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

Atsuko Shinhara, Motomu Matsui, Kiriko Hiraoka, Wataru Nomura, Reiko Hirano, Kenji Nakahigashi, Masaru Tomita, Hirotada Mori, Akio Kanai

研究成果: Article査読

41 被引用数 (Scopus)

抄録

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.

本文言語English
論文番号428
ジャーナルBMC Genomics
12
DOI
出版ステータスPublished - 2011 8 24

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

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