TY - JOUR
T1 - Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli
AU - Shinhara, Atsuko
AU - Matsui, Motomu
AU - Hiraoka, Kiriko
AU - Nomura, Wataru
AU - Hirano, Reiko
AU - Nakahigashi, Kenji
AU - Tomita, Masaru
AU - Mori, Hirotada
AU - Kanai, Akio
N1 - Funding Information:
We thank Dr. Kosuke Fujishima and Ms. Yuki Takai (Institute for Advanced Biosciences, Keio University, Japan) for critical reading of the manuscript and for technical assistance, respectively. We also thank Drs. Teppei Morita and Hiroji Aiba (Suzuka University of Medical Sciences, Japan), and all the members of the RNA group (Institute for Advanced Biosciences, Keio University, Japan) for their insightful discussions. This work was supported by the Japan Society for the Promotion of Science; a grant from the Ministry of Education, Culture, Sports, Science and Technology of Japan (The 21st Century Centre of Excellence Program, entitled Understanding and Control of Life’s Function via Systems Biology); by research funds from the Yamagata Prefectural Government; and by research funds from Tsuruoka City, Japan.
PY - 2011/8/24
Y1 - 2011/8/24
N2 - 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.
AB - 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.
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U2 - 10.1186/1471-2164-12-428
DO - 10.1186/1471-2164-12-428
M3 - Article
C2 - 21864382
AN - SCOPUS:80052035218
VL - 12
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
M1 - 428
ER -