-
1
-
-
4644223259
-
Mechanisms of gene silencing by double-stranded RNA
-
• ] provide an up-to-date summary of current knowledge of the molecular mechanisms of gene silencing induced by siRNAs and miRNAs.
-
(2004)
Nature
, vol.431
, pp. 343-349
-
-
Meister, G.1
Tuschl, T.2
-
3
-
-
3142615372
-
The RNAi revolution
-
C.D. Novina, and P.A. Sharp The RNAi revolution Nature 430 2004 161 164
-
(2004)
Nature
, vol.430
, pp. 161-164
-
-
Novina, C.D.1
Sharp, P.A.2
-
4
-
-
0037686295
-
Killing the messenger: Short RNAs that silence gene expression
-
D.M. Dykxhoorn, C.D. Novina, and P.A. Sharp Killing the messenger: short RNAs that silence gene expression Nat Rev Mol Cell Biol 4 2003 457 467
-
(2003)
Nat Rev Mol Cell Biol
, vol.4
, pp. 457-467
-
-
Dykxhoorn, D.M.1
Novina, C.D.2
Sharp, P.A.3
-
6
-
-
0035859046
-
Gene silencing as an adaptive defence against viruses
-
P.M. Waterhouse, M.B. Wang, and T. Lough Gene silencing as an adaptive defence against viruses Nature 411 2001 834 842
-
(2001)
Nature
, vol.411
, pp. 834-842
-
-
Waterhouse, P.M.1
Wang, M.B.2
Lough, T.3
-
7
-
-
0037123606
-
RNA silencing: The genome's immune system
-
R.H. Plasterk RNA silencing: the genome's immune system Science 296 2002 1263 1265
-
(2002)
Science
, vol.296
, pp. 1263-1265
-
-
Plasterk, R.H.1
-
8
-
-
0035942736
-
Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells
-
S.M. Elbashir, J. Harborth, W. Lendeckel, A. Yalcin, K. Weber, and T. Tuschl Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells Nature 411 2001 494 498
-
(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
-
9
-
-
0141843656
-
The nuclear RNase III Drosha initiates microRNA processing
-
Y. Lee, C. Ahn, J. Han, H. Choi, J. Kim, J. Yim, J. Lee, P. Provost, O. Radmark, and S. Kim The nuclear RNase III Drosha initiates microRNA processing Nature 425 2003 415 419
-
(2003)
Nature
, vol.425
, pp. 415-419
-
-
Lee, Y.1
Ahn, C.2
Han, J.3
Choi, H.4
Kim, J.5
Yim, J.6
Lee, J.7
Provost, P.8
Radmark, O.9
Kim, S.10
-
10
-
-
4644312235
-
The role of RNA interference in heterochromatic silencing
-
Z. Lippman, and R. Martienssen The role of RNA interference in heterochromatic silencing Nature 431 2004 364 370
-
(2004)
Nature
, vol.431
, pp. 364-370
-
-
Lippman, Z.1
Martienssen, R.2
-
11
-
-
1942471652
-
Those interfering little RNAs! Silencing and eliminating chromatin
-
V. Schramke, and R. Allshire Those interfering little RNAs! Silencing and eliminating chromatin Curr Opin Genet Dev 14 2004 174 180
-
(2004)
Curr Opin Genet Dev
, vol.14
, pp. 174-180
-
-
Schramke, V.1
Allshire, R.2
-
12
-
-
0035313137
-
Viral suppressors of RNA silencing
-
W.X. Li, and S.W. Ding Viral suppressors of RNA silencing Curr Opin Biotechnol 12 2001 150 154
-
(2001)
Curr Opin Biotechnol
, vol.12
, pp. 150-154
-
-
Li, W.X.1
Ding, S.W.2
-
13
-
-
0035425379
-
RNA silencing as a plant immune system against viruses
-
O. Voinnet RNA silencing as a plant immune system against viruses Trends Genet 17 2001 449 459
-
(2001)
Trends Genet
, vol.17
, pp. 449-459
-
-
Voinnet, O.1
-
14
-
-
1442360415
-
RNase III enzymes and the initiation of gene silencing
-
M.A. Carmell, and G.J. Hannon RNase III enzymes and the initiation of gene silencing Nat Struct Mol Biol 11 2004 214 218
-
(2004)
Nat Struct Mol Biol
, vol.11
, pp. 214-218
-
-
Carmell, M.A.1
Hannon, G.J.2
-
15
-
-
3142613181
-
Single processing center models for human Dicer and bacterial RNase III
-
H. Zhang, F.A. Kolb, L. Jaskiewicz, E. Westhof, and W. Filipowicz Single processing center models for human Dicer and bacterial RNase III Cell 118 2004 57 68 This paper provides an excellent biochemical characterization of the RNase III activity of human Dicer, and shows that prokaryotic and eukaryotic RNase III enzymes have only a single center for processing dsRNA.
-
(2004)
Cell
, vol.118
, pp. 57-68
-
-
Zhang, H.1
Kolb, F.A.2
Jaskiewicz, L.3
Westhof, E.4
Filipowicz, W.5
-
16
-
-
0036828639
-
The Argonaute family: Tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis
-
M.A. Carmell, Z. Xuan, M.Q. Zhang, and G.J. Hannon The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis Genes Dev 16 2002 2733 2742
-
(2002)
Genes Dev
, vol.16
, pp. 2733-2742
-
-
Carmell, M.A.1
Xuan, Z.2
Zhang, M.Q.3
Hannon, G.J.4
-
17
-
-
0034306266
-
Domains in gene silencing and cell differentiation proteins: The novel PAZ domain and redefinition of the Piwi domain
-
L. Cerutti, N. Mian, and A. Bateman Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the Piwi domain Trends Biochem Sci 25 2000 481 482
-
(2000)
Trends Biochem Sci
, vol.25
, pp. 481-482
-
-
Cerutti, L.1
Mian, N.2
Bateman, A.3
-
18
-
-
0642345790
-
Structure and conserved RNA binding of the PAZ domain
-
•• ] present three-dimensional structures of the PAZ domains from Drosophila Ago1 and Ago2, and demonstrate that the PAZ domain binds single-stranded nucleic acids in vitro. The binding site is mapped by NMR chemical shift perturbations and mutational analyses. The nucleic acid ligand specificity is explored and shown to require a single-stranded 3′ overhang. Blunt-ended dsRNAs or dsRNAs with 5′ overhangs are not recognized.
-
(2003)
Nature
, vol.426
, pp. 468-474
-
-
Yan, K.S.1
Yan, S.2
Farooq, A.3
Han, A.4
Zeng, L.5
Zhou, M.M.6
-
20
-
-
0345490960
-
The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes
-
••].
-
(2003)
Nat Struct Biol
, vol.10
, pp. 1026-1032
-
-
Song, J.J.1
Liu, J.2
Tolia, N.H.3
Schneiderman, J.4
Smith, S.K.5
Martienssen, R.A.6
Hannon, G.J.7
Joshua-Tor, L.8
-
21
-
-
2442679207
-
Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain
-
J.B. Ma, K. Ye, and D.J. Patel Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain Nature 429 2004 318 322 The crystal structure of the PAZ domain of HsAgo1 bound to a small siRNA mimic shows that the characteristic 2-nt single-stranded 3′ overhang of siRNAs is recognized. Additional contacts involving the phosphates of the siRNA duplex region are required for high-affinity binding.
-
(2004)
Nature
, vol.429
, pp. 318-322
-
-
Ma, J.B.1
Ye, K.2
Patel, D.J.3
-
22
-
-
2542461104
-
Nucleic acid 3′-end recognition by the Argonaute2 PAZ domain
-
A. Lingel, B. Simon, E. Izaurralde, and M. Sattler Nucleic acid 3′-end recognition by the Argonaute2 PAZ domain Nat Struct Mol Biol 11 2004 576 577 NMR solution structures of the PAZ domain of DmAgo2 bound to 5-nt single-stranded RNA and DNA oligomers show that the two 3′-terminal nucleotides are recognized in a sequence-independent manner, without discrimination between RNA and DNA.
-
(2004)
Nat Struct Mol Biol
, vol.11
, pp. 576-577
-
-
Lingel, A.1
Simon, B.2
Izaurralde, E.3
Sattler, M.4
-
23
-
-
2442664066
-
Structural basis of single-stranded RNA recognition
-
A.C. Messias, and M. Sattler Structural basis of single-stranded RNA recognition Acc Chem Res 37 2004 279 287
-
(2004)
Acc Chem Res
, vol.37
, pp. 279-287
-
-
Messias, A.C.1
Sattler, M.2
-
24
-
-
1842505081
-
Structural basis for telomeric single-stranded DNA recognition by yeast Cdc13
-
R.M. Mitton-Fry, E.M. Anderson, D.L. Theobald, L.W. Glustrom, and D.S. Wuttke Structural basis for telomeric single-stranded DNA recognition by yeast Cdc13 J Mol Biol 338 2004 241 255
-
(2004)
J Mol Biol
, vol.338
, pp. 241-255
-
-
Mitton-Fry, R.M.1
Anderson, E.M.2
Theobald, D.L.3
Glustrom, L.W.4
Wuttke, D.S.5
-
26
-
-
0345304903
-
DNA self-recognition in the structure of Pot1 bound to telomeric single-stranded DNA
-
M. Lei, E.R. Podell, P. Baumann, and T.R. Cech DNA self-recognition in the structure of Pot1 bound to telomeric single-stranded DNA Nature 426 2003 198 203
-
(2003)
Nature
, vol.426
, pp. 198-203
-
-
Lei, M.1
Podell, E.R.2
Baumann, P.3
Cech, T.R.4
-
28
-
-
0029643952
-
Recombining the structures of HIV integrase, RuvC and RNase H
-
W. Yang, and T.A. Steitz Recombining the structures of HIV integrase, RuvC and RNase H Structure 3 1995 131 134
-
(1995)
Structure
, vol.3
, pp. 131-134
-
-
Yang, W.1
Steitz, T.A.2
-
29
-
-
0035937257
-
Structural biochemistry of a type 2 RNase H: RNA primer recognition and removal during DNA replication
-
B.R. Chapados, Q. Chai, D.J. Hosfield, J. Qiu, B. Shen, and J.A. Tainer Structural biochemistry of a type 2 RNase H: RNA primer recognition and removal during DNA replication J Mol Biol 307 2001 541 556
-
(2001)
J Mol Biol
, vol.307
, pp. 541-556
-
-
Chapados, B.R.1
Chai, Q.2
Hosfield, D.J.3
Qiu, J.4
Shen, B.5
Tainer, J.A.6
-
30
-
-
0029190888
-
Functions and structures of ribonuclease H enzymes
-
S. Kanaya, and M. Ikehara Functions and structures of ribonuclease H enzymes Subcell Biochem 24 1995 377 422
-
(1995)
Subcell Biochem
, vol.24
, pp. 377-422
-
-
Kanaya, S.1
Ikehara, M.2
-
31
-
-
0027184481
-
A general two-metal-ion mechanism for catalytic RNA
-
T.A. Steitz, and J.A. Steitz A general two-metal-ion mechanism for catalytic RNA Proc Natl Acad Sci USA 90 1993 6498 6502
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 6498-6502
-
-
Steitz, T.A.1
Steitz, J.A.2
-
32
-
-
0025605872
-
Ribonucleases H of retroviral and cellular origin
-
U. Wintersberger Ribonucleases H of retroviral and cellular origin Pharmacol Ther 48 1990 259 280
-
(1990)
Pharmacol Ther
, vol.48
, pp. 259-280
-
-
Wintersberger, U.1
-
33
-
-
2442495329
-
RISC is a 5′ phosphomonoester-producing RNA endonuclease
-
J. Martinez, and T. Tuschl RISC is a 5′ phosphomonoester-producing RNA endonuclease Genes Dev 18 2004 975 980
-
(2004)
Genes Dev
, vol.18
, pp. 975-980
-
-
Martinez, J.1
Tuschl, T.2
-
35
-
-
0034616993
-
Three-dimensional structure of the Tn5 synaptic complex transposition intermediate
-
D.R. Davies, I.Y. Goryshin, W.S. Reznikoff, and I. Rayment Three-dimensional structure of the Tn5 synaptic complex transposition intermediate Science 289 2000 77 85
-
(2000)
Science
, vol.289
, pp. 77-85
-
-
Davies, D.R.1
Goryshin, I.Y.2
Reznikoff, W.S.3
Rayment, I.4
-
36
-
-
0035863097
-
RNA interference is mediated by 21- and 22-nucleotide RNAs
-
S.M. Elbashir, W. Lendeckel, and T. Tuschl RNA interference is mediated by 21- and 22-nucleotide RNAs Genes Dev 15 2001 188 200
-
(2001)
Genes Dev
, vol.15
, pp. 188-200
-
-
Elbashir, S.M.1
Lendeckel, W.2
Tuschl, T.3
-
37
-
-
4444368187
-
Argonaute2 is the catalytic engine of mammalian RNAi
-
J. Liu, M.A. Carmell, F.V. Rivas, C.G. Marsden, J.M. Thomson, J.J. Song, S.M. Hammond, L. Joshua-Tor, and G.J. Hannon Argonaute2 is the catalytic engine of mammalian RNAi Science 305 2004 1437 1441 The function and biochemical activities of the four human Argonaute paralogs are studied. The authors show that mutation of two putative catalytic residues in the Piwi (RNase H) domain of HsAgo2 abolishes Slicer activity in human cells.
-
(2004)
Science
, vol.305
, pp. 1437-1441
-
-
Liu, J.1
Carmell, M.A.2
Rivas, F.V.3
Marsden, C.G.4
Thomson, J.M.5
Song, J.J.6
Hammond, S.M.7
Joshua-Tor, L.8
Hannon, G.J.9
-
38
-
-
9644260528
-
Function of the trypanosome argonaute 1 protein in RNA interference requires the N-terminal RGG domain and arginine 735 in the piwi domain
-
H. Shi, E. Ullu, and C. Tschudi Function of the trypanosome argonaute 1 protein in RNA interference requires the N-terminal RGG domain and arginine 735 in the piwi domain J Biol Chem 279 2004 49889 49893
-
(2004)
J Biol Chem
, vol.279
, pp. 49889-49893
-
-
Shi, H.1
Ullu, E.2
Tschudi, C.3
-
39
-
-
0035868713
-
Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA
-
S.G. Sarafianos, K. Das, C. Tantillo, A.D. Clark Jr., J. Ding, J.M. Whitcomb, P.L. Boyer, S.H. Hughes, and E. Arnold Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA EMBO J 20 2001 1449 1461
-
(2001)
EMBO J
, vol.20
, pp. 1449-1461
-
-
Sarafianos, S.G.1
Das, K.2
Tantillo, C.3
Clark Jr., A.D.4
Ding, J.5
Whitcomb, J.M.6
Boyer, P.L.7
Hughes, S.H.8
Arnold, E.9
-
40
-
-
3242736704
-
Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs
-
G. Meister, M. Landthaler, A. Patkaniowska, Y. Dorsett, G. Teng, and T. Tuschl Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs Mol Cell 15 2004 185 197 The authors show that the endonucleolytic Slicer activity co-purifies exclusively with complexes containing HsAgo2 in human cells and demonstrate that exogenously introduced siRNAs associate with HsAgo2 to guide mRNA cleavage.
-
(2004)
Mol Cell
, vol.15
, pp. 185-197
-
-
Meister, G.1
Landthaler, M.2
Patkaniowska, A.3
Dorsett, Y.4
Teng, G.5
Tuschl, T.6
-
41
-
-
0042838304
-
Recognition of double-stranded RNA by proteins and small molecules
-
C.B. Carlson, O.M. Stephens, and P.A. Beal Recognition of double-stranded RNA by proteins and small molecules Biopolymers 70 2003 86 102
-
(2003)
Biopolymers
, vol.70
, pp. 86-102
-
-
Carlson, C.B.1
Stephens, O.M.2
Beal, P.A.3
-
42
-
-
0034192148
-
Proteins binding to duplexed RNA: One motif, multiple functions
-
I. Fierro-Monti, and M.B. Mathews Proteins binding to duplexed RNA: one motif, multiple functions Trends Biochem Sci 25 2000 241 246
-
(2000)
Trends Biochem Sci
, vol.25
, pp. 241-246
-
-
Fierro-Monti, I.1
Mathews, M.B.2
-
43
-
-
3042704491
-
Structural basis for recognition of the AGNN tetraloop RNA fold by the double-stranded RNA-binding domain of Rnt1p RNase III
-
H. Wu, A. Henras, G. Chanfreau, and J. Feigon Structural basis for recognition of the AGNN tetraloop RNA fold by the double-stranded RNA-binding domain of Rnt1p RNase III Proc Natl Acad Sci USA 101 2004 8307 8312
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 8307-8312
-
-
Wu, H.1
Henras, A.2
Chanfreau, G.3
Feigon, J.4
-
44
-
-
0035662491
-
Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage
-
J. Blaszczyk, J.E. Tropea, M. Bubunenko, K.M. Routzahn, D.S. Waugh, D.L. Court, and X. Ji Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage Structure (Camb) 9 2001 1225 1236
-
(2001)
Structure (Camb)
, vol.9
, pp. 1225-1236
-
-
Blaszczyk, J.1
Tropea, J.E.2
Bubunenko, M.3
Routzahn, K.M.4
Waugh, D.S.5
Court, D.L.6
Ji, X.7
-
45
-
-
0036845374
-
Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP
-
H. Zhang, F.A. Kolb, V. Brondani, E. Billy, and W. Filipowicz Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP EMBO J 21 2002 5875 5885
-
(2002)
EMBO J
, vol.21
, pp. 5875-5885
-
-
Zhang, H.1
Kolb, F.A.2
Brondani, V.3
Billy, E.4
Filipowicz, W.5
-
46
-
-
0347985826
-
Size selective recognition of siRNA by an RNA silencing suppressor
-
••], presents crystal structures of the viral p19 protein bound to prototypical siRNAs. The structures and biochemical analyses demonstrate that the p19 homodimer measures the size of a 19 bp dsRNA helix. Recognition of the 5′ monophosphates facilitates the interaction and the RNA is bound without sequence specificity. The structures represent spectacular examples of size-selective siRNA recognition.
-
(2003)
Cell
, vol.115
, pp. 799-811
-
-
Vargason, J.M.1
Szittya, G.2
Burgyan, J.3
Tanaka Hall, T.M.4
-
48
-
-
0037312936
-
Structure of the L1 protuberance in the ribosome
-
A. Nikulin, I. Eliseikina, S. Tishchenko, N. Nevskaya, N. Davydova, O. Platonova, W. Piendl, M. Selmer, A. Liljas, and D. Drygin Structure of the L1 protuberance in the ribosome Nat Struct Biol 10 2003 104 108
-
(2003)
Nat Struct Biol
, vol.10
, pp. 104-108
-
-
Nikulin, A.1
Eliseikina, I.2
Tishchenko, S.3
Nevskaya, N.4
Davydova, N.5
Platonova, O.6
Piendl, W.7
Selmer, M.8
Liljas, A.9
Drygin, D.10
-
49
-
-
0347988235
-
Nuclear export of microRNA precursors
-
E. Lund, S. Guttinger, A. Calado, J.E. Dahlberg, and U. Kutay Nuclear export of microRNA precursors Science 303 2004 95 98
-
(2004)
Science
, vol.303
, pp. 95-98
-
-
Lund, E.1
Guttinger, S.2
Calado, A.3
Dahlberg, J.E.4
Kutay, U.5
-
50
-
-
4444230672
-
Structural requirements for pre-microRNA binding and nuclear export by Exportin 5
-
Y. Zeng, and B.R. Cullen Structural requirements for pre-microRNA binding and nuclear export by Exportin 5 Nucleic Acids Res 32 2004 4776 4785
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 4776-4785
-
-
Zeng, Y.1
Cullen, B.R.2
-
51
-
-
1842608548
-
MicroRNA precursors in motion: Exportin-5 mediates their nuclear export
-
V.N. Kim MicroRNA precursors in motion: exportin-5 mediates their nuclear export Trends Cell Biol 14 2004 156 159
-
(2004)
Trends Cell Biol
, vol.14
, pp. 156-159
-
-
Kim, V.N.1
-
52
-
-
0142165224
-
Functional siRNAs and miRNAs exhibit strand bias
-
A. Khvorova, A. Reynolds, and S.D. Jayasena Functional siRNAs and miRNAs exhibit strand bias Cell 115 2003 209 216
-
(2003)
Cell
, vol.115
, pp. 209-216
-
-
Khvorova, A.1
Reynolds, A.2
Jayasena, S.D.3
-
53
-
-
10744225153
-
Asymmetry in the assembly of the RNAi enzyme complex
-
D.S. Schwarz, G. Hutvagner, T. Du, Z. Xu, N. Aronin, and P.D. Zamore Asymmetry in the assembly of the RNAi enzyme complex Cell 115 2003 199 208
-
(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
-
54
-
-
0029881007
-
MOLMOL: A program for display and analysis of macromolecular structures
-
R. Koradi, M. Billeter, and K. Wüthrich MOLMOL: a program for display and analysis of macromolecular structures J Mol Graph 14 1996 51 55
-
(1996)
J Mol Graph
, vol.14
, pp. 51-55
-
-
Koradi, R.1
Billeter, M.2
Wüthrich, K.3
-
55
-
-
11244279683
-
Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity
-
in press.
-
Parker JS, Roe SM, Barford D: Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J 2004, in press. The crystal structure of an archaeal Piwi protein reveals two structural domains that are also present in PfAgo (Piwi and middle domains), but lacks a PAZ domain. The resemblance between the Piwi domain and the RNase H fold is confirmed. A putative 5′-phosphate-binding site is identified and is involved in siRNA binding.
-
(2004)
EMBO J
-
-
Parker, J.S.1
Roe, S.M.2
Barford, D.3
|