A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome

Argaman, 2001, Novel small RNA-encoding genes in the intergenic regions of Escherichia coli, Current Biol., 11, 941, 10.1016/S0960-9822(01)00270-6 Bucher, 1996, A flexible search technique based on generalized profiles, Comput. Chem., 20, 3, 10.1016/S0097-8485(96)80003-9 Carter, 2001, A computational approach to identify genes for functional RNAs in genomic sequences, Nucleic Acids Res., 29, 3928, 10.1093/nar/29.19.3928 Delihas, 1995, Regulation of gene expression by trans-encoded antisense RNAs, Mol. Microbiol., 15, 411, 10.1111/j.1365-2958.1995.tb02254.x Draper, 1996, Translational initiation, 902 Gojobori, 1981, Inter-RNA homology and possible roles of small RNAs, J. Mol. Evol., 17, 245, 10.1007/BF01732762 Guigueno, 2001, Oversynthesis of a new Escherichia coli small RNA suppresses export toxicity of DsbA′-PhoA unfoldable periplasmic proteins, J. Bacteriol., 183, 1147, 10.1128/JB.183.4.1147-1158.2001 Gusarov, 1999, The mechanism of intrinsic transcription termination, Mol. Cell., 3, 49, 10.1016/S1097-2765(00)80477-3 Keiler, 1996, Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA, Science, 271, 990, 10.1126/science.271.5251.990 Komine, 1994, A tRNA-like structure is present in 10SaRNA, a small stable RNA from Escherichia coli, Proc. Natl. Acad. Sci. USA, 91, 9223, 10.1073/pnas.91.20.9223 Lesnik, 2001, Prediction of Rho-independent transcription terminators in Escherichia coli genome, Nucleic Acids Res., 29, 3583, 10.1093/nar/29.17.3583 Lewin, 1994, 461 Macke, 2001, RNAMotif, an RNA secondary structure definition and search algorithm, Nucleic Acids Res., 29, 4724, 10.1093/nar/29.22.4724 Majdalani, 2001, Regulation of RpoS by a novel small RNA: the characterization of RprA, Mol. Microbiol., 39, 1382, 10.1111/j.1365-2958.2001.02329.x Mulligan, 1984, Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity, Nucleic Acids Res., 12, 789, 10.1093/nar/12.1Part2.789 Okamoto, 1986, Mechanism of the autogenous control of the crp operon: transcriptional inhibition by a divergent RNA transcript, Proc. Natl. Acad. Sci. USA, 83, 5000, 10.1073/pnas.83.14.5000 Rivas, 2001, Computational identification of noncoding RNAs in E. coli by comparative genomics, Current Biol., 11, 1369, 10.1016/S0960-9822(01)00401-8 Rudd, 1999, Novel intergenic repeats of Escherichia coli K-12, Res. Microbiol., 150, 653, 10.1016/S0923-2508(99)00126-6 Salgado, 2000, Operons in Escherichia coli: genomic analyses and predictions, Proc. Natl. Acad. Sci. USA, 97, 6652, 10.1073/pnas.110147297 Selinger, 2000, RNA expression analysis using a 30 base pair resolution Eschericia coli genome array, Nat. Biotechnol., 18, 1262, 10.1038/82367 Urbanowski, 2000, The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport system in Eschericia coli, Mol. Microbiol., 37, 856, 10.1046/j.1365-2958.2000.02051.x Vanet, 1999, Promoter sequences and algorithmical methods for identifying them, Res. Microbiol., 150, 779, 10.1016/S0923-2508(99)00115-1 Wassarman, 1999, Small RNAs in Escherichia coli, Trends Microbiol., 7, 37, 10.1016/S0966-842X(98)01379-1 Wassarman, 2001, Identification of novel small RNAs using comparative genomics and microarrays, Genes Dev., 15, 1637, 10.1101/gad.901001 Yada, 1999, Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models, Bioinformatics, 15, 987, 10.1093/bioinformatics/15.12.987