Identification of novel small RNAs using comparative genomics and microarrays
- Karen M. Wassarman1,4,
- Francis Repoila2,4,
- Carsten Rosenow3,
- Gisela Storz1,5, and
- Susan Gottesman2,5
- 1Cell Biology and Metabolism Branch, National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; 2Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA; 3Affymetrix, Santa Clara, California 95051, USA
Abstract
A burgeoning list of small RNAs with a variety of regulatory functions has been identified in both prokaryotic and eukaryotic cells. However, it remains difficult to identify small RNAs by sequence inspection. We used the high conservation of small RNAs among closely related bacterial species, as well as analysis of transcripts detected by high-density oligonucleotide probe arrays, to predict the presence of novel small RNA genes in the intergenic regions of theEscherichia coli genome. The existence of 23 distinct new RNA species was confirmed by Northern analysis. Of these, six are predicted to encode short ORFs, whereas 17 are likely to be novel functional small RNAs. We discovered that many of these small RNAs interact with the RNA-binding protein Hfq, pointing to a global role of the Hfq protein in facilitating small RNA function. The approaches used here should allow identification of small RNAs in other organisms.
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Footnotes
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↵4 Both authors contributed equally to this work.
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↵5 Corresponding authors.
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E-MAIL storz{at}helix.nih.gov; FAX (301) 402-0078.
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E-MAIL susang{at}helix.nih.gov; FAX (301) 496-3875.
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Article and publication are at http://www.genesdev.org/cgi/doi/10.1101/gad.901001.
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- Received April 3, 2001.
- Accepted May 9, 2001.
- Cold Spring Harbor Laboratory Press
