Predicting sRNAs and Their Targets in Bacteria

Genomics, Proteomics and Bioinformatics

Volumn 10, Issue 5, 2012, Pages 276-284

  Li, Wuju ^a   Ying, Xiaomin ^a   Lu, Qixuan ^a,b   Chen, Linxi ^b  

^a INSTITUTE OF BASIC MEDICAL SCIENCES   (China)

^b UNIVERSITY OF SOUTH CHINA   (China)

Author keywords

Bacterial; Bioinformatics; Prediction; SRNA; Target

Indexed keywords

BACTERIAL RNA; NUCLEOTIDE; TRANSFER RNA;

BACTERIAL GENETICS; BIOINFORMATICS; CONTROLLED STUDY; ENVIRONMENTAL CHANGE; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE TARGETING; GENOMICS; PHYLOGENY; PREDICTION; PROTEIN TARGETING; REGULATORY RNA SEQUENCE; REVIEW; RNA STRUCTURE; VALIDATION PROCESS;

ARTIFICIAL INTELLIGENCE; BACTERIA; BACTERIAL PROTEINS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GENES, BACTERIAL; MODELS, GENETIC; NUCLEIC ACID CONFORMATION; RNA, BACTERIAL; RNA, MESSENGER;

BACTERIA (MICROORGANISMS);

EID: 84870324468     PISSN: 16720229     EISSN: 22103244     Source Type: Journal    
DOI: 10.1016/j.gpb.2012.09.004     Document Type: Review

References (88)

1. Huang H.Y., Chang H.Y., Chou C.H., Tseng C.P., Ho S.Y., Yang C.D., et al. SRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. Nucleic Acids Res 2009, 37:D150-D154.
2. Livny J., Waldor M.K. Identification of small RNAs in diverse bacterial species. Curr Opin Microbiol 2007, 10:96-101.
3. Gottesman S., Storz G. Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 2011, 3.
4. Vanderpool C.K., Balasubramanian D., Lloyd C.R. Dual-function RNA regulators in bacteria. Biochimie 2011, 93:1943-1949.
5. Cao Y., Wu J., Liu Q., Zhao Y., Ying X., Cha L., et al. SRNATarBase: a comprehensive database of bacterial sRNA targets verified by experiments. RNA 2010, 16:2051-2057.
6. Guillier M., Gottesman S. Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs. Mol Microbiol 2006, 59:231-247.
7. Valentin-Hansen P., Johansen J., Rasmussen A.A. Small RNAs controlling outer membrane porins. Curr Opin Microbiol 2007, 10:152-155.
8. Massé E., Vanderpool C.K., Gottesman S. Effect of RyhB small RNA on global iron use in Escherichia coli. J Bacteriol 2005, 187:6962-6971.
9. Massé E., Salvail H., Desnoyers G., Arguin M. Small RNAs controlling iron metabolism. Curr Opin Microbiol 2007, 10:140-145.
10. Večerek B., Moll I., Bläsi U. Control of Fur synthesis by the non-coding RNA RyhB and iron-responsive decoding. EMBO J 2007, 26:965-975.
11. Lenz D.H., Miller M.B., Zhu J., Kulkarni R.V., Bassler B.L. CsrA and three redundant small RNAs regulate quorum sensing in Vibrio cholerae. Mol Microbiol 2005, 58:1186-1202.
12. Tu K.C., Bassler B.L. Multiple small RNAs act additively to integrate sensory information and control quorum sensing in Vibrio harveyi. Genes Dev 2007, 21:221-233.
13. Romby P., Vandenesch F., Wagner E.G.H. The role of RNAs in the regulation of virulence-gene expression. Curr Opin Microbiol 2006, 9:229-236.
14. Toledo-Arana A., Repoila F., Cossart P. Small noncoding RNAs controlling pathogenesis. Curr Opin Microbiol 2007, 10:182-188.
15. Voss B., Georg J., Schön V., Ude S., Hess W.R. Biocomputational prediction of non-coding RNAs in model cyanobacteria. BMC Genomics 2009, 10:123.
16. Acebo P., Martin-Galiano A.J., Navarro S., Zaballos Á., Amblar M. Identification of 88 regulatory small RNAs in the TIGR4 strain of the human pathogen Streptococcus pneumoniae. RNA 2012, 18:530-546.
17. Rivas E., Eddy S. Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2001, 2:8.
18. Washietl S., Hofacker I.L., Stadler P.F. Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A 2005, 102:2454-2459.
19. Pedersen J.S., Bejerano G., Siepel A., Rosenbloom K., Lindblad-Toh K., Lander E.S., et al. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol 2006, 2:e33.
20. Livny J., Teonadi H., Livny M., Waldor M.K. High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS One 2008, 3:e3197.
21. Livny J., Fogel M.A., Davis B.M., Waldor M.K. SRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes. Nucleic Acids Res 2005, 33:4096-4105.
22. Marchais A., Naville M., Bohn C., Bouloc P., Gautheret D. Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles. Genome Res 2009, 19:1084-1092.
23. Carter R.J., Dubchak I., Holbrook S.R. A computational approach to identify genes for functional RNAs in genomic sequences. Nucleic Acids Res 2001, 29:3928-3938.
24. Sætrom P., Sneve R., Kristiansen K.I., Snøve O., Grünfeld T., Rognes T., et al. Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming. Nucleic Acids Res 2005, 33:3263-3270.
25. Wang C., Ding C., Meraz R.F., Holbrook S.R. PSoL: a positive sample only learning algorithm for finding non-coding RNA genes. Bioinformatics 2006, 22:2590-2596.
26. Tran T.T., Zhou F., Marshburn S., Stead M., Kushner S.R., Xu Y. De novo computational prediction of non-coding RNA genes in prokaryotic genomes. Bioinformatics 2009, 25:2897-2905.
27. Wagner E.G.H. Kill the messenger: bacterial antisense RNA promotes mRNA decay. Nat Struct Mol Biol 2009, 16:804-806.
28. Zhang Y., Sun S., Wu T., Wang J., Liu C., Chen L., et al. Identifying Hfq-binding small RNA targets in Escherichia coli. Biochem Biophys Res Commun 2006, 343:950-955.
29. Tjaden B., Goodwin S.S., Opdyke J.A., Guillier M., Fu D.X., Gottesman S., et al. Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Res 2006, 34:2791-2802.
30. Tjaden B. TargetRNA: a tool for predicting targets of small RNA action in bacteria. Nucleic Acids Res 2008, 36:W109-W113.
31. Mandin P., Repoila F., Vergassola M., Geissmann T., Cossart P. Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets. Nucleic Acids Res 2007, 35:962-974.
32. Busch A., Richter A.S., Backofen R. IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics 2008, 24:2849-2856.
33. Zhao Y., Li H., Hou Y., Cha L., Cao Y., Wang L., et al. Construction of two mathematical models for prediction of bacterial sRNA targets. Biochem Biophys Res Commun 2008, 372:346-350.
34. Cao Y., Zhao Y., Cha L., Ying X., Wang L., Shao N., et al. sRNATarget: a web server for prediction of bacterial sRNA targets. Bioinformation 2009, 3:364-366.
35. Eggenhofer F., Tafer H., Stadler P.F., Hofacker I.L. RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Res 2011, 39:W149-W154.
36. Ying X., Cao Y., Wu J., Liu Q., Cha L., Li W. STarPicker: a method for efficient prediction of bacterial sRNA targets based on a two-step model for hybridization. PLoS One 2011, 6:e22705.
37. Vogel J., Wagner E.G.H. Target identification of small noncoding RNAs in bacteria. Curr Opin Microbiol 2007, 10:262-270.
38. Pichon C., Felden B. Small RNA gene identification and mRNA target predictions in bacteria. Bioinformatics 2008, 24:2807-2813.
39. Backofen R., Hess W.R. Computational prediction of sRNAs and their targets in bacteria. RNA Biol 2010, 7:33-42.
40. Sharma C.M., Vogel J. Experimental approaches for the discovery and characterization of regulatory small RNA. Curr Opin Microbiol 2009, 12:536-546.
41. Kozomara A., Griffiths-Jones S. MiRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011, 39:D152-D157.
42. Eddy S.R. Computational genomics of noncoding RNA genes. Cell 2002, 109:137-140.
43. Storz G., Altuvia S., Wassarman K.M. An abundance of RNA regulators. Annu Rev Biochem 2005, 74:199-217.
44. Hershberg R., Altuvia S., Margalit H. A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res 2003, 31:1813-1820.
45. Vogel J., Sharma C.M. How to find small non-coding RNAs in bacteria. Biol Chem 2005, 386:1219-1238.
46. Argaman L., Hershberg R., Vogel J., Bejerano G., Wagner E.G.H., Margalit H., et al. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol 2001, 11:941-950.
47. Rivas E., Klein R.J., Jones T.A., Eddy S.R. Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr Biol 2001, 11:1369-1373.
48. Rose D., Hertel J., Reiche K., Stadler P.F., Hackermüller J. NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences. Genomics 2008, 92:65-74.
49. Lu X., Goodrich-Blair H., Tjaden B. Assessing computational tools for the discovery of small RNA genes in bacteria. RNA 2011, 17:1635-1647.
50. Li W., Xiong M.M. Tclass: tumor classification system based on gene expression profile. Bioinformatics 2002, 18:325-326.
51. Richter A.S., Schleberger C., Backofen R., Steglich C. Seed-based IntaRNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1. Bioinformatics 2010, 26:1-5.
52. Storz G., Opdyke J.A., Zhang A. Controlling mRNA stability and translation with small, noncoding RNAs. Curr Opin Microbiol 2004, 7:140-144.
53. Hofacker I.L., Fontana W., Stadler P.F., Bonhoeffer L.S., Tacker M., Schuster P. Fast folding and comparison of RNA secondary structures. Monatsh Chem 1994, 125:167-188.
54. Lorenz R., Bernhart S.H., Höner Zu Siederdissen C., Tafer H., Flamm C., Stadler P.F., et al. ViennaRNA package 2.0. Algorithms Mol Biol 2011, 6:26.
55. Rehmsmeier M., Steffen P., Höchsmann M., Giegerich R. Fast and effective prediction of microRNA/target duplexes. RNA 2004, 10:1507-1517.
56. Kruger J., Rehmsmeier M. RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 2006, 34:W451-W454.
57. Tafer H., Hofacker I.L. RNAplex: a fast tool for RNA-RNA interaction search. Bioinformatics 2008, 24:2657-2663.
58. Muckstein U., Tafer H., Hackermuller J., Bernhart S.H., Stadler P.F., Hofacker I.L. Thermodynamics of RNA-RNA binding. Bioinformatics 2006, 22:1177-1182.
59. Alkan C., Karakoc E., Nadeau J.H., Sahinalp S.C., Zhang K. RNA-RNA interaction prediction and antisense RNA target search. J Comput Biol 2006, 13:267-282.
60. Chitsaz H., Salari R., Sahinalp S.C., Backofen R. A partition function algorithm for interacting nucleic acid strands. Bioinformatics 2009, 25:i365-i373.
61. Salari R., Backofen R., Sahinalp S.C. Fast prediction of RNA-RNA interaction. Algorithms Mol Biol 2010, 5:5.
62. Huang F.W.D., Qin J., Reidys C.M., Stadler P.F. Partition function and base pairing probabilities for RNA-RNA interaction prediction. Bioinformatics 2009, 25:2646-2654.
63. Kato Y., Sato K., Hamada M., Watanabe Y., Asai K., Akutsu T. RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinformatics 2010, 26:i460-i466.
64. Li A.X., Marz M., Qin J., Reidys C.M. RNA-RNA interaction prediction based on multiple sequence alignments. Bioinformatics 2011, 27:456-463.
65. Seemann S.E., Richter A.S., Gesell T., Backofen R., Gorodkin J. PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences. Bioinformatics 2011, 27:211-219.
66. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31:3406-3415.
67. Sharma C.M., Darfeuille F., Plantinga T.H., Vogel J. A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites. Genes Dev 2007, 21:2804-2817.
68. Muckstein U., Tafer H., Bernhart S.H., Hernandez-Rosales M., Vogel J., Stadler P.F., et al. Translational control by RNA-RNA interaction: improved computation of RNA-RNA binding thermodynamics. Bioinformatics research and development 2008, vol. 13:114-127. Springer, Berlin, Heidelberg.
69. Bompfünewerer A.F., Backofen R., Bernhart S.H., Hertel J., Hofacker I.L., Stadler P.F., et al. Variations on RNA folding and alignment: lessons from Benasque. J Math Biol 2008, 56:129-144.
70. Stephan B., Ullrike M., Ivo H. RNA accessibility in cubic time. Algorithms Mol Biol 2011, 6:3.
71. Gardner P.P., Daub J., Tate J.G., Nawrocki E.P., Kolbe D.L., Lindgreen S., et al. Rfam: updates to the RNA families database. Nucleic Acids Res 2009, 37:D136-D140.
72. Muppirala U.K., Honavar V.G., Dobbs D. Predicting RNA-protein interactions using only sequence information. BMC Bioinformatics 2011, 12:489.
73. Pellin D., Miotto P., Ambrosi A., Cirillo D.M., Di Serio C. A genome-wide identification analysis of small regulatory RNAs in mycobacterium tuberculosis by RNA-Seq and conservation analysis. PLoS One 2012, 7:e32723.
74. Oliver H.F., Orsi R.H., Ponnala L., Keich U., Wang W., Sun Q., et al. Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs. BMC Genomics 2009, 10:641.
75. Yoder-Himes D.R., Chain P.S.G., Zhu Y., Wurtzel O., Rubin E.M., Tiedje J.M., et al. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci U S A 2009, 106:3976.
76. Camarena L., Bruno V., Euskirchen G., Poggio S., Snyder M. Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing. PLoS Pathog 2010, 6:e1000834.
77. Kolev N.G., Franklin J.B., Carmi S., Shi H., Michaeli S., Tschudi C. The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution. PLoS Pathog 2010, 6:e1001090.
78. Sharma C.M., 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.
79. Raghavan R., Groisman E.A., Ochman H. Genome-wide detection of novel regulatory RNAs in E. coli. Genome Res 2011, 21:1487-1497.
80. Atsuko S., Motomu M., Kiriko H., Wataru N., Reiko H., Kenji N., et al. Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. BMC Genomics 2011, 12:428.
81. Kumar R., Lawrence M.L., Watt J., Cooksey A.M., Burgess S.C., Nanduri B. RNA-Seq based transcriptional map of bovine respiratory disease pathogen " Histophilus somni 2336" PloS One 2012, 7:e29435.
82. Chi S.W., Zang J.B., Mele A., Darnell R.B. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 2009, 460:479-486.
83. Sittka A., Lucchini S., Papenfort K., Sharma C.M., Rolle K., Binnewies T.T., et al. Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet 2008, 4:e1000163.
84. Hafner M., Landthaler M., Burger L., Khorshid M., Hausser J., Berninger P., et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010, 141:129-141.
85. Zhang C., Darnell R.B. Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat Biotechnol 2011, 29:607-614.
86. Mauger D.M., Weeks K.M. Toward global RNA structure analysis. Nat Biotechnol 2010, 28:1178-1179.
87. Underwood J.G., Uzilov A.V., Katzman S., Onodera C.S., Mainzer J.E., Mathews D.H., et al. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods 2010, 7:995-1001.
88. Kertesz M., Wan Y., Mazor E., Rinn J.L., Nutter R.C., Chang H.Y., et al. Genome-wide measurement of RNA secondary structure in yeast. Nature 2010, 467:103-107.