Transcription as a source of genome instability. Nat Rev Genet 13: 204–214.
102. VenkitaramanAR (2014) Cancer suppression by the chromosome custodians, BRCA1 and BRCA2. Science 343: 1470–1475.
103. MasseE, DroletM (1999) R-loop-dependent hypernegative supercoiling in Escherichia coli topA mutants preferentially occurs at low temperatures and correlates with growth inhibition. J Mol Biol 294: 321–332.
104. MasseE, DroletM (1999) Escherichia coli DNA topoisomerase I inhibits R-loop formation by relaxing transcription-induced negative supercoiling. J Biol Chem 274: 16659–16664.
105. UsongoV, DroletM (2014) Roles of type 1A topoisomerases in genome maintenance in Escherichia coli. PLoS Genet 10: e1004543.
106. BoccardF, EsnaultE, ValensM (2005) Spatial arrangement and macrodomain organization of bacterial chromosomes. Mol Microbiol 57: 9–16.
107. RochaEP (2008) The organization of the bacterial genome. Annu Rev Genet 42: 211–233.
108. MercierR, PetitMA, SchbathS, RobinS, El KarouiM, et al. (2008) The MatP/matS site-specific system organizes the terminus region of the E. coli chromosome into a macrodomain. Cell 135: 475–485.
109. DameRT, KalmykowaOJ, GraingerDC (2011) Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in Gram negative bacteria. PLoS Genet 7: e1002123.
110. KuzminovA (2013) The chromosome cycle of prokaryotes. Mol Microbiol 90: 214–227.
111. YoungrenB, NielsenHJ, JunS, AustinS (2014) The multifork Escherichia coli chromosome is a self-duplicating and self-segregating thermodynamic ring polymer. Genes Dev 28: 71–84.
112. Zakrzewska-CzerwinskaJ, JakimowiczD, Zawilak-PawlikA, MesserW (2007) Regulation of the initiation of chromosomal replication in bacteria. FEMS Microbiol Rev 31: 378–387.
113. KatayamaT, OzakiS, KeyamuraK, FujimitsuK (2010) Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC. Nat Rev Microbiol 8: 163–170.
114. HassanAK, MoriyaS, OguraM, TanakaT, KawamuraF, et al. (1997) Suppression of initiation defects of chromosome replication in Bacillus subtilis dnaA and oriC-deleted mutants by integration of a plasmid replicon into the chromosomes. J Bacteriol 179: 2494–2502.
115. MoriyaS, HassanAK, KadoyaR, OgasawaraN (1997) Mechanism of anucleate cell production in the oriC-deleted mutants of Bacillus subtilis. DNA Res 4: 115–126.
116. PetitMA, DervynE, RoseM, EntianKD, McGovernS, et al. (1998) PcrA is an essential DNA helicase of Bacillus subtilis fulfilling functions both in repair and rolling-circle replication. Mol Microbiol 29: 261–273.
117. PetitMA, EhrlichD (2002) Essential bacterial helicases that counteract the toxicity of recombination proteins. EMBO J 21: 3137–3147.
118. MerrikhC, MerrikhH (2014) The B. subtilis accessory helicase PcrA facilitates replication through transcription units genome-wide. FASEB J 28 Supp. LB126
119. GabbaiCB, MariansKJ (2010) Recruitment to stalled replication forks of the PriA DNA helicase and replisome-loading activities is essential for survival. DNA Repair 9: 202–209.
120. MerrikhH, MachonC, GraingerWH, GrossmanAD, SoultanasP (2011) Co-directional replication-transcription conflicts lead to replication restart. Nature 470: 554–557.
121. AyoraS, CarrascoB, CardenasPP, CesarCE, CanasC, et al. (2011) Double-strand break repair in bacteria: a view from Bacillus subtilis. FEMS Microbiol Rev 35: 1055–1081.
122. CarrAM, LambertS (2013) Replication stress-induced genome instability: the dark side of replication maintenance by homologous recombination. J Mol Biol 425: 4733–4744.
123. JasinM, RothsteinR (2013) Repair of strand breaks by homologous recombination. Cold Spring Harb Perspect Biol 5: a012740.
124. DaleyJM, KwonY, NiuH, SungP (2013) Investigations of homologous recombination pathways and their regulation. Yale J Biol Med 86: 453–461.
125. AzeA, ZhouJC, CostaA, CostanzoV (2013) DNA replication and homologous recombination factors: acting together to maintain genome stability. Chromosoma 122: 401–413.
126. WillisNA, ChandramoulyG, HuangB, KwokA, FollonierC, et al. (2014) BRCA1 controls homologous recombination at Tus/Ter-stalled mammalian replication forks. Nature 510: 556–559.
127. YeelesJT, DillinghamMS (2010) The processing of double-stranded DNA breaks for recombinational repair by helicase-nuclease complexes. DNA Repair 9: 276–285.
128. WigleyDB (2013) Bacterial DNA repair: recent insights into the mechanism of RecBCD, AddAB and AdnAB. Nat Rev Microbiol 11: 9–13.
129. BlackwoodJK, RzechorzekNJ, BraySM, MamanJD, PellegriniL, et al. (2013) End-resection at DNA double-strand breaks in the three domains of life. Biochem Soc Trans 41: 314–320.
130. MimitouEP, SymingtonLS (2011) DNA end resection–unraveling the tail. DNA Repair 10: 344–348.
131. SymingtonLS (2014) End resection at double-strand breaks: mechanism and regulation. Cold Spring Harb Perspect Biol 6: a016436.
132. SharplesGJ, InglestonSM, LloydRG (1999) Holliday junction processing in bacteria: insights from the evolutionary conservation of RuvABC, RecG, and RusA. J Bacteriol 181: 5543–5550.
133. Lo PianoA, Martinez-JimenezMI, ZecchiL, AyoraS (2011) Recombination-dependent concatemeric viral DNA replication. Virus Res 160: 1–14.
134. ZecchiL, Lo PianoA, SuzukiY, CanasC, TakeyasuK, et al. (2012) Characterization of the Holliday junction resolving enzyme encoded by the Bacillus subtilis bacteriophage SPP1. PLoS One 7: e48440.
135. MaricM, MaculinsT, De PiccoliG, LabibK (2014) Cdc48 and a ubiquitin ligase drive disassembly of the CMG helicase at the end of DNA replication. Science 346: 440.
136. MorenoSP, BaileyR, CampionN, HerronS, GambusA (2014) Polyubiquitylation drives replisome disassembly at the termination of DNA replication. Science 346: 477–481.
137. WangJD, BerkmenMB, GrossmanAD (2007) Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis. Proc Natl Acad Sci U S A 104: 5608–5613.
138. SrivatsanA, TehranchiA, MacAlpineDM, WangJD (2010) Co-orientation of replication and transcription preserves genome integrity. PLoS Genet 6: e1000810.
139. HuvetM, NicolayS, TouchonM, AuditB, d'Aubenton-CarafaY, et al. (2007) Human gene organization driven by the coordination of replication and transcription. Genome Res 17: 1278–1285.
140. NicolasP, MaderU, DervynE, RochatT, LeducA, et al. (2012) Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 335: 1103–1106.
141. ChanYA, AristizabalMJ, LuPYT, LuoZ, HamzaA, et al. (2014) Genome-wide profiling of yeast DNA: RNA hybrid prone sites with DRIP-Chip. PLoS Genet 10: e1004288.
142. El HageA, WebbS, KerrA, TollerveyD (2014) Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons and mitochondria. PLoS Genet 10: e1004716.
143. El HageA, FrenchSL, BeyerAL, TollerveyD (2010) Loss of topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis. Genes Dev 24: 1546–1558.
144. FukushimaS, ItayaM, KatoH, OgasawaraN, YoshikawaH (2007) Reassessment of the in vivo functions of DNA polymerase I and RNase H in bacterial cell growth. J Bacteriol 189: 8575–8583.
145. TadokoroT, KanayaS (2009) Ribonuclease H: molecular diversities, substrate binding domains, and catalytic mechanism of the prokaryotic enzymes. FEBS J 276: 1482–1493.
146. CerritelliSM, CrouchRJ (2009) Ribonuclease H: the enzymes in eukaryotes. FEBS J 276: 1494–1505.
147. WenQ, MahdiAA, BriggsGS, SharplesGJ, LloydRG (2005) Conservation of RecG activity from pathogens to hyperthermophiles. DNA Repair 4: 23–31.
148. SanchezH, CarrascoB, CozarMC, AlonsoJC (2007) Bacillus subtilis RecG branch migration translocase is required for DNA repair and chromosomal segregation. Mol Microbiol 65: 920–935.