title: Novel small RNA-encoding genes in the intergenic regions of Escherichia coli.
abstract: BACKGROUND
  Small, untranslated RNA molecules were identified initially in bacteria, but examples can be found in all kingdoms of life. These RNAs carry out diverse functions, and many of them are regulators of gene expression. Genes encoding small, untranslated RNAs are difficult to detect experimentally or to predict by traditional sequence analysis approaches. Thus, in spite of the rising recognition that such RNAs may play key roles in bacterial physiology, many of the small RNAs known to date were discovered fortuitously.
  
  
  RESULTS
  To search the Escherichia coli genome sequence for genes encoding small RNAs, we developed a computational strategy employing transcription signals and genomic features of the known small RNA-encoding genes. The search, for which we used rather restrictive criteria, has led to the prediction of 24 putative sRNA-encoding genes, of which 23 were tested experimentally. Here we report on the discovery of 14 genes encoding novel small RNAs in E. coli and their expression patterns under a variety of physiological conditions. Most of the newly discovered RNAs are abundant. Interestingly, the expression level of a significant number of these RNAs increases upon entry into stationary phase.
  
  
  CONCLUSIONS
  Based on our results, we conclude that small RNAs are much more widespread than previously imagined and that these versatile molecules may play important roles in the fine-tuning of cell responses to changing environments.
authors.affiliation: Department of Molecular Genetics and Biotechnology, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel.
authors.forename: L
authors.initials: L
authors.lastname: Argaman
authors.forename: R
authors.initials: R
authors.lastname: Hershberg
authors.forename: J
authors.initials: J
authors.lastname: Vogel
authors.forename: G
authors.initials: G
authors.lastname: Bejerano
authors.forename: E G
authors.initials: EG
authors.lastname: Wagner
authors.forename: H
authors.initials: H
authors.lastname: Margalit
authors.forename: S
authors.initials: S
authors.lastname: Altuvia
mesh_terms: D015152:Blotting, Northern; D002874:Chromosome Mapping; D021901:DNA, Intergenic; D004926:Escherichia coli / Q000235:genetics*; D009838:Oligodeoxyribonucleotides / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D021901:DNA, Intergenic; D009838:Oligodeoxyribonucleotides; D012329:RNA, Bacterial; D022661:RNA, Untranslated