Almagro Armenteros JJ, Tsirigos KD, Sønderby CK, Petersen TN, Winther O, Brunak S, von Heijne G, Nielsen H (2019) SignalP 5.0 improves signal peptide predictions using deep neural networks, Nat. Biotechnol. 37:420–423. https://doi.org/10.1038/s41587-019-0036-z
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Article CAS PubMed Google Scholar
Andrews S (2010) FastQC: A Quality Control Tool for High Throughput Sequence Data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Arnvig KB, Comas I, Thomson NR, Houghton J, Boshoff HI, Croucher NJ, Rose G, Perkins TT, Parkhill J, Dougan G, Young DB (2011) Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis. PLoS Pathog 7:e1002342. https://doi.org/10.1371/journal.ppat.1002342
Article CAS PubMed PubMed Central Google Scholar
Bagchi G, Chauhan S, Sharma D, Tyagi JS (2005) Transcription and autoregulation of the Rv3134c-devR-devS operon of mycobacterium tuberculosis. Microbiology 151(12):4045–4053. https://doi.org/10.1099/mic.0.28333-0
Article CAS PubMed Google Scholar
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37:W202–W208. https://doi.org/10.1093/nar/gkp335
Article CAS PubMed PubMed Central Google Scholar
Banerjee A, Dubnau E, Quemard A, Balasubramanian V, Um KS, Wilson T, Collins D, De Lisle G, Jacobs WR (1994) inhA, a gene encoding a target for isoniazid and ethionamide in mycobacterium tuberculosis. Science 263(5144):227–230. https://doi.org/10.1126/science.8284673
Article CAS PubMed Google Scholar
Berthet FX, Rasmussen PB, Rosenkrands I, Andersen P, Gicquel B (1998) A mycobacterium tuberculosis operon encoding ESAT-6 and a novel low-molecular-mass culture filtrate protein (CFP-10). Microbiology 144(11):3195–3203. https://doi.org/10.1099/00221287-144-11-3195
Article CAS PubMed Google Scholar
Bigi F, Alito A, Romano MI, Zumarraga M, Caimi K, Cataldi A (2000) The gene encoding P27 lipoprotein and a putative antibiotic-resistance gene form an operon in mycobacterium tuberculosis and Mycobacterium bovis. Microbiology 146(4):1011–1018. https://doi.org/10.1099/00221287-146-4-1011
Article CAS PubMed Google Scholar
Blum M, Chang H-Y, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD (2020) The InterPro protein families and domains database: 20 years on. Nucleic Acids Res 49:D344–D354. https://doi.org/10.1093/nar/gkaa977
Article CAS PubMed Central Google Scholar
Brosius J (2014) The persistent contributions of RNA to eukaryotic Gen(om)e architecture and cellular function. Cold Spring Harb Perspect Biol 6:a016089. https://doi.org/10.1101/cshperspect.a016089
Article CAS PubMed PubMed Central Google Scholar
Brosius J, Raabe CA (2016) What is an RNA? A Top Layer for RNA Classification. RNA Biol 13:140–144. https://doi.org/10.1080/15476286.2015.1128064
Article PubMed PubMed Central Google Scholar
Brosius J, Tiedge H (2004) RNomenclature. RNA Biol 1:81–83. https://doi.org/10.4161/rna.1.2.1228
Article CAS PubMed Google Scholar
Callen BP, Shearwin KE, Egan JB (2004) Transcriptional interference between convergent promoters caused by elongation over the promoter. Mol Cell 14:647–656. https://doi.org/10.1016/j.molcel.2004.05.010
Article CAS PubMed Google Scholar
Casali N, White AM, Riley LW (2006) Regulation of the mycobacterium tuberculosis mce1 operon. J Bacteriol 188(2):441–449. https://doi.org/10.1128/JB.188.2.441-449.2006
Article CAS PubMed PubMed Central Google Scholar
Chao Y, Vogel J (2016) A 3’UTR-derived small RNA provides the regulatory noncoding arm of the inner membrane stress response. Mol Cell 61:352–363. https://doi.org/10.1016/j.molcel.2015.12.023
Article CAS PubMed Google Scholar
Chao Y, Papenfort K, Reinhardt R, Sharma CM, Vogel J (2012) An atlas of Hfq-bound transcripts reveals 3′ UTRs as a genomic reservoir of regulatory small RNAs: Hfq-dependent small RNAs from 3′ UTRs. EMBO J 31:4005–4019. https://doi.org/10.1038/emboj.2012.229
Article CAS PubMed PubMed Central Google Scholar
Chauhan R, Ravi J, Datta P, Chen T, Schnappinger D, Bassler KE, Balázsi G, Gennaro ML (2016) Reconstruction and topological characterization of the sigma factor regulatory network of Mycobacterium tuberculosis. Nat Commun 7:1–12. https://doi.org/10.1038/ncomms11062
Cheah H-L, Raabe CA, Lee L-P, Rozhdestvensky TS, Citartan M, Ahmed SA, Tang T-H (2018) Bacterial regulatory RNAs: complexity, function, and putative drug targeting. Crit Rev Biochem Mol Biol 53:335–355. https://doi.org/10.1080/10409238.2018.1473330
Article CAS PubMed Google Scholar
Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K, Osborne J, Quail MA, Rajandream M-A, Rogers J, Rutter S, Seeger K, Skelton J, Squares R, Squares S, Sulston JE, Taylor K, Whitehead S, Barrell BG (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537–544. https://doi.org/10.1038/31159
Article CAS PubMed Google Scholar
Cortes T, Schubert OT, Rose G, Arnvig KB, Comas I, Aebersold R, Young DB (2013) Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis. Cell Rep 5:1121–1131. https://doi.org/10.1016/j.celrep.2013.10.031
Article CAS PubMed PubMed Central Google Scholar
Dar D, Sorek (2018) Extensive reshaping of bacterial operons by programmed mRNA decay, PLoS Genet. 14. https://doi.org/10.1371/journal.pgen.1007354
Desgranges E, Caldelari I, Marzi S, Lalaouna D (2020). Navigation through the twists and turns of RNA sequencing technologies: Application to bacterial regulatory RNAs. Biochimica et Biophysica Acta (BBA) - Gene Regul Mech 1863(3), 194506. https://doi.org/10.1016/j.bbagrm.2020.194506
Dugar G, Herbig A, Förstner KU, Heidrich N, Reinhardt R, Nieselt K, Sharma CM (2013) High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates, PLoS Genet. 9. https://doi.org/10.1371/journal.pgen.1003495
Ewels P, Magnusson M, Lundin S, Käller M (2016) MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32:3047–3048. https://doi.org/10.1093/bioinformatics/btw354
Article CAS PubMed PubMed Central Google Scholar
Förstner KU, Vogel J, Sharma CM (2014) READemption-a tool for the computational analysis of deep-sequencing-based transcriptome data. Bioinforma Oxf Engl 30:3421–3423. https://doi.org/10.1093/bioinformatics/btu533
Ganapathy U, Marrero J, Calhoun S, Eoh H, de Carvalho LPS, Rhee K, Ehrt S (2015) Two enzymes with redundant fructose bisphosphatase activity sustain gluconeogenesis and virulence in Mycobacterium tuberculosis. Nat Commun 6(1):7912. https://doi.org/10.1038/ncomms8912
Article CAS PubMed PubMed Central Google Scholar
Gao LY, Pak M, Kish R, Kajihara K, Brown EJ (2006) A mycobacterial operon essential for virulence in vivo and invasion and intracellular persistence in macrophages. Infect Immun 74(3):1757–1767. https://doi.org/10.1128/IAI.74.3.1757-1767.2006
Article CAS PubMed PubMed Central Google Scholar
Gardner PP, Barquist L, Bateman A, Nawrocki EP, Weinberg Z (2011) RNIE: Genome-wide prediction of bacterial intrinsic terminators. Nucleic Acids Res 39:5845–5852. https://doi.org/10.1093/nar/gkr168
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