-
1
-
-
33646188259
-
3′ UTR seed matches, but not overall identity are associated with RNAi off-targets
-
doi:10.1038/nmeth854
-
Birmingham A, Anderson EM, Reynolds A, Ilsley-Tyree D, Leake D, Fedorov Y, Baskerville S, Maksimova E, Robinson K, Karpilow J, Marshall WS, Khvorova A (2006) 3′ UTR seed matches, but not overall identity are associated with RNAi off-targets. Nat Methods 3: 199-204. doi: 10. 1038/nmeth854.
-
(2006)
Nat Methods
, vol.3
, pp. 199-204
-
-
Birmingham, A.1
Anderson, E.M.2
Reynolds, A.3
Ilsley-Tyree, D.4
Leake, D.5
Fedorov, Y.6
Baskerville, S.7
Maksimova, E.8
Robinson, K.9
Karpilow, J.10
Marshall, W.S.11
Khvorova, A.12
-
2
-
-
34250674830
-
RNAi-mediated resistance to bean golden mosaic virus in genetically engineered common bean (Phaseolus vulgaris)
-
doi:10.1094/MPMI-20-6-0717
-
Bonfim K, Faria JC, Nogueira OPL, Mendes EA, Aragao FJL (2007) RNAi-mediated resistance to bean golden mosaic virus in genetically engineered common bean (Phaseolus vulgaris). Mol Plant Microbe Interact 20: 717-726. doi: 10. 1094/MPMI-20-6-0717.
-
(2007)
Mol Plant Microbe Interact
, vol.20
, pp. 717-726
-
-
Bonfim, K.1
Faria, J.C.2
Nogueira, O.P.L.3
Mendes, E.A.4
Aragao, F.J.L.5
-
3
-
-
15044358407
-
A systematic analysis of the silencing effects of an active siRNA at all single-nucleotide mismatched target sites
-
doi:10.1093/nar/gki312
-
Du Q, Thonberg H, Wang J, Wahlestedt C, Liang Z (2005) A systematic analysis of the silencing effects of an active siRNA at all single-nucleotide mismatched target sites. Nucleic Acids Res 33: 1671-1677. doi: 10. 1093/nar/gki312.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 1671-1677
-
-
Du, Q.1
Thonberg, H.2
Wang, J.3
Wahlestedt, C.4
Liang, Z.5
-
4
-
-
0035942736
-
Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells
-
doi:10.1038/35078107
-
Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411: 494-498. doi: 10. 1038/35078107.
-
(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
-
5
-
-
0032545933
-
Potent and specific genetic interference by double-stranded RNA in C. elegans
-
doi:10.1038/35888
-
Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in C. elegans. Nature 391: 806-811. doi: 10. 1038/35888.
-
(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
-
6
-
-
33745141582
-
Intron-hairpin RNA derived from replication associated protein C1 gene confers immunity to tomato yellow leaf curl virus infection in transgenic tomato plants
-
doi:10.1007/s11248-005-5238-0
-
Fuentes A, Ramos PL, Fiallo E, Callard D, Sanchez Y, Peral R, Rodriguez R, Pujol M (2006) Intron-hairpin RNA derived from replication associated protein C1 gene confers immunity to tomato yellow leaf curl virus infection in transgenic tomato plants. Transgenic Res 15: 291-304. doi: 10. 1007/s11248-005-5238-0.
-
(2006)
Transgenic Res
, vol.15
, pp. 291-304
-
-
Fuentes, A.1
Ramos, P.L.2
Fiallo, E.3
Callard, D.4
Sanchez, Y.5
Peral, R.6
Rodriguez, R.7
Pujol, M.8
-
7
-
-
24944510549
-
MicroRNA directs mRNA cleavage of the transcription factor NAC1 to down regulate auxin signals for Arabidopsis lateral root development
-
doi:10.1105/tpc.105.030841
-
Guo HS, Xie Q, Fei JF, Chua NH (2005) MicroRNA directs mRNA cleavage of the transcription factor NAC1 to down regulate auxin signals for Arabidopsis lateral root development. Plant Cell 17: 1376-1386. doi: 10. 1105/tpc. 105. 030841.
-
(2005)
Plant Cell
, vol.17
, pp. 1376-1386
-
-
Guo, H.S.1
Xie, Q.2
Fei, J.F.3
Chua, N.H.4
-
8
-
-
11844286931
-
Constructs and methods for hairpin RNA-mediated gene silencing in plants
-
Helliwell CA, Waterhouse PM (2003) Constructs and methods for hairpin RNA-mediated gene silencing in plants. Methods Enzymol 329: 24-35.
-
(2003)
Methods Enzymol
, vol.329
, pp. 24-35
-
-
Helliwell, C.A.1
Waterhouse, P.M.2
-
9
-
-
3242891277
-
DEQOR: A web-based tool for the design and quality control of siRNAs
-
doi:10.1093/nar/gkh408
-
Henschel A, Buchilz F, Habermann B (2004) DEQOR: a web-based tool for the design and quality control of siRNAs. Nucleic Acids Res 32: 113-120. doi: 10. 1093/nar/gkh408.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 113-120
-
-
Henschel, A.1
Buchilz, F.2
Habermann, B.3
-
10
-
-
73949142128
-
-
Hofacker and Stadler (2005) RNAfold
-
Hofacker and Stadler (2005) RNAfold www. tbi. univie. ac. at/~ivo/RNA/. html.
-
-
-
-
11
-
-
0037089135
-
Positional effects of short interfering RNAs targeting the human coagulation trigger tissue factor
-
doi:10.1093/nar/30.8.1757
-
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. doi: 10. 1093/nar/30. 8. 1757.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 1757-1766
-
-
Holen, T.1
Amarzguioui, M.2
Wiiger, M.T.3
Babaie, E.4
Prydz, H.5
-
12
-
-
0037685280
-
Expression profiling reveals off-target gene regulation by RNAi
-
doi:10.1038/nbt831
-
Jackson AL, Bartz SR, Helter J, Kobayashi SV, Burchard J, Mao M, Li B, Cavet G, Linsley PS (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol 21: 635-637. doi: 10. 1038/nbt831.
-
(2003)
Nat Biotechnol
, vol.21
, pp. 635-637
-
-
Jackson, A.L.1
Bartz, S.R.2
Helter, J.3
Kobayashi, S.V.4
Burchard, J.5
Mao, M.6
Li, B.7
Cavet, G.8
Linsley, P.S.9
-
13
-
-
58749113430
-
A three-dimensional view of the molecular machinery of RNA interference
-
doi:10.1038/nature07755
-
Jinek M, Doudna JA (2009) A three-dimensional view of the molecular machinery of RNA interference. Nature 457: 405-412. doi: 10. 1038/nature07755.
-
(2009)
Nature
, vol.457
, pp. 405-412
-
-
Jinek, M.1
Doudna, J.A.2
-
14
-
-
0002565608
-
Selection of hybridization probes for real-time quantification and genetic analysis
-
S. Meuer, C. Wittwer, and K. Nakagawara (Eds.), Berlin: Springer Verlag
-
Landt O (2001) Selection of hybridization probes for real-time quantification and genetic analysis. In: Meuer S, Wittwer C, Nakagawara K (eds) Rapid cycle real-time PCR: methods and applications. Springer Verlag, Berlin, pp 35-41.
-
(2001)
Rapid Cycle Real-Time PCR: Methods and Applications
, pp. 35-41
-
-
Landt, O.1
-
15
-
-
4444275405
-
MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems
-
doi:10.1242/dev.01320
-
Laufs P, Peaucelle A, Morin H, Traas J (2004) MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems. Development 131: 4311-4322. doi: 10. 1242/dev. 01320.
-
(2004)
Development
, vol.131
, pp. 4311-4322
-
-
Laufs, P.1
Peaucelle, A.2
Morin, H.3
Traas, J.4
-
17
-
-
23344438420
-
SiRNA-mediated off-target gene silencing triggered by a 7 nt complementation
-
doi:10.1093/nar/gki762
-
Lin X, Ruan X, Anderson MG, McDowell JA, Kroeger PE, Fesik SW, Shen Y (2005) siRNA-mediated off-target gene silencing triggered by a 7 nt complementation. Nucleic Acids Res 33: 4527-4535. doi: 10. 1093/nar/gki762.
-
(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
-
18
-
-
16544394479
-
RNA silencing in plants by the expression of siRNA duplexes
-
doi:10.1093/nar/gnh170
-
Lu S, Shi R, Tsao C, Yi X, Li L, Chiang VL (2004) RNA silencing in plants by the expression of siRNA duplexes. Nucleic Acids Res 32: e171. doi: 10. 1093/nar/gnh170.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Lu, S.1
Shi, R.2
Tsao, C.3
Yi, X.4
Li, L.5
Chiang, V.L.6
-
19
-
-
4444363152
-
MicroRNA control of PHABULOSA in leaf development: Importance of pairing to the microRNA 50 region
-
doi:10.1038/sj.emboj.7600340
-
Mallory AC, Reinhart BJ, Jones-Rhoades MW, Tang G, Zamore PD, Barton MK, Bartel DP (2004) MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 50 region. EMBO J 23: 3356-3364. doi: 10. 1038/sj. emboj. 7600340.
-
(2004)
EMBO J
, vol.23
, pp. 3356-3364
-
-
Mallory, A.C.1
Reinhart, B.J.2
Jones-Rhoades, M.W.3
Tang, G.4
Zamore, P.D.5
Barton, M.K.6
Bartel, D.P.7
-
20
-
-
0001869253
-
Transformation of tomato with Agrobacterium tumefaciens
-
McCormick S (1991) Transformation of tomato with Agrobacterium tumefaciens. Plant Tissue Cult Man B6: 1-9.
-
(1991)
Plant Tissue Cult Man
, vol.B6
, pp. 1-9
-
-
McCormick, S.1
-
21
-
-
2342577446
-
Simple RNAi vectors for stable and transient suppression of gene function in rice
-
doi:10.1093/pcp/pch048
-
Miki D, Shimamoto K (2004) Simple RNAi vectors for stable and transient suppression of gene function in rice. Plant Cell Physiol 45: 490-495. doi: 10. 1093/pcp/pch048.
-
(2004)
Plant Cell Physiol
, vol.45
, pp. 490-495
-
-
Miki, D.1
Shimamoto, K.2
-
22
-
-
33846007585
-
Minimizing off-target effects by using diced siRNAs for RNA interference
-
Myers JW, Jen-Tsan C, Delquin G, Schaner ME, Brown PO, Ferrell JE Jr (2006) Minimizing off-target effects by using diced siRNAs for RNA interference. J RNAi Gene Silencing 2: 181-194.
-
(2006)
J RNAi Gene Silencing
, vol.2
, pp. 181-194
-
-
Myers, J.W.1
Jen-Tsan, C.2
Delquin, G.3
Schaner, M.E.4
Brown, P.O.5
Ferrell Jr., J.E.6
-
23
-
-
28244479938
-
Hairpin RNA-mediated silencing of Plum pox virus P1 and HC-Pro genes for efficient and predictable resistance to the virus
-
doi:10.1007/s11248-005-1773-y
-
Nicola-Negri E, Brunetti A, Tavazza M, Ilardi V (2005) Hairpin RNA-mediated silencing of Plum pox virus P1 and HC-Pro genes for efficient and predictable resistance to the virus. Transgenic Res 14: 989-994. doi: 10. 1007/s11248-005-1773-y.
-
(2005)
Transgenic Res
, vol.14
, pp. 989-994
-
-
Nicola-Negri, E.1
Brunetti, A.2
Tavazza, M.3
Ilardi, V.4
-
24
-
-
34447121300
-
Identification of novel small RNAs in tomato (Solanum lycopersicum)
-
doi:10.1007/s00425-007-0518-y
-
Pilcher RL, Moxon S, Pakseresht N, Moulton V, Manning K, Seymour G, Dalmay T (2007) Identification of novel small RNAs in tomato (Solanum lycopersicum). Planta 226: 709-717. doi: 10. 1007/s00425-007-0518-y.
-
(2007)
Planta
, vol.226
, pp. 709-717
-
-
Pilcher, R.L.1
Moxon, S.2
Pakseresht, N.3
Moulton, V.4
Manning, K.5
Seymour, G.6
Dalmay, T.7
-
25
-
-
13944261560
-
Antisense suppression of replicase gene expression recovers tomato plants from leaf curl virus infection
-
doi:10.1016/j.plantsci.2004.12.008
-
Praveen S, Mishra AK, Dasgupta A (2005) Antisense suppression of replicase gene expression recovers tomato plants from leaf curl virus infection. Plant Sci 168: 1011-1101. doi: 10. 1016/j. plantsci. 2004. 12. 008.
-
(2005)
Plant Sci
, vol.168
, pp. 1011-1101
-
-
Praveen, S.1
Mishra, A.K.2
Dasgupta, A.3
-
26
-
-
45549096479
-
Behavior of RNAi suppressor protein 2b of cucumber mosaic virus in planta in presence and absence of virus
-
doi:10.1007/s11262-008-0232-2
-
Praveen S, Mangrauthia SK, Singh P, Mishra AK (2008) Behavior of RNAi suppressor protein 2b of cucumber mosaic virus in planta in presence and absence of virus. Virus Genes 37: 96-102. doi: 10. 1007/s11262-008-0232-2.
-
(2008)
Virus Genes
, vol.37
, pp. 96-102
-
-
Praveen, S.1
Mangrauthia, S.K.2
Singh, P.3
Mishra, A.K.4
-
27
-
-
34547215335
-
Hairpin RNA mediated strategies for silencing of tomato leaf curl virus AC1 and AC4 genes for effective resistance in plants
-
doi:10.1089/oli.2006.0063
-
Ramesh SV, Mishra AK, Praveen S (2007) Hairpin RNA mediated strategies for silencing of tomato leaf curl virus AC1 and AC4 genes for effective resistance in plants. Oligonucleotide 17: 251-257. doi: 10. 1089/oli. 2006. 0063.
-
(2007)
Oligonucleotide
, vol.17
, pp. 251-257
-
-
Ramesh, S.V.1
Mishra, A.K.2
Praveen, S.3
-
28
-
-
16244398080
-
Specific effects of microRNAs on the plant transcriptome
-
doi:10.1016/j.devcel.2005.01.018
-
Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8: 517-527. doi: 10. 1016/j. devcel. 2005. 01. 018.
-
(2005)
Dev Cell
, vol.8
, pp. 517-527
-
-
Schwab, R.1
Palatnik, J.F.2
Riester, M.3
Schommer, C.4
Schmid, M.5
Weigel, D.6
-
29
-
-
58749096360
-
On the road to reading the RNA-interference code
-
doi:10.1038/nature07754
-
Siomi H, Siomi MC (2009) On the road to reading the RNA-interference code. Nature 457: 396-404. doi: 10. 1038/nature07754.
-
(2009)
Nature
, vol.457
, pp. 396-404
-
-
Siomi, H.1
Siomi, M.C.2
-
30
-
-
0034699247
-
Total silencing by intron-spliced hairpin RNAs
-
doi:10.1038/35036500
-
Smith N, Singh S, Wang MB, Stoutjesdijk P, Green A, Waterhouse PM (2000) Total silencing by intron-spliced hairpin RNAs. Nature 407: 319-320. doi: 10. 1038/35036500.
-
(2000)
Nature
, vol.407
, pp. 319-320
-
-
Smith, N.1
Singh, S.2
Wang, M.B.3
Stoutjesdijk, P.4
Green, A.5
Waterhouse, P.M.6
-
31
-
-
0042924332
-
Short interfering RNA-mediated interference of gene expression and viral DNA accumulation in cultured plant cells
-
doi:10.1073/pnas.1733874100
-
Vanitharani R, Chellappan P, Fauquet CM (2003) Short interfering RNA-mediated interference of gene expression and viral DNA accumulation in cultured plant cells. Proc Natl Acad Sci USA 100: 9632-9636. doi: 10. 1073/pnas. 1733874100.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 9632-9636
-
-
Vanitharani, R.1
Chellappan, P.2
Fauquet, C.M.3
-
32
-
-
0001412080
-
A single copy of a virus-derived transgene encoding hairpin RNA gives immunity to barley yellow dwarf virus
-
doi:10.1046/j.1364-3703.2000.00038.x
-
Wang MB, Abbott DC, Waterhouse PM (2000) A single copy of a virus-derived transgene encoding hairpin RNA gives immunity to barley yellow dwarf virus. Mol Plant Pathol 1: 347-356. doi: 10. 1046/j. 1364-3703. 2000. 00038. x.
-
(2000)
Mol Plant Pathol
, vol.1
, pp. 347-356
-
-
Wang, M.B.1
Abbott, D.C.2
Waterhouse, P.M.3
-
33
-
-
27744596243
-
Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis
-
doi:10.1105/tpc.105.033076
-
Wang JW, Wang LJ, Mao YB, Cai WJ, Xue HW, Chen XY (2005) Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis. Plant Cell 17: 2204-2216. doi: 10. 1105/tpc. 105. 033076.
-
(2005)
Plant Cell
, vol.17
, pp. 2204-2216
-
-
Wang, J.W.1
Wang, L.J.2
Mao, Y.B.3
Cai, W.J.4
Xue, H.W.5
Chen, X.Y.6
-
34
-
-
0032506226
-
Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA
-
doi:10.1073/pnas.95.23.13959
-
Waterhouse PM, Graham MW, Wang MB (1998) Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. Proc Natl Acad Sci USA 96: 13959-13964. doi: 10. 1073/pnas. 95. 23. 13959.
-
(1998)
Proc Natl Acad Sci USA
, vol.96
, pp. 13959-13964
-
-
Waterhouse, P.M.1
Graham, M.W.2
Wang, M.B.3
-
35
-
-
0035859046
-
Gene silencing as an adaptive defence against viruses
-
doi:10.1038/35081168
-
Waterhouse PM, Wang MB, Lough T (2001) Gene silencing as an adaptive defence against viruses. Nature 411: 834-842. doi: 10. 1038/35081168.
-
(2001)
Nature
, vol.411
, pp. 834-842
-
-
Waterhouse, P.M.1
Wang, M.B.2
Lough, T.3
-
36
-
-
0034800385
-
Construct design for efficient, effective and high-throughput gene silencing in plants
-
doi:10.1046/j.1365-313X.2001.01105.x
-
Wesley V, Helliwell CA, Smith NA, Wang MB, Rouse DT, Liu Q, Gooding PS, Singh SP, Abbott D, Stoutjesdijk PA, Robinson SP, Gleave AP, Green AG, Waterhouse PM (2001) Construct design for efficient, effective and high-throughput gene silencing in plants. Plant J 27: 581-591. doi: 10. 1046/j. 1365-313X. 2001. 01105. x.
-
(2001)
Plant J
, vol.27
, pp. 581-591
-
-
Wesley, V.1
Helliwell, C.A.2
Smith, N.A.3
Wang, M.B.4
Rouse, D.T.5
Liu, Q.6
Gooding, P.S.7
Singh, S.P.8
Abbott, D.9
Stoutjesdijk, P.A.10
Robinson, S.P.11
Gleave, A.P.12
Green, A.G.13
Waterhouse, P.M.14
-
37
-
-
33750061917
-
Computational estimation and experimental verification of off-target silencing during posttranscriptional gene silencing in plants
-
doi:10.1104/pp.106.083295
-
Xu P, Zhang Y, Kang L, Roossinck MJ, Mysore KS (2006) Computational estimation and experimental verification of off-target silencing during posttranscriptional gene silencing in plants. Plant Physiol 142: 429-440. doi: 10. 1104/pp. 106. 083295.
-
(2006)
Plant Physiol
, vol.142
, pp. 429-440
-
-
Xu, P.1
Zhang, Y.2
Kang, L.3
Roossinck, M.J.4
Mysore, K.S.5
-
38
-
-
46949106572
-
A one-step real time RT-PCR assay for quantifying rice stripe virus in rice and in the small brown planthopper (Laodelphax striatellus Fallen)
-
doi:10.1016/j.jviromet.2008.05.024
-
Zhang X, Wang X, Zhou G (2008) A one-step real time RT-PCR assay for quantifying rice stripe virus in rice and in the small brown planthopper (Laodelphax striatellus Fallen). J Virol Methods 151: 181-187. doi: 10. 1016/j. jviromet. 2008. 05. 024.
-
(2008)
J Virol Methods
, vol.151
, pp. 181-187
-
-
Zhang, X.1
Wang, X.2
Zhou, G.3
|