Published online 17 February 2005
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Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli
1 Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development Building 18T, Room 101, Bethesda, MD 20892-5430, USA 2 Molecular Microbiology Department, Biotechnology Institute, National University of Mexico Av. Universidad #2001, Col. Chamilpa, CP. 62210, Cuernavaca, Morelos, Mexico
*To whom correspondence should be addressed. Tel: +1 301 402 0968; Fax: +1 301 402 0078; Email: storz{at}helix.nih.gov
Received December 3, 2004. Revised January 30, 2005. Accepted January 30, 2005.
Evidence is accumulating that small, noncoding RNAs are important regulatory molecules. Computational and experimental searches have led to the identification of 
60 small RNA genes in Escherichia coli. However, most of these studies focused on the intergenic regions and assumed that small RNAs were >50 nt. Thus, the previous screens missed small RNAs encoded on the antisense strand of protein-coding genes and small RNAs of <50 nt. To identify additional small RNAs, we carried out a cloning-based screen focused on RNAs of 30–65 nt. In this screen, we identified RNA species corresponding to fragments of rRNAs, tRNAs and known small RNAs. Several of the small RNAs also corresponded to 5'- and 3'-untranslated regions (UTRs) and internal fragments of mRNAs. Four of the 3'-UTR-derived RNAs were highly abundant and two showed expression patterns that differed from the corresponding mRNAs, suggesting independent functions for the 3'-UTR-derived small RNAs. We also detected three previously unidentified RNAs encoded in intergenic regions and RNAs from the long direct repeat and hok/sok elements. In addition, we identified a few small RNAs that are expressed opposite protein-coding genes and could base pair with 5' or 3' ends of the mRNAs with perfect complementarity.
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