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Volumn 11, Issue 6, 2010, Pages

Design and evaluation of genome-wide libraries for RNA interference screens

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA; LIPID PHOSPHATASE; PHOSPHATASE; SMALL INTERFERING RNA; UNCLASSIFIED DRUG; PHOSPHOPROTEIN PHOSPHATASE;

EID: 78049437928     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2010-11-6-r61     Document Type: Article
Times cited : (67)

References (58)
  • 1
    • 0032545933 scopus 로고    scopus 로고
    • Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans.
    • 10.1038/35888, 9486653
    • Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998, 391:806-811. 10.1038/35888, 9486653.
    • (1998) Nature , vol.391 , pp. 806-811
    • Fire, A.1    Xu, S.2    Montgomery, M.K.3    Kostas, S.A.4    Driver, S.E.5    Mello, C.C.6
  • 2
    • 35348996554 scopus 로고    scopus 로고
    • Specialization and evolution of endogenous small RNA pathways.
    • 10.1038/nrg2179, 17943195
    • Chapman EJ, Carrington JC. Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet 2007, 8:884-896. 10.1038/nrg2179, 17943195.
    • (2007) Nat Rev Genet , vol.8 , pp. 884-896
    • Chapman, E.J.1    Carrington, J.C.2
  • 3
    • 45549089565 scopus 로고    scopus 로고
    • The art and design of genetic screens: RNA interference.
    • 10.1038/nrg2364, 18521077
    • Boutros M, Ahringer J. The art and design of genetic screens: RNA interference. Nat Rev Genet 2008, 9:554-566. 10.1038/nrg2364, 18521077.
    • (2008) Nat Rev Genet , vol.9 , pp. 554-566
    • Boutros, M.1    Ahringer, J.2
  • 5
    • 33745941420 scopus 로고    scopus 로고
    • Cellular phenotyping by RNAi.
    • 10.1093/bfgp/ell007, 16769679
    • Fuchs F, Boutros M. Cellular phenotyping by RNAi. Brief Funct Genomic Proteomic 2006, 5:52-56. 10.1093/bfgp/ell007, 16769679.
    • (2006) Brief Funct Genomic Proteomic , vol.5 , pp. 52-56
    • Fuchs, F.1    Boutros, M.2
  • 6
    • 1642273831 scopus 로고    scopus 로고
    • An algorithm for selection of functional siRNA sequences.
    • 10.1016/j.bbrc.2004.02.157, 15044091
    • Amarzguioui M, Prydz H. An algorithm for selection of functional siRNA sequences. Biochem Biophys Res Commun 2004, 316:1050-1058. 10.1016/j.bbrc.2004.02.157, 15044091.
    • (2004) Biochem Biophys Res Commun , vol.316 , pp. 1050-1058
    • Amarzguioui, M.1    Prydz, H.2
  • 7
    • 0036752785 scopus 로고    scopus 로고
    • RNAi in human cells: basic structural and functional features of small interfering RNA.
    • 10.1016/S1097-2765(02)00652-4, 12408823
    • Chiu YL, Rana TM. RNAi in human cells: basic structural and functional features of small interfering RNA. Mol Cell 2002, 10:549-561. 10.1016/S1097-2765(02)00652-4, 12408823.
    • (2002) Mol Cell , vol.10 , pp. 549-561
    • Chiu, Y.L.1    Rana, T.M.2
  • 8
    • 0142165224 scopus 로고    scopus 로고
    • Functional siRNAs and miRNAs exhibit strand bias.
    • 10.1016/S0092-8674(03)00801-8, 14567918
    • Khvorova A, Reynolds A, Jayasena SD. Functional siRNAs and miRNAs exhibit strand bias. Cell 2003, 115:209-216. 10.1016/S0092-8674(03)00801-8, 14567918.
    • (2003) Cell , vol.115 , pp. 209-216
    • Khvorova, A.1    Reynolds, A.2    Jayasena, S.D.3
  • 10
    • 10744225153 scopus 로고    scopus 로고
    • Asymmetry in the assembly of the RNAi enzyme complex.
    • 10.1016/S0092-8674(03)00759-1, 14567917
    • Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD. Asymmetry in the assembly of the RNAi enzyme complex. Cell 2003, 115:199-208. 10.1016/S0092-8674(03)00759-1, 14567917.
    • (2003) Cell , vol.115 , pp. 199-208
    • Schwarz, D.S.1    Hutvagner, G.2    Du, T.3    Xu, Z.4    Aronin, N.5    Zamore, P.D.6
  • 11
    • 1642346273 scopus 로고    scopus 로고
    • Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference.
    • 10.1093/nar/gkh247, 373388, 14769950
    • Ui-Tei K, Naito Y, Takahashi F, Haraguchi T, Ohki-Hamazaki H, Juni A, Ueda R, Saigo K. Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res 2004, 32:936-948. 10.1093/nar/gkh247, 373388, 14769950.
    • (2004) Nucleic Acids Res , vol.32 , pp. 936-948
    • Ui-Tei, K.1    Naito, Y.2    Takahashi, F.3    Haraguchi, T.4    Ohki-Hamazaki, H.5    Juni, A.6    Ueda, R.7    Saigo, K.8
  • 12
    • 34347229441 scopus 로고    scopus 로고
    • SIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database.
    • 10.1186/1471-2105-8-178, 1896181, 17540034
    • Shah JK, Garner HR, White MA, Shames DS, Minna JD. sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database. BMC Bioinformatics 2007, 8:178. 10.1186/1471-2105-8-178, 1896181, 17540034.
    • (2007) BMC Bioinformatics , vol.8 , pp. 178
    • Shah, J.K.1    Garner, H.R.2    White, M.A.3    Shames, D.S.4    Minna, J.D.5
  • 13
    • 75649110049 scopus 로고    scopus 로고
    • Selection of hyperfunctional siRNAs with improved potency and specificity.
    • 10.1093/nar/gkp864, 2794195, 19846596
    • Wang X, Varma RK, Beauchamp L, Magdaleno S, Sendera TJ. Selection of hyperfunctional siRNAs with improved potency and specificity. Nucleic Acids Res 2009, 37:e152. 10.1093/nar/gkp864, 2794195, 19846596.
    • (2009) Nucleic Acids Res , vol.37
    • Wang, X.1    Varma, R.K.2    Beauchamp, L.3    Magdaleno, S.4    Sendera, T.J.5
  • 14
    • 49649114607 scopus 로고    scopus 로고
    • RNAi screening in cultured Drosophila cells.
    • full_text, 18641945
    • Steinbrink S, Boutros M. RNAi screening in cultured Drosophila cells. Methods Mol Biol 2008, 420:139-153. full_text, 18641945.
    • (2008) Methods Mol Biol , vol.420 , pp. 139-153
    • Steinbrink, S.1    Boutros, M.2
  • 15
    • 0034612276 scopus 로고    scopus 로고
    • Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways.
    • 10.1073/pnas.110149597, 18635, 10823906
    • Clemens JC, Worby CA, Simonson-Leff N, Muda M, Maehama T, Hemmings BA, Dixon JE. Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways. Proc Natl Acad Sci USA 2000, 97:6499-6503. 10.1073/pnas.110149597, 18635, 10823906.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 6499-6503
    • Clemens, J.C.1    Worby, C.A.2    Simonson-Leff, N.3    Muda, M.4    Maehama, T.5    Hemmings, B.A.6    Dixon, J.E.7
  • 16
    • 0035942736 scopus 로고    scopus 로고
    • Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells.
    • 10.1038/35078107, 11373684
    • Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 2001, 411:494-498. 10.1038/35078107, 11373684.
    • (2001) Nature , vol.411 , pp. 494-498
    • Elbashir, S.M.1    Harborth, J.2    Lendeckel, W.3    Yalcin, A.4    Weber, K.5    Tuschl, T.6
  • 17
    • 0042972933 scopus 로고    scopus 로고
    • Activation of the interferon system by short-interfering RNAs.
    • 10.1038/ncb1038, 12942087
    • Sledz CA, Holko M, de Veer MJ, Silverman RH, Williams BR. Activation of the interferon system by short-interfering RNAs. Nat Cell Biol 2003, 5:834-839. 10.1038/ncb1038, 12942087.
    • (2003) Nat Cell Biol , vol.5 , pp. 834-839
    • Sledz, C.A.1    Holko, M.2    de Veer, M.J.3    Silverman, R.H.4    Williams, B.R.5
  • 18
    • 33747776448 scopus 로고    scopus 로고
    • ShRNA libraries and their use in cancer genetics.
    • 10.1038/nmeth921, 16929315
    • Bernards R, Brummelkamp TR, Beijersbergen RL. shRNA libraries and their use in cancer genetics. Nat Methods 2006, 3:701-706. 10.1038/nmeth921, 16929315.
    • (2006) Nat Methods , vol.3 , pp. 701-706
    • Bernards, R.1    Brummelkamp, T.R.2    Beijersbergen, R.L.3
  • 19
    • 33747754760 scopus 로고    scopus 로고
    • Lessons from Nature: microRNA-based shRNA libraries.
    • 10.1038/nmeth923, 16929316
    • Chang K, Elledge SJ, Hannon GJ. Lessons from Nature: microRNA-based shRNA libraries. Nat Methods 2006, 3:707-714. 10.1038/nmeth923, 16929316.
    • (2006) Nat Methods , vol.3 , pp. 707-714
    • Chang, K.1    Elledge, S.J.2    Hannon, G.J.3
  • 20
    • 33747794587 scopus 로고    scopus 로고
    • Genome-scale loss-of-function screening with a lentiviral RNAi library.
    • 10.1038/nmeth924, 16929317
    • Root DE, Hacohen N, Hahn WC, Lander ES, Sabatini DM. Genome-scale loss-of-function screening with a lentiviral RNAi library. Nat Methods 2006, 3:715-719. 10.1038/nmeth924, 16929317.
    • (2006) Nat Methods , vol.3 , pp. 715-719
    • Root, D.E.1    Hacohen, N.2    Hahn, W.C.3    Lander, E.S.4    Sabatini, D.M.5
  • 21
    • 38649099969 scopus 로고    scopus 로고
    • Strand-specific 5'-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity.
    • 10.1261/rna.789808, 2212253, 18094121
    • Chen PY, Weinmann L, Gaidatzis D, Pei Y, Zavolan M, Tuschl T, Meister G. Strand-specific 5'-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity. RNA 2008, 14:263-274. 10.1261/rna.789808, 2212253, 18094121.
    • (2008) RNA , vol.14 , pp. 263-274
    • Chen, P.Y.1    Weinmann, L.2    Gaidatzis, D.3    Pei, Y.4    Zavolan, M.5    Tuschl, T.6    Meister, G.7
  • 22
    • 24344500241 scopus 로고    scopus 로고
    • Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing.
    • 10.1089/108729003321629638, 12804036
    • Harborth J, Elbashir SM, Vandenburgh K, Manninga H, Scaringe SA, Weber K, Tuschl T. Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing. Antisense Nucleic Acid Drug Dev 2003, 13:83-105. 10.1089/108729003321629638, 12804036.
    • (2003) Antisense Nucleic Acid Drug Dev , vol.13 , pp. 83-105
    • Harborth, J.1    Elbashir, S.M.2    Vandenburgh, K.3    Manninga, H.4    Scaringe, S.A.5    Weber, K.6    Tuschl, T.7
  • 24
    • 33747762617 scopus 로고    scopus 로고
    • Enzymatically prepared RNAi libraries.
    • 10.1038/nmeth912, 16929314
    • Buchholz F, Kittler R, Slabicki M, Theis M. Enzymatically prepared RNAi libraries. Nat Methods 2006, 3:696-700. 10.1038/nmeth912, 16929314.
    • (2006) Nat Methods , vol.3 , pp. 696-700
    • Buchholz, F.1    Kittler, R.2    Slabicki, M.3    Theis, M.4
  • 25
    • 23144441141 scopus 로고    scopus 로고
    • E-RNAi: a web application to design optimized RNAi constructs.
    • 10.1093/nar/gki468, 1160229, 15980541
    • Arziman Z, Horn T, Boutros M. E-RNAi: a web application to design optimized RNAi constructs. Nucleic Acids Res 2005, 33:W582-588. 10.1093/nar/gki468, 1160229, 15980541.
    • (2005) Nucleic Acids Res , vol.33
    • Arziman, Z.1    Horn, T.2    Boutros, M.3
  • 26
    • 3242891277 scopus 로고    scopus 로고
    • DEQOR: a web-based tool for the design and quality control of siRNAs.
    • 10.1093/nar/gkh408, 441546, 15215362
    • Henschel A, Buchholz F, Habermann B. DEQOR: a web-based tool for the design and quality control of siRNAs. Nucleic Acids Res 2004, 32:W113-120. 10.1093/nar/gkh408, 441546, 15215362.
    • (2004) Nucleic Acids Res , vol.32
    • Henschel, A.1    Buchholz, F.2    Habermann, B.3
  • 27
    • 33748939584 scopus 로고    scopus 로고
    • Prevalence of off-target effects in Drosophila RNA interference screens.
    • 10.1038/nature05179, 16964239
    • Ma Y, Creanga A, Lum L, Beachy PA. Prevalence of off-target effects in Drosophila RNA interference screens. Nature 2006, 443:359-363. 10.1038/nature05179, 16964239.
    • (2006) Nature , vol.443 , pp. 359-363
    • Ma, Y.1    Creanga, A.2    Lum, L.3    Beachy, P.A.4
  • 28
    • 84855519090 scopus 로고    scopus 로고
    • Mdust software
    • mdust software. , http://compbio.dfci.harvard.edu/tgi/software/
  • 29
    • 0035905766 scopus 로고    scopus 로고
    • Role for a bidentate ribonuclease in the initiation step of RNA interference.
    • 10.1038/35053110, 11201747
    • Bernstein E, Caudy AA, Hammond SM, Hannon GJ. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 2001, 409:363-366. 10.1038/35053110, 11201747.
    • (2001) Nature , vol.409 , pp. 363-366
    • Bernstein, E.1    Caudy, A.A.2    Hammond, S.M.3    Hannon, G.J.4
  • 31
    • 23344438420 scopus 로고    scopus 로고
    • SiRNA-mediated off-target gene silencing triggered by a 7 nt complementation.
    • 10.1093/nar/gki762, 1184219, 16091630
    • Lin X, Ruan X, Anderson MG, McDowell JA, Kroeger PE, Fesik SW, Shen Y. siRNA-mediated off-target gene silencing triggered by a 7 nt complementation. Nucleic Acids Res 2005, 33:4527-4535. 10.1093/nar/gki762, 1184219, 16091630.
    • (2005) Nucleic Acids Res , vol.33 , pp. 4527-4535
    • Lin, X.1    Ruan, X.2    Anderson, M.G.3    McDowell, J.A.4    Kroeger, P.E.5    Fesik, S.W.6    Shen, Y.7
  • 36
    • 0033990048 scopus 로고    scopus 로고
    • Primer3 on the www for general users and for biologist programmers.
    • Rozen S, Skaletsky H. Primer3 on the www for general users and for biologist programmers. Methods Mol Biol 2000, 132:365-386.
    • (2000) Methods Mol Biol , vol.132 , pp. 365-386
    • Rozen, S.1    Skaletsky, H.2
  • 37
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
    • 10.1186/gb-2009-10-3-r25, 2690996, 19261174
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 38
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - the BLAST-like alignment tool.
    • 187518, 11932250
    • Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res 2002, 12:656-664. 187518, 11932250.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 41
    • 38449084517 scopus 로고    scopus 로고
    • Design and implementation of high-throughput RNAi screens in cultured Drosophila cells.
    • 10.1038/nprot.2007.250, 17853882
    • Ramadan N, Flockhart I, Booker M, Perrimon N, Mathey-Prevot B. Design and implementation of high-throughput RNAi screens in cultured Drosophila cells. Nat Protoc 2007, 2:2245-2264. 10.1038/nprot.2007.250, 17853882.
    • (2007) Nat Protoc , vol.2 , pp. 2245-2264
    • Ramadan, N.1    Flockhart, I.2    Booker, M.3    Perrimon, N.4    Mathey-Prevot, B.5
  • 42
    • 49649116149 scopus 로고    scopus 로고
    • FlyBase: a database for the Drosophila research community.
    • full_text, 18641940
    • Drysdale R. FlyBase: a database for the Drosophila research community. Methods Mol Biol 2008, 420:45-59. full_text, 18641940.
    • (2008) Methods Mol Biol , vol.420 , pp. 45-59
    • Drysdale, R.1
  • 44
    • 84855483977 scopus 로고    scopus 로고
    • NEXT-RNAi webpage
    • NEXT-RNAi webpage. , http://www.nextrnai.org/
  • 45
    • 33846066203 scopus 로고    scopus 로고
    • BeetleBase: the model organism database for Tribolium castaneum.
    • 10.1093/nar/gkl776, 1669707, 17090595
    • Wang L, Wang S, Li Y, Paradesi MS, Brown SJ. BeetleBase: the model organism database for Tribolium castaneum. Nucleic Acids Res 2007, 35:D476-479. 10.1093/nar/gkl776, 1669707, 17090595.
    • (2007) Nucleic Acids Res , vol.35
    • Wang, L.1    Wang, S.2    Li, Y.3    Paradesi, M.S.4    Brown, S.J.5
  • 48
    • 0035831034 scopus 로고    scopus 로고
    • Conserved role of a complement-like protein in phagocytosis revealed by dsRNA knockout in cultured cells of the mosquito, Anopheles gambiae.
    • 10.1016/S0092-8674(01)00267-7, 11257225
    • Levashina EA, Moita LF, Blandin S, Vriend G, Lagueux M, Kafatos FC. Conserved role of a complement-like protein in phagocytosis revealed by dsRNA knockout in cultured cells of the mosquito, Anopheles gambiae. Cell 2001, 104:709-718. 10.1016/S0092-8674(01)00267-7, 11257225.
    • (2001) Cell , vol.104 , pp. 709-718
    • Levashina, E.A.1    Moita, L.F.2    Blandin, S.3    Vriend, G.4    Lagueux, M.5    Kafatos, F.C.6
  • 50
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.
    • 10.1093/nar/gkl842, 1716718, 17130148
    • Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, 35:D61-65. 10.1093/nar/gkl842, 1716718, 17130148.
    • (2007) Nucleic Acids Res , vol.35
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 54
    • 84855479604 scopus 로고    scopus 로고
    • DRSC webpage
    • DRSC webpage. , http://www.flyrnai.org/
  • 55
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server.
    • 10.1093/nar/gkg599, 169005, 12824340
    • Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res 2003, 31:3429-3431. 10.1093/nar/gkg599, 169005, 12824340.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 56
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq.
    • 10.1093/bioinformatics/btp120, 2672628, 19289445
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111. 10.1093/bioinformatics/btp120, 2672628, 19289445.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 57
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
    • 10.1038/nbt.1621, 20436464
    • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28:511-515. 10.1038/nbt.1621, 20436464.
    • (2010) Nat Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    van Baren, M.J.6    Salzberg, S.L.7    Wold, B.J.8    Pachter, L.9
  • 58
    • 58149307466 scopus 로고    scopus 로고
    • QuantPrime - a flexible tool for reliable high-throughput primer design for quantitative PCR.
    • 10.1186/1471-2105-9-465, 2612009, 18976492
    • Arvidsson S, Kwasniewski M, Riano-Pachon DM, Mueller-Roeber B. QuantPrime - a flexible tool for reliable high-throughput primer design for quantitative PCR. BMC Bioinformatics 2008, 9:465. 10.1186/1471-2105-9-465, 2612009, 18976492.
    • (2008) BMC Bioinformatics , vol.9 , pp. 465
    • Arvidsson, S.1    Kwasniewski, M.2    Riano-Pachon, D.M.3    Mueller-Roeber, B.4


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