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Volumn 38, Issue 5, 2009, Pages 1504-1514

Mining regulatory 5′UTRs from cDNA deep sequencing datasets

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; FATTY ACID; GREEN FLUORESCENT PROTEIN; PEPTIDOGLYCAN; RNA; AMINO ACID;

EID: 77950465576     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1121     Document Type: Article
Times cited : (19)

References (47)
  • 1
    • 60149089144 scopus 로고    scopus 로고
    • Regulatory RNAs in bacteria
    • Waters, L.S. and Storz, G. (2009) Regulatory RNAs in bacteria. Cell, 136, 615-628.
    • (2009) Cell , vol.136 , pp. 615-628
    • Waters, L.S.1    Storz, G.2
  • 2
    • 63749126957 scopus 로고    scopus 로고
    • Expanding roles for metabolite-sensing regulatory RNAs
    • Dambach, M.D. and Winkler, W.C. (2009) Expanding roles for metabolite-sensing regulatory RNAs. Curr. Opin. Microbiol., 12, 161-169.
    • (2009) Curr. Opin. Microbiol. , vol.12 , pp. 161-169
    • Dambach, M.D.1    Winkler, W.C.2
  • 4
    • 0035984639 scopus 로고    scopus 로고
    • Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions
    • Henkin, T.M. and Yanofsky, C. (2002) Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions. Bioessays, 24, 700-707.
    • (2002) Bioessays , vol.24 , pp. 700-707
    • Henkin, T.M.1    Yanofsky, C.2
  • 5
    • 0043166304 scopus 로고    scopus 로고
    • Transcriptional and post-transcriptional control of cold-shock genes
    • Gualerzi, C.O., Giuliodori, A.M. and Pon, C.L. (2003) Transcriptional and post-transcriptional control of cold-shock genes. J. Mol. Biol., 331, 527-539.
    • (2003) J. Mol. Biol. , vol.331 , pp. 527-539
    • Gualerzi, C.O.1    Giuliodori, A.M.2    Pon, C.L.3
  • 7
    • 20444478991 scopus 로고    scopus 로고
    • Riboswitches as versatile gene control elements
    • Tucker, B.J. and Breaker, R.R. (2005) Riboswitches as versatile gene control elements. Curr. Opin. Struct. Biol., 15, 342-348.
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 342-348
    • Tucker, B.J.1    Breaker, R.R.2
  • 8
    • 0027234192 scopus 로고
    • tRNA as a positive regulator of transcription antitermination in B. subtilis
    • Grundy, F.J. and Henkin, T.M. (1993) tRNA as a positive regulator of transcription antitermination in B. subtilis. Cell, 74, 475-482.
    • (1993) Cell , vol.74 , pp. 475-482
    • Grundy, F.J.1    Henkin, T.M.2
  • 10
    • 42149126162 scopus 로고    scopus 로고
    • Evolution of bacterial trp operons and their regulation
    • Merino, E., Jensen, R.A. and Yanofsky, C. (2008) Evolution of bacterial trp operons and their regulation. Curr. Opin. Microbiol., 11, 78-86.
    • (2008) Curr. Opin. Microbiol. , vol.11 , pp. 78-86
    • Merino, E.1    Jensen, R.A.2    Yanofsky, C.3
  • 13
    • 23144463910 scopus 로고    scopus 로고
    • RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements
    • Abreu-Goodger, C. and Merino, E. (2005) RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements. Nucleic Acids Res., 33, W690-W692.
    • (2005) Nucleic Acids Res , vol.33
    • Abreu-Goodger, C.1    Merino, E.2
  • 15
    • 42549108780 scopus 로고    scopus 로고
    • A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism
    • Regulski, E.E., Moy, R.H., Weinberg, Z., Barrick, J.E., Yao, Z., Ruzzo, W.L. and Breaker, R.R. (2008) A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Mol. Microbiol., 68, 918-932.
    • (2008) Mol. Microbiol. , vol.68 , pp. 918-932
    • Regulski, E.E.1    Moy, R.H.2    Weinberg, Z.3    Barrick, J.E.4    Yao, Z.5    Ruzzo, W.L.6    Breaker, R.R.7
  • 17
    • 64549149245 scopus 로고    scopus 로고
    • Experimental discovery of sRNAs in Vibrio cholerae by direct cloning. 5S/tRNA depletion and parallel sequencing
    • Liu, J.M., Livny, J., Lawrence, M.S., Kimball, M.D., Waldor, M.K. and Camilli, A. (2009) Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res., 37, e46.
    • (2009) Nucleic Acids Res. , vol.37
    • Liu, J.M.1    Livny, J.2    Lawrence, M.S.3    Kimball, M.D.4    Waldor, M.K.5    Camilli, A.6
  • 21
    • 52449093583 scopus 로고    scopus 로고
    • High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs
    • Livny, J., Teonadi, H., Livny, M. and Waldor, M.K. (2008) High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS ONE, 3, e3197.
    • (2008) PLoS ONE , vol.3
    • Livny, J.1    Teonadi, H.2    Livny, M.3    Waldor, M.K.4
  • 24
    • 33847386673 scopus 로고    scopus 로고
    • Translational control and target recognition by Escherichia coli small RNAs in vivo
    • Urban, J.H. and Vogel, J. (2007) Translational control and target recognition by Escherichia coli small RNAs in vivo. Nucleic Acids Res., 35, 1018-1037.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 1018-1037
    • Urban, J.H.1    Vogel, J.2
  • 25
    • 22844436749 scopus 로고    scopus 로고
    • sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes
    • Livny, J., Fogel, M.A., Davis, B.M. and Waldor, M.K. (2005) sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes. Nucleic Acids Res., 33, 4096-4105.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 4096-4105
    • Livny, J.1    Fogel, M.A.2    Davis, B.M.3    Waldor, M.K.4
  • 26
    • 0043210342 scopus 로고    scopus 로고
    • msDNA-St85, a multicopy single-stranded DNA isolated from Salmonella enterica serovar Typhimurium LT2 with the genomic analysis of its retron
    • Ahmed, A.M. and Shimamoto, T. (2003) msDNA-St85, a multicopy single-stranded DNA isolated from Salmonella enterica serovar Typhimurium LT2 with the genomic analysis of its retron. FEMS Microbiol. Lett., 224, 291-297.
    • (2003) FEMS Microbiol. Lett. , vol.224 , pp. 291-297
    • Ahmed, A.M.1    Shimamoto, T.2
  • 28
    • 34548348934 scopus 로고    scopus 로고
    • 6S RNA: a regulator of transcription
    • Wassarman, K.M. (2007) 6S RNA: a regulator of transcription. Mol. Microbiol., 65, 1425-1431.
    • (2007) Mol. Microbiol. , vol.65 , pp. 1425-1431
    • Wassarman, K.M.1
  • 29
    • 0029965652 scopus 로고    scopus 로고
    • Pseudoknot and translational control in the expression of the S15 ribosomal protein
    • Benard, L., Philippe, C., Ehresmann, B., Ehresmann, C. and Portier, C. (1996) Pseudoknot and translational control in the expression of the S15 ribosomal protein. Biochimie, 78, 568-576.
    • (1996) Biochimie , vol.78 , pp. 568-576
    • Benard, L.1    Philippe, C.2    Ehresmann, B.3    Ehresmann, C.4    Portier, C.5
  • 30
    • 0037206833 scopus 로고    scopus 로고
    • Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression
    • Winkler, W., Nahvi, A. and Breaker, R.R. (2002) Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature, 419, 952-956.
    • (2002) Nature , vol.419 , pp. 952-956
    • Winkler, W.1    Nahvi, A.2    Breaker, R.R.3
  • 31
    • 0019376173 scopus 로고
    • Control of leu operon expression in Escherichia coli by a transcription attenuation mechanism
    • Wessler, S.R. and Calvo, J.M. (1981) Control of leu operon expression in Escherichia coli by a transcription attenuation mechanism. J. Mol. Biol., 149, 579-597.
    • (1981) J. Mol. Biol. , vol.149 , pp. 579-597
    • Wessler, S.R.1    Calvo, J.M.2
  • 32
    • 0022997615 scopus 로고
    • Transcription attenuation in Salmonella typhimurium: the significance of rare leucine codons in the leu leader
    • Carter, P.W., Bartkus, J.M. and Calvo, J.M. (1986) Transcription attenuation in Salmonella typhimurium: the significance of rare leucine codons in the leu leader. Proc. Natl Acad. Sci. USA, 83, 8127-8131.
    • (1986) Proc. Natl Acad. Sci. USA , vol.83 , pp. 8127-8131
    • Carter, P.W.1    Bartkus, J.M.2    Calvo, J.M.3
  • 33
    • 0025880640 scopus 로고
    • Regulation of pheA expression by the pheR product in Escherichia coli is mediated through attenuation of transcription
    • Gavini, N. and Davidson, B.E. (1991) Regulation of pheA expression by the pheR product in Escherichia coli is mediated through attenuation of transcription. J. Biol. Chem., 266, 7750-7753.
    • (1991) J. Biol. Chem. , vol.266 , pp. 7750-7753
    • Gavini, N.1    Davidson, B.E.2
  • 34
    • 0028797303 scopus 로고
    • RNase E autoregulates its synthesis by controlling the degradation rate of its own mRNA in Escherichia coli: unusual sensitivity of the rne transcript to RNase E activity
    • Jain, C. and Belasco, J.G. (1995) RNase E autoregulates its synthesis by controlling the degradation rate of its own mRNA in Escherichia coli: unusual sensitivity of the rne transcript to RNase E activity. Genes Dev., 9, 84-96.
    • (1995) Genes Dev. , vol.9 , pp. 84-96
    • Jain, C.1    Belasco, J.G.2
  • 35
    • 0037783314 scopus 로고    scopus 로고
    • Translational repression mechanisms in prokaryotes
    • Schlax, P.J. and Worhunsky, D.J. (2003) Translational repression mechanisms in prokaryotes. Mol. Microbiol., 48, 1157-1169.
    • (2003) Mol. Microbiol. , vol.48 , pp. 1157-1169
    • Schlax, P.J.1    Worhunsky, D.J.2
  • 36
    • 0035803559 scopus 로고    scopus 로고
    • PNPase autocontrols its expression by degrading a double-stranded structure in the pnp mRNA leader
    • Jarrige, A.C., Mathy, N. and Portier, C. (2001) PNPase autocontrols its expression by degrading a double-stranded structure in the pnp mRNA leader. EMBO J., 20, 6845-6855.
    • (2001) EMBO J , vol.20 , pp. 6845-6855
    • Jarrige, A.C.1    Mathy, N.2    Portier, C.3
  • 37
    • 0026654962 scopus 로고
    • E. coli polynucleotide phosphorylase expression is autoregulated through an RNase III-dependent mechanism
    • Robert-Le Meur, M. and Portier, C. (1992) E. coli polynucleotide phosphorylase expression is autoregulated through an RNase III-dependent mechanism. EMBO J., 11, 2633-2641.
    • (1992) EMBO J , vol.11 , pp. 2633-2641
    • Robert-Le Meur, M.1    Portier, C.2
  • 38
    • 0028358101 scopus 로고
    • Polynucleotide phosphorylase of Escherichia coli induces the degradation of its RNase III processed messenger by preventing its translation
    • Robert-Le Meur, M. and Portier, C. (1994) Polynucleotide phosphorylase of Escherichia coli induces the degradation of its RNase III processed messenger by preventing its translation. Nucleic Acids Res., 22, 397-403.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 397-403
    • Robert-Le Meur, M.1    Portier, C.2
  • 39
    • 0020340153 scopus 로고
    • Autogenous control: ribosomal protein L10-L12 complex binds to the leader sequence of its mRNA
    • Johnsen, M., Christensen, T., Dennis, P.P. and Fiil, N.P. (1982) Autogenous control: ribosomal protein L10-L12 complex binds to the leader sequence of its mRNA. EMBO J., 1, 999-1004.
    • (1982) EMBO J , vol.1 , pp. 999-1004
    • Johnsen, M.1    Christensen, T.2    Dennis, P.P.3    Fiil, N.P.4
  • 40
    • 36048942754 scopus 로고    scopus 로고
    • Guanine riboswitch variants from Mesoplasma florum selectively recognize 2′-deoxyguanosine
    • Kim, J.N., Roth, A. and Breaker, R.R. (2007) Guanine riboswitch variants from Mesoplasma florum selectively recognize 2(-deoxyguanosine. Proc. Natl Acad. Sci. USA, 104, 16092-16097.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 16092-16097
    • Kim, J.N.1    Roth, A.2    Breaker, R.R.3
  • 41
    • 0028251157 scopus 로고
    • Diverse mechanisms for regulating ribosomal protein synthesis in Escherichia coli
    • Zengel, J.M. and Lindahl, L. (1994) Diverse mechanisms for regulating ribosomal protein synthesis in Escherichia coli. Prog. Nucleic Acid Res. Mol. Biol., 47, 331-370.
    • (1994) Prog. Nucleic Acid Res. Mol. Biol. , vol.47 , pp. 331-370
    • Zengel, J.M.1    Lindahl, L.2
  • 42
    • 4344637329 scopus 로고    scopus 로고
    • Regulation of ribosomal protein synthesis in Vibrio cholerae
    • Allen, T.D., Watkins, T., Lindahl, L. and Zengel, J.M. (2004) Regulation of ribosomal protein synthesis in Vibrio cholerae. J. Bacteriol., 186, 5933-5937.
    • (2004) J. Bacteriol. , vol.186 , pp. 5933-5937
    • Allen, T.D.1    Watkins, T.2    Lindahl, L.3    Zengel, J.M.4
  • 44
    • 5044234799 scopus 로고    scopus 로고
    • 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
  • 45
    • 0015818661 scopus 로고
    • Transport systems for alanine, serine, and glycine in Escherichia coli K-12
    • Robbins, J.C. and Oxender, D.L. (1973) Transport systems for alanine, serine, and glycine in Escherichia coli K-12. J. Bacteriol., 116, 12-18.
    • (1973) J. Bacteriol. , vol.116 , pp. 12-18
    • Robbins, J.C.1    Oxender, D.L.2
  • 46
    • 0027991987 scopus 로고
    • Penicillin-binding protein 7/8 of Escherichia coli is a DD-endopeptidase
    • Romeis, T. and Holtje, J.V. (1994) Penicillin-binding protein 7/8 of Escherichia coli is a DD-endopeptidase. Eur. J. Biochem., 224, 597-604.
    • (1994) Eur. J. Biochem. , vol.224 , pp. 597-604
    • Romeis, T.1    Holtje, J.V.2
  • 47
    • 0030878532 scopus 로고    scopus 로고
    • Characterization of thiI, a new gene involved in thiazole biosynthesis in Salmonella typhimurium
    • Webb, E., Claas, K. and Downs, D.M. (1997) Characterization of thiI, a new gene involved in thiazole biosynthesis in Salmonella typhimurium. J. Bacteriol., 179, 4399-4402.
    • (1997) J. Bacteriol. , vol.179 , pp. 4399-4402
    • Webb, E.1    Claas, K.2    Downs, D.M.3


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