Methods for selecting effective siRNA target sequences using a variety of statistical and analytical techniques

Methods in Molecular Biology

Volumn 942, Issue , 2013, Pages 17-55

  Takasaki, Shigeru ^a  

^a NONE

Author keywords

AiRNA; Average gene silencing; Bayes' theorem; Decision tree learning; Estimation of gene silencing; Gene silencing; Hidden Markov model; RNA interference; SiRNA design

Indexed keywords

SMALL INTERFERING RNA;

ALGORITHM; ANALYTIC METHOD; ARTICLE; BAYES THEOREM; DECISION TREE; GENE; GENE SILENCING; HIDDEN MARKOV MODEL; MAMMAL; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROBABILITY; RNA SEQUENCE; SEQUENCE ANALYSIS; STATISTICAL ANALYSIS;

EID: 84934439072     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-119-6_2     Document Type: Article

References (56)

1. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans . Nature 391: 806-811
2. Sharp PA (2001) RNA interference-2001. Genes Dev 15:485-490
3. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in mammalian cell culture. Nature 411: 494-498
4. Elbashir SM, Lendeckel W, Tuschl T (2001) RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev 15:188-200
5. Dykxhoorn DM, Navia CD, Sharp PA (2003) Killing the messenger: short RNAs that silence gene expression. Nat Rev 4:457-467
6. Hannon GJ (2002) RNA interference. Nature 418:244-251
7. Holen T, Amarzguioui M, Wiiger MT, Babaie E, Prydz H (2002) Positional effects of short interfering RNAs targeting the human coagulation trigger tissue factor. Nucleic Acids Res 30:1757-1766
8. Elbashir SM, Martinez J, Patkaniowska A, Lendeckel W, Tuschl T (2001) Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J 20:6877-6888
9. Kumar R, Conklin DS, Mittal V (2003) Highthroughput selection of effective RNAi probes for gene silencing. Genome Res 13:2333-2340
10. Mittal V (2004) Improving the efficiency of RNA interference in mammals. Nat Rev Genet 5:355-365
11. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115:199-208
12. Khvorova A, Reynolds A, Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115:209-216
13. Chalk AM, Wahlestedt C, Sonnhammer ELL (2004) Improved and automated prediction of effective siRNA. Biochem Biophys Res Commun 319:264-274
14. Teramoto R, Aoki M, Kimura T, Kanaoka M (2005) Prediction of siRNA functionality using generalized string kernel and support vector machine. FEBS Lett 579:2878-2882
15. Naito Y, Yamada T, Ui-Tei K, Morishita S, Saigo K (2004) siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference. Nucleic Acids Res 32:W124-W129
16. Santoyo J, Vaguerizas JM, Dapozo J (2004) Highly specific and accurate selection of siRNAs for high-throughput functional assays. Bioinformatics 21:1376-1382
17. Truss M, Swat M, Kielbasa SM, Schafer R, Herzed H, Hagemeier C (2005) HuSiDa-the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells. Nucleic Acids Res 33:D108-D111
18. Reynolds A, Leake D, Boese Q, Scaringe S, Marshall WS, Khvorova A (2004) Rational siRNA design for RNA interference. Nat Biotechnol 22:326-330
19. Ui-Tei K, Naito Y, Takahashi F, Haraguchi T, Ohki-Hamazaki H, Juni A, Ueda R, Saigou K (2004) Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res 32: 936-948
20. Amarzguioui M, Prydz H (2004) An algorithm for selection of functional siRNA sequences. Biochem Biophys Res Commun 316: 1050-1058
21. Hsieh AC, Bo R, Monola J, Vazquez F, Bare O, Khvorova A, Scaringe S, Sellers WR (2004) A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: determinants of gene silencing for use in cell-based screens. Nucleic Acids Res 32:893-901
22. Jagla B, Aulner N, Kelly PD, Song D, Volchuk A, Zatorski A, Shum D, Mayer T, De Angelis DA, Ouerfelli O, Rutishauser U, Rothman JE (2005) Sequence characteristics of functional siRNAs. RNA 11:864-872
23. Huesken D, Lange J, Mikanin C, Weiler J, Asselbergs F, Warner J, Meloon B, Engel S, Rosenberg A, Cohen D, Labow M, Reinhardt M, Natt F, Hall J (2005) Design of a genome-wide siRNA library using an artificial neural network. Nat Biotechnol 23:995-1001
24. Snove O Jr, Nedland M, Fjeldstad SH, Humberset H, Birkeland OR, Grunfeld T, Saetrom PO (2004) Designing effective siRNAs with off-target control. Biochem Biophys Res Commun 325:769-773
25. Durbin R, Eddy SR, Krogh A, Mitchison G (1998) Biological sequence analysis- probabilistic models of proteins and nucleic acids. Cambridge University Press, Cambridge
26. Takasaki S (2009) Selecting effective siRNA target sequences by using Bayes' theorem. Comput Biol Chem 33:368-372
27. Takasaki S, Kawamura Y, Konagaya A (2006) Selecting effective siRNA sequences by using radial basis function network and decision tree learning. BMC Bioinform 7(Suppl 5):S22
28. Takasaki S, Kotani S, Konagaya A (2004) An effective method for selecting siRNA target sequences in mammalian cells. Cell Cycle 3: 790-795
29. Takasaki S, Kotani S, Konagaya A (2005) Selecting effective siRNA target sequences for mammalian genes. RNA Biol 2:21-27
30. Takasaki S, Kawamura Y, Konagaya A (2006) Selecting effective siRNA sequences based on the self-organizing map and statistical techniques. Comput Biol Chem 30:169-178
31. Takasaki S, Konagaya A (2006) Comparative analyses for selecting effective siRNA sequences. Chem-Bioinform J 6:69-84
32. Takasaki S, Kawamura Y (2007) Using radial basis function networks and significance testing to select effective siRNA sequences, Comput . Stat Data Anal 51:6476-6487
33. Elbashir SM, Harborth J, Weber K, Tuschl T (2002) Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods 26:199-213
34. Ladunga I (2007) More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature. Nucleic Acids Res 35:433-440
35. Holen T (2006) Efficient prediction of siRNAs with siRNA rules 1.0: an open-source JAVA approach to siRNA algorithms. RNA 12: 1620-1625
36. Heale BSE, Sifer HS, Bowers C, Rossi JJ (2005) siRNA target site secondary structure predictions using local stable substructures. Nucleic Acids Res 33:e-30
37. Luo KQ, Chang DC (2004) The gene silencing efficacy of siRNA is strongly dependent on the local structure of mRNA at the target region. Biochem Biophys Res Commun 318:303-310
38. Bohula EA, Salisbury AJ, Sohail M, Playford MP, Riedemann J, Southern EM, Macaulay VM (2003) The efficacy of small interfering RNAs targeted to the type I insulin-like growth factor receptor (IGFIR) is in fluenced by secondary structure in the IGFIR transcript. J Biol Chem 278:15991-15997
39. Chan CY, Carmack CS, Long DD, Maliyekkel A, Shao Y, Roninson IB, Ding Y (2009) A structural interpretation of the effect of GC-content on efficiency of RNA interference. BMC Bioinform 10(Suppl 1):S33
40. Vig K, Lewis N, Moore EG, Pillai S, Dennis VA, Singh SR (2009) Secondary RNA structure and its role in RNA interference to silence the respiratory syncytial virus fusion protein gene. Mol Biotechnol 43:200-211
41. Saetrom P, Snove O Jr (2004) A comparison of siRNA efficacy predictors. Biochem Biophys Res Commun 321:247-253
42. Shabalina SA, Spiridonov AN, Ogurtsov AY (2006) Computational models with thermodynamic and composition features improve siRNA design. BMC Bioinform 7:65
43. Vert J, Foveau N, Lajaunie C, Vandenbrouck Y (2006) An accurate and interpretable model for siRNA efficacy prediction. BMC Bioinform 7:520
44. Matveeva O, Nechipurenko Y, Rossi L, Moore B, Sactrom P, Ogurtsov AY, Atkins JF, Shabalina SA (2007) Comparison of approaches for rational siRNA design leading to a new efficient and transparent method. Nucleic Acids Res 35:e63
45. Lu ZJ, Mathews DH (2008) Efficient siRNA selection using hybridization thermodynamics. Nucleic Acids Res 36:640-647
46. Wang X, Wang X, Varma RK, Beauchamp L, Magdaleno S, Sendera TJ (2009) Selection of hyperfunctional siRNAs with improved potency and specificity. Nucleic Acids Res 37:e152
47. Klingelhoefer JW, Moutsianas L, Holmes C (2009) Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency. Bioinformatics 25:1594-1601
48. Gong W, Ren Y, Zhou H, Wang Y, Kang S, Li T (2008) siDRM: an effective and generally applicable online siRNA design tool. Bioinformatics 24:2405-2406
49. Patzel V (2007) In silico selection of active siRNA. Drug Discov Today 12:139-148
50. Tafer H, Ameres SL, Obemosterer G, Gebeshuber CA, Schroeder R (2008) The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol 26: 578-583
51. Walton SP, Wu M, Gredell JA, Chan C (2010) Designing highly active siRNAs for therapeutic applications. FEBS J 277:4806-4813
52. Ahmed F, Raghava GP (2011) Designing of highly effective complementary and mismatch siRNAs for silencing a gene. PLoS One 6: e23443
53. Chaudhary A, Srivastava S, Garg S (2011) Development of a software tool and criteria evaluation for efficient design of small interfering RNA. Biochem Biophys Res Commun 404: 313-320
54. Katoh T, Suzuki T (2007) Specific residues at every third position of siRNA shape its efficient RNAi activity. Nucleic Acids Res 35:e27
55. Quinlan JR (1986) Induction of decision trees. Mach Learn 1:81-106
56. Saetrom P (2004) Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming. Bioinformatics 20:3055-3063