Exploring the transcription start sites and other genomic features facilitates the accurate identification and annotation of small RNAs across multiple stress conditions in Mycobacterium tuberculosis

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

Article  CAS  Google Scholar 

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

Article  CAS  Google Scholar 

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

Article  CAS  PubMed  PubMed Central  Google Scholar 

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