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The ribosomal protein S1-dependent standby site in tisB mRNA consists of a single-stranded region and a 5' structure element.

Romilly C, Deindl S, Wagner EGH.

Proc Natl Acad Sci U S A. 2019 Aug 6;116(32):15901-15906. doi: 10.1073/pnas.1904309116. Epub 2019 Jul 18.


Hfq-dependent mRNA unfolding promotes sRNA-based inhibition of translation.

Hoekzema M, Romilly C, Holmqvist E, Wagner EGH.

EMBO J. 2019 Apr 1;38(7). pii: e101199. doi: 10.15252/embj.2018101199. Epub 2019 Mar 4.


Unstructured 5'-tails act through ribosome standby to override inhibitory structure at ribosome binding sites.

Sterk M, Romilly C, Wagner EGH.

Nucleic Acids Res. 2018 May 4;46(8):4188-4199. doi: 10.1093/nar/gky073.


Impact of bacterial sRNAs in stress responses.

Holmqvist E, Wagner EGH.

Biochem Soc Trans. 2017 Dec 15;45(6):1203-1212. doi: 10.1042/BST20160363. Epub 2017 Nov 3. Review.


RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study.

Berghoff BA, Karlsson T, Källman T, Wagner EGH, Grabherr MG.

BioData Min. 2017 Sep 5;10:30. doi: 10.1186/s13040-017-0150-8. eCollection 2017.


Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition.

Amlinger L, Hoekzema M, Wagner EGH, Koskiniemi S, Lundgren M.

Sci Rep. 2017 Sep 4;7(1):10392. doi: 10.1038/s41598-017-10876-z.


RNA-based regulation in type I toxin-antitoxin systems and its implication for bacterial persistence.

Berghoff BA, Wagner EGH.

Curr Genet. 2017 Dec;63(6):1011-1016. doi: 10.1007/s00294-017-0710-y. Epub 2017 May 30. Review.


Two regulatory RNA elements affect TisB-dependent depolarization and persister formation.

Berghoff BA, Hoekzema M, Aulbach L, Wagner EG.

Mol Microbiol. 2017 Mar;103(6):1020-1033. doi: 10.1111/mmi.13607. Epub 2017 Jan 13.


One Gene and Two Proteins: a Leaderless mRNA Supports the Translation of a Shorter Form of the Shigella VirF Regulator.

Di Martino ML, Romilly C, Wagner EG, Colonna B, Prosseda G.

MBio. 2016 Nov 8;7(6). pii: e01860-16. doi: 10.1128/mBio.01860-16.


Small RNAs in bacteria and archaea: who they are, what they do, and how they do it.

Wagner EGH, Romby P.

Adv Genet. 2015;90:133-208. doi: 10.1016/bs.adgen.2015.05.001. Epub 2015 Jul 3. Review.


A method to map changes in bacterial surface composition induced by regulatory RNAs in Escherichia coli and Staphylococcus aureus.

Hammann P, Parmentier D, Cerciat M, Reimegård J, Helfer AC, Boisset S, Guillier M, Vandenesch F, Wagner EG, Romby P, Fechter P.

Biochimie. 2014 Nov;106:175-9. doi: 10.1016/j.biochi.2014.07.011. Epub 2014 Jul 18.


Differential translation tunes uneven production of operon-encoded proteins.

Quax TE, Wolf YI, Koehorst JJ, Wurtzel O, van der Oost R, Ran W, Blombach F, Makarova KS, Brouns SJ, Forster AC, Wagner EG, Sorek R, Koonin EV, van der Oost J.

Cell Rep. 2013 Sep 12;4(5):938-44. doi: 10.1016/j.celrep.2013.07.049. Epub 2013 Sep 5.


Massive functional mapping of a 5'-UTR by saturation mutagenesis, phenotypic sorting and deep sequencing.

Holmqvist E, Reimegård J, Wagner EG.

Nucleic Acids Res. 2013 Jul;41(12):e122. doi: 10.1093/nar/gkt267. Epub 2013 Apr 22.


Cycling of RNAs on Hfq.

Wagner EG.

RNA Biol. 2013 Apr;10(4):619-26. doi: 10.4161/rna.24044. Epub 2013 Mar 6. Review.


The toxin-antitoxin system tisB-istR1: Expression, regulation, and biological role in persister phenotypes.

Wagner EG, Unoson C.

RNA Biol. 2012 Dec;9(12):1513-9. doi: 10.4161/rna.22578. Epub 2012 Oct 23. Review.


MicroRNAs in Amoebozoa: deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs.

Avesson L, Reimegård J, Wagner EG, Söderbom F.

RNA. 2012 Oct;18(10):1771-82. doi: 10.1261/rna.033175.112. Epub 2012 Aug 8.


A mixed double negative feedback loop between the sRNA MicF and the global regulator Lrp.

Holmqvist E, Unoson C, Reimegård J, Wagner EG.

Mol Microbiol. 2012 May;84(3):414-27. doi: 10.1111/j.1365-2958.2012.07994.x. Epub 2012 Feb 13.


RNAs actively cycle on the Sm-like protein Hfq.

Fender A, Elf J, Hampel K, Zimmermann B, Wagner EG.

Genes Dev. 2010 Dec 1;24(23):2621-6. doi: 10.1101/gad.591310.


H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO.

Westra ER, Pul U, Heidrich N, Jore MM, Lundgren M, Stratmann T, Wurm R, Raine A, Mescher M, Van Heereveld L, Mastop M, Wagner EG, Schnetz K, Van Der Oost J, Wagner R, Brouns SJ.

Mol Microbiol. 2010 Sep;77(6):1380-93. doi: 10.1111/j.1365-2958.2010.07315.x. Epub 2010 Aug 18.


Novel role for a bacterial nucleoid protein in translation of mRNAs with suboptimal ribosome-binding sites.

Park HS, Ostberg Y, Johansson J, Wagner EG, Uhlin BE.

Genes Dev. 2010 Jul 1;24(13):1345-50. doi: 10.1101/gad.576310.


Two antisense RNAs target the transcriptional regulator CsgD to inhibit curli synthesis.

Holmqvist E, Reimegård J, Sterk M, Grantcharova N, Römling U, Wagner EG.

EMBO J. 2010 Jun 2;29(11):1840-50. doi: 10.1038/emboj.2010.73. Epub 2010 Apr 20.


Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA.

Djupedal I, Kos-Braun IC, Mosher RA, Söderholm N, Simmer F, Hardcastle TJ, Fender A, Heidrich N, Kagansky A, Bayne E, Wagner EG, Baulcombe DC, Allshire RC, Ekwall K.

EMBO J. 2009 Dec 16;28(24):3832-44. doi: 10.1038/emboj.2009.351.


Kill the messenger: bacterial antisense RNA promotes mRNA decay.

Wagner EG.

Nat Struct Mol Biol. 2009 Aug;16(8):804-6. doi: 10.1038/nsmb0809-804. No abstract available.


Sensory ataxic neuropathy in golden retriever dogs is caused by a deletion in the mitochondrial tRNATyr gene.

Baranowska I, Jäderlund KH, Nennesmo I, Holmqvist E, Heidrich N, Larsson NG, Andersson G, Wagner EG, Hedhammar A, Wibom R, Andersson L.

PLoS Genet. 2009 May;5(5):e1000499. doi: 10.1371/journal.pgen.1000499. Epub 2009 May 29.


A small SOS-induced toxin is targeted against the inner membrane in Escherichia coli.

Unoson C, Wagner EG.

Mol Microbiol. 2008 Oct;70(1):258-70. doi: 10.1111/j.1365-2958.2008.06416.x. Epub 2008 Aug 29.


Dealing with stable structures at ribosome binding sites: bacterial translation and ribosome standby.

Unoson C, Wagner EG.

RNA Biol. 2007 Nov;4(3):113-7. Epub 2007 Nov 29. Review.


Exploring the complex world of RNA regulation.

Romby P, Wagner EG.

Biol Cell. 2008 Jan;100(1):e1-3. No abstract available.


The small RNA repertoire of Dictyostelium discoideum and its regulation by components of the RNAi pathway.

Hinas A, Reimegård J, Wagner EG, Nellen W, Ambros VR, Söderbom F.

Nucleic Acids Res. 2007;35(20):6714-26. Epub 2007 Oct 4.


Target identification of small noncoding RNAs in bacteria.

Vogel J, Wagner EG.

Curr Opin Microbiol. 2007 Jun;10(3):262-70. Epub 2007 Jun 15. Review.


An antisense RNA inhibits translation by competing with standby ribosomes.

Darfeuille F, Unoson C, Vogel J, Wagner EG.

Mol Cell. 2007 May 11;26(3):381-92.


Structure probing of tmRNA in distinct stages of trans-translation.

Ivanova N, Lindell M, Pavlov M, Holmberg Schiavone L, Wagner EG, Ehrenberg M.

RNA. 2007 May;13(5):713-22. Epub 2007 Mar 30.


RNA antitoxins.

Gerdes K, Wagner EG.

Curr Opin Microbiol. 2007 Apr;10(2):117-24. Epub 2007 Mar 21. Review.


Sigma E controls biogenesis of the antisense RNA MicA.

Udekwu KI, Wagner EG.

Nucleic Acids Res. 2007;35(4):1279-88. Epub 2007 Jan 31.


The role of RNAs in the regulation of virulence-gene expression.

Romby P, Vandenesch F, Wagner EG.

Curr Opin Microbiol. 2006 Apr;9(2):229-36. Epub 2006 Mar 10. Review.


Paenibacillus polymyxa invades plant roots and forms biofilms.

Timmusk S, Grantcharova N, Wagner EG.

Appl Environ Microbiol. 2005 Nov;71(11):7292-300.


Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA.

Udekwu KI, Darfeuille F, Vogel J, Reimegård J, Holmqvist E, Wagner EG.

Genes Dev. 2005 Oct 1;19(19):2355-66.


Lead(II) cleavage analysis of RNase P RNA in vivo.

Lindell M, Brännvall M, Wagner EG, Kirsebom LA.

RNA. 2005 Sep;11(9):1348-54. Epub 2005 Jul 25.


The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide.

Vogel J, Argaman L, Wagner EG, Altuvia S.

Curr Biol. 2004 Dec 29;14(24):2271-6.


A repeated GGA motif is critical for the activity and stability of the riboregulator RsmY of Pseudomonas fluorescens.

Valverde C, Lindell M, Wagner EG, Haas D.

J Biol Chem. 2004 Jun 11;279(24):25066-74. Epub 2004 Mar 18.


RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria.

Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jäger JG, Hüttenhofer A, Wagner EG.

Nucleic Acids Res. 2003 Nov 15;31(22):6435-43.


Characterization of phiA, a gene essential for phialide development in Aspergillus nidulans.

Melin P, Schnürer J, Wagner EG.

Fungal Genet Biol. 2003 Dec;40(3):234-41.


Loop swapping in an antisense RNA/target RNA pair changes directionality of helix progression.

Slagter-Jäger JG, Wagner EG.

J Biol Chem. 2003 Sep 12;278(37):35558-63. Epub 2003 Jun 20.


Antisense RNAs everywhere?

Wagner EG, Flärdh K.

Trends Genet. 2002 May;18(5):223-6.


Lead(II) as a probe for investigating RNA structure in vivo.

Lindell M, Romby P, Wagner EG.

RNA. 2002 Apr;8(4):534-41.


Antisense RNAs in bacteria and their genetic elements.

Wagner EG, Altuvia S, Romby P.

Adv Genet. 2002;46:361-98. Review.


Bulged residues promote the progression of a loop-loop interaction to a stable and inhibitory antisense-target RNA complex.

Kolb FA, Westhof E, Ehresmann C, Ehresmann B, Wagner EG, Romby P.

Nucleic Acids Res. 2001 Aug 1;29(15):3145-53.


Novel small RNA-encoding genes in the intergenic regions of Escherichia coli.

Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S.

Curr Biol. 2001 Jun 26;11(12):941-50.

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