title: Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli.
abstract: BACKGROUND
  In Escherichia coli, approximately 100 regulatory small RNAs (sRNAs) have been identified experimentally and many more have been predicted by various methods. To provide a comprehensive overview of sRNAs, we analysed the low-molecular-weight RNAs (< 200 nt) of E. coli with deep sequencing, because the regulatory RNAs in bacteria are usually 50-200 nt in length.
  
  
  RESULTS
  We discovered 229 novel candidate sRNAs (≥ 50 nt) with computational or experimental evidence of transcription initiation. Among them, the expression of seven intergenic sRNAs and three cis-antisense sRNAs was detected by northern blot analysis. Interestingly, five novel sRNAs are expressed from prophage regions and we note that these sRNAs have several specific characteristics. Furthermore, we conducted an evolutionary conservation analysis of the candidate sRNAs and summarised the data among closely related bacterial strains.
  
  
  CONCLUSIONS
  This comprehensive screen for E. coli sRNAs using a deep sequencing approach has shown that many as-yet-undiscovered sRNAs are potentially encoded in the E. coli genome. We constructed the Escherichia coli Small RNA Browser (ECSBrowser; http://rna.iab.keio.ac.jp/), which integrates the data for previously identified sRNAs and the novel sRNAs found in this study.
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan.
authors.forename: Atsuko
authors.initials: A
authors.lastname: Shinhara
authors.forename: Motomu
authors.initials: M
authors.lastname: Matsui
authors.forename: Kiriko
authors.initials: K
authors.lastname: Hiraoka
authors.forename: Wataru
authors.initials: W
authors.lastname: Nomura
authors.forename: Reiko
authors.initials: R
authors.lastname: Hirano
authors.forename: Kenji
authors.initials: K
authors.lastname: Nakahigashi
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
authors.forename: Hirotada
authors.initials: H
authors.lastname: Mori
authors.forename: Akio
authors.initials: A
authors.lastname: Kanai
mesh_terms: D019295:Computational Biology / Q000379:methods; D021901:DNA, Intergenic / Q000235:genetics; D030541:Databases, Genetic; D004926:Escherichia coli / Q000235:genetics*; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D016372:RNA, Antisense / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D021901:DNA, Intergenic; D016372:RNA, Antisense; D012329:RNA, Bacterial