NocoRNAc: Characterization of non-coding RNAs in prokaryotes

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Herbig, Alexander ^a   Nieselt, Kay ^a  

^a UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PROCESS; EXPERIMENTAL TECHNIQUES; EXPRESSION PATTERNS; INTERGENIC REGIONS; MICROBIAL GENOMES; PROTEIN CODING REGIONS; PROTEIN-CODING GENES; STREPTOMYCES COELICOLOR;

BACTERIA; FORECASTING; GENES; PROTEINS; TRANSCRIPTION;

NUCLEIC ACIDS;

BACTERIA (MICROORGANISMS); PROKARYOTA; STREPTOMYCES COELICOLOR;

BACTERIAL RNA; COMPLEMENTARY RNA; UNTRANSLATED RNA;

ARTICLE; CLASSIFICATION; COMPUTER PROGRAM; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETICS; PROMOTER REGION; REGULATOR GENE; STREPTOMYCES COELICOLOR;

GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS, GENETIC; RNA, ANTISENSE; RNA, BACTERIAL; RNA, UNTRANSLATED; SOFTWARE; STREPTOMYCES COELICOLOR; TERMINATOR REGIONS, GENETIC;

EID: 79251567076     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-40     Document Type: Article

References (66)

1. Eddy SR. Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2001, 2(12):919-929. 10.1038/35103511, 11733745.
2. Storz G. An expanding universe of noncoding RNAs. Science 2002, 296(5571):1260-1263. 10.1126/science.1072249, 12016301.
3. Repoila F, Darfeuille F. Small regulatory non-coding RNAs in bacteria: physiology and mechanistic aspects. Biol Cell 2009, 101(2):117-131. 10.1042/BC20070137, 19076068.
4. Barrandon C, Spiluttini B, Bensaude O. Non-coding RNAs regulating the transcriptional machinery. Biol Cell 2008, 100(2):83-95. 10.1042/BC20070090, 18199047.
5. Wang X, Song X, Glass CK, Rosenfeld MG. The Long Arm of Long Noncoding RNAs: Roles as Sensors Regulating Gene Transcriptional Programs. Cold Spring Harb Perspect Biol 2011, 3.
6. Pichon C, Felden B. Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. Proc Natl Acad Sci USA 2005, 102(40):14249-14254. 10.1073/pnas.0503838102, 1242290, 16183745.
7. Giangrossi M, Prosseda G, Tran CN, Brandi A, Colonna B, Falconi M. A novel antisense RNA regulates at transcriptional level the virulence gene icsA of Shigella flexneri. Nucleic Acids Res 2010, 38(10):3362-3375. 10.1093/nar/gkq025, 2879508, 20129941.
8. Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C, Schrenzel J, Francçis P, Vandenesch F, Gaspin C, Romby P. A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Res 2009, 37(21):7239-7257. 10.1093/nar/gkp668, 2790875, 19786493.
9. Abu-Qatouseh LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J, Rozhdestvensky TS, Peters G, von Eiff C, Becker K. Identification of differentially expressed small non-protein-coding RNAs in Staphylococcus aureus displaying both the normal and the small-colony variant phenotype. J Mol Med 2010, 88(6):565-575. 10.1007/s00109-010-0597-2, 20151104.
10. Muffler A, Fischer D, Hengge-Aronis R. The RNA-binding protein HF-I, known as a host factor for phage Qbeta RNA replication, is essential for rpoS translation in Escherichia coli. Genes Dev 1996, 10(9):1143-1151. 10.1101/gad.10.9.1143, 8654929.
11. Zhang A, Altuvia S, Tiwari A, Argaman L, Hengge-Aronis R, Storz G. The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein. EMBO J 1998, 17(20):6061-6068. 10.1093/emboj/17.20.6061, 1170932, 9774349.
12. Sledjeski DD, Whitman C, Zhang A. Hfq is necessary for regulation by the untranslated RNA DsrA. J Bacteriol 2001, 183(6):1997-2005. 10.1128/JB.183.6.1997-2005.2001, 95095, 11222598.
13. Brantl S. Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr Opin Microbiol 2007, 10(2):102-109. 10.1016/j.mib.2007.03.012, 17387036.
14. Hüttenhofer A, Vogel J. Experimental approaches to identify non-coding RNAs. Nucleic Acids Res 2006, 34(2):635-646. 1351373, 16436800.
15. Altuvia S. Identification of bacterial small non-coding RNAs: experimental approaches. Curr Opin Microbiol 2007, 10(3):257-261. 10.1016/j.mib.2007.05.003, 17553733.
16. Sharma CM, Vogel J. Experimental approaches for the discovery and characterization of regulatory small RNA. Curr Opin Microbiol 2009, 12(5):536-546. 10.1016/j.mib.2009.07.006, 19758836.
17. Sittka A, Sharma CM, Rolle K, Vogel J. Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes. RNA Biol 2009, 6(3):266-275. 10.4161/rna.6.3.8332, 19333007.
18. Albrecht M, Sharma CM, Reinhardt R, Vogel J, Rudel T. Deep sequencing-based discovery of the Chlamy-dia trachomatis transcriptome. Nucleic Acids Res 2010, 38(3):868-877. 10.1093/nar/gkp1032, 2817459, 19923228.
19. Irnov I, Sharma CM, Vogel J, Winkler WC. Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res 2010, 38(19):6637-6651. 10.1093/nar/gkq454, 2965217, 20525796.
20. Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J. The primary transcriptome of the major human pathogen Heli-cobacter pylori. Nature 2010, 464(7286):250-255. 10.1038/nature08756, 20164839.
21. Schlüter J, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Jänicke S, Becker J, Giegerich R, Becker A. A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genomics 2010, 17:245.
22. Vogel J, Sharma CM. How to find small non-coding RNAs in bacteria. Biol Chem 2005, 386(12):1219-1238. 10.1515/BC.2005.140, 16336117.
23. Pichon C, Felden B. Small RNA gene identification and mRNA target predictions in bacteria. Bioinformatics 2008, 24(24):2807-2813. 10.1093/bioinformatics/btn560, 18974076.
24. Washietl S, Hofacker IL, Stadler PF. Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci USA 2005, 102(7):2454-2459. 10.1073/pnas.0409169102, 548974, 15665081.
25. Gruber AR, Findeiss S, Washietl S, Hofacker IL, Stadler PF. RNAZ 2.0: IMPROVED NONCODING RNA DETECTION. Pac Symp Biocomput 2010, 15:69-79.
26. Rivas E, Eddy SR. Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2001, 2:8-8. 10.1186/1471-2105-2-8, 64605, 11801179.
27. Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol 2006, 2:e33. 10.1371/journal.pcbi.0020033, 1440920, 16628248.
28. Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, Tompa M, Ruzzo WL. A computational pipeline for high-throughput discovery of cis-regulatory noncoding RNA in prokaryotes. PLoS Comput Biol 2007, 3(7). 10.1371/journal.pcbi.0030126, 1913097, 17616982.
29. Uzilov AV, Keegan JM, Mathews DH. Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change. BMC Bioinformatics 2006, 7:173-173. 10.1186/1471-2105-7-173, 1570369, 16566836.
30. Tseng HH, Weinberg Z, Gore J, Breaker RR, Ruzzo WL. Finding non-coding RNAs through genome-scale clustering. J Bioinform Comput Biol 2009, 7(2):373-388. 10.1142/S0219720009004126, 19340921.
31. Childs L, Nikoloski Z, May P, Walther D. Identification and classification of ncRNA molecules using graph properties. Nucleic Acids Res 2009, 37(9). 10.1093/nar/gkp206, 2685108, 19339518.
32. Tran TT, Zhou F, Marshburn S, Stead M, Kushner SR, Xu Y. De novo computational prediction of non-coding RNA genes in prokaryotic genomes. Bioinformatics 2009, 25(22):2897-2905. 10.1093/bioinformatics/btp537, 2773258, 19744996.
33. Saetrom P, Sneve R, Kristiansen KI, Snove O, Grünfeld T, Rognes T, Seeberg E. Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming. Nucleic Acids Res 2005, 33(10):3263-3270. 10.1093/nar/gki644, 1143698, 15942029.
34. Yachie N, Numata K, Saito R, Kanai A, Tomita M. Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model. Gene 2006, 372:171-181. 10.1016/j.gene.2005.12.034, 16564143.
35. Salari R, Aksay C, Karakoc E, Unrau PJ, Hajirasouliha I, Sahinalp SC. smyRNA: a novel Ab initio ncRNA gene finder. PLoS One 2009, 4(5). 10.1371/journal.pone.0005433, 2673033, 19415115.
36. Livny J, Teonadi H, Livny M, Waldor MK. High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS One 2008, 3(9). 10.1371/journal.pone.0003197, 2527527, 18787707.
37. Tjaden B. Prediction of small, noncoding RNAs in bacteria using heterogeneous data. J Math Biol 2008, 56(1-2):183-200. 10.1007/s00285-007-0079-5, 17354017.
38. Livny J, Brencic A, Lory S, Waldor MK. Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2. Nucleic Acids Res 2006, 34(12):3484-3493. 10.1093/nar/gkl453, 1524904, 16870723.
39. Sridhar J, Narmada SR, Sabarinathan R, Ou HY, Deng Z, Sekar K, Rafi ZA, Rajakumar K. sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes. PLoS One 2010, 5(8). 10.1371/journal.pone.0011970, 2916834, 20700540.
40. Bentley SD, Chater KF, Cerdeño-Tárraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 2002, 417(6885):141-147. 10.1038/417141a, 12000953.
41. Axmann IM, Kensche P, Vogel J, Kohl S, Herzel H, Hess WR. Identification of cyanobacterial non-coding RNAs by comparative genome analysis. Genome Biol 2005, 6(9). 10.1186/gb-2005-6-9-r73, 1242208, 16168080.
42. Voss B, Georg J, Schön V, Ude S, Hess WR. Biocomputational prediction of non-coding RNAs in model cyanobacteria. BMC Genomics 2009, 10:123-123. 10.1186/1471-2164-10-123, 2662882, 19309518.
43. Xiao B, Li W, Guo G, Li B, Liu Z, Jia K, Guo Y, Mao X, Zou Q. Identification of small noncoding RNAs in Helicobacter pylori by a bioinformatics-based approach. Curr Microbiol 2009, 58(3):258-263. 10.1007/s00284-008-9318-2, 19123032.
44. Kingsford CL, Ayanbule K, Salzberg SL. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol 2007, 8(2). 10.1186/gb-2007-8-2-r22, 1852404, 17313685.
45. Benham CJ, Bi C. The analysis of stress-induced duplex destabilization in long genomic DNA sequences. J Comput Biol 2004, 11(4):519-543. 10.1089/cmb.2004.11.519, 15579230.
46. Wang H, Noordewier M, Benham CJ. Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters. Genome Res 2004, 14(8):1575-1584. 10.1101/gr.2080004, 509266, 15289476.
47. Wang H, Benham CJ. Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress. BMC Bioinformatics 2006, 7:248-248. 10.1186/1471-2105-7-248, 1468432, 16677393.
48. Pánek J, Bobek J, Mikulík K, Basler M, J V. Biocomputational prediction of small non-coding RNAs in Streptomyces. BMC Genomics 2008, 9:217-217. 2422843, 18477385.
49. Swiercz JP, Bobek J, Bobek J, Haiser HJ, Di Berardo C, Tjaden B, Elliot MA. Small non-coding RNAs in Streptomyces coelicolor. Nucleic Acids Res 2008, 36(22):7240-7251. 10.1093/nar/gkn898, 2602773, 19008244.
50. D'Alia D, Nieselt K, Steigele S, Müller J, Verburg I, Takano E. Noncoding RNA of glutamine synthetase I modulates antibiotic production in Streptomyces coelicolor A3(2). J Bacteriol 2010, 192(4):1160-1164. 2812974, 19966003.
51. Battke F, Herbig A, Wentzel A, Jakobsen T, Bonin M, Hodgson D, Wohlleben W, Ellingsen T, Nieselt K. SysMO Stream Consortium A Technical Platform for Generating Reproducible Expression Data from Streptomyces Coelicolor Batch Cultivations. Software Tools and Algorithms for Biological Systems 2010, Springer, Arabnia H, SysMO Stream Consortium.
52. Nieselt K, Battke F, Herbig A, Bruheim P, Wentzel A, Jakobsen T, Sletta H, Alam MT, Merlo ME, Moore J, Omara WA, Morrissey ER, Juarez-Hermosillo MA, Rodríguez-García A, Nentwich M, Thomas L, Iqbal M, Legaie R, Gaze WH, Challis GL, Jansen RC, Dijkhuizen L, Rand DA, Wild DL, Bonin M, Reuther J, Wohlleben W, Smith MC, Burroughs NJ, Martin JF, Hodgson DA, Takano E, Breitling R, Ellingsen TE, Wellington EM. The dynamic architecture of the metabolic switch in Streptomyces coelicolor. BMC Genomics 2010, 11:10-10. 10.1186/1471-2164-11-10, 2824715, 20053288.
53. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A. Rfam: updates to the RNA families database. Nucleic Acids Res 2009, (37 Database):136-140.
54. Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics 2009, 25(10):1335-1337. 10.1093/bioinformatics/btp157, 2732312, 19307242.
55. Gautheret D, Lambert A. Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. J Mol Biol 2001, 313(5):1003-1011. 10.1006/jmbi.2001.5102, 11700055.
56. R Development Core Team R: A Language and Environment for Statistical Computing 2009, R Foundation for Statistical Computing, Vienna, Austria, [ISBN 3-900051-07-0], R Development Core Team.
57. Gentleman R, Carey V, Bates D, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini A, Sawitzki G, Smith C, Smyth G, Tierney L, Yang J, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biology 2004, 5(10):R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
58. Busch A, Richter AS, Backofen R. IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics 2008, 24(24):2849-2856. 10.1093/bioinformatics/btn544, 2639303, 18940824.
59. Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004, 14(7):1394-1403. 10.1101/gr.2289704, 442156, 15231754.
60. Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 2010, 5(6).
61. Battke F, Symons S, Nieselt K. Mayday-integrative analytics for expression data. BMC Bioinformatics 2010, 11:121-121. 2848234, 20214778.
62. Rodríguez-García A, Barreiro C, Santos-Beneit F, Sola-Landa A, Martín JF. Genome-wide transcriptomic and proteomic analysis of the primary response to phosphate limitation in Streptomyces coelicolor M145 and in a DeltaphoP mutant. Proteomics 2007, 7(14):2410-2429.
63. Bode J, Winkelmann S, Götze S, Spiker S, Tsutsui K, Bi C, A K P, Benham C. Correlations between scaffold/matrix attachment region (S/MAR) binding activity and DNA duplex destabilization energy. J Mol Biol 2006, 358(2):597-613. 10.1016/j.jmb.2005.11.073, 16516920.
64. Polonskaya Z, Benham CJ, Hearing J. Role for a region of helically unstable DNA within the Epstein-Barr virus latent cycle origin of DNA replication oriP in origin function. Virology 2004, 328(2):282-291. 10.1016/j.virol.2004.07.023, 15464848.
65. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25(5):955-964. 10.1093/nar/25.5.955, 146525, 9023104.
66. Rederstorff M, Bernhart SH, Tanzer A, Zywicki M, Perfler K, Lukasser M, Hofacker IL, Hüttenhofer A. RN-Pomics: defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles. Nucleic Acids Res 2010, 38(10). 10.1093/nar/gkq057, 2879528, 20150415.