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Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli

Atsuko Shinhara12, Motomu Matsui12, Kiriko Hiraoka1, Wataru Nomura3, Reiko Hirano1, Kenji Nakahigashi1, Masaru Tomita124, Hirotada Mori13 and Akio Kanai124*

Author Affiliations

1 Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan

2 Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan

3 Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Ikoma, 630-0192, Japan

4 Faculty of Environment and Information Studies, Keio University, Fujisawa 252-0882, Japan

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BMC Genomics 2011, 12:428  doi:10.1186/1471-2164-12-428

Published: 24 August 2011



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.


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.


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; webcite), which integrates the data for previously identified sRNAs and the novel sRNAs found in this study.