-
1
-
-
70349199881
-
Riboswitches: From ancient gene-control systems to modern drug targets
-
Breaker RR. Riboswitches: from ancient gene-control systems to modern drug targets. Future Microbiol 2009; 4:771-3.
-
(2009)
Future Microbiol
, vol.4
, pp. 771-773
-
-
Breaker, R.R.1
-
2
-
-
46349083026
-
The distributions, mechanisms and structures of metabolite-binding riboswitches
-
Barrick JE, Breaker RR. The distributions, mechanisms and structures of metabolite-binding riboswitches. Genome Biol 2007; 8:239.
-
(2007)
Genome Biol
, vol.8
, pp. 239
-
-
Barrick, J.E.1
Breaker, R.R.2
-
3
-
-
63749126957
-
Expanding roles for metabolite-sensing regulatory RNAs
-
Dambach MD, Winkler WC. Expanding roles for metabolite-sensing regulatory RNAs. Curr Opin Microbiol 2009; 12:161-9.
-
(2009)
Curr Opin Microbiol
, vol.12
, pp. 161-169
-
-
Dambach, M.D.1
Winkler, W.C.2
-
4
-
-
67650713931
-
The structural and functional diversity of metabolite-binding riboswitches
-
Roth A, Breaker RR. The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem 2009; 78:305-34.
-
(2009)
Annu Rev Biochem
, vol.78
, pp. 305-334
-
-
Roth, A.1
Breaker, R.R.2
-
5
-
-
70350771280
-
A trans-acting riboswitch controls expression of the virulence regulator PrfA in listeria monocytogenes
-
Loh E, Dussurget O, Gripenland J, Vaitkevicius K, Tiensuu T, Mandin P, et al. A trans-acting riboswitch controls expression of the virulence regulator PrfA in listeria monocytogenes. Cell 2009; 139:770-9.
-
(2009)
Cell
, vol.139
, pp. 770-779
-
-
Loh, E.1
Dussurget, O.2
Gripenland, J.3
Vaitkevicius, K.4
Tiensuu, T.5
Mandin, P.6
-
6
-
-
85011940612
-
Riboswitch-mediated control of gene expression in eukaryotes
-
Wachter A. Riboswitch-mediated control of gene expression in eukaryotes. RNA Biol 2010; 7:67-76.
-
(2010)
RNA Biol
, vol.7
, pp. 67-76
-
-
Wachter, A.1
-
8
-
-
37849045636
-
Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs
-
Wachter A, Tunc-Ozdemir M, Grove BC, Green PJ, Shintani DK, Breaker RR. Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs. Plant Cell 2007; 19:3437-50.
-
(2007)
Plant Cell
, vol.19
, pp. 3437-3450
-
-
Wachter, A.1
Tunc-Ozdemir, M.2
Grove, B.C.3
Green, P.J.4
Shintani, D.K.5
Breaker, R.R.6
-
9
-
-
34249278470
-
Control of alternative RNA splicing and gene expression by eukaryotic riboswitches
-
DOI 10.1038/nature05769, PII NATURE05769
-
Cheah MT, Wachter A, Sudarsan N, Breaker RR. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 2007; 447:497-500. (Pubitemid 46816734)
-
(2007)
Nature
, vol.447
, Issue.7143
, pp. 497-500
-
-
Cheah, M.T.1
Wachter, A.2
Sudarsan, N.3
Breaker, R.R.4
-
10
-
-
0345531094
-
Regulation of lysine biosynthesis and transport genes in bacteria: Yet another RNA riboswitch?
-
Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? Nucleic Acids Res 2003; 31:6748-57.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 6748-6757
-
-
Rodionov, D.A.1
Vitreschak, A.G.2
Mironov, A.A.3
Gelfand, M.S.4
-
11
-
-
2342511433
-
New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control
-
DOI 10.1073/pnas.0308014101
-
Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, et al. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc Natl Acad Sci USA 2004; 101:6421-6. (Pubitemid 38585989)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.17
, pp. 6421-6426
-
-
Barrick, J.E.1
Corbino, K.A.2
Winkler, W.C.3
Nahvi, A.4
Mandal, M.5
Collins, J.6
Lee, M.7
Roth, A.8
Sudarsan, N.9
Jona, I.10
Wickiser, J.K.11
Breaker, R.R.12
-
12
-
-
34547873145
-
Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline
-
DOI 10.1093/nar/gkm487
-
Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, et al. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res 2007; 35:4809-19. (Pubitemid 47250352)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.14
, pp. 4809-4819
-
-
Weinberg, Z.1
Barrick, J.E.2
Yao, Z.3
Roth, A.4
Kim, J.N.5
Gore, J.6
Wang, J.X.7
Lee, E.R.8
Block, K.F.9
Sudarsan, N.10
Neph, S.11
Tompa, M.12
Ruzzo, W.L.13
Breaker, R.R.14
-
13
-
-
34547558201
-
A computational pipeline for highthroughput discovery of cis-regulatory noncoding RNA in prokaryotes
-
Yao Z, Barrick J, Weinberg Z, Neph S, Breaker RR, Tompa M, et al. A computational pipeline for highthroughput discovery of cis-regulatory noncoding RNA in prokaryotes. PLoS Comput Biol 2007; 3:126.
-
(2007)
PLoS Comput Biol
, vol.3
, pp. 126
-
-
Yao, Z.1
Barrick, J.2
Weinberg, Z.3
Neph, S.4
Breaker, R.R.5
Tompa, M.6
-
14
-
-
65449156827
-
Finding non-coding RNAs through genome-scale clustering
-
Tseng H, Weinberg Z, Gore J, Breaker RR, Ruzzo WL. Finding non-coding RNAs through genome-scale clustering. J Bioinform Comput Biol 2009; 7:373-88.
-
(2009)
J Bioinform Comput Biol
, vol.7
, pp. 373-388
-
-
Tseng, H.1
Weinberg, Z.2
Gore, J.3
Breaker, R.R.4
Ruzzo, W.L.5
-
15
-
-
77951606278
-
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes
-
Weinberg Z, Wang J, Bogue J, Yang J, Corbino K, Moy R, et al. Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes. Genome Biol 2010; 11:31.
-
(2010)
Genome Biol
, vol.11
, pp. 31
-
-
Weinberg, Z.1
Wang, J.2
Bogue, J.3
Yang, J.4
Corbino, K.5
Moy, R.6
-
16
-
-
0242298623
-
An mRNA structure in bacteria that controls gene expression by binding lysine
-
DOI 10.1101/gad.1140003
-
Sudarsan N, Wickiser JK, Nakamura S, Ebert MS, Breaker RR. An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev 2003; 17:2688-97. (Pubitemid 37363073)
-
(2003)
Genes and Development
, vol.17
, Issue.21
, pp. 2688-2697
-
-
Sudarsan, N.1
Wickiser, J.K.2
Nakamura, S.3
Ebert, M.S.4
Breaker, R.R.5
-
17
-
-
5044234799
-
A glycine-dependent riboswitch that uses cooperative binding to control gene expression
-
DOI 10.1126/science.1100829
-
Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, et al. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 2004; 306:275-9. (Pubitemid 39336872)
-
(2004)
Science
, vol.306
, Issue.5694
, pp. 275-279
-
-
Mandal, M.1
Lee, M.2
Barrick, J.E.3
Weinberg, Z.4
Emilsson, G.M.5
Ruzzo, W.L.6
Breaker, R.R.7
-
18
-
-
0017235084
-
Identification of nitrogen as a growth-limiting nutrient in wastewaters and coastal marine waters through continuous culture algal assays
-
Goldman JC. Identification of nitrogen as a growth-limiting nutrient in wastewaters and coastal marine waters through continuous culture algal assays. Water Res 1976; 10:97-104.
-
(1976)
Water Res
, vol.10
, pp. 97-104
-
-
Goldman, J.C.1
-
20
-
-
34249816497
-
Glutamine signalling in bacteria
-
DOI 10.2741/2069
-
Forchhammer K. Glutamine signalling in bacteria. Front Biosci 2007; 12:358-70. (Pubitemid 46852845)
-
(2007)
Frontiers in Bioscience
, vol.12
, Issue.1
, pp. 358-370
-
-
Forchhammer, K.1
-
21
-
-
0035851149
-
Cyanobacteria perceive nitrogen status by sensing intracellular 2-oxoglutarate levels
-
Muro-Pastor MI, Reyes JC, Florencio FJ. Cyanobacteria perceive nitrogen status by sensing intracellular 2-oxoglutarate levels. J Biol Chem 2001; 276:38320-8.
-
(2001)
J Biol Chem
, vol.276
, pp. 38320-38328
-
-
Muro-Pastor, M.I.1
Reyes, J.C.2
Florencio, F.J.3
-
22
-
-
0142062422
-
Carbon supply and 2-oxoglutarate effects on expression of nitrate reductase and nitrogen-regulated genes in Synechococcus sp. strain PCC 7942
-
DOI 10.1016/S0378-1097(03)00208-8
-
Vázquez-Bermúdez MF, Herrero A, Flores E. Carbon supply and 2-oxoglutarate effects on expression of nitrate reductase and nitrogen-regulated genes in Synechococcus sp. strain PCC 7942. FEMS Microbiol Lett 2003; 221:155-9. (Pubitemid 41123056)
-
(2003)
FEMS Microbiology Letters
, vol.221
, Issue.2
, pp. 155-159
-
-
Vazquez-Bermudez, M.F.1
Herrero, A.2
Flores, E.3
-
23
-
-
2642530192
-
II signal transduction in cyanobacteria: From signals to targets
-
II signal transduction in cyanobacteria: from signals to targets. FEMS Microbiol Rev 2004; 28:319-33.
-
(2004)
FEMS Microbiol Rev
, vol.28
, pp. 319-333
-
-
Forchhammer, K.1
-
24
-
-
68049100110
-
Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
-
Bennett BD, Kimball EH, Gao M, Osterhout R, Van Dien SJ, Rabinowitz JD. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol 2009; 5:593-9.
-
(2009)
Nat Chem Biol
, vol.5
, pp. 593-599
-
-
Bennett, B.D.1
Kimball, E.H.2
Gao, M.3
Osterhout, R.4
Van Dien, S.J.5
Rabinowitz, J.D.6
-
25
-
-
33749986680
-
Tandem riboswitch architectures exhibit complex gene control functions
-
DOI 10.1126/science.1130716
-
Sudarsan N, Hammond MC, Block KF, Welz R, Barrick JE, Roth A, et al. Tandem riboswitch architectures exhibit complex gene control functions. Science 2006; 314:300-4. (Pubitemid 44571975)
-
(2006)
Science
, vol.314
, Issue.5797
, pp. 300-304
-
-
Sudarsan, N.1
Hammond, M.C.2
Block, K.F.3
Welz, R.4
Barrick, J.E.5
Roth, A.6
Breaker, R.R.7
-
26
-
-
33947714417
-
Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis
-
DOI 10.1261/rna.407707
-
Welz R, Breaker RR. Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis. RNA 2007; 13:573-82. (Pubitemid 46506940)
-
(2007)
RNA
, vol.13
, Issue.4
, pp. 573-582
-
-
Welz, R.1
Breaker, R.R.2
-
27
-
-
38049025288
-
Chemical basis of glycine riboswitch cooperativity
-
Kwon M, Strobel SA. Chemical basis of glycine riboswitch cooperativity. RNA 2008; 14:25-34.
-
(2008)
RNA
, vol.14
, pp. 25-34
-
-
Kwon, M.1
Strobel, S.A.2
-
28
-
-
71449108155
-
Structural basis of ligand binding by a c-di-GMP riboswitch
-
Smith KD, Lipchock SV, Ames TD, Wang J, Breaker RR, Strobel SA. Structural basis of ligand binding by a c-di-GMP riboswitch. Nat Struct Mol Biol 2009; 16:1218-23.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 1218-1223
-
-
Smith, K.D.1
Lipchock, S.V.2
Ames, T.D.3
Wang, J.4
Breaker, R.R.5
Strobel, S.A.6
-
29
-
-
1642586299
-
Control of gene expression by a natural metabolite-responsive ribozyme
-
DOI 10.1038/nature02362
-
Winkler WC, Nahvi A, Roth A, Collins JA, Breaker RR. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 2004; 428:281-6. (Pubitemid 38418792)
-
(2004)
Nature
, vol.428
, Issue.6980
, pp. 281-286
-
-
Winkler, W.C.1
Nahvi, A.2
Roth, A.3
Collins, J.A.4
Breaker, R.R.5
-
30
-
-
65249184394
-
Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme
-
Cochrane JC, Lipchock SV, Smith KD, Strobel SA. Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme. Biochemistry 2009; 48:3239-46.
-
(2009)
Biochemistry
, vol.48
, pp. 3239-3246
-
-
Cochrane, J.C.1
Lipchock, S.V.2
Smith, K.D.3
Strobel, S.A.4
-
31
-
-
26444620938
-
The kinetics of ligand binding by an adenine-sensing riboswitch
-
DOI 10.1021/bi051008u
-
Wickiser JK, Cheah MT, Breaker RR, Crothers DM. The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry 2005; 44:13404-14. (Pubitemid 41429463)
-
(2005)
Biochemistry
, vol.44
, Issue.40
, pp. 13404-13414
-
-
Wickiser, J.K.1
Cheah, M.T.2
Breaker, R.R.3
Crothers, D.M.4
-
32
-
-
15944382675
-
The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch
-
DOI 10.1016/j.molcel.2005.02.032
-
Wickiser JK, Winkler WC, Breaker RR, Crothers DM. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol Cell 2005; 18:49-60. (Pubitemid 40444647)
-
(2005)
Molecular Cell
, vol.18
, Issue.1
, pp. 49-60
-
-
Wickiser, J.K.1
Winkler, W.C.2
Breaker, R.R.3
Crothers, D.M.4
-
33
-
-
33646768226
-
Thermodynamic and Kinetic Characterization of Ligand Binding to the Purine Riboswitch Aptamer Domain
-
DOI 10.1016/j.jmb.2006.04.003, PII S0022283606004517
-
Gilbert SD, Stoddard CD, Wise SJ, Batey RT. Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. J Mol Biol 2006; 359:754-68. (Pubitemid 43767264)
-
(2006)
Journal of Molecular Biology
, vol.359
, Issue.3
, pp. 754-768
-
-
Gilbert, S.D.1
Stoddard, C.D.2
Wise, S.J.3
Batey, R.T.4
-
34
-
-
0032831634
-
Relationship between internucleotide linkage geometry and the stability of RNA
-
DOI 10.1017/S1355838299990891
-
Soukup GA, Breaker RR. Relationship between internucleotide linkage geometry and the stability of RNA. RNA 1999; 5:1308-25. (Pubitemid 29489813)
-
(1999)
RNA
, vol.5
, Issue.10
, pp. 1308-1325
-
-
Soukup, G.A.1
Breaker, R.R.2
-
35
-
-
84897585709
-
In-line probing analysis of riboswitches
-
Regulski EE, Breaker RR. In-line probing analysis of riboswitches. Methods Mol Biol 2008; 419:53-67.
-
(2008)
Methods Mol Biol
, vol.419
, pp. 53-67
-
-
Regulski, E.E.1
Breaker, R.R.2
-
36
-
-
13944278373
-
SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments
-
DOI 10.1261/rna.7214405
-
Das R, Laederach A, Pearlman SM, Herschlag D, Altman RB. SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA 2005; 11:344-54. (Pubitemid 40270826)
-
(2005)
RNA
, vol.11
, Issue.3
, pp. 344-354
-
-
Das, R.1
Laederach, A.2
Pearlman, S.M.3
Herschlag, D.4
Altman, R.B.5
|