Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation

References

• Storz G, Vogel J, Wassarman KM. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 2011; 43:880 - 91; http://dx.doi.org/10.1016/j.molcel.2011.08.022; PMID: 21925377
   PubMed Web of Science ®Google Scholar
• Papenfort K, Vogel J. Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level. Res Microbiol 2009; 160:278 - 87; http://dx.doi.org/10.1016/j.resmic.2009.03.004; PMID: 19366629
   PubMed Web of Science ®Google Scholar
• Chao Y, Papenfort K, Reinhardt R, Sharma CM, Vogel J. An atlas of Hfq-bound transcripts reveals 3′ UTRs as a genomic reservoir of regulatory small RNAs. EMBO J 2012; 31:4005 - 19; http://dx.doi.org/10.1038/emboj.2012.229; PMID: 22922465
   PubMed Web of Science ®Google Scholar
• Lalaouna D, Simoneau-Roy M, Lafontaine D, Massé E. Regulatory RNAs and target mRNA decay in prokaryotes. Biochim Biophys Acta 2013; 1829:742 - 7; http://dx.doi.org/10.1016/j.bbagrm.2013.02.013; PMID: 23500183
   PubMed Web of Science ®Google Scholar
• Schroeder R, Barta A, Semrad K. Strategies for RNA folding and assembly. Nat Rev Mol Cell Biol 2004; 5:908 - 19; http://dx.doi.org/10.1038/nrm1497; PMID: 15520810
   PubMed Web of Science ®Google Scholar
• Wagner EGH. Cycling of RNAs on Hfq. RNA Biol 2013; 10:619 - 26; http://dx.doi.org/10.4161/rna.24044; PMID: 23466677
   PubMed Web of Science ®Google Scholar
• Soper TJ, Woodson SA. The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA. RNA 2008; 14:1907 - 17; http://dx.doi.org/10.1261/rna.1110608; PMID: 18658123
   PubMed Web of Science ®Google Scholar
• Salim NN, Feig AL. An upstream Hfq binding site in the fhlA mRNA leader region facilitates the OxyS-fhlA interaction. PLoS One 2010; 5:1 - 11; http://dx.doi.org/10.1371/journal.pone.0013028; PMID: 20927406
   PubMed Web of Science ®Google Scholar
• Lorenz C, Gesell T, Zimmermann B, Schoeberl U, Bilusic I, Rajkowitsch L, Waldsich C, von Haeseler A, Schroeder R. Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts. Nucleic Acids Res 2010; 38:3794 - 808; http://dx.doi.org/10.1093/nar/gkq032; PMID: 20348540
   PubMed Web of Science ®Google Scholar
• Georg J, Hess WR. cis-antisense RNA, another level of gene regulation in bacteria. Microbiol Mol Biol Rev 2011; 75:286 - 300; http://dx.doi.org/10.1128/MMBR.00032-10; PMID: 21646430
   PubMed Web of Science ®Google Scholar
• Dornenburg JE, Devita AM, Palumbo MJ, Wade JT. Widespread antisense transcription in Escherichia coli. MBio 2010; 1:1 - 4; http://dx.doi.org/10.1128/mBio.00024-10; PMID: 20689751
   PubMed Web of Science ®Google Scholar
• Raghavan R, Sloan DB, Ochman H. Antisense transcription is pervasive but rarely conserved in enteric bacteria. MBio 2012; 3; http://dx.doi.org/10.1128/mBio.00156-12; PMID: 22872780
   PubMed Web of Science ®Google Scholar
• Lybecker M, Zimmermann B, Bilusic I, Tukhtubaeva N, Schroeder R. The double-stranded transcriptome of Escherichia coli. Proc Natl Acad Sci U S A 2014; 111:3134 - 9; http://dx.doi.org/10.1073/pnas.1315974111; PMID: 24453212
   PubMed Web of Science ®Google Scholar
• Christiansen JK, Nielsen JS, Ebersbach T, Valentin-Hansen P, Søgaard-Andersen L, Kallipolitis BH. Identification of small Hfq-binding RNAs in Listeria monocytogenes. RNA 2006; 12:1383 - 96; http://dx.doi.org/10.1261/rna.49706; PMID: 16682563
   PubMed Web of Science ®Google Scholar
• Zhang A, Wassarman KM, Rosenow C, Tjaden BC, Storz G, Gottesman S. Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol 2003; 50:1111 - 24; http://dx.doi.org/10.1046/j.1365-2958.2003.03734.x; PMID: 14622403
   PubMed Web of Science ®Google Scholar
• Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, Hinton JCD, Vogel J. Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet 2008; 4:e1000163; http://dx.doi.org/10.1371/journal.pgen.1000163; PMID: 18725932
   PubMed Web of Science ®Google Scholar
• Dambach M, Irnov I, Winkler WC. Association of RNAs with Bacillus subtilis Hfq. PLoS One 2013; 8:e55156; http://dx.doi.org/10.1371/journal.pone.0055156; PMID: 23457461
   PubMed Web of Science ®Google Scholar
• Soper T, Mandin P, Majdalani N, Gottesman S, Woodson SA. Positive regulation by small RNAs and the role of Hfq. Proc Natl Acad Sci U S A 2010; 107:9602 - 7; http://dx.doi.org/10.1073/pnas.1004435107; PMID: 20457943
   PubMed Web of Science ®Google Scholar
• Ikeda Y, Yagi M, Morita T, Aiba H. Hfq binding at RhlB-recognition region of RNase E is crucial for the rapid degradation of target mRNAs mediated by sRNAs in Escherichia coli. Mol Microbiol 2011; 79:419 - 32; http://dx.doi.org/10.1111/j.1365-2958.2010.07454.x; PMID: 21219461
   PubMed Web of Science ®Google Scholar
• Le Derout J, Folichon M, Briani F, Dehò G, Régnier P, Hajnsdorf E. Hfq affects the length and the frequency of short oligo(A) tails at the 3′ end of Escherichia coli rpsO mRNAs. Nucleic Acids Res 2003; 31:4017 - 23; http://dx.doi.org/10.1093/nar/gkg456; PMID: 12853618
   PubMed Web of Science ®Google Scholar
• Mohanty BK, Maples VF, Kushner SR. The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli. Mol Microbiol 2004; 54:905 - 20; http://dx.doi.org/10.1111/j.1365-2958.2004.04337.x; PMID: 15522076
   PubMed Web of Science ®Google Scholar
• Scheibe M, Bonin S, Hajnsdorf E, Betat H, Mörl M. Hfq stimulates the activity of the CCA-adding enzyme. BMC Mol Biol 2007; 8:92; http://dx.doi.org/10.1186/1471-2199-8-92; PMID: 17949481
   PubMed Web of Science ®Google Scholar
• Sukhodolets MV, Garges S. Interaction of Escherichia coli RNA polymerase with the ribosomal protein S1 and the Sm-like ATPase Hfq. Biochemistry 2003; 42:8022 - 34; http://dx.doi.org/10.1021/bi020638i; PMID: 12834354
   PubMed Web of Science ®Google Scholar
• Raghavan R, Groisman EA, Ochman H. Genome-wide detection of novel regulatory RNAs in E. coli. Genome Res 2011; 21:1487 - 97; http://dx.doi.org/10.1101/gr.119370.110; PMID: 21665928
   PubMed Web of Science ®Google Scholar
• Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP. Next generation software for functional trend analysis. Bioinformatics 2009; 25:3043 - 4; http://dx.doi.org/10.1093/bioinformatics/btp498; PMID: 19717575
   PubMed Web of Science ®Google Scholar
• Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S. Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev 2001; 15:1637 - 51; http://dx.doi.org/10.1101/gad.901001; PMID: 11445539
   PubMed Web of Science ®Google Scholar
• Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jäger JG, Hüttenhofer A, Wagner EG. RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. Nucleic Acids Res 2003; 31:6435 - 43; http://dx.doi.org/10.1093/nar/gkg867; PMID: 14602901
   PubMed Web of Science ®Google Scholar
• De Lay N, Schu DJ, Gottesman S. Bacterial small RNA-based negative regulation: Hfq and its accomplices. J Biol Chem 2013; 288:7996 - 8003; http://dx.doi.org/10.1074/jbc.R112.441386; PMID: 23362267
   PubMed Web of Science ®Google Scholar
• Lasa I, Toledo-Arana A, Dobin A, Villanueva M, de los Mozos IR, Vergara-Irigaray M, Segura V, Fagegaltier D, Penadés JR, Valle J, et al. Genome-wide antisense transcription drives mRNA processing in bacteria. Proc Natl Acad Sci U S A 2011; 108:20172 - 7; http://dx.doi.org/10.1073/pnas.1113521108; PMID: 22123973
   PubMed Web of Science ®Google Scholar
• Ross JA, Wardle SJ, Haniford DB. Tn10/IS10 transposition is downregulated at the level of transposase expression by the RNA-binding protein Hfq. Mol Microbiol 2010; 78:607 - 21; http://dx.doi.org/10.1111/j.1365-2958.2010.07359.x; PMID: 20815820
   PubMed Web of Science ®Google Scholar
• Ross JA, Ellis MJ, Hossain S, Haniford DB. Hfq restructures RNA-IN and RNA-OUT and facilitates antisense pairing in the Tn10/IS10 system. RNA 2013; 19:670 - 84; http://dx.doi.org/10.1261/rna.037747.112; PMID: 23510801
   PubMed Web of Science ®Google Scholar
• Opdyke JA, Kang JG, Storz G. GadY, a small-RNA regulator of acid response genes in Escherichia coli. J Bacteriol 2004; 186:6698 - 705; http://dx.doi.org/10.1128/JB.186.20.6698-6705.2004; PMID: 15466020
   PubMed Web of Science ®Google Scholar
• Opdyke JA, Fozo EM, Hemm MR, Storz G. RNase III participates in GadY-dependent cleavage of the gadX-gadW mRNA. J Mol Biol 2011; 406:29 - 43; http://dx.doi.org/10.1016/j.jmb.2010.12.009; PMID: 21147125
   PubMed Web of Science ®Google Scholar
• Thomason MK, Storz G. Bacterial antisense RNAs: how many are there, and what are they doing?. Annu Rev Genet 2010; 44:167 - 88; http://dx.doi.org/10.1146/annurev-genet-102209-163523; PMID: 20707673
   PubMed Web of Science ®Google Scholar
• Singh SS, Singh N, Bonocora RP, Fitzgerald DM, Wade JT, Grainger DC. Widespread suppression of intragenic transcription initiation by H-NS. Genes Dev 2014; 28:214 - 9; http://dx.doi.org/10.1101/gad.234336.113; PMID: 24449106
   PubMed Web of Science ®Google Scholar
• Papenfort K, Said N, Welsink T, Lucchini S, Hinton JCD, Vogel J. Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA. Mol Microbiol 2009; 74:139 - 58; http://dx.doi.org/10.1111/j.1365-2958.2009.06857.x; PMID: 19732340
   PubMed Web of Science ®Google Scholar
• Davis BM, Waldor MK. RNase E-dependent processing stabilizes MicX, a Vibrio cholerae sRNA. Mol Microbiol 2007; 65:373 - 85; http://dx.doi.org/10.1111/j.1365-2958.2007.05796.x; PMID: 17590231
   PubMed Web of Science ®Google Scholar
• Møller T, Franch T, Højrup P, Keene DR, Bächinger HP, Brennan RG, Valentin-Hansen P. Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction. Mol Cell 2002; 9:23 - 30; http://dx.doi.org/10.1016/S1097-2765(01)00436-1; PMID: 11804583
   PubMed Web of Science ®Google Scholar
• Tétart F, Bouché JP. Regulation of the expression of the cell-cycle gene ftsZ by DicF antisense RNA. Division does not require a fixed number of FtsZ molecules. Mol Microbiol 1992; 6:615 - 20; http://dx.doi.org/10.1111/j.1365-2958.1992.tb01508.x; PMID: 1372677
   PubMed Web of Science ®Google Scholar
• Faubladier M, Cam K, Bouché JP. Escherichia coli cell division inhibitor DicF-RNA of the dicB operon. Evidence for its generation in vivo by transcription termination and by RNase III and RNase E-dependent processing. J Mol Biol 1990; 212:461 - 71; http://dx.doi.org/10.1016/0022-2836(90)90325-G; PMID: 1691299
   PubMed Web of Science ®Google Scholar
• Arraiano CM, Mauxion F, Viegas SC, Matos RG, Séraphin B. Intracellular ribonucleases involved in transcript processing and decay: precision tools for RNA. Biochim Biophys Acta 2013; 1829:491 - 513; http://dx.doi.org/10.1016/j.bbagrm.2013.03.009; PMID: 23545199
   PubMed Web of Science ®Google Scholar
• Lee T, Feig AL. The RNA binding protein Hfq interacts specifically with tRNAs. RNA 2008; 14:514 - 23; http://dx.doi.org/10.1261/rna.531408; PMID: 18230766
   PubMed Web of Science ®Google Scholar
• Salim NN, Faner MA, Philip JA, Feig AL. Requirement of upstream Hfq-binding (ARN)x elements in glmS and the Hfq C-terminal region for GlmS upregulation by sRNAs GlmZ and GlmY. Nucleic Acids Res 2012; 40:8021 - 32; http://dx.doi.org/10.1093/nar/gks392; PMID: 22661574
   PubMed Web of Science ®Google Scholar
• Serganov A, Nudler E. A decade of riboswitches. Cell 2013; 152:17 - 24; http://dx.doi.org/10.1016/j.cell.2012.12.024; PMID: 23332744
   PubMed Web of Science ®Google Scholar
• Loh E, Dussurget O, Gripenland J, Vaitkevicius K, Tiensuu T, Mandin P, Repoila F, Buchrieser C, Cossart P, Johansson J. A trans-acting riboswitch controls expression of the virulence regulator PrfA in Listeria monocytogenes. Cell 2009; 139:770 - 9; http://dx.doi.org/10.1016/j.cell.2009.08.046; PMID: 19914169
   PubMed Web of Science ®Google Scholar
• Sedlazeck FJ, Rescheneder P, von Haeseler A. NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Bioinformatics 2013; 29:2790 - 1; http://dx.doi.org/10.1093/bioinformatics/btt468; PMID: 23975764
   PubMed Web of Science ®Google Scholar
• Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 2010; 26:2204 - 7; http://dx.doi.org/10.1093/bioinformatics/btq351; PMID: 20639541
   PubMed Web of Science ®Google Scholar
• Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010; 26:139 - 40; http://dx.doi.org/10.1093/bioinformatics/btp616; PMID: 19910308
   PubMed Web of Science ®Google Scholar