-
1
-
-
4344579113
-
The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock
-
Allen, T.A., Von Kaenel, S., Goodrich, J.A., and Kugel, J.F. 2004. The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat. Struct. Mol. Biol. 11: 816-821.
-
(2004)
Nat. Struct. Mol. Biol.
, vol.11
, pp. 816-821
-
-
Allen, T.A.1
Von Kaenel, S.2
Goodrich, J.A.3
Kugel, J.F.4
-
2
-
-
0037154430
-
Expression of a small RNA, BS203 RNA, from the yocI-yocJ intergenic region of the Bacillus subtilis genome
-
Ando, Y., Asari, S., Suzuma, S., Yamane, K., and Nakamura, K. 2002. Expression of a small RNA, BS203 RNA, from the yocI-yocJ intergenic region of the Bacillus subtilis genome. FEMS Microbiol. Lett. 207: 29-33.
-
(2002)
FEMS Microbiol. Lett.
, vol.207
, pp. 29-33
-
-
Ando, Y.1
Asari, S.2
Suzuma, S.3
Yamane, K.4
Nakamura, K.5
-
3
-
-
0042531680
-
Methenyltetrahydrofolate synthetase regulates folate turnover and accumulation
-
Anguera, M.C., Suh, J.R., Ghandour, H., Nasrallah, I.M., Selhub, J., and Stover, P.J. 2003. Methenyltetrahydrofolate synthetase regulates folate turnover and accumulation. J. Biol. Chem. 278: 29856-29862.
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 29856-29862
-
-
Anguera, M.C.1
Suh, J.R.2
Ghandour, H.3
Nasrallah, I.M.4
Selhub, J.5
Stover, P.J.6
-
4
-
-
2342511433
-
New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control
-
Barrick, J.E., Corbino, K.A., Winkler, W.C., Nahvi, A., Mandal, M., Collins, J., Lee, M., Roth, A., Sudarsan, N., Jona, I., et al. 2004. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl. Acad. Sci. 101: 6421-6426.
-
(2004)
Proc. Natl. Acad. Sci.
, vol.101
, 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
-
5
-
-
0029930365
-
More Haemophilus and Mycoplasma genes
-
Brosius, J. 1996. More Haemophilus and Mycoplasma genes. Science 271: 1302-1302.
-
(1996)
Science
, vol.271
, pp. 1302-1302
-
-
Brosius, J.1
-
6
-
-
0015208767
-
Sequence of 6S RNA of E. coli
-
Brownlee, G.G. 1971. Sequence of 6S RNA of E. coli. Nat. New Biol. 229: 147-149.
-
(1971)
Nat. New Biol.
, vol.229
, pp. 147-149
-
-
Brownlee, G.G.1
-
7
-
-
0037251969
-
The Ribosomal Database Project (RDP-II): Previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
-
Cole, J.R., Chai, B., Marsh, T.L., Farris, R.J., Wang, Q., Kulam, S.A., Chandra, S., McGarrell, D.M., Schmidt, T.M., Garrity, G.M., et al. 2003. The Ribosomal Database Project (RDP-II): Previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 31: 442-443.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 442-443
-
-
Cole, J.R.1
Chai, B.2
Marsh, T.L.3
Farris, R.J.4
Wang, Q.5
Kulam, S.A.6
Chandra, S.7
McGarrell, D.M.8
Schmidt, T.M.9
Garrity, G.M.10
-
8
-
-
0002300369
-
The recent evolution of mammalian repetitive DNA elements
-
Deininger, P.L. and Daniels, G.R. 1986. The recent evolution of mammalian repetitive DNA elements. Trends Genet. 2: 76-80.
-
(1986)
Trends Genet.
, vol.2
, pp. 76-80
-
-
Deininger, P.L.1
Daniels, G.R.2
-
9
-
-
0028272315
-
RNA sequence analysis using covariance models
-
Eddy, S.R. and Durbin, R. 1994. RNA sequence analysis using covariance models. Nucleic Acids Res. 22: 2079-2088.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 2079-2088
-
-
Eddy, S.R.1
Durbin, R.2
-
10
-
-
4344583992
-
B2 RNA binds directly to RNA polymerase II to repress transcript synthesis
-
Espinoza, C.A., Allen, T.A., Hieb, A.R., Kugel, J.F., and Goodrich, J.A. 2004. B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat. Struct. Mol. Biol. 11: 822-829.
-
(2004)
Nat. Struct. Mol. Biol.
, vol.11
, pp. 822-829
-
-
Espinoza, C.A.1
Allen, T.A.2
Hieb, A.R.3
Kugel, J.F.4
Goodrich, J.A.5
-
11
-
-
0038606991
-
Effect of DNA bases and backbone on σ70 holoenzyme binding and isomerization using fork junction probes
-
Fenton, M.S. and Gralla, J.D. 2003. Effect of DNA bases and backbone on σ70 holoenzyme binding and isomerization using fork junction probes. Nucleic Acids Res. 31: 2745-2750.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 2745-2750
-
-
Fenton, M.S.1
Gralla, J.D.2
-
12
-
-
0031711821
-
Ribonuclease P: Unity and diversity in a tRNA processing ribozyme
-
Frank, D.N. and Pace, N.R. 1998. Ribonuclease P: Unity and diversity in a tRNA processing ribozyme. Annu. Rev. Biochem. 67: 153-180.
-
(1998)
Annu. Rev. Biochem.
, vol.67
, pp. 153-180
-
-
Frank, D.N.1
Pace, N.R.2
-
13
-
-
0028221642
-
Volume changes in protein evolution
-
Gerstein, M., Sonnhammer, E.L.L., and Chothia, C. 1994. Volume changes in protein evolution. J. Mol. Biol. 236: 1067-1078.
-
(1994)
J. Mol. Biol.
, vol.236
, pp. 1067-1078
-
-
Gerstein, M.1
Sonnhammer, E.L.L.2
Chothia, C.3
-
14
-
-
0037252684
-
Rfam: An RNA family database
-
Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A., and Eddy, S.R. 2003. Rfam: An RNA family database. Nucleic Acids Res. 31: 439-441.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 439-441
-
-
Griffiths-Jones, S.1
Bateman, A.2
Marshall, M.3
Khanna, A.4
Eddy, S.R.5
-
15
-
-
18344418394
-
Protein-nucleic acid interactions during open complex formation investigated by systematic alteration of the protein and DNA binding partners
-
Helmann, J.D. and deHaseth, P.L. 1999. Protein-nucleic acid interactions during open complex formation investigated by systematic alteration of the protein and DNA binding partners. Biochemistry 38: 5959-5967.
-
(1999)
Biochemistry
, vol.38
, pp. 5959-5967
-
-
Helmann, J.D.1
DeHaseth, P.L.2
-
16
-
-
0014220139
-
32P-labelled ribonucleic acids on polyacrylamide gels and their characterization by fingerprinting
-
32P-labelled ribonucleic acids on polyacrylamide gels and their characterization by fingerprinting. J. Mol. Biol. 30: 125-136.
-
(1967)
J. Mol. Biol.
, vol.30
, pp. 125-136
-
-
Hindley, J.1
-
17
-
-
0021913190
-
Escherichia coli 6S RNA gene is part of a dual-function transcription unit
-
Hsu, L.M., Zagorski, J., Wang, Z., and Fournier, M.J. 1985. Escherichia coli 6S RNA gene is part of a dual-function transcription unit. J. Bacteriol. 161: 1162-1170.
-
(1985)
J. Bacteriol.
, vol.161
, pp. 1162-1170
-
-
Hsu, L.M.1
Zagorski, J.2
Wang, Z.3
Fournier, M.J.4
-
18
-
-
0033021173
-
Modulation of the nucleoid, the transcription apparatus, and the translation machinery in bacteria for stationary phase survival
-
Ishihama, A. 1999. Modulation of the nucleoid, the transcription apparatus, and the translation machinery in bacteria for stationary phase survival. Genes Cells 4: 135-143.
-
(1999)
Genes Cells
, vol.4
, pp. 135-143
-
-
Ishihama, A.1
-
19
-
-
0033765113
-
Functional modulation of Escherichia coli RNA polymerase
-
_. 2000. Functional modulation of Escherichia coli RNA polymerase. Annu. Rev. Microbiol. 54: 499-518.
-
(2000)
Annu. Rev. Microbiol.
, vol.54
, pp. 499-518
-
-
-
20
-
-
2942576138
-
Evolution of bacterial RNA polymerase: Implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer
-
Iyer, L.M., Koonin, E.V., and Aravind, L. 2004. Evolution of bacterial RNA polymerase: Implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. Gene 335: 73-88.
-
(2004)
Gene
, vol.335
, pp. 73-88
-
-
Iyer, L.M.1
Koonin, E.V.2
Aravind, L.3
-
21
-
-
11344264898
-
Regulation of 6S RNA biogenesis by switching utilization of both sigma factors and endoribonucleases
-
Kim, K.S. and Lee, Y. 2004. Regulation of 6S RNA biogenesis by switching utilization of both sigma factors and endoribonucleases. Nucleic Acids Res. 32: 6057-6068.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 6057-6068
-
-
Kim, K.S.1
Lee, Y.2
-
22
-
-
4644225942
-
In search of RNase P RNA from microbial genomes
-
Li, Y. and Altman, S. 2004. In search of RNase P RNA from microbial genomes. RNA 10: 1533-1540.
-
(2004)
RNA
, vol.10
, pp. 1533-1540
-
-
Li, Y.1
Altman, S.2
-
23
-
-
0032539857
-
3′ Exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli
-
Li, Z., Pandit, S., and Deutscher, M.P. 1998. 3′ Exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli. Proc. Natl. Acad. Sci. 95: 2856-2861.
-
(1998)
Proc. Natl. Acad. Sci.
, vol.95
, pp. 2856-2861
-
-
Li, Z.1
Pandit, S.2
Deutscher, M.P.3
-
24
-
-
5044234799
-
A glycine-dependent riboswitch that uses cooperative binding to control gene expression
-
Mandal, M., Lee, M., Barrick, J.E., Weinberg, Z., Emilsson, G.M., Ruzzo, W.L., and Breaker, R.R. 2004. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306: 275-279.
-
(2004)
Science
, vol.306
, 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
-
25
-
-
0037123602
-
Structural basis of transcription initiation: An RNA polymerase holoenzyme-DNA complex
-
Murakami, K.S., Masuda, S., Campbell, E.A., Muzzin, O., and Darst, S.A. 2002. Structural basis of transcription initiation: An RNA polymerase holoenzyme-DNA complex. Science 296: 1285-1290.
-
(2002)
Science
, vol.296
, pp. 1285-1290
-
-
Murakami, K.S.1
Masuda, S.2
Campbell, E.A.3
Muzzin, O.4
Darst, S.A.5
-
27
-
-
0037150071
-
Characterization of a viroid-derived RNA promoter for the DNA-dependent RNA polymerase from Escherichia coli
-
Pelchat, M., Grenier, C., and Perreault, J.P. 2002. Characterization of a viroid-derived RNA promoter for the DNA-dependent RNA polymerase from Escherichia coli. Biochemistry 41: 6561-6571.
-
(2002)
Biochemistry
, vol.41
, pp. 6561-6571
-
-
Pelchat, M.1
Grenier, C.2
Perreault, J.P.3
-
28
-
-
2342442328
-
Gene expression in Escherichia coli biofilms
-
Ren, D., Bedzyk, L.A., Thomas, S.M., Ye, R.W., and Wood, T.K. 2004. Gene expression in Escherichia coli biofilms. Appl. Microbiol. Biotechnol. 64: 515-524.
-
(2004)
Appl. Microbiol. Biotechnol.
, vol.64
, pp. 515-524
-
-
Ren, D.1
Bedzyk, L.A.2
Thomas, S.M.3
Ye, R.W.4
Wood, T.K.5
-
29
-
-
0032831634
-
Relationship between inter-nucleotide linkage geometry and the stability of RNA
-
Soukup, G.A. and Breaker, R.R. 1999. Relationship between inter-nucleotide linkage geometry and the stability of RNA. RNA 5: 1308-1325.
-
(1999)
RNA
, vol.5
, pp. 1308-1325
-
-
Soukup, G.A.1
Breaker, R.R.2
-
30
-
-
0036667443
-
Identification and characterization of novel small RNAs in the aspS-yrvM intergenic region of the Bacillus subtilis genome
-
Suzuma, S., Asari, S., Bunai, K., Yoshino, K., Ando, Y., Kakeshita, H., Fujita, M., Nakamura, K., and Yamane, K. 2002. Identification and characterization of novel small RNAs in the aspS-yrvM intergenic region of the Bacillus subtilis genome. Microbiology 148: 2591-2598.
-
(2002)
Microbiology
, vol.148
, pp. 2591-2598
-
-
Suzuma, S.1
Asari, S.2
Bunai, K.3
Yoshino, K.4
Ando, Y.5
Kakeshita, H.6
Fujita, M.7
Nakamura, K.8
Yamane, K.9
-
31
-
-
3242807381
-
6S RNA function enhances long-term cell survival
-
Trotochaud, A.E. and Wassarman, K.M. 2004. 6S RNA function enhances long-term cell survival. J. Bact. 186: 4978-4985.
-
(2004)
J. Bact.
, vol.186
, pp. 4978-4985
-
-
Trotochaud, A.E.1
Wassarman, K.M.2
-
32
-
-
11144354360
-
Environmental genome shotgun sequencing of the Sargasso Sea
-
Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., Wu, D.Y., Paulsen, I., Nelson, K.E., Nelson, W., et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
-
(2004)
Science
, vol.304
, pp. 66-74
-
-
Venter, J.C.1
Remington, K.2
Heidelberg, J.F.3
Halpern, A.L.4
Rusch, D.5
Eisen, J.A.6
Wu, D.Y.7
Paulsen, I.8
Nelson, K.E.9
Nelson, W.10
-
33
-
-
0023650987
-
The sequence of the 6S RNA gene of Pseudomonas aeruginosa
-
Vogel, D.W., Hartmann, R.K., Struck, J.C.R., Ulbrich, N., and Erdmann, V.A. 1987. The sequence of the 6S RNA gene of Pseudomonas aeruginosa. Nucleic Acids Res. 15: 4583-4591.
-
(1987)
Nucleic Acids Res.
, vol.15
, pp. 4583-4591
-
-
Vogel, D.W.1
Hartmann, R.K.2
Struck, J.C.R.3
Ulbrich, N.4
Erdmann, V.A.5
-
34
-
-
0037133946
-
Small RNAs in bacteria: Diverse regulators of gene expression in response to environmental changes
-
Wassarman, K.M. 2002. Small RNAs in bacteria: Diverse regulators of gene expression in response to environmental changes. Cell 109: 141-144.
-
(2002)
Cell
, vol.109
, pp. 141-144
-
-
Wassarman, K.M.1
-
35
-
-
0034625237
-
6S RNA regulates E. coli RNA polymerase activity
-
Wassarman, K.M. and Storz, G. 2000. 6S RNA regulates E. coli RNA polymerase activity. Cell 101: 613-623.
-
(2000)
Cell
, vol.101
, pp. 613-623
-
-
Wassarman, K.M.1
Storz, G.2
-
36
-
-
0030695907
-
A novel small stable RNA, 6Sa RNA, from the cyanobacterium Synechococcus sp. strain PCC6301
-
Watanabe, T., Sugiura, R., and Sugita, M. 1997. A novel small stable RNA, 6Sa RNA, from the cyanobacterium Synechococcus sp. strain PCC6301. FEBS Lett. 416: 302-306.
-
(1997)
FEBS Lett.
, vol.416
, pp. 302-306
-
-
Watanabe, T.1
Sugiura, R.2
Sugita, M.3
-
37
-
-
13444287763
-
Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy
-
Weinberg, Z. and Ruzzo, W.L. 2004a. Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy. Bioinformatics 20 (Suppl. 1): i334-i341.
-
(2004)
Bioinformatics
, vol.20
, Issue.1 SUPPL.
-
-
Weinberg, Z.1
Ruzzo, W.L.2
-
39
-
-
0035916889
-
RNA species that replicate with DNA-dependent RNA polymerase from Escherichia coli
-
Wettich, A. and Biebricher, C.K. 2001. RNA species that replicate with DNA-dependent RNA polymerase from Escherichia coli. Biochemistry 40: 3308-3315.
-
(2001)
Biochemistry
, vol.40
, pp. 3308-3315
-
-
Wettich, A.1
Biebricher, C.K.2
-
40
-
-
0033597435
-
Mechanism of intrinsic transcription termination and antitermination
-
Yarnell, W.S. and Roberts, J.W. 1999. Mechanism of intrinsic transcription termination and antitermination. Science 284: 611-615.
-
(1999)
Science
, vol.284
, pp. 611-615
-
-
Yarnell, W.S.1
Roberts, J.W.2
|