References
- Serganov A, Nudler E. A decade of riboswitches. Cell. 2013;152:17–24.
- Mccown PJ, Corbino KA, Stav S, et al. Riboswitch diversity and distribution. Rna. 2017;23:995–1011.
- Montange RK, Batey RT. Riboswitches: emerging themes in RNA structure and function. Annu Rev Biophys. 2008;37:117–133.
- Pan T, Sosnick T. RNA folding during transcription. Annu Rev Biophys Biomol Struct. 2006;35:161–175.
- Zhang J, Landick R. A two-way street: regulatory interplay between RNA polymerase and nascent RNA structure. Trends Biochem Sci. 2016;41:293–310.
- Wickiser JK, Winkler WC, Breaker RR, et al. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol Cell. 2005;18:49–60.
- Lemay JF, Desnoyers G, Blouin S, et al. Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms. PLoS Genet. 2011;7:e1001278.
- Hollands K, Proshkin S, Sklyarova S, et al. Riboswitch control of Rho-dependent transcription termination. Proc Natl Acad Sci U S A. 2012;109:5376–5381.
- Chauvier A, Picard-Jean F, Berger-Dancause J-C, et al. Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation. Nat Commun. 2017;8:13892.
- Perdrizet GA, Artsimovitch I, Furman R, et al. Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch. Proc Natl Acad Sci. 2012;109:3323–3328.
- Guedich S, Puffer-Enders B, Baltzinger M, et al. Quantitative and predictive model of kinetic regulation by E. coli TPP riboswitches. RNA Biol. 2016;13:373–390.
- Wong TN, Pan T. RNA folding during transcription: protocols and studies. Methods Enzym. 2009;468:167–193.
- Artsimovitch I, Landick R. Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Proc Natl Acad Sci U S A. 2000;97:7090–7095.
- Sen R, Chalissery J, Qayyum MZ, et al. Nus factors of Escherichia coli. EcoSal Plus. 2013. DOI:10.1128/ecosalplus.4.5.3.1
- Yakhnin AV, Babitzke P. NusA-stimulated RNA polymerase pausing and termination participates in the Bacillus subtilis trp operon attenuation mechanism invitro. Proc Natl Acad Sci U S A. 2002;99:11067–11072.
- Mondal S, Yakhnin AV, Sebastian A, et al. NusA-dependent transcription termination prevents misregulation of global gene expression. Nat Microbiol. 2016;1:15007.
- Pan T, Artsimovitch I, Fang XW, et al. Folding of a large ribozyme during transcription and the effect of the elongation factor NusA. Proc Natl Acad Sci U S A. 1999;96:9545–9550.
- Toulokhonov I, Artsimovitch I, Landick R. Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science. 2001;292:730–733.
- Shankar S, Hatoum A, Roberts JW. A transcription antiterminator constructs a NusA-dependent shield to the emerging transcript. Mol Cell. 2007;27:914–927.
- Ha KS, Toulokhonov I, Vassylyev DG, et al. The NusA N-terminal domain is necessary and sufficient for enhancement of transcriptional pausing via interaction with the RNA exit channel of RNA polymerase. J Mol Biol. 2010;401:708–725.
- Guo X, Myasnikov AG, Chen J, et al. Structural basis for NusA stabilized transcriptional pausing. Mol Cell. 2018;69:802–819.e1.
- Begley TP, Downs DM, Ealick SE, et al. Thiamin biosynthesis in prokaryotes. Arch Microbiol. 1999;171:293–300.
- Winkler W, Nahvi A, Breaker RR. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature. 2002;419:952–956.
- Chauvier A, Lafontaine D. Probing of nascent riboswitch transcript. In: DNA-protein interactions: principles and protocols. 4th ed. Humana Press. 2015. p. 1–347. https://www.springer.com/cn/book/9781493928767
- Kang JY, Mishanina TV, Bellecourt MJ, et al. RNA polymerase accommodates a pause RNA hairpin by global conformational rearrangements that prolong pausing. Mol Cell. 2018;69:802–815.
- Chan CL, Landick R. Dissection of the his leader pause site by base substitution reveals a multipartite signal that includes a pause RNA hairpin. J Mol Biol. 1993;233:25–42.
- Landick R, Yanofsky C. Stability of an RNA secondary structure affects in vitro transcription pausing in the trp operon leader region. J Biol Chem. 1984;259:11550–11555.
- Larson MH, Mooney RA, Peters JM, et al. A pause sequence enriched at translation start sites drives transcription dynamics in vivo. Science. 2014;344:1042–1047.
- Massé E, Gottesman S. A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci U S A. 2002;99:4620–4625.
- Simons RW, Houman F, Kleckner N. Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene. 1987;53:85–96.
- Powell BS, Courtl DL, Nakamura3 Y, et al. Rapid confirmation of single copy lambda prophage integration by PCR. Nucleic Acid Research. 1994;22:5765–5766.
- Landick R, Wang D, Chan CL. Quantitative analysis of transcriptional pausing by Escherichia coli RNA polymerase: his leader pause site as paradigm. Methods Enzymol. 1996;274:334–353.
- Caron M-P, Bastet L, Lussier A, et al. Dual-acting riboswitch control of translation initiation and mRNA decay. Proc Natl Acad Sci U S A. 2012;109:E3444–53.
- Prévost K, Salvail H, Desnoyers G, et al. The small RNA RyhB activates the translation of shiA mRNA encoding a permease of shikimate, a compound involved in siderophore synthesis. Mol Microbiol. 2007;64:1260–1273.
- Zhou Y, Gottesman S. Regulation of proteolysis of the stationary-phase sigma factor RpoS. J Bacteriol. 1998;180:1154–1158.
- Nudler E, Gusarov I, Bar-Nahum G. Methods of walking with the RNA polymerase. Methods Enzymol. 2003;371:160–169.