Identification of novel small RNAs using comparative genomics and microarrays.
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 the Escherichia 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.
Wassarman
K M
KM
Cell Biology and Metabolism Branch, National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA.
Repoila
F
F
Rosenow
C
C
Storz
G
G
Gottesman
S
S
D001419:Bacteria / Q000235:genetics*; D015152:Blotting, Northern / Q000379:methods; D002352:Carrier Proteins / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D035001:Host Factor 1 Protein; D034982:Integration Host Factors; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames; D011485:Protein Binding; D012329:RNA, Bacterial / Q000032:analysis* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism; D012269:Ribosomal Proteins / Q000235:genetics; D017423:Sequence Analysis, RNA
D002352:Carrier Proteins; D035001:Host Factor 1 Protein; D034982:Integration Host Factors; D012329:RNA, Bacterial; D016601:RNA-Binding Proteins; D012269:Ribosomal Proteins; C023509:ribosomal protein S16