Starpicker: A method for efficient prediction of bacterial sRNA targets based on a Two-Step model for hybridization

PLoS ONE

Volumn 6, Issue 7, 2011, Pages

  Ying, Xiaomin ^a   Cao, Yuan ^b   Wu, Jiayao ^a   Liu, Qian ^a   Cha, Lei ^a   Li, Wuju ^a  

^a INSTITUTE OF BASIC MEDICAL SCIENCES   (China)

^b 90th Hospital of Jinan   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; DOUBLE STRANDED RNA; MESSENGER RNA; TRANSFER RNA; BACTERIAL PROTEIN;

ACCURACY; ARTICLE; CLASSIFIER; COMPUTER PREDICTION; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; GENE INTERACTION; GENE TARGETING; GENETIC MODEL; GENETIC SCREENING; GENETIC STABILITY; MATHEMATICAL COMPUTING; NONHUMAN; NUCLEOTIDE BINDING SITE; NUCLEOTIDE SEQUENCE; QUANTITATIVE ANALYSIS; RNA HYBRIDIZATION; THERMOSTABILITY; ARTIFICIAL INTELLIGENCE; BASE PAIRING; BIOLOGICAL MODEL; CHEMISTRY; GENETICS; GENOMICS; METABOLISM; NUCLEIC ACID HYBRIDIZATION; PROCHLOROCOCCUS; REGULATORY RNA SEQUENCE; RNA STABILITY;

BACTERIA (MICROORGANISMS);

ARTIFICIAL INTELLIGENCE; BACTERIAL PROTEINS; BASE PAIRING; GENOMICS; MODELS, GENETIC; NUCLEIC ACID HYBRIDIZATION; PROCHLOROCOCCUS; REGULATORY SEQUENCES, RIBONUCLEIC ACID; RNA STABILITY; RNA, BACTERIAL; RNA, MESSENGER;

EID: 79960694944     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0022705     Document Type: Article

References (44)

1. Vogel J, Sharma CM, (2005) How to find small noncoding RNAs in bacteria. Biol Chem 386: 1219-1238.
2. Huang HY, Chang HY, Chou CH, Tseng CP, Ho SY, et al. (2009) sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. Nucleic Acids Res 37: D150-D154.
3. Guillier M, Gottesman S, (2006) Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs. Mol Microbiol 59: 231-247.
4. Lenz DH, Miller MB, Zhu J, Kulkarni RV, Bassler BL, (2005) CsrA and three redundant small RNAs regulate quorum sensing in Vibrio cholerae. Mol Microbiol 58: 1186-1202.
5. Tu KC, Bassler BL, (2007) Multiple small RNAs act additively to integrate sensory information and control quorum sensing in Vibrio harveyi. Genes Dev 21: 221-233.
6. Toledo-Arana A, Repoila F, Cossart P, (2007) Small noncoding RNAs controlling pathogenesis. Curr Opin Microbiol 10: 182-188.
7. Romby P, Vandenesch F, Wagner EG, (2006) The role of RNAs in the regulation of virulence-gene expression. Curr Opin Microbiol 9: 229-236.
8. Storz G, Altuvia S, Wassarman KM, (2005) An abundance of RNA regulators. Annu Rev Biochem 74: 199-217.
9. Storz G, Opdyke JA, Zhang A, (2004) Controlling mRNA stability and translation with small, noncoding RNAs. Curr Opin Microbiol 7: 140-144.
10. Sun X, Zhulin I, Wartell RM, (2002) Predicted structure and phyletic distribution of the RNA-binding protein Hfq, Nucleic Acids Res 30: 3662-3671.
11. Valentin-Hansen P, Eriksen M, Udesen C, (2004) The bacterial Sm-like protein Hfq: a key player in RNA transactions, Mol Microbiol 51: 1525-1533.
12. Cao Y, Wu J, Liu Q, Zhao Y, Ying X, et al. (2010) sRNATarBase: A comprehensive database of bacterial sRNA targets verified by experiments. RNA 16: 2051-2057.
13. Zhang Y, Sun S, Wu T, Wang J, Liu C, et al. (2006) Identifying Hfq-binding small RNA targets in Escherichia coli. Biochem Biophys Res Commun 343: 950-955.
14. Tjaden B, Goodwin SS, Opdyke JA, Guillier M, Fu DX, et al. (2006) Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Res 34: 2791-2802.
15. Tjaden B, (2008) TargetRNA: a tool for predicting targets of small RNA action in bacteria. Nucleic Acids Res 36: W109-W113.
16. Mandin P, Repoila F, Vergassola M, Geissmann T, Cossart P, (2007) Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets. Nucl Acids Res 35: 962-974.
17. Zhao Y, Li H, Hou Y, Cha L, Cao Y, et al. (2008) Construction of two mathematical models for prediction of bacterial sRNA targets. Biochem Biophys Res Commun 372: 346-350.
18. Cao Y, Zhao Y, Cha L, Ying X, Wang L, et al. (2009) sRNATarget: a web server for prediction of bacterial sRNA targets. Bioinformation 3: 364-366.
19. Li W, Xiong M, (2002) Tclass: tumor classification system based on gene expression profile. Bioinformatics 18: 325-326.
20. Alkan C, Karakoc E, Nadeau JH, Sahinalp SC, Zhang K, (2006) RNA-RNA interaction prediction and antisense RNA target search. J Comput Biol 13: 267-282.
21. Krüger J, Rehmsmeier M, (2006) RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 34: 451-454.
22. Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R, (2004) Fast and effective prediction of microRNA/target duplexes. RNA 10: 1507-1517.
23. Sharma CM, Darfeuille F, Plantinga TH, Vogel J, (2007) A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites. Genes & Development 21: 2804-2817.
24. Tafer H, Hofacker IL, (2008) RNAplex: a fast tool for RNA-RNA interaction search. Bioinformatics 24: 2657-2663.
25. Mückstein U, Tafer H, Bernhart SH, Hernandez-Rosales M, Vogel J, et al. (2008) Translational Control by RNA-RNA Interaction Improved Computation of RNA-RNA Binding Thermodynamics. In Elloumi,M,et al (eds) Bioinformatics Research and Development, Vol 13 of Communications in Computer and Information Science Springer, Berlin, Heidelberg, 114-127.
26. Busch A, Richter AS, Backofen R, (2008) IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics 24: 2849-2856.
27. Ameres SL, Martinez J, Schroeder R, (2007) Molecular basis for target RNA recognition and cleavage by human RISC. Cell 130: 101-112.
28. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E, (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39: 1278-1284.
29. Köberle C, Kaufmann SHE, Patzel V, (2006) Selecting effective siRNAs based on guide RNA structure. Nat Protocols 1: 1832-1839.
30. Kretschmer-Kazemi Far R, Sczakiel G, (2003) The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides. Nucl Acids Res 31: 4417-4424.
31. Long D, Lee R, Williams P, Chan CY, Ambros V, et al. (2007) Potent effect of target structure on microRNA function. Nat Struct Mol Biol 14: 287-294.
32. Schubert S, Grünweller A, Erdmann VA, Kurreck J, (2005) Local RNA Target Structure Influences siRNA Efficacy: Systematic Analysis of Intentionally Designed Binding Regions. Journal of Molecular Biology 348: 883-893.
33. Shao Y, Chan CY, Maliyekkel A, Lawrence CE, Roninson IB, et al. (2007) Effect of target secondary structure on RNAi efficiency. RNA 13: 1631-1640.
34. Rajewsky N, (2006) microRNA target predictions in animals. Nat Genet 38 (Suppl): 8-13.
35. Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL, (2008) The Vienna RNA websuite. Nucleic Acids Res 36: W70-W74.
36. Lu ZJ, Mathews DH, (2008) Efficient siRNA selection using hybridization thermodynamics. Nucl Acids Res 36: 640-647.
37. Zhao Y, Samal E, Srivastava D, (2005) Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436: 214-220.
38. Richter AS, Schleberger C, Backofen R, Steglich C, (2010) Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1. Bioinformatics 26: 1-5.
39. Gerlach W, Giegerich R, (2006) GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. Bioinformatics 22: 762-764.
40. Wu B, Cha L, Du Z, Ying X, Li H, et al. (2007) Construction of mathematical model for high-level expression of foreign genes in pPIC9 vector and its verification. Biochem Biophys Res Commun 354: 498-504.
41. Storz G, Opdyke JA, Zhang A, (2004) Controlling mRNA stability and translation with small, noncoding RNAs. Current Opinion in Microbiology 7: 140-144.
42. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW, (2010) GenBank. Nucl Acids Res 38: D46-D51.
43. Xia T, SantaLucia J, Burkard ME, Kierzek R, Schroeder SJ, et al. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37: 14719-14735.
44. Sharma CM, Darfeuille F, Plantinga TH, Vogel J, (2007) A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites. Genes Dev 21: 2804-2817.