References
- Jacob F, Perrin D, Sanchez C, Monod J. Operon: a group of genes with the expression coordinated by an operator. C R Hebd Seances Acad Sci 1960;250:1727-1729.
- Ishihama A. Functional modulation of Escherichia coli RNA polymerase. Annu Rev Microbiol 2000;54:499-518. https://doi.org/10.1146/annurev.micro.54.1.499
- Pérez-Rueda E, Collado-Vides J. The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res 2000;28:1838-1847. https://doi.org/10.1093/nar/28.8.1838
- Waters LS, Storz G. Regulatory RNAs in bacteria. Cell 2009; 136:615-628. https://doi.org/10.1016/j.cell.2009.01.043
- Ma JC, Newman AJ, Hayward RS. Internal promoters of the rpoBC operon of Escherichia coli. Mol Gen Genet 1981;184: 548-550. https://doi.org/10.1007/BF00352538
- Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, et al. Transcriptome complexity in a genome- reduced bacterium. Science 2009;326:1268-1271. https://doi.org/10.1126/science.1176951
- Qiu Y, Cho BK, Park YS, Lovley D, Palsson BØ, Zengler K. Structural and operational complexity of the Geobacter sulfurreducens genome. Genome Res 2010;20:1304-1311. https://doi.org/10.1101/gr.107540.110
- Sorek R, Cossart P. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet 2010;11:9-16.
- Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, et al. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 2010;464:250-255. https://doi.org/10.1038/nature08756
- Cho BK, Zengler K, Qiu Y, Park YS, Knight EM, Barrett CL, et al. The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol 2009;27:1043-1049. https://doi.org/10.1038/nbt.1582
- Selinger DW, Cheung KJ, Mei R, Johansson EM, Richmond CS, Blattner FR, et al. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol 2000;18:1262-1268. https://doi.org/10.1038/82367
- Toledo-Arana A, Solano C. Deciphering the physiological blueprint of a bacterial cell: revelations of unanticipated complexity in transcriptome and proteome. Bioessays 2010;32: 461-467. https://doi.org/10.1002/bies.201000020
- Rasmussen S, Nielsen HB, Jarmer H. The transcriptionally active regions in the genome of Bacillus subtilis. Mol Microbiol 2009;73:1043-1057. https://doi.org/10.1111/j.1365-2958.2009.06830.x
- Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, et al. Prevalence of transcription promoters within archaeal operons and coding sequences. Mol Syst Biol 2009;5:285.
- McGrath PT, Lee H, Zhang L, Iniesta AA, Hottes AK, Tan MH, et al. High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons. Nat Biotechnol 2007;25:584-592. https://doi.org/10.1038/nbt1294
- Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet- Revillet H, Balestrino D, et al. The Listeria transcriptional landscape from saprophytism to virulence. Nature 2009;459: 950-956. https://doi.org/10.1038/nature08080
- Pinto AC, Melo-Barbosa HP, Miyoshi A, Silva A, Azevedo V. Application of RNA-seq to reveal the transcript profile in bacteria. Genet Mol Res 2011;10:1707-1718. https://doi.org/10.4238/vol10-3gmr1554
- Pareek CS, Smoczynski R, Tretyn A. Sequencing technologies and genome sequencing. J Appl Genet 2011;52:413-435. https://doi.org/10.1007/s13353-011-0057-x
- Metzker ML. Sequencing technologies: the next generation. Nat Rev Genet 2010;11:31-46. https://doi.org/10.1038/nrg2626
- Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009;10:57-63. https://doi.org/10.1038/nrg2484
- Soon WW, Hariharan M, Snyder MP. High-throughput sequencing for biology and medicine. Mol Syst Biol 2013;9:640.
- Mamanova L, Andrews RM, James KD, Sheridan EM, Ellis PD, Langford CF, et al. FRT-seq: amplification-free, strand-specific transcriptome sequencing. Nat Methods 2010;7:130-132. https://doi.org/10.1038/nmeth.1417
- Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 2010; 7:709-715. https://doi.org/10.1038/nmeth.1491
- Loudig O, Brandwein-Gensler M, Kim RS, Lin J, Isayeva T, Liu C, et al. Illumina whole-genome complementary DNA-mediated annealing, selection, extension and ligation platform: assessing its performance in formalin-fixed, paraffin-embedded samples and identifying invasion pattern-related genes in oral squamous cell carcinoma. Hum Pathol 2011;42:1911-1922. https://doi.org/10.1016/j.humpath.2011.02.011
- Zhu YY, Machleder EM, Chenchik A, Li R, Siebert PD. Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. Biotechniques 2001;30: 892-897.
- Armour CD, Castle JC, Chen R, Babak T, Loerch P, Jackson S, et al. Digital transcriptome profiling using selective hexamer priming for cDNA synthesis. Nat Methods 2009;6:647-649. https://doi.org/10.1038/nmeth.1360
- He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW. The antisense transcriptomes of human cells. Science 2008;322:1855-1857. https://doi.org/10.1126/science.1163853
- Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, et al. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 2009;37:e123. https://doi.org/10.1093/nar/gkp596
- Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, et al. Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet 2008;4:e1000163. https://doi.org/10.1371/journal.pgen.1000163
- Liu JM, Livny J, Lawrence MS, Kimball MD, Waldor MK, Camilli A. Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res 2009;37:e46. https://doi.org/10.1093/nar/gkp080
- Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J, et al. Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res 2012;40:2020-2031. https://doi.org/10.1093/nar/gkr904
- Raghavan R, Groisman EA, Ochman H. Genome-wide detection of novel regulatory RNAs in E. coli. Genome Res 2011;21:1487-1497. https://doi.org/10.1101/gr.119370.110
- Mitschke J, Vioque A, Haas F, Hess WR, Muro-Pastor AM. Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120. Proc Natl Acad Sci U S A 2011;108:20130-20135. https://doi.org/10.1073/pnas.1112724108
- Jager D, Sharma CM, Thomsen J, Ehlers C, Vogel J, Schmitz RA. Deep sequencing analysis of the Methanosarcina mazei Go1 transcriptome in response to nitrogen availability. Proc Natl Acad Sci U S A 2009;106:21878-21882. https://doi.org/10.1073/pnas.0909051106
- Filiatrault MJ, Stodghill PV, Myers CR, Bronstein PA, Butcher BG, Lam H, et al. Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. PLoS One 2011;6:e29335. https://doi.org/10.1371/journal.pone.0029335
- Irnov I, Sharma CM, Vogel J, Winkler WC. Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res 2010; 38:6637-6651. https://doi.org/10.1093/nar/gkq454
- Berk AJ, Sharp PA. Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell 1977;12:721-732. https://doi.org/10.1016/0092-8674(77)90272-0
- Voorhies M, Foo CK, Sil A. Experimental annotation of the human pathogen Histoplasma capsulatum transcribed regions using high-resolution tiling arrays. BMC Microbiol 2011;11:216 https://doi.org/10.1186/1471-2180-11-216
- Herring CD, Raffaelle M, Allen TE, Kanin EI, Landick R, Ansari AZ, et al. Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays. J Bacteriol 2005;187: 6166-6174. https://doi.org/10.1128/JB.187.17.6166-6174.2005
- Mitschke J, Georg J, Scholz I, Sharma CM, Dienst D, Bantscheff J, et al. An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci U S A 2011;108:2124- 2129. https://doi.org/10.1073/pnas.1015154108
- Sesto N, Wurtzel O, Archambaud C, Sorek R, Cossart P. The excludon: a new concept in bacterial antisense RNA-mediated gene regulation. Nat Rev Microbiol 2013;11:75-82.
- Guell M, Yus E, Lluch-Senar M, Serrano L. Bacterial transcriptomics: what is beyond the RNA horiz-ome? Nat Rev Microbiol 2011;9:658-669. https://doi.org/10.1038/nrmicro2620
- Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, Rubin EM, Tiedje JM, et al. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci U S A 2009;106:3976-3981. https://doi.org/10.1073/pnas.0813403106
- Perkins TT, Kingsley RA, Fookes MC, Gardner PP, James KD, Yu L, et al. A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet 2009;5:e1000569. https://doi.org/10.1371/journal.pgen.1000569
- Dornenburg JE, Devita AM, Palumbo MJ, Wade JT. Widespread antisense transcription in Escherichia coli. MBio 2010;1.
- Lasa I, Toledo-Arana A, Dobin A, Villanueva M, de los Mozos IR, Vergara-Irigaray M, et al. Genome-wide antisense transcription drives mRNA processing in bacteria. Proc Natl Acad Sci U S A 2011;108:20172-20177. https://doi.org/10.1073/pnas.1113521108
- Hirakawa H, Harwood CS, Pechter KB, Schaefer AL, Greenberg EP. Antisense RNA that affects Rhodopseudomonas palustris quorum-sensing signal receptor expression. Proc Natl Acad Sci U S A 2012;109:12141-12146. https://doi.org/10.1073/pnas.1200243109
- Chen BS, Hsu CY, Liou JJ. Robust design of biological circuits: evolutionary systems biology approach. J Biomed Biotechnol 2011;2011:304236.
Cited by
- Regulatory genomics: Combined experimental and computational approaches vol.51, pp.4, 2015, https://doi.org/10.1134/S1022795415040067
- : transcriptomic and metabolomic landscapes reveal highly integrated physiological networks vol.284, pp.1857, 2017, https://doi.org/10.1098/rspb.2017.0360
- Comparative Transcriptome Analysis of Vibrio splendidus JZ6 Reveals the Mechanism of Its Pathogenicity at Low Temperatures vol.82, pp.7, 2016, https://doi.org/10.1128/AEM.03486-15