References
- Gordon AJE, Halliday JA. Inversions with deletions and duplications. Genetics. 1995;140:411–414.
- Traverse CC, Ochman H. Genome-wide spectra of transcription insertions and deletions reveal that slippage depends on RNA:DNA hybrid complementarity. mBio. 2017;8:e01230–17–13.
- Nudler E, Mustaev A, Lukhtanov E, et al. RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell. 1997;89:33–41.
- Epshtein V, Kamarthapu V, McGary K, et al. UvrD facilitates DNA repair by pulling RNA polymerase backwards. Nature. 2014;505:372–377.
- Komissarova N, Kashlev M. Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3ʹ end of the RNA intact and extruded. Proc Natl Acad Sci USA. 1997;94:1755–1760.
- Borukhov S, Sagitov V, Goldfarb A. Transcript cleavage factors from E.coli. Cell. 1993;72:459–466.
- Erie DA, Hajiseyedjavadi O, Young MC, et al. Multiple RNA polymerase conformations and GreA: control of the fidelity of transcription. Science. 1993;262:867–873.
- Imashimizu M, Oshima T, Lubkowska L, et al. Direct assessment of transcription fidelity by high-resolution RNA sequencing. Nucleic Acids Res. 2013;41:9090–9104.
- Imashimizu M, Takahashi H, Oshima T, et al. Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo. Genome Biol. 2015;16:98.
- James K, Gamba P, Cockell SJ, et al. Misincorporation by RNA polymerase is a major source of transcription pausing in vivo. Nucleic Acids Res. 2017;45:1105–1113.
- Tehranchi AK, Blankschien MD, Zhang Y, et al. The transcription factor DksA prevents conflicts between DNA replication and transcription machinery. Cell. 2010;141:595–605.
- Sivaramakrishnan P, Sepúlveda LA, Halliday JA, et al. The transcription fidelity factor GreA impedes DNA break repair. Nature. 2017;550:214–218.
- Koulich D, Orlova M, Malhotra A, et al. Domain organization of Escherichia coli transcript cleavage factors GreA and GreB. J Biol Chem. 1997;272:7201–7210.
- Vinella D, Potrykus K, Murphy H, et al. Effects on growth by changes of the balance between GreA, GreB, and DksA suggest mutual competition and functional redundancy in Escherichia coli. J Bacteriol. 2012;194:261–273.
- Roghanian M, Zenkin N, Yuzenkova Y. Bacterial global regulators DksA/ppGpp increase fidelity of transcription. Nucleic Acids Res. 2015;43:1529–1536.
- Satory D, Gordon AJE, Wang M, et al. DksA involvement in transcription fidelity buffers stochastic epigenetic change. Nucleic Acids Res. 2015;43:10190–10199.
- Dillingham MS, Kowalczykowski SC. RecBCD enzyme and the repair of double-stranded DNA breaks. Microbiol Mol Biol Rev. 2008;72:642–671.
- Branch P, Aquilina G, Bignami M, et al. Defective mismatch binding and a mutator phenotype in cells tolerant to DNA damage. Nature. 1993;362:652–654.
- Kamarthapu V, Epshtein V, Benjamin B, et al. ppGpp couples transcription to DNA repair in E. coli. Science. 2016;352:993–996.
- Gordon AJE, Satory D, Halliday JA, et al. Lost in transcription: transient errors in information transfer. Curr Opin Microbiol. 2015;24:80–87.
- Gordon AJE, Halliday JA, Blankschien MD, et al. Transcriptional infidelity promotes heritable phenotypic change in a bistable gene network. PLoS Biol. 2009;7:e44.
- Novick A, Weiner M. Enzyme induction as an all-or-none phenomenon. Proc Natl Acad Sci USA. 1957;43:553–566.
- Cai L, Friedman N, Xie XS. Stochastic protein expression in individual cells at the single molecule level. Nature. 2006;440:358–362.
- Gordon AJE, Satory D, Halliday JA, et al. Heritable change caused by transient transcription errors. PLoS Genet. 2013;9:e1003595.
- Gordon AJE, Satory D, Wang M, et al. Removal of 8-oxo-GTP by MutT hydrolase is not a major contributor to transcriptional fidelity. Nucleic Acids Res. 2014;42:12015–12026.
- Taddei F, Hayakawa H, Bouton M, et al. Counteraction by MutT protein of transcriptional errors caused by oxidative damage. Science. 1997;278:128–130.
- Satory D, Gordon AJE, Halliday JA, et al. Epigenetic switches: can infidelity govern fate in microbes? Curr Opin Microbiol. 2011;14:212–217.
- Bubunenko MG, Court CB, Rattray AJ, et al. A Cre transcription fidelity reporter identifies GreA as a major RNA proofreading factor in Escherichia coli. Genetics. 2017;206:179–187.
- Dutta D, Shatalin K, Epshtein V, et al. Linking RNA polymerase backtracking to genome instability in E. coli. Cell. 2011;146:533–543.
- Epshtein V, Nudler E. Cooperation between RNA polymerase molecules in transcription elongation. Science. 2003;300:801–805.
- Epshtein V, Toulmé F, Rahmouni AR, et al. Transcription through the roadblocks: the role of RNA polymerase cooperation. EMBO J. 2003;22:4719–4727.
- Gamba P, Zenkin N. Transcription fidelity and its roles in the cell. Curr Opin Microbiol. 2017;42:13–18.
- Gamba P, James K, Zenkin N. A link between transcription fidelity and pausing in vivo. Transcription. 2017;8:99–105.
- Mellon I, Hanawalt PC. Induction of the Escherichia coli lactose operon selectively increases repair of its transcribed DNA strand. Nature. 1989;342:95–98.