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

Research output: Contribution to journalArticle

38 Citations (Scopus)

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.

Original languageEnglish
Article number428
JournalBMC Genomics
Volume12
DOIs
Publication statusPublished - 2011 Aug 24

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High-Throughput Nucleotide Sequencing
RNA
Escherichia coli
Prophages
Antisense RNA

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Shinhara, A., Matsui, M., Hiraoka, K., Nomura, W., Hirano, R., Nakahigashi, K., ... Kanai, A. (2011). Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. BMC Genomics, 12, [428]. https://doi.org/10.1186/1471-2164-12-428

Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. / Shinhara, Atsuko; Matsui, Motomu; Hiraoka, Kiriko; Nomura, Wataru; Hirano, Reiko; Nakahigashi, Kenji; Tomita, Masaru; Mori, Hirotada; Kanai, Akio.

In: BMC Genomics, Vol. 12, 428, 24.08.2011.

Research output: Contribution to journalArticle

Shinhara, A, Matsui, M, Hiraoka, K, Nomura, W, Hirano, R, Nakahigashi, K, Tomita, M, Mori, H & Kanai, A 2011, 'Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli', BMC Genomics, vol. 12, 428. https://doi.org/10.1186/1471-2164-12-428
Shinhara A, Matsui M, Hiraoka K, Nomura W, Hirano R, Nakahigashi K et al. Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. BMC Genomics. 2011 Aug 24;12. 428. https://doi.org/10.1186/1471-2164-12-428
Shinhara, Atsuko ; Matsui, Motomu ; Hiraoka, Kiriko ; Nomura, Wataru ; Hirano, Reiko ; Nakahigashi, Kenji ; Tomita, Masaru ; Mori, Hirotada ; Kanai, Akio. / Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. In: BMC Genomics. 2011 ; Vol. 12.
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